Article
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publication date
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author
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author name string
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published in
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Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution.
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2023-05-18
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Jürg Bähler Ian Goodhead Valerie Wood
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Brian T Wilhelm Samuel Marguerat Stephen Watt Falk Schubert Christopher J Penkett Jane Rogers Jürg Bähler
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Nature
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The transcriptional landscape of the yeast genome defined by RNA sequencing
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2023-06-06
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Mark Bender Gerstein
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Ugrappa Nagalakshmi Zhong Wang Karl Waern Chong Shou Debasish Raha Michael Snyder
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Science
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A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome
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2023-07-03
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Stefan Haas
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Marc Sultan Marcel H Schulz Hugues Richard Alon Magen Andreas Klingenhoff Matthias Scherf Martin Seifert Tatjana Borodina Aleksey Soldatov Dmitri Parkhomchuk Dominic Schmidt Sean O'Keeffe Martin Vingron Hans Lehrach Marie-Laure Yaspo
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Science
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RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays
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Biology Direct
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2010-12-31
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Johan Flygare Harvey Lodish
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Lingbo Zhang Piu Wong Bing Lim
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Genes & Development
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Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples
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2011
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Celina Sanchez Rivers Zora Modrusan Brock A Peters
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Serban Nacu Wenlin Yuan Zhengyan Kan Deepali Bhatt Jeremy Stinson Kenneth Jung Somasekar Seshagiri Thomas D Wu
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BMC Medical Genomics
|
Thousands of Novel Transcripts Identified in Mouse Cerebrum, Testis, and ES Cells Based on ribo-minus RNA Sequencing
|
2011
|
Songnian Hu
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Wanfei Liu Yuhui Zhao Peng Cui Qiang Lin Feng Ding Chengqi Xin Xinyu Tan Shuhui Song Jun Yu
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Frontiers in Genetics
|
RNA-seq analyses of blood-induced changes in gene expression in the mosquito vector species, Aedes aegypti
|
2011
|
Mariangela Bonnizoni Osvaldo Marinotti
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W Augustine Dunn Corey L Campbell Ken E Olson Michelle T Dimon Anthony A James
|
BMC Genomics
|
Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans
|
2011
|
Matthew Berriman Karen Mungall Gary Saunders Anna V Protasio Martin Hunt Roz Laing Michael Andrew Quail
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Steven Laing Frank Jackson Robin Beech John S Gilleard
|
PLOS ONE
|
The post-apoptotic fate of RNAs identified through high-throughput sequencing of human hair
|
2011
|
Benjamin Yu
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Gloria K Lefkowitz Anandaroop Mukhopadhyay Christopher Cowing-Zitron
|
PLOS ONE
|
A low-cost library construction protocol and data analysis pipeline for Illumina-based strand-specific multiplex RNA-seq
|
2011
|
Thomas Brutnell
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Lin Wang Yaqing Si Lauren K Dedow Ying Shao Peng Liu
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PLOS ONE
|
ENCODE whole-genome data in the UCSC genome browser (2011 update)
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2011-01
|
David Haussler Venkat S Malladi Angie S. Hinrichs Donna Karolchik Hiram Clawson Ann S Zweig
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Brian J Raney Melissa S Cline Kate R Rosenbloom Timothy R Dreszer Katrina Learned Galt P Barber Laurence R Meyer Cricket A Sloan Krishna M Roskin Bernard B Suh Vanessa Kirkup Pauline A Fujita Brooke Rhead Kayla E Smith Andy Pohl Robert M Kuhn W James Kent
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Nucleic Acids Research
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Insights into global mechanisms and disease by gene expression profiling.
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2011-01-01
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Hubert Hackl Johannes Rainer Ana Dopazo
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Fátima Sánchez-Cabo Zlatko Trajanoski
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Methods in Molecular Biology
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Identifying mRNA editing deaminase targets by RNA-Seq.
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2011-01-01
|
Nina Papavasiliou
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Brad R Rosenberg Scott Dewell F Nina Papavasiliou
|
Methods in Molecular Biology
|
The NBP Negative Binomial Model for Assessing Differential Gene Expression from RNA-Seq
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2011-01-12
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Jeff H. Chang
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Yanming Di Daniel W Schafer Jason S Cumbie
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Statistical Applications in Genetics and Molecular Biology
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A pipeline for RNA-seq data processing and quality assessment
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2011-01-13
|
Alvis Brazma Angela Goncalves
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Andrew Tikhonov Misha Kapushesky
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Bioinformatics
|
RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts
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2011-01-17
|
Katherine Lontok
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Michelle T Dimon Joseph L DeRisi
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Nucleic Acids Research
|
Length bias correction for RNA-seq data in gene set analyses
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2011-01-19
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Xiangqin Cui
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Liyan Gao Zhide Fang Kui Zhang Degui Zhi
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Bioinformatics
|
Identification of fusion genes in breast cancer by paired-end RNA-sequencing.
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2011-01-19
|
Olli-Pekka Kallioniemi Anne-Lise Børresen-Dale Sara Kangaspeska Vesa Hongisto Kristine Kleivi
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Henrik Edgren Astrid Murumagi Sara Kangaspeska Daniel Nicorici Vesa Hongisto Inga H Rye Sandra Nyberg Maija Wolf
|
Genome Biology
|
Understanding the pathogenesis of Alzheimer's disease: will RNA-Seq realize the promise of transcriptomics?
|
2011-01-19
|
Greg T. Sutherland Jillian J. Kril
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Michal Janitz
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Journal of Neurochemistry
|
Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array
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2011-01-21
|
Shikai Liu Eric Peatman Huseyin Kucuktas Ludmilla Kaltenboeck Shaolin Wang Zhanjiang Liu
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Zunchun Zhou Jianguo Lu Fanyue Sun Hong Liu Yanliang Jiang
|
BMC Genomics
|
Augmented annotation of the Schizosaccharomyces pombe genome reveals additional genes required for growth and viability.
|
2011-01-26
|
Agnes Grallert Valerie Wood Iain M. Hagan Crispin J. Miller
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Danny A Bitton Paul J Scutt Tim Yates Duncan L Smith
|
Genetics
|
In vitro culture and characterization of putative porcine embryonic germ cells derived from domestic breeds and Yucatan mini pig embryos at Days 20-24 of gestation.
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2011-01-31
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Hendrik Marks Yu Gao Poul Hyttel
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Stoyan G Petkov Tino Klein Rodrigo S Garcia Henk Stunnenberg
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Stem Cell Research
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Transcriptome-wide sequencing reveals numerous APOBEC1 mRNA-editing targets in transcript 3' UTRs
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2011-02
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Nina Papavasiliou
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Brad R Rosenberg Claire E Hamilton Michael M Mwangi Scott Dewell F Nina Papavasiliou
|
Nature Structural & Molecular Biology
|
General lack of global dosage compensation in ZZ/ZW systems? Broadening the perspective with RNA-seq
|
2011-02-01
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Jochen Wolf Jarosław Bryk
|
Jochen Bw Wolf
|
BMC Genomics
|
The next generation: using new sequencing technologies to analyse gene regulation.
|
2011-02-01
|
Olivia Alder Pamela A. Hoodless
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Rebecca Cullum
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Respirology
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Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-seq.
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2011-02-08
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Michael Eisen S E Lott
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Jacqueline E Villalta Gary P Schroth Shujun Luo Leath A Tonkin
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PLOS Biology
|
Identification and optimization of small molecules that restore E-cadherin expression and reduce invasion in colorectal carcinoma cells.
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2011-02-09
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Robert Daniel Beauchamp Craig W Lindsley
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Sydney L Stoops A Scott Pearson Connie Weaver Alex G Waterson Emily Days Chris Farmer Suzanne Brady C David Weaver
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ACS Chemical Biology
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Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads.
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2011-02-10
|
Ernest Turro Angela Goncalves Lachlan Coin Sylvia Richardson Alexandra M. Lewin
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Shu-Yi Su
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Genome Biology
|
Isoform-level microRNA-155 target prediction using RNA-seq
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2011-02-11
|
Erik K Flemington
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Nan Deng Adriane Puetter Kun Zhang Kristen Johnson Zhiyu Zhao Christopher Taylor Dongxiao Zhu
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Nucleic Acids Research
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Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes.
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2011-02-15
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Peggy Farnham
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Kimberly R Blahnik Lei Dou Lorigail Echipare Sushma Iyengar Henriette O'Geen Erica Sanchez Yongjun Zhao Marco A Marra Martin Hirst Joseph F Costello Ian Korf
|
PLOS ONE
|
Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.
|
2011-02-16
|
Vineet Bafna Olivier Harismendy
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Marcus Kinsella Masakazu Nakano Kelly A Frazer
|
Bioinformatics
|
Targeted disruption of py235ebp-1: invasion of erythrocytes by Plasmodium yoelii using an alternative Py235 erythrocyte binding protein.
|
2011-02-17
|
Thomas D Otto Arnab Pain Anthony A Holder Rita Tewari
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Solabomi A Ogun Steven A Howell Ellen Knuepfer Deirdre A Cunningham Zhengyao Xu
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PLOS Pathogens
|
RNA-seq reveals cooperative metabolic interactions between two termite-gut spirochete species in co-culture
|
2011-02-17
|
Avigdor Eldar
|
Adam Z Rosenthal Eric G Matson Jared R Leadbetter
|
The ISME Journal
|
ACT: aggregation and correlation toolbox for analyses of genome tracks.
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2011-02-23
|
Joel Rozowsky Kevin Y Yip Lucas Lochovsky
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Justin Jee Robert Bjornson Guoneng Zhong Zhengdong Zhang Yutao Fu Jie Wang Zhiping Weng Mark Gerstein
|
Bioinformatics
|
Method for improved Illumina sequencing library preparation using NuGEN Ovation RNA-Seq System.
|
2011-03-01
|
Traver Hart
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Steven R Head H Kiyomi Komori John Shimashita Lana Schaffer Daniel R Salomon Phillip T Ordoukhanian
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BioTechniques
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Accurate estimation of expression levels of homologous genes in RNA-seq experiments.
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2011-03-01
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Bogdan Pasaniuc Noah Zaitlen
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Eran Halperin
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Journal of Computational Biology
|
The carbonic anhydrase isoforms of Chlamydomonas reinhardtii: intracellular location, expression, and physiological roles.
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2011-03-02
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Bratati Mukherjee
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James V Moroney Yunbing Ma Wesley D Frey Katelyn A Fusilier Trang T Pham Tiffany A Simms Robert J DiMario Jing Yang
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Photosynthesis Research
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Improving RNA-Seq expression estimates by correcting for fragment bias.
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2011-03-16
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Lior Pachter John L. Rinn
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Adam Roberts Cole Trapnell Julie Donaghey
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Genome Biology
|
MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers
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2011-03-17
|
Louis M Staudt Ujunwa C Okoye Pedro Farinha Anke van den Berg Steven Jones
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Christian Steidl Sohrab P Shah Bruce W Woolcock Lixin Rui Masahiro Kawahara Nathalie A Johnson Yongjun Zhao Adele Telenius Susana Ben Neriah Andrew McPherson Barbara Meissner Arjan Diepstra Mark Sun Gillian Leung Joseph M Connors David G Huntsman Kerry J Savage Lisa M Rimsza Douglas E Horsman Ulrich Steidl Marco A Marra Randy D Gascoyne
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Nature
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A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii.
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2011-03-21
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Sabeeha Merchant Matteo Pellegrini David Casero
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Janette Kropat Anne Hong-Hermesdorf Petr Ent Madeli Castruita Davin Malasarn
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The Plant Journal
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ExpEdit: a webserver to explore human RNA editing in RNA-Seq experiments.
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2011-03-22
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Graziano Pesole Ernesto Picardi
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Mattia D'Antonio Danilo Carrabino Tiziana Castrignanò
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Bioinformatics
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Composite transcriptome assembly of RNA-seq data in a sheep model for delayed bone healing
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2011-03-24
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Peter Robinson Stefan Mundlos
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Marten Jäger Claus-Eric Ott Johannes Grünhagen Jochen Hecht Hanna Schell Stefan Mundlos Georg N Duda Jasmin Lienau
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BMC Genomics
|
Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays
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2011-03-24
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Nicole A Walter Jessica Ezzell Hunter Michael A Mooney Shannon K McWeeney
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Daniel Bottomly Priscila Darakjian Sunita Kawane Kari J Buck Robert P Searles Robert Hitzemann
|
PLOS ONE
|
Effects of nickel treatment on H3K4 trimethylation and gene expression.
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2011-03-24
|
Stuart M. Brown Phillip R Smith
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Kam-Meng Tchou-Wong Kathrin Kiok Zuojian Tang Thomas Kluz Adriana Arita Max Costa
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PLOS ONE
|
Developmental changes in transcriptional profiles.
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2011-03-30
|
Gad Shaulsky
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William F Loomis
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Development, Growth and Differentiation
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RNA-Seq analysis in mutant zebrafish reveals role of U1C protein in alternative splicing regulation.
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2011-04-05
|
Vladimir Benes Gunnar Rätsch
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Tanja Dorothe Rösel Lee-Hsueh Hung Jan Medenbach Katrin Donde Stefan Starke Albrecht Bindereif
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The EMBO Journal
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Network-guided analysis of genes with altered somatic copy number and gene expression reveals pathways commonly perturbed in metastatic melanoma.
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2011-04-08
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Stylianos Antonarakis Christian Iseli Carlo Rivolta Ioannis Xenarios Jacques S. Beckmann Armand Valsesia
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Donata Rimoldi Danielle Martinet Mark Ibberson Paola Benaglio Manfredo Quadroni Patrice Waridel Muriel Gaillard Mireille Pidoux Blandine Rapin Andrew J G Simpson C Victor Jongeneel Brian J Stevenson
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PLOS ONE
|
Genome-wide analysis of the 5' and 3' ends of vaccinia virus early mRNAs delineates regulatory sequences of annotated and anomalous transcripts.
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2011-04-13
|
Bernard Moss
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Zhilong Yang Daniel P Bruno Craig A Martens Stephen F Porcella
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Journal of Virology
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A multiplex RNA-seq strategy to profile poly(A+) RNA: application to analysis of transcription response and 3' end formation.
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2011-04-15
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Jeremy Davis-Turak Yu Zhou
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Kristi Fox-Walsh Hairi Li Xiang-Dong Fu
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Genomics
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Design and validation issues in RNA-seq experiments.
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2011-04-15
|
Xiangqin Cui
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Zhide Fang
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Briefings in Bioinformatics
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Systems biology approach in Chlamydomonas reveals connections between copper nutrition and multiple metabolic steps.
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2011-04-15
|
David Casero Sabeeha Merchant Matteo Pellegrini Astrid Vieler Christoph Benning
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Madeli Castruita Steven J Karpowicz Janette Kropat Scott I Hsieh Weihong Yan Shawn Cokus Joseph A Loo
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The Plant Cell
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Estimation of alternative splicing isoform frequencies from RNA-Seq data
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2011-04-19
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Ion I. Mandoiu Alexander Zelikovsky
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Marius Nicolae Serghei Mangul
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Algorithms for Molecular Biology
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Massive-scale RNA-Seq analysis of non ribosomal transcriptome in human trisomy 21.
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2011-04-20
|
Luciana D'Apice Aldo Donizetti Monica Rienzo Paola Salvatore Stefania Crispi Valerio Costa Piergiuseppe De Berardinis Teresa Infante Claudia Angelini Marco Picardi Berardo Sarubbi Raffaele Calabrò Claudio Napoli Amelia Casamassimi
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Margherita Mutarelli Linda Sommese Maria Assunta Gallo Marianna Aprile Roberta Esposito Luigi Leone Alfredo Ciccodicola
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PLOS ONE
|
BM-map: Bayesian mapping of multireads for next-generation sequencing data.
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2011-04-22
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Yuan Yuan Han Liang
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Yuan Ji Yanxun Xu Qiong Zhang Kam-Wah Tsui Clift Norris Shoudan Liang
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Biometrics
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Contribution of Hfq to photooxidative stress resistance and global regulation in Rhodobacter sphaeroides.
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2011-04-27
|
Cynthia Sharma Jörg Vogel Gabriele Klug
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Bork A Berghoff Jens Glaeser Monica Zobawa Friedrich Lottspeich
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Molecular Microbiology
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FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq.
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2011-05-05
|
Jeremy Chien Jian Ma
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Yang Li David I Smith
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Bioinformatics
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Protocol dependence of sequencing-based gene expression measurements
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2011-05-06
|
John F Thompson
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Tal Raz Philipp Kapranov Doron Lipson Stan Letovsky Patrice M Milos
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PLOS ONE
|
Detecting copy number status and uncovering subclonal markers in heterogeneous tumor biopsies.
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2011-05-11
|
Antonella Bacchiocchi
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Fabio Parisi Stephan Ariyan Deepak Narayan Kathleen Hoyt Elaine Cheng Fang Xu Peining Li Ruth Halaban Yuval Kluger
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BMC Genomics
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The sensitivity of massively parallel sequencing for detecting candidate infectious agents associated with human tissue
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2011-05-13
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Curtis A. Suttle Julia A Gustavsen Jan M Friedman Robert A Holt
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Richard A Moore René L Warren J Douglas Freeman Caroline Chénard Yongjun Zhao
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PLOS ONE
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NSMAP: a method for spliced isoforms identification and quantification from RNA-Seq.
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2011-05-16
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Zheng Xia
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Jianguo Wen Chung-Che Chang Xiaobo Zhou
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BMC Bioinformatics
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FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution.
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2011-05-18
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Wolfgang Hoeck
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Huanying Ge Kejun Liu Todd Juan Fang Fang Matthew Newman
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Bioinformatics
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deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data.
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2011-05-19
|
Malachi Griffith Gavin Ha
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Andrew McPherson Fereydoun Hormozdiari Abdalnasser Zayed Ryan Giuliany Mark G F Sun Alireza Heravi Moussavi Janine Senz Nataliya Melnyk Marina Pacheco Marco A Marra Martin Hirst Torsten O Nielsen S Cenk Sahinalp David Huntsman Sohrab P Shah
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PLOS Computational Biology
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Genome-wide RNA-seq analysis of human and mouse platelet transcriptomes.
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2011-05-19
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A S Weyrich
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Jesse W Rowley Andrew J Oler Neal D Tolley Benjamin N Hunter Elizabeth N Low David A Nix Christian C Yost Guy A Zimmerman
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Blood
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The zebrafish transcriptome during early development.
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2011-05-24
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Juha Kere Outi Hovatta Liselotte Vesterlund
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Hong Jiao Per Unneberg Outi Hovatta
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BMC Developmental Biology
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Transcriptome profiling of chemosensory appendages in the malaria vector Anopheles gambiae reveals tissue- and sex-specific signatures of odor coding
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2011-05-27
|
Antonis Rokas Laurence J. Zwiebel
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R Jason Pitts David C Rinker Patrick L Jones
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BMC Genomics
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Pyrosequencing-based expression profiling and identification of differentially regulated genes from Manduca sexta, a lepidopteran model insect.
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2011-05-27
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Haobo Jiang
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Shuguang Zhang Ramesh T Gunaratna Xiufeng Zhang Fares Najar Yang Wang Bruce Roe
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Insect Biochemistry and Molecular Biology
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Megakaryocytes differentially sort mRNAs for matrix metalloproteinases and their inhibitors into platelets: a mechanism for regulating synthetic events.
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2011-05-31
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Loredana Bury A S Weyrich Paolo Gresele
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Luca Cecchetti Neal D Tolley Noemi Michetti
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Blood
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Characterizing the impact of smoking and lung cancer on the airway transcriptome using RNA-Seq
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2011-06
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Frank Schembri Jennifer Beane Yuriy O Alekseyev Avrum Spira Marc E Lenburg Shawn Levy
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Jessica Vick Christina Anderlind Adam Gower Joshua Campbell Lingqi Luo Xiao Hui Zhang Ji Xiao Shenglong Wang Pierre P Massion
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Cancer Prevention Research
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RNA-seq: technical variability and sampling.
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2011-06-06
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Lauren McIntyre
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Kenneth K Lopiano Alison M Morse Victor Amin Ann L Oberg Linda J Young Sergey V Nuzhdin
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BMC Genomics
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Proportion statistics to detect differentially expressed genes: a comparison with log-ratio statistics.
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2011-06-07
|
Tracy L Bergemann
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Jason Wilson
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BMC Bioinformatics
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RNA sequencing reveals two major classes of gene expression levels in metazoan cells.
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2011-06-07
|
Sarah Teichmann Alexander van Oudenaarden Muxin Gu Varodom Charoensawan Daniel Hebenstreit
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Miaoqing Fang
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Molecular Systems Biology
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PR-domain-containing Mds1-Evi1 is critical for long-term hematopoietic stem cell function.
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2011-06-10
|
Subhash Juneja
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Yi Zhang Sandra Stehling-Sun Kimberly Lezon-Geyda Lucie Coillard Gouri Chatterjee Charles A Wuertzer Fernando Camargo Archibald S Perkins
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Blood
|
Poly (A)+ transcriptome assessment of ERBB2-induced alterations in breast cell lines.
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2011-06-22
|
Dirce Carraro Emmanuel Dias-Neto Helena Brentani Renata Pasqualini
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Elisa Napolitano Ferreira Gustavo de Campos Molina Renato David Puga Eduardo Fernandes Abrantes Adriana Priscila Trapé Bedrich L Eckhardt Diana Noronha Nunes Maria Mitzi Brentani Wadih Arap Ricardo Renzo Brentani
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PLOS ONE
|
Deterministic and stochastic allele specific gene expression in single mouse blastomeres
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2011-06-23
|
Azim Surani
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Fuchou Tang Catalin Barbacioru Ellen Nordman Siqin Bao Caroline Lee Xiaohui Wang Brian B Tuch Edith Heard Kaiqin Lao
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PLOS ONE
|
Transcription factor TEAD4 regulates expression of myogenin and the unfolded protein response genes during C2C12 cell differentiation
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2011-06-24
|
Gabrielle Mengus Irwin Davidson
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A Benhaddou C Keime T Ye A Morlon I Michel B Jost
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Cell Death & Differentiation
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Directional RNA deep sequencing sheds new light on the transcriptional response of Anabaena sp. strain PCC 7120 to combined-nitrogen deprivation.
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2011-06-28
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Filip Van Nieuwerburgh James W Golden
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Britt L Flaherty Steven R Head
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BMC Genomics
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Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq
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2011-07
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Sten Linnarsson Peter Lönnerberg
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Saiful Islam Una Kjällquist Annalena Moliner Pawel Zajac Jian-Bing Fan
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Genome Research
|
Full-length transcriptome assembly from RNA-Seq data without a reference genome
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2011-07
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Kerstin Lindblad-Toh Aviv Regev Chad Nusbaum Andreas Gnirke Evan Mauceli Nir Friedman Nicholas Rhind Nir Hacohen Raktima Raychowdhury
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Manfred G Grabherr Brian J Haas Moran Yassour Joshua Z Levin Dawn A Thompson Ido Amit Xian Adiconis Lin Fan Raktima Raychowdhury Qiandong Zeng Zehua Chen Federica di Palma Bruce W Birren
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Nature Biotechnology
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Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling.
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2011-07-01
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Paweł P Łabaj Steven Wiley D Kreil
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Germán G Leparc Bryan E Linggi Lye Meng Markillie
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Bioinformatics
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Global transcriptome changes underlying colony growth in the opportunistic human pathogen Aspergillus fumigatus.
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2011-07-01
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Antonis Rokas
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John G Gibbons Anne Beauvais Remi Beau Kriston L McGary Jean-Paul Latgé
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Eukaryotic Cell
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Exploring the Schistosoma mansoni adult male transcriptome using RNA-seq.
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2011-07-02
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Ricardo DeMarco Sergio Verjovski-Almeida
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Giulliana Tessarin Almeida Murilo Sena Amaral Felipe Cesar Ferrarezi Beckedorff João Paulo Kitajima
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Experimental Parasitology
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An efficient approach to finding Siraitia grosvenorii triterpene biosynthetic genes by RNA-seq and digital gene expression analysis.
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2011-07-05
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Iain W Wilson
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Qi Tang Xiaojun Ma Changming Mo Cai Song Huan Zhao Yanfang Yang Wei Fu Deyou Qiu
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BMC Genomics
|
A comparative analysis of DNA methylation across human embryonic stem cell lines.
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2011-07-06
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Matteo Pellegrini
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Pao-Yang Chen Suhua Feng Jong Wha Joanne Joo Steve E Jacobsen
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Genome Biology
|
SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data
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2011-07-07
|
Tak-Wah Lam
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Songbo Huang Jinbo Zhang Ruiqiang Li Wenqian Zhang Zengquan He Zhiyu Peng Siu-Ming Yiu
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Frontiers in Genetics
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Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data.
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2011-07-12
|
David Casero Matteo Pellegrini Sabeeha Merchant
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David Lopez Shawn J Cokus
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BMC Bioinformatics
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De novo assembly of expressed transcripts and global analysis of the Phalaenopsis aphrodite transcriptome.
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2011-07-19
|
Ya-Ting Chao
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Chun-lin Su Yao-Chien Alex Chang Wan-Chieh Chen Chun-Yi Chen Ann-Ying Lee Kee Tuan Hwa Ming-Che Shih
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Plant and Cell Physiology
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Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM).
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2011-07-19
|
Angel Pizarro Gregory R Grant Eric A Pierce
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Michael H Farkas Nicholas F Lahens Jonathan Schug Brian P Brunk Christian J Stoeckert John B Hogenesch
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Bioinformatics
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RseqFlow: workflows for RNA-Seq data analysis.
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2011-07-27
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Ewa Deelman
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Ying Wang Gaurang Mehta Rajiv Mayani Jingxi Lu Tade Souaiaia Yangho Chen Andrew Clark Hee Jae Yoon Lin Wan Oleg V Evgrafov James A Knowles Ting Chen
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Bioinformatics
|
Detection of splicing events and multiread locations from RNA-seq data based on a geometric-tail (GT) distribution of intron length
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2011-07-27
|
Jing Woei Li Stephen Kwok-Wing Tsui T F Chan
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Shao-Ke Lou Hao Qin Aldrin Kay-Yuen Yim Leung-Yau Lo Bing Ni Kwong-Sak Leung
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BMC Bioinformatics
|
ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data.
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2011-07-28
|
Tom Maniatis Brad Friedman
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Genome Biology
|
Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure.
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2011-07-29
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Mikhail Matz
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E Meyer G V Aglyamova
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Molecular Ecology
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Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression
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2011-07-31
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John R. Prensner Qi Cao Irfan Asangani Nallasivam Palanisamy
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Matthew K Iyer O Alejandro Balbin Saravana M Dhanasekaran J Chad Brenner Bharathi Laxman Catherine S Grasso Hal D Kominsky Xuhong Cao Xiaojun Jing Xiaoju Wang Javed Siddiqui John T Wei Daniel Robinson Hari K Iyer Christopher A Maher Arul M Chinnaiyan
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Nature Biotechnology
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RNA-Seq-based monitoring of infection-linked changes in Vibrio cholerae gene expression.
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2011-08-01
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Jennifer M Ritchie
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Anjali Mandlik Jonathan Livny William P Robins John J Mekalanos Matthew K Waldor
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Cell Host & Microbe
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AlleleSeq: analysis of allele-specific expression and binding in a network framework.
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2011-08-02
|
Yong Kong Alexej Abyzov Joel Rozowsky Mark Rubin Mark Bender Gerstein
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Jing Wang Pedro Alves Debasish Raha Arif Harmanci Jing Leng Robert Bjornson Naoki Kitabayashi Nitin Bhardwaj Michael Snyder
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Molecular Systems Biology
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Synthetic spike-in standards for RNA-seq experiments.
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2011-08-04
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Thomas R. Gingeras
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Lichun Jiang Felix Schlesinger Carrie A Davis Yu Zhang Renhua Li Marc Salit Brian Oliver
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Genome Research
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Quantitative RNA-seq analysis of the Campylobacter jejuni transcriptome
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2011-08-04
|
Paul P. Gardner Roy R Chaudhuri Jyoti Choudhary
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Lu Yu Alpa Kanji Timothy T Perkins Duncan J Maskell Andrew J Grant
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Microbiology
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RNA-seq discovery, functional characterization, and comparison of sesquiterpene synthases from Solanum lycopersicum and Solanum habrochaites trichomes
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2011-08-05
|
Eran Pichersky
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Petra M Bleeker Eleni A Spyropoulou Paul J Diergaarde Hanne Volpin Michiel T J De Both Philipp Zerbe Joerg Bohlmann Vasiliki Falara Yuki Matsuba Eran Pichersky Michel A Haring Robert C Schuurink
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Plant Molecular Biology
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FDM: a graph-based statistical method to detect differential transcription using RNA-seq data.
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2011-08-08
|
Derek Y Chiang
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Darshan Singh Christian F Orellana Yin Hu Corbin D Jones Yufeng Liu Jinze Liu Jan F Prins
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Bioinformatics
|
TopHat-Fusion: an algorithm for discovery of novel fusion transcripts
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2011-08-11
|
Steven Salzberg
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Daehwan Kim
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Genome Biology
|
Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation.
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2011-08-11
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Jason Gertz Katherine E Varley Timothy E Reddy
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Kevin M Bowling Florencia Pauli Stephanie L Parker Katerina S Kucera Huntington F Willard Richard M Myers
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PLOS Genetics
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Genome-Wide Gene Expression Profiling of Nucleus Accumbens Neurons Projecting to Ventral Pallidum Using both Microarray and Transcriptome Sequencing
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2011-08-12
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Robert W. Williams
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Hao Chen Zhimin Liu Suzhen Gong Xingjun Wu William L Taylor Shannon G Matta Burt M Sharp
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Frontiers in Neuroscience
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Local and global factors affecting RNA sequencing analysis.
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2011-08-16
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Graham D Johnson
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Edward Sendler Stephen A Krawetz
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Analytical Biochemistry
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Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma
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2011-08-18
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Martin Hirst Yaron Butterfield Angela Brooks-Wilson Eric Y Zhao Malachi Griffith Andrew Mungall
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Ryan D Morin Maria Mendez-Lago Rodrigo Goya Karen L Mungall Richard D Corbett Nathalie A Johnson Tesa M Severson Readman Chiu Matthew Field Shaun Jackman Martin Krzywinski David W Scott Diane L Trinh Jessica Tamura-Wells Sa Li Marlo R Firme Sanja Rogic Susanna Chan Oleksandr Yakovenko Irmtraud M Meyer Duane Smailus Michelle Moksa Suganthi Chittaranjan Lisa Rimsza John J Spinelli Susana Ben-Neriah Barbara Meissner Bruce Woolcock Merrill Boyle Helen McDonald Angela Tam Yongjun Zhao Allen Delaney Thomas Zeng Kane Tse Inanç Birol Rob Holt Jacqueline Schein Douglas E Horsman Richard Moore Steven J M Jones Joseph M Connors Randy D Gascoyne Marco A Marra
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Nature
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An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype
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2011-08-18
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Michele Balsamo
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Irina M Shapiro Albert W Cheng Nicholas C Flytzanis John S Condeelis Maja H Oktay Christopher B Burge Frank B Gertler
|
PLOS Genetics
|
Transcriptional profiling of psoriasis using RNA-seq reveals previously unidentified differentially expressed genes.
|
2011-08-18
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Ali Jabbari
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Mayte Suárez-Fariñas Scott Dewell James G Krueger
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Journal of Investigative Dermatology
|
The disequilibrium of nucleosomes distribution along chromosomes plays a functional and evolutionarily role in regulating gene expression
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2011-08-19
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Songnian Hu
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Peng Cui Qiang Lin Lingfang Zhang Feng Ding Chengqi Xin Daoyong Zhang Fanglin Sun Jun Yu
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PLOS ONE
|
Lignin metabolism has a central role in the resistance of cotton to the wilt fungus Verticillium dahliae as revealed by RNA-Seq-dependent transcriptional analysis and histochemistry.
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2011-08-23
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Daojun Yuan Xianlong Zhang
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Li Xu Longfu Zhu Lili Tu Linlin Liu Li Jin Lu Long
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Journal of Experimental Botany
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Bioaccumulation and effects of CdTe/CdS quantum dots on Chlamydomonas reinhardtii - nanoparticles or the free ions?
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2011-08-25
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Rute F. Domingos Kevin J Wilkinson
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Dana F Simon Charles Hauser
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Environmental Science & Technology
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A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data.
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2011-08-26
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Daniel A Skelly
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Marnie Johansson Jennifer Madeoy Jon Wakefield Joshua M Akey
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Genome Research
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Preservation of the Y transcriptome in a 10-million-year-old plant sex chromosome system.
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2011-09-01
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Deborah Charlesworth
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Roberta Bergero
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Current Biology
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Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
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2011-09-02
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Loyal Goff Magdalena J Koziol John L. Rinn
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Moran N Cabili Cole Trapnell Barbara Tazon-Vega Aviv Regev
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Genes & Development
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Wnt gene loss in flatworms.
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2011-09-03
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Nick Riddiford
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Peter D Olson
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Development Genes and Evolution
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SpliceTrap: a method to quantify alternative splicing under single cellular conditions.
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2011-09-06
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W. Richard McCombie Adrian Robert Krainer
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Jie Wu Martin Akerman Shuying Sun Michael Q Zhang
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Bioinformatics
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Genome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factor erythroid Kruppel-like factor during erythrocyte differentiation.
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2011-09-06
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Ross C Hardison James C Mullikin
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Andre M Pilon Subramanian S Ajay Swathi Ashok Kumar Laurie A Steiner Praveen F Cherukuri Stephen Wincovitch Stacie M Anderson NISC Comparative Sequencing Center Patrick G Gallagher Elliott H Margulies David M Bodine
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Blood
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wapRNA: a web-based application for the processing of RNA sequences.
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2011-09-06
|
Songnian Hu
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Wenming Zhao Wanfei Liu Dongmei Tian Bixia Tang Yanqing Wang Caixia Yu Rujiao Li Yunchao Ling Jiayan Wu Shuhui Song
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Bioinformatics
|
RNA-Seq of human neurons derived from iPS cells reveals candidate long non-coding RNAs involved in neurogenesis and neuropsychiatric disorders.
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2011-09-07
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Deyou Zheng
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Mingyan Lin Erika Pedrosa Abhishek Shah Anastasia Hrabovsky Shahina Maqbool Herbert M Lachman
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PLOS ONE
|
Differential expression in RNA-seq: a matter of depth.
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2011-09-08
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Joaquín Dopazo Ana Conesa Sonia Tarazona Alberto Ferrer
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Fernando García-Alcalde
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Genome Research
|
Proteomic and phosphoproteomic comparison of human ES and iPS cells.
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2011-09-11
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Justin Brumbaugh
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Douglas H Phanstiel Craig D Wenger Shulan Tian Mitchell D Probasco Derek J Bailey Danielle L Swaney Mark A Tervo Jennifer M Bolin Victor Ruotti Ron Stewart James A Thomson Joshua J Coon
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Nature Methods
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Identification of common carp innate immune genes with whole-genome sequencing and RNA-Seq data.
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2011-09-12
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Elia Stupka Christiaan V. Henkel Herman P Spaink
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Yanju Zhang Hans J Jansen Fons J Verbeek
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Journal of integrative bioinformatics
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Integrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes.
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2011-09-13
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Jurian Schuijers Michal Mokry
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Pantelis Hatzis Nico Lansu Frans-Paul Ruzius Hans Clevers Edwin Cuppen
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Nucleic Acids Research
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Integrative approach involving RNA-Seq, foliar traits and growth measurements revealed genotype-specific plasticity on Eucalyptus subjected to seasonal water shortage.
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2011-09-13
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Christophe Plomion
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Emilie Villar Jean-Marc Gion
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BMC Proceedings
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Pronounced and extensive microtubule defects in a Saccharomyces cerevisiae DIS3 mutant.
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2011-09-15
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Daniel L Kiss
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Sarah B Smith Edward Turk Alan M Tartakoff Erik D Andrulis
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Yeast
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RNA-Seq methods for imperfect samples: development, evaluation and applications
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2011-09-19 2011
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Aviv Regev Chad Nusbaum Gad Getz
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Xian Adiconis Lin Fan David DeLuca Andrey Sivachenko Nathalie Pochet Aaron Berlin Sarah Young Andreas Gnirke Joshua Z Levin
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Genome Biology
|
Differential Expression for RNA Sequencing (RNA-Seq) Data: Mapping, Summarization, Statistical Analysis, and Experimental Design
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2011-09-22
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Davis J McCarthy Alicia Oshlack Gordon K Smyth
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Matthew D. Young Matthew J. Wakefield Mark D. Robinson
|
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Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals.
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2011-09-25
|
Vincent Lynch Gunter P Wagner
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Robert D Leclerc Gemma May
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Nature Genetics
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From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.).
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2011-09-28
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Thomas Schmutzer Martin Mascher Uwe Scholz Nils Stein Klaus Mayer Eva Bauer
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Grit Haseneyer Michael Seidel Ruonan Zhou Chris-Carolin Schön Stefan Taudien
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BMC Plant Biology
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Accurate identification of A-to-I RNA editing in human by transcriptome sequencing.
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2011-09-29
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Jae-Hyung Lee Guangdun Peng Xinshu Xiao
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Jae Hoon Bahn Gang Li Christopher Greer
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Genome Research
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Genome-wide transcriptome analysis in murine neural retina using high-throughput RNA sequencing.
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2011-10-01
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Ece D. Gamsiz Eric M. Morrow
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Qing Ouyang Michael Schmidt Shailender Nagpal
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Genomics
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RNA-Seq analysis in MeV.
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2011-10-05
|
John Quackenbush
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Eleanor A Howe Raktim Sinha Daniel Schlauch
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Bioinformatics
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RNA-seq analysis of small RNPs in Trypanosoma brucei reveals a rich repertoire of non-coding RNAs
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2011-10-05
|
Tirza Doniger
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Shulamit Michaeli Sachin Kumar Gupta Omri Wurtzel Mali Romano Damian Visnovezky Rotem Sorek Ron Unger Elisabetta Ullu
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Nucleic Acids Research
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GENE-counter: a computational pipeline for the analysis of RNA-Seq data for gene expression differences.
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2011-10-06
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Jeff H. Chang Jeffrey A Kimbrel James C. Carrington
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Jason S Cumbie Yanming Di Daniel W Schafer Larry J Wilhelm Samuel E Fox Christopher M Sullivan Aron D Curzon Todd C Mockler
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PLOS ONE
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S-MART, a software toolbox to aid RNA-Seq data analysis
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2011-10-06
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Hadi Quesneville
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Matthias Zytnicki
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PLOS ONE
|
Nonrandom gene loss from the Drosophila miranda neo-Y chromosome.
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2011-10-10
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Doris Bachtrog
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Vera B Kaiser Qi Zhou
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Genome Biology and Evolution
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The role of CYP3A4 mRNA transcript with shortened 3'-untranslated region in hepatocyte differentiation, liver development, and response to drug induction.
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2011-10-13
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Gaedigk R Steven N. Hart
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Dan Li J Steven Leeder Xiao-bo Zhong
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Molecular Pharmacology
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RNA-Seq for Plant Pathogenic Bacteria.
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2011-10-13
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Jeffrey A Kimbrel Jeff H. Chang
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Yanming Di Jason S Cumbie
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Genes
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Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens.
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2011-10-18
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Charles D. Johnson Ulisses Braga Neto
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Ying Wang Noushin Ghaffari Hui Wang Rui Chen Huaijun Zhou
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BMC Bioinformatics
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The crystal structure of necrosis- and ethylene-inducing protein 2 from the causal agent of cacao's Witches' Broom disease reveals key elements for its activity
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2011-10-21
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Paulo José Pereira Lima Teixeira Joan Barau Antonio Costa-filho
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Gustavo Zaparoli Mario Ramos de Oliveira Barsottini Juliana Ferreira de Oliveira Fabio Dyszy Odalys Garcia Andre Luis Berteli Ambrosio Gonçalo Amarante Guimarães Pereira Sandra Martha Gomes Dias
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Biochemistry
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Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster.
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2011-10-23
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Thomas R. Gingeras Jay Shendure David Sturgill
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Xinxian Deng Joseph B Hiatt Di Kim Nguyen Sevinc Ercan LaDeana W Hillier Felix Schlesinger Carrie A Davis Valerie J Reinke Robert H Waterston Brian Oliver Jason D Lieb Christine M Disteche
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Nature Genetics
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Identification of gene fusion transcripts by transcriptome sequencing in BRCA1-mutated breast cancers and cell lines
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2011-10-27
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Anne Vincent-Salomon William D Foulkes Jorge Reis-Filho Rachael Natrajan Alan Ashworth
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Kevin C H Ha Emilie Lalonde Lili Li Luca Cavallone Maryou B Lambros Costas Mitsopoulos Jarle Hakas Iwanka Kozarewa Kerry Fenwick Chris J Lord Mark Basik Jacek Majewski
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BMC Medical Genomics
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RNA-Seq reveals an integrated immune response in nucleated erythrocytes.
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2011-10-27
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Nerea Roher Laia Ribas Joan C Balasch Sebastian Boltana Steven B. Roberts Simon Mackenzie
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Davinia Morera Carmen Doñate Agnes Callol Giles Goetz Frederick W Goetz
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PLOS ONE
|
The transcriptome of the reference potato genome Solanum tuberosum Group Phureja clone DM1-3 516R44.
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2011-10-28
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Giovanni Giuliano Kevin L. Childs
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Alicia N Massa Haining Lin Glenn J Bryan C Robin Buell
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PLOS ONE
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RNA-Seq reveals genotype-specific molecular responses to water deficit in eucalyptus
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2011-11-02
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Christophe Plomion Evandro Novaes
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Emilie Villar Christophe Klopp Céline Noirot Matias Kirst Jean-Marc Gion
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BMC Genomics
|
RNA-Seq improves annotation of protein-coding genes in the cucumber genome.
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2011-11-02
|
Zhen Li Sanwen Huang
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Zhonghua Zhang Pengcheng Yan Zhangjun Fei Kui Lin
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BMC Genomics
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deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns.
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2011-11-03
|
Peter F. Stadler Jan Gorodkin David Langenberger Claus T. Ekstrøm Sachin Pundhir
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Steve Hoffmann
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Bioinformatics
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Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain.
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2011-11-06
|
Adam Ameur Ulf Gyllensten
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Ammar Zaghlool Jonatan Halvardson Anna Wetterbom Lucia Cavelier Lars Feuk
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Nature Structural & Molecular Biology
|
Exploring the gonad transcriptome of two extreme male pigs with RNA-seq
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2011-11-08
|
Giovanni Bussotti Robert Kofler Cedric Notredame Miguel Perez-Enciso Anna Esteve-Codina
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Nicola Palmieri
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BMC Genomics
|
Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq.
|
2011-11-08
|
Ming Hu Zhaohui Steve Qin
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Yu Zhu Jeremy M G Taylor Jun S Liu
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Bioinformatics
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An RNA-Seq strategy to detect the complete coding and non-coding transcriptome including full-length imprinted macro ncRNAs.
|
2011-11-10
|
Andreas Sommer Irena Vlatkovic Hendrik Marks Robert Kralovics
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Ru Huang Markus Jaritz Philipp Guenzl Ido M Tamir Thorsten Klampfl Hendrik G Stunnenberg Denise P Barlow Florian M Pauler
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PLOS ONE
|
Non-laser capture microscopy approach for the microdissection of discrete mouse brain regions for total RNA isolation and downstream next-generation sequencing and gene expression profiling.
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2011-11-13
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Norman Atkins
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Charlie M Miller Joseph R Owens Fred W Turek
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Journal of Visualized Experiments
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ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets.
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2011-11-16
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Jeffrey T. Leek Ben Langmead
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Alyssa C Frazee
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BMC Bioinformatics
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Identification of new viral genes and transcript isoforms during Epstein-Barr virus reactivation using RNA-Seq.
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2011-11-16
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Melody Baddoo Dale Hedges Erik K Flemington
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Monica Concha Xia Wang Subing Cao Melody Baddoo Claire Fewell Zhen Lin William Hulme Dale Hedges Jane McBride
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Journal of Virology
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Genetic variation of pre-mRNA alternative splicing in human populations
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2011-11-17
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Zhi-xiang Lu
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Peng Jiang Yi Xing
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Wiley interdisciplinary reviews. RNA
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Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis.
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2011-11-22
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Aviv Regev Eivind Valen Albin Sandelin John L. Rinn
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Andrea Pauli Michael F Lin Manuel Garber Nadine L Vastenhouw Joshua Z Levin Lin Fan Alexander F Schier
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Genome Research
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RNA-Seq and find: entering the RNA deep field.
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2011-11-22
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Lior Pachter
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Adam Roberts
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Genome Medicine
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Estimation of alternative splicing variability in human populations.
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2011-11-23
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Roderic Guigó i Serra Michael Sammeth
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Mar Gonzàlez-Porta Miquel Calvo
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Genome Research
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RNA-Seq reveals infection-related global gene changes in Phytophthora phaseoli, the causal agent of lima bean downy mildew.
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2011-11-24
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Blake Meyers
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Sridhara G Kunjeti Thomas A Evans Adam G Marsh Nancy F Gregory Saritha Kunjeti Venugopal S Kalavacharla Nicole M Donofrio
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Molecular Plant Pathology
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Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data.
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2011-11-28
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Robert Tibshirani
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Jun Li
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Statistical Methods in Medical Research
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Cell walls of developing wheat starchy endosperm: comparison of composition and RNA-Seq transcriptome.
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2011-11-28
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Paola Tosi J Paul Knox Jackie Freeman
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Till K Pellny Alison Lovegrove Christopher G Love Peter R Shewry Rowan A C Mitchell
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Plant Physiology
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Transposase mediated construction of RNA-seq libraries.
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2011-11-29
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Jason Gertz Katherine E Varley
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Nicholas S Davis Bradley J Baas Igor Y Goryshin Ramesh Vaidyanathan Scott Kuersten Richard M Myers
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Genome Research
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Comparative analysis of human protein-coding and noncoding RNAs between brain and 10 mixed cell lines by RNA-Seq.
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2011-11-30
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Jian Luo Mingyao Liu
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Geng Chen Kangping Yin Leming Shi Yuanzhang Fang Ya Qi Peng Li Bing He Tieliu Shi
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PLOS ONE
|
Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in Anabaena sp. PCC7120
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2011-11-30
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Agustín Vioque Fabian Haas Wolfgang R Hess Alicia María Muro-Pastor
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Jan Mitschke
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Proceedings of the National Academy of Sciences of the United States of America
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Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation.
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2011-12-01
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Jingyi Jessica Li
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Ci-Ren Jiang James B Brown Haiyan Huang Peter J Bickel
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Proceedings of the National Academy of Sciences of the United States of America
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EpiRegNet: constructing epigenetic regulatory network from high throughput gene expression data for humans.
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2011-12-01
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Jing Qin Junwen Wang
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Lily Yan Wang Panwen Wang Mulin Jun Li Xiaowo Wang Michael Q Zhang
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Epigenetics
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RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.).
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2011-12-02
|
Jérôme Salse
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Caroline Pont Florent Murat Carole Confolent Sandrine Balzergue
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Genome Biology
|
X-chromosome hyperactivation in mammals via nonlinear relationships between chromatin states and transcription
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2011-12-04
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Ruslan I Sadreyev
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Eda Yildirim Stefan F Pinter Jeannie T Lee
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Nature Structural & Molecular Biology
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Isoform diversity and its importance for axon regeneration.
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2011-12-13
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John L. Bixby Vance P. Lemmon
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Jessica K Lerch
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Neuropathology
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Protein identification using customized protein sequence databases derived from RNA-Seq data.
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2011-12-14
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David Tabb Daniel C. Liebler
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Xiaojing Wang Robbert J C Slebos Dong Wang Patrick J Halvey Bing Zhang
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Journal of Proteome Research
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Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study.
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2011-12-14
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Qiong-Yi Zhao
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Yi Wang Yi-Meng Kong Da Luo Xuan Li Pei Hao
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BMC Bioinformatics
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GC-content normalization for RNA-Seq data
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2011-12-17
|
Gavin Sherlock Davide Risso
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Katja Schwartz Sandrine Dudoit
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BMC Bioinformatics
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Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis
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2011-12-22
|
Desmond G. Higgins Geraldine Butler Sarah L Maguire Matthew Berriman
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Alessandro Guida Claudia Lindstädt Chen Ding Nicola J Corton
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BMC Genomics
|
Characterization of a highly conserved histone related protein, Ydl156w, and its functional associations using quantitative proteomic analyses.
|
2011-12-22
|
Laurence Florens Swaminathan Venkatesh Michael P. Washburn
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Joshua M Gilmore Mihaela E Sardiu Brent Stutzman Allison Peak Chris W Seidel Jerry L Workman
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Molecular & Cellular Proteomics
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Statistical methods on detecting differentially expressed genes for RNA-seq data.
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2011-12-23
|
Saralees Nadarajah
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Zhongxue Chen Jianzhong Liu Hon Keung Tony Ng Saralees Nadarajah Howard L Kaufman Jack Y Yang Youping Deng
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BMC Systems Biology
|
Modulation of NF-κB-dependent gene transcription using programmable DNA minor groove binders
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2011-12-27
|
Jordan L Meier Peter Dervan
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Jevgenij A Raskatov James W Puckett Fei Yang Parameswaran Ramakrishnan
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Proceedings of the National Academy of Sciences of the United States of America
|
Detection, annotation and visualization of alternative splicing from RNA-Seq data with SplicingViewer.
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2011-12-28
|
Fangqing Zhao
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Qi Liu Chong Chen Enjian Shen Zhongsheng Sun Jinyu Wu
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Genomics
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Cytoskeleton remodeling and alterations in smooth muscle contractility in the bovine jejunum during nematode infection.
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2011-12-28
|
Steven G Schroeder
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Robert W Li
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Functional and Integrative Genomics
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Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas.
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2011-12-29
|
Steven B. Roberts
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Mackenzie R Gavery
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Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics
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Adaptation of the black yeast Wangiella dermatitidis to ionizing radiation: molecular and cellular mechanisms
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2012
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Christina A Cuomo
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Kelly L Robertson Anahita Mostaghim Carissa M Soto Nikolai Lebedev Robert F Bailey Zheng Wang
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PLOS ONE
|
Isoform diversity and regulation in peripheral and central neurons revealed through RNA-Seq
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2012
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John L. Bixby Vance P. Lemmon Dario Motti
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Jessica K Lerch Frank Kuo Richard Morris
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PLOS ONE
|
Genes associated with MUC5AC expression in small airway epithelium of human smokers and non-smokers
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2012
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Jacqueline Salit
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Guoqing Wang Zhibo Xu Rui Wang Mohammed Al-Hijji Yael Strulovici-Barel Ann E Tilley Jason G Mezey Ronald G Crystal
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BMC Medical Genomics
|
The transcriptional landscape of the deep-sea bacterium Photobacterium profundum in both a toxR mutant and its parental strain
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2012
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Andrea Telatin Stefano Campanaro Giorgio Valle
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Fabio De Pascale Riccardo Schiavon Douglas H Bartlett
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BMC Genomics
|
Computational analysis of noncoding RNAs
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2012
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Manolis Kellis Stefan Washietl Bonnie Berger John L. Rinn
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Sebastian Will David A. Hendrix Loyal A. Goff
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Wiley interdisciplinary reviews. RNA
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Transcriptome analysis reveals strain-specific and conserved stemness genes in Schmidtea mediterranea
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2012
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Brenton R. Graveley
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Alissa M Resch Dasaradhi Palakodeti Yi-Chien Lu Michael Horowitz
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PLOS ONE
|
RNA-seq-based metatranscriptomic and microscopic investigation reveals novel metalloproteases of Neobodo sp. as potential virulence factors for soft tunic syndrome in Halocynthia roretzi
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2012
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Tae Sung Jung
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Ho Bin Jang Young Kyu Kim Carmelo S Del Castillo Seong Won Nho In Seok Cha Seong Bin Park Mi Ae Ha Jun-Ichi Hikima Sung Jong Hong Takashi Aoki
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PLOS ONE
|
GABAergic gene expression in postmortem hippocampus from alcoholics and cocaine addicts; corresponding findings in alcohol-naïve P and NP rats
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2012
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David Goldman
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Mary-Anne Enoch Zhifeng Zhou Mitsuru Kimura Deborah C Mash Qiaoping Yuan
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PLOS ONE
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Tcf7 is an important regulator of the switch of self-renewal and differentiation in a multipotential hematopoietic cell line
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2012
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Mark Bender Gerstein Vincent Schulz
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Jia Qian Wu Montrell Seay Manoj Hariharan David Tuck Jin Lian Jiang Du Minyi Shi Zhijia Ye Michael P Snyder Sherman Weissman
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PLOS Genetics
|
Gene expression profiling of liver cancer stem cells by RNA-sequencing
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2012
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Timothy Wan
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David W Y Ho Zhen Fan Yang Kang Yi Chi Tat Lam Michael N P Ng Wan Ching Yu Joyce Lau Xiaoqi Wang Zhixiang Yan Hang Liu Yong Zhang Sheung Tat Fan
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PLOS ONE
|
Nrac, a novel nutritionally-regulated adipose and cardiac-enriched gene
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2012
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Feng Gao Abdul B Abou-Samra
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Ren Zhang Fayi Yao
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PLOS ONE
|
RNA-seq analysis reveals different dynamics of differentiation of human dermis- and adipose-derived stromal stem cells
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2012
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Sten Linnarsson
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Kersti Jääger Saiful Islam Pawel Zajac Toomas Neuman
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PLOS ONE
|
Stable gene targeting in human cells using single-strand oligonucleotides with modified bases
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2012
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George M. Church
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Xavier Rios Adrian W Briggs Danos Christodoulou Josh M Gorham Jonathan G Seidman
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PLOS ONE
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Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data
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2012
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Jean-Baptiste Veyrieras Daniel J Gaffney
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Jean-Baptiste Veyrieras Joseph K Pickrell Yoav Gilad Matthew Stephens Jonathan K Pritchard
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PLOS ONE
|
Comparing Bowtie and BWA to Align Short Reads from a RNA-Seq Experiment
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2012
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Honghuang Lin
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N. Medina-Medina A. Broka S. Lacey E. S. Klings C. T. Baldwin M. H. Steinberg P. Sebastiani
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Advances in Intelligent and Soft Computing
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DBTSS: DataBase of Transcriptional Start Sites progress report in 2012
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2012-01
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Sumio Sugano
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Riu Yamashita Yutaka Suzuki Kenta Nakai
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Nucleic Acids Research
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Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes
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2012-01-01
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Andreas Gnirke Georgia Giannoukos Ashlee Earl Chad Nusbaum Dirk Gevers
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Dawn M Ciulla Katherine Huang Brian J Haas Jacques Izard Joshua Z Levin Jonathan Livny Doyle V Ward Bruce W Birren
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Genome Biology
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How to analyze gene expression using RNA-sequencing data.
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2012-01-01
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Daniel Ramsköld Rickard Sandberg
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Ersen Kavak
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Methods in Molecular Biology
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Detection and quantification of alternative splicing variants using RNA-seq.
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2012-01-01
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Henry D Priest
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Douglas W Bryant Todd C Mockler
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Methods in Molecular Biology
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Retinal transcriptome profiling by directional next-generation sequencing using 100 ng of total RNA.
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2012-01-01
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Anand Swaroop
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Matthew J Brooks Harsha Karur Rajasimha
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Methods in Molecular Biology
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Sex-biased transcriptome evolution in Drosophila.
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2012-01-01
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Doris Bachtrog
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Raquel Assis Qi Zhou
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Genome Biology and Evolution
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Defining the molecular profile of planarian pluripotent stem cells using a combinatorial RNAseq, RNA interference and irradiation approach.
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2012-01-01
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Jordi Solana Aziz A. Aboobaker
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Damian Kao Yuliana Mihaylova Farah Jaber-Hijazi Sunir Malla Ray Wilson
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Genome Biology
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Genome-wide mapping of nucleosome occupancy, histone modifications, and gene expression using next-generation sequencing technology.
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2012-01-01
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Gangqing Hu
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Gang Wei Kairong Cui Keji Zhao
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Methods in Enzymology
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Direct isolation and RNA-seq reveal environment-dependent properties of engrafted neural stem/progenitor cells.
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2012-01-01
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Yasuyuki Ohkawa Kazu Kobayakawa Seiji Okada Hideyuki Okano
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Hiromi Kumamaru Hirokazu Saiwai Hisakata Yamada Kensuke Kubota Koichi Akashi Yukihide Iwamoto
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Nature Communications
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Computational analysis of RNA-seq.
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2012-01-01
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Scott A. Givan
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Christopher A Bottoms William G Spollen
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Methods in Molecular Biology
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Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution.
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2012-01-03
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Robert K. Bradley
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Jason Merkin Nicole J Lambert Christopher B Burge
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PLOS Biology
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Sequencing and de novo analysis of the Chinese Sika deer antler-tip transcriptome during the ossification stage using Illumina RNA-Seq technology.
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2012-01-03
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Baojin Yao
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Yu Zhao Haishan Zhang Mei Zhang Meichen Liu Hailong Liu Juan Li
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Biotechnology Letters
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PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data.
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2012-01-04
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Zemin Ning Peter A.C. 't Hoen Pieternella E Slagboom
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Yanju Zhang Eric-Wubbo Lameijer Kai Ye
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Bioinformatics
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IQSeq: integrated isoform quantification analysis based on next-generation sequencing.
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2012-01-06
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Andrea Sboner Mark Bender Gerstein
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Jiang Du Jing Leng Lukas Habegger Drew McDermott
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PLOS ONE
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Detection of murine leukemia virus in the Epstein-Barr virus-positive human B-cell line JY, using a computational RNA-Seq-based exogenous agent detection pipeline, PARSES.
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2012-01-11
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Melody Baddoo Erik K Flemington
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Zhen Lin Adriane Puetter Joseph Coco Guorong Xu Michael J Strong Xia Wang Claire Fewell Melody Baddoo Christopher Taylor
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Journal of Virology
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Transcriptomic analysis of Chinese bayberry (Myrica rubra) fruit development and ripening using RNA-Seq.
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2012-01-13
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Andrew C. Allan Xue-ren Yin
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Chao Feng Ming Chen Chang-jie Xu Lin Bai Xian Li Ian B Ferguson Kun-song Chen
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BMC Genomics
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Next-generation sequencing identifies TGF-β1-associated gene expression profiles in renal epithelial cells reiterated in human diabetic nephropathy
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2012-01-14
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Peadar Ó Gaora Helen M Roche
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Eoin P Brennan Melissa J Morine David W Walsh Sarah A Roxburgh Maja T Lindenmeyer Derek P Brazil Denise M Sadlier Clemens D Cohen GENIE Consortium Catherine Godson Finian Martin
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Biochimica et Biophysica Acta
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The architecture and ppGpp-dependent expression of the primary transcriptome of Salmonella Typhimurium during invasion gene expression.
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2012-01-17
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Cynthia Sharma
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Vinoy K Ramachandran Neil Shearer Jobin J Jacob Arthur Thompson
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BMC Genomics
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FX: an RNA-Seq analysis tool on the cloud.
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2012-01-17
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Young Seok Ju Thomas Bleazard
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Dongwan Hong Arang Rhie Sung-Soo Park Jongkeun Lee Sujung Kim Saet-Byeol Yu Hyun-Seok Park Hwanseok Rhee Hyonyong Chong Kap-Seok Yang Yeon-Su Lee In-Hoo Kim Jin Soo Lee Jong-Il Kim Jeong-Sun Seo
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Bioinformatics
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MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data.
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2012-01-20
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Zhi-xiang Lu Jian Huang
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Shihao Shen Juw Won Park Kimberly A Dittmar Qing Zhou Russ P Carstens Yi Xing
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Nucleic Acids Research
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Application of RNA-Seq transcriptome analysis: CD151 is an Invasion/Migration target in all stages of epithelial ovarian cancer.
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2012-01-24
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Sergio Marchini Robert Fruscio Maurizio D'Incalci
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Rebecca A Mosig Li Lin Emir Senturk Hardik Shah Fei Huang Peter Schlosshauer Samantha Cohen Ravi Sachidanandam Peter Dottino John A Martignetti
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Journal of Ovarian Research
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A powerful method for transcriptional profiling of specific cell types in eukaryotes: laser-assisted microdissection and RNA sequencing.
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2012-01-26
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Philip Rosenstiel Ueli Grossniklaus Marc W Schmid
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Anja Schmidt Ulrich C Klostermeier Matthias Barann
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PLOS ONE
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Comparison between Normalised and Unnormalised 454-Sequencing Libraries for Small-Scale RNA-Seq Studies.
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2012-01-26
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Robert Ekblom Jon Slate Terry Burke
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Gavin J Horsburgh Tim Birkhead
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Comparative and Functional Genomics
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Pepitome: evaluating improved spectral library search for identification complementarity and quality assessment.
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2012-01-27
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David Tabb
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Surendra Dasari Matthew C Chambers Misti A Martinez Kristin L Carpenter Amy-Joan L Ham Lorenzo J Vega-Montoto
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Journal of Proteome Research
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Removing technical variability in RNA-seq data using conditional quantile normalization.
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2012-01-27
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Kasper D. Hansen Zhijin Wu
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Rafael A Irizarry
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Biostatistics
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The Transcriptome Analysis and Comparison Explorer--T-ACE: a platform-independent, graphical tool to process large RNAseq datasets of non-model organisms.
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2012-01-27
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Lars Kraemer Philip Rosenstiel
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E E R Philipp D Mountfort M Schilhabel S Schreiber
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Bioinformatics
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A new approach to bias correction in RNA-Seq
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2012-01-28
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Walter L. Ruzzo
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Daniel C Jones Xinxia Peng Michael G Katze
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Bioinformatics
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Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation.
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2012-01-28
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Davis J McCarthy Gordon K Smyth
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Yunshun Chen
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Nucleic Acids Research
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SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data.
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2012-01-31
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Asa Ben-Hur
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Mark F Rogers Julie Thomas Anireddy Sn Reddy
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Genome Biology
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Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae).
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2012-02-01
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W. Richard McCombie Norman J Wickett Mark W. Chase
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Michael R McKain Yeting Zhang Saravanaraj Ayyampalayam J Chris Pires Claude W dePamphilis Jim Leebens-Mack
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American Journal of Botany
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Spt4 is selectively required for transcription of extended trinucleotide repeats.
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2012-02-01
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Yijuang Chern
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Chia-Rung Liu Chuang-Rung Chang Tzu-Han Wang Wen-Chieh Hsieh Wen-Chuan Shen Chi-Yuan Chang I-Chieh Chu Ning Deng Stanley N Cohen Tzu-Hao Cheng
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Cell
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The Pseudomonas aeruginosa transcriptome in planktonic cultures and static biofilms using RNA sequencing.
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2012-02-03
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Andreas Dötsch Denitsa Eckweiler Susanne Häussler
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Monika Schniederjans Ariane Zimmermann Vanessa Jensen Maren Scharfe Robert Geffers
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PLOS ONE
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Transcriptome analysis of the model protozoan, Tetrahymena thermophila, using Deep RNA sequencing.
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2012-02-07
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Miao Tian
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Jie Xiong Xingyi Lu Zhemin Zhou Yue Chang Dongxia Yuan Zhigang Zhou Lei Wang Chengjie Fu Eduardo Orias Wei Miao
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PLOS ONE
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Genome-wide transcriptional profiling of appressorium development by the rice blast fungus Magnaporthe oryzae.
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2012-02-09
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Nick Talbot
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Darren M Soanes Apratim Chakrabarti Konrad H Paszkiewicz Angus L Dawe
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PLOS Pathogens
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Nuclear matrix factor hnRNP U/SAF-A exerts a global control of alternative splicing by regulating U2 snRNP maturation.
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2012-02-09
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Jie Huang Yu Zhou Changwei Shao Yi Zhang
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Rui Xiao Peng Tang Bo Yang Hairi Li Hui Sun Xiang-Dong Fu
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Molecular Cell
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Genome-wide analysis of STAT3 binding in vivo predicts effectors of the anti-inflammatory response in macrophages.
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2012-02-09
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Andrew Paul Hutchins Stéphane Poulain
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Diego Miranda-Saavedra
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Blood
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Specific and sensitive mRNA biomarkers for the identification of skin in 'touch DNA' evidence.
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2012-02-09
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Cordula Haas
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E Hanson R Jucker J Ballantyne
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Forensic Science International: Genetics
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Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome.
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2012-02-12
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Jun Wang Bertrand Chin-Ming Tan Zhiyu Peng
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Yanbing Cheng Lin Kang Zhijian Tian Yuankun Zhu Wenwei Zhang Yu Liang Xueda Hu Xuemei Tan Jing Guo Zirui Dong Yan Liang Li Bao
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Nature Biotechnology
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Uterine gene expression in the live-bearing lizard, Chalcides ocellatus, reveals convergence of squamate reptile and mammalian pregnancy mechanisms
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2012-02-14
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Dan L. Warren Michael B Thompson Gunter P Wagner
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Matthew C Brandley Rebecca L Young
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Genome Biology and Evolution
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RNA-Seq Atlas--a reference database for gene expression profiling in normal tissue by next-generation sequencing.
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2012-02-17
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Jens U Marquardt Ugur Sahin
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Markus Krupp Peter R Galle John Castle Andreas Teufel
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Bioinformatics
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RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus.
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2012-02-17
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Eric Peatman
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Chao Li Yu Zhang Ruijia Wang Jianguo Lu Samiran Nandi Sriprakash Mohanty Jeffery Terhune Zhanjiang Liu
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Fish and Shellfish Immunology
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RNA-seq analysis of the functional compartments within the rat placentation site.
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2012-02-21
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Kartik Shankar
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Ying Zhong Ping Kang Michael L Blackburn Michael J Soares Thomas M Badger Horacio Gomez-Acevedo
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Endocrinology
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RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings.
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2012-02-21
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Jian-Hua Mao Jun Wang Huanming Yang
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Shancheng Ren Zhiyu Peng Yongwei Yu Changjun Yin Xin Gao Zilian Cui Jibin Zhang Kang Yi Weidong Xu Chao Chen Fubo Wang Xinwu Guo Ji Lu Jun Yang Min Wei Zhijian Tian Yinghui Guan Liang Tang Chuanliang Xu Linhui Wang Xu Gao Wei Tian Jian Wang Yinghao Sun
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Cell Research
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Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data.
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2012-02-29
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Alexey I Nesvizhskii
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Kang Ning Damian Fermin
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Journal of Proteome Research
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RNA-Seq quantification of the human small airway epithelium transcriptome
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2012-02-29
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Juan L Rodriguez-Flores
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Neil R Hackett Marcus W Butler Renat Shaykhiev Jacqueline Salit Larsson Omberg Jason G Mezey Yael Strulovici-Barel Guoqing Wang Lukas Didon Ronald G Crystal
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BMC Genomics
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FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads.
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2012-02-29
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Angelo Valleriani
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Gong Zhang Ivan Fedyunin Sebastian Kirchner Chuanle Xiao Zoya Ignatova
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Nucleic Acids Research
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Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
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2012-03
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Loyal Goff Steven Salzberg Lior Pachter Harold Pimentel John L. Rinn
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Cole Trapnell Adam Roberts Geo Pertea Daehwan Kim David R Kelley
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Nature Protocols
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Characterization and differential expression analysis of complete coding sequences of Vitis vinifera L. sirtuin genes.
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2012-03-03
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Giacomo Morreale Matteo Busconi Luigi Bavaresco
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M Cucurachi A Zanetti C Fogher
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Plant Physiology and Biochemistry
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A new subtype of bone sarcoma defined by BCOR-CCNB3 gene fusion.
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2012-03-04
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Franck Tirode Olivier Delattre
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Gaëlle Pierron Carlo Lucchesi Stéphanie Reynaud Stelly Ballet Sarah Cohen-Gogo Virginie Perrin Jean-Michel Coindre
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Nature Genetics
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The human pancreatic islet transcriptome: expression of candidate genes for type 1 diabetes and the impact of pro-inflammatory cytokines.
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2012-03-08
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Gerton Lunter Izortze Santin Michael Sammeth Miriam Cnop Lorella Marselli Piero Marchetti Fernanda Ortis Mark McCarthy
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Décio L Eizirik Thomas Bouckenooghe Guy Bottu Giorgia Sisino Mariana Igoillo-Esteve Maikel L Colli Jenny Barthson Luc Bouwens Linda Hughes Lorna Gregory
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PLOS Genetics
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HnRNP L and L-like cooperate in multiple-exon regulation of CD45 alternative splicing.
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2012-03-08
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Vladimir Benes Gunnar Rätsch Hans-Martin Jäck
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Marco Preussner Silke Schreiner Lee-Hsueh Hung Martina Porstner Albrecht Bindereif
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Nucleic Acids Research
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Application of the whole-transcriptome shotgun sequencing approach to the study of Philadelphia-positive acute lymphoblastic leukemia.
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2012-03-09
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Annalisa Lonetti Giovanni Malerba Alberto Ferrarini Luciano Xumerle Anna Ferrari Cristina Papayannidis Simona Soverini
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I Iacobucci M Sazzini E Giacomelli D Luiselli A Boattini P Garagnani A Vitale F Pane M Baccarani M Delledonne G Martinelli
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Blood Cancer Journal
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An Interspecies Regulatory Network Inferred from Simultaneous RNA-seq of Candida albicans Invading Innate Immune Cells.
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2012-03-12
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Sascha Brunke Karl Kuchler Reinhard Guthke
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Lanay Tierney Jörg Linde Sebastian Müller Juan Camilo Molina Bernhard Hube Ulrike Schöck
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Frontiers in Microbiology
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A new RNASeq-based reference transcriptome for sugar beet and its application in transcriptome-scale analysis of vernalization and gibberellin responses.
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2012-03-19
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Effie Mutasa-Göttgens Berthold Gottgens
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Anagha Joshi Helen F Holmes Peter Hedden
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BMC Genomics
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Transcriptome landscape of the human placenta
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2012-03-27
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Zhi-xiang Lu Jin-kai Wang
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Jinsil Kim Keyan Zhao Peng Jiang Jeffrey C Murray Yi Xing
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BMC Genomics
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Characterization of the longissimus lumborum transcriptome response to adding propionate to the diet of growing Angus beef steers.
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2012-03-27
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Jennifer Thomson Cong-Jun Li
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Ransom L Baldwin Robert W Li Brian J Bequette
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Physiological Genomics
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Alternative splicing networks regulated by signaling in human T cells.
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2012-03-27
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Nicole M Martinez
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Qun Pan Brian S Cole Christopher A Yarosh Grace A Babcock Florian Heyd William Zhu Sandya Ajith Benjamin J Blencowe Kristen W Lynch
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RNA
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RNA-Seq analysis uncovers transcriptomic variations between morphologically similar in vivo- and in vitro-derived bovine blastocysts
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2012-03-28
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Francisco Peñagaricano
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Ashley M Driver Wen Huang Khawaja R Ahmad Katie S Hackbart Milo C Wiltbank Hasan Khatib
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BMC Genomics
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A genome-wide identification analysis of small regulatory RNAs in Mycobacterium tuberculosis by RNA-Seq and conservation analysis
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2012-03-28
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Paolo Miotto Alessandro Ambrosi
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Danilo Pellin Daniela Maria Cirillo Clelia Di Serio
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PLOS ONE
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Identification of allele-specific alternative mRNA processing via transcriptome sequencing.
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2012-03-29
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Jae-Hyung Lee Guangdun Peng Xinshu Xiao
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Gang Li Jae Hoon Bahn Zugen Chen Stanley F Nelson
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Nucleic Acids Research
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Comparative analyses of H3K4 and H3K27 trimethylations between the mouse cerebrum and testis.
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2012-04-01
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Songnian Hu
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Peng Cui Wanfei Liu Yuhui Zhao Qiang Lin Daoyong Zhang Feng Ding Chengqi Xin Zhang Zhang Shuhui Song Fanglin Sun Jun Yu
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Genomics Proteomics and Bioinformatics
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Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity.
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2012-04-01
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Ellen V. Rothenberg
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Jingli A Zhang Ali Mortazavi Brian A Williams Barbara J Wold
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Cell
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A zinc-finger-family transcription factor, AbVf19, is required for the induction of a gene subset important for virulence in Alternaria brassicicola.
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2012-04-01
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Igor V Grigoriev
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Akhil Srivastava Robin A Ohm Lindsay Oxiles Fred Brooks Christopher B Lawrence Yangrae Cho
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Molecular Plant-Microbe Interactions
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Identification of shortened 3' untranslated regions from expression arrays.
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2012-04-01
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Andrei Zinovyev Loredana Martignetti Emmanuel Barillot
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Journal of Bioinformatics and Computational Biology
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Improving RNA-Seq Precision with MapAl.
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2012-04-02
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D Kreil
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Paweł P Labaj Bryan E Linggi H Steven Wiley
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Frontiers in Genetics
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RNA-Seq analysis of developing nasturtium seeds (Tropaeolum majus): identification and characterization of an additional galactosyltransferase involved in xyloglucan biosynthesis
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2012-04-02
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Alex Schultink Jacob K Jensen Markus Pauly
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Kenneth Keegstra Curtis G Wilkerson
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Plant Physiology Journal
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Deep sequencing the circadian and diurnal transcriptome of Drosophila brain
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2012-04-03
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Gregory R Grant
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Michael E Hughes Christina Paquin Jack Qian Michael N Nitabach
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Genome Research
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The clonal and mutational evolution spectrum of primary triple-negative breast cancers
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2012-04-04
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Gavin Ha D Yap Daniel Lai Inanc Birol Malachi Griffith Gregg B Morin Suet-feung Chin Christina Curtis Mackey JR Wyeth W Wasserman Steven Jones
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Sohrab P Shah Andrew Roth Rodrigo Goya Arusha Oloumi Yongjun Zhao Gulisa Turashvili Jiarui Ding Kane Tse Gholamreza Haffari Ali Bashashati Leah M Prentice Jaswinder Khattra Angela Burleigh Virginie Bernard Andrew McPherson Karey Shumansky Anamaria Crisan Ryan Giuliany Alireza Heravi-Moussavi Jamie Rosner Richard Varhol Angela Tam Noreen Dhalla Thomas Zeng Kevin Ma Simon K Chan Annie Moradian S-W Grace Cheng Peter Watson Karen Gelmon Stephen Chia Oscar M Rueda Paul D Pharoah Sambasivarao Damaraju Kelly Hoon Timothy Harkins Vasisht Tadigotla Mahvash Sigaroudinia Philippe Gascard Thea Tlsty Joseph F Costello Irmtraud M Meyer Connie J Eaves David Huntsman Martin Hirst Carlos Caldas Marco A Marra Samuel Aparicio
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Nature
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Spatial proximity and similarity of the epigenetic state of genome domains.
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2012-04-04
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Ekaterina E Khrameeva Gennady G Fedonin Mikhail S Gelfand
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Andrey A Mironov Philipp Khaitovich
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PLOS ONE
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Computational inference of mRNA stability from histone modification and transcriptome profiles
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2012-04-10
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Yong Zhang
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Chengyang Wang Rui Tian Qian Zhao Han Xu Clifford A Meyer Cheng Li X Shirley Liu
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Nucleic Acids Research
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Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data.
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2012-04-12
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J Duitama
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Pramod K Srivastava Ion I Măndoiu
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BMC Genomics
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Rapid de novo evolution of X chromosome dosage compensation in Silene latifolia, a plant with young sex chromosomes.
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2012-04-17
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Niklaus Zemp
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Aline Muyle Clothilde Deschamps Sylvain Mousset Alex Widmer Gabriel A B Marais
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PLOS Biology
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KISSPLICE: de-novo calling alternative splicing events from RNA-seq data
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2012-04-19
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Pierre Peterlongo Marie-France Sagot
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Gustavo A T Sacomoto Janice Kielbassa Rayan Chikhi Raluca Uricaru Pavlos Antoniou Vincent Lacroix
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BMC Bioinformatics
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A context-based approach to identify the most likely mapping for RNA-seq experiments.
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2012-04-19
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Ralf Zimmer
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Thomas Bonfert Gergely Csaba Caroline C Friedel
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BMC Bioinformatics
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A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy
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2012-04-24
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Daniel S. Rokhsar Kranthi Varala
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Kankshita Swaminathan Won Byoung Chae Therese Mitros Liang Xie Adam Barling Katarzyna Glowacka Megan Hall Stanislaw Jezowski Ray Ming Matthew Hudson John A Juvik Stephen P Moose
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BMC Genomics
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RNA-SeQC: RNA-seq metrics for quality control and process optimization
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2012-04-25
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Gad Getz Wendy Winckler
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David S DeLuca Joshua Z Levin Andrey Sivachenko Timothy Fennell Marc-Danie Nazaire Chris Williams Michael Reich
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Bioinformatics
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Transcriptome profiling of the intoxication response of Tenebrio molitor larvae to Bacillus thuringiensis Cry3Aa protoxin
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2012-04-25
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Ana Conesa Diana Huestis Jeffrey A Fabrick Juan Luis Jurat-Fuentes
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Brenda Oppert Scot E Dowd Pascal Bouffard Lewyn Li Marcé D Lorenzen Michelle Toutges Jeremy Marshall Cris Oppert
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PLOS ONE
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Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution.
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2012-04-26
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Ralf Zimmer
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Lukas Windhager Thomas Bonfert Kaspar Burger Zsolt Ruzsics Stefan Krebs Stefanie Kaufmann Georg Malterer Anne L'Hernault Markus Schilhabel Stefan Schreiber Philip Rosenstiel Dirk Eick Caroline C Friedel Lars Dölken
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Genome Research
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Transcriptome sequencing revealed significant alteration of cortical promoter usage and splicing in schizophrenia.
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2012-04-27
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Jingqin Wu Xi Wang Murray J Cairns
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Natalie J Beveridge Paul A Tooney Rodney J Scott Vaughan J Carr
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PLOS ONE
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Comprehensive Genomic Profiling Of The Lung Transcriptome In Emphysema And IPF Using RNA-Seq
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2012-05
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John Quackenbush Naftali Kaminski
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Rebecca L. Kusko John Brothers II Gang Liu Lingqi Luo Brenda J. Guardela John R. Tedrow Yuriy Aleksyev Ivana V. Yang Mick Correll Mark Geraci Frank C. Sciurba Marc Lenburg David A. Schwartz Jennifer Beane Avrum Spira
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Concordant signaling pathways produced by pesticide exposure in mice correspond to pathways identified in human Parkinson's disease
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2012-05-01
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Olivier Elemento
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Seema Gollamudi Ashu Johri Noel Y Calingasan Lichuan Yang M Flint Beal
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PLOS ONE
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Utilizing RNA-Seq data for de novo coexpression network inference
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2012-05-03
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Shannon K McWeeney
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Ovidiu D Iancu Sunita Kawane Daniel Bottomly Robert Searles Robert Hitzemann
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Bioinformatics
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Identifying differentially expressed transcripts from RNA-seq data with biological variation.
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2012-05-03
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Magnus Rattray Antti Honkela
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Peter Glaus Antti Honkela
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Bioinformatics
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PhenoLink--a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains.
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2012-05-04
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Douwe Molenaar
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Jumamurat R Bayjanov Vesela Tzeneva Roland J Siezen Sacha A F T van Hijum
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BMC Genomics
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RNA-Seq identifies SNP markers for growth traits in rainbow trout
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2012-05-04
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Timothy D Leeds
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Mohamed Salem Roger L Vallejo Yniv Palti Sixin Liu Annas Sabbagh Caird E Rexroad Jianbo Yao
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PLOS ONE
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Gene mapping via bulked segregant RNA-Seq (BSR-Seq).
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2012-05-07
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Cheng-Ting Yeh Dan Nettleton Patrick S Schnable
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Sanzhen Liu Ho Man Tang
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PLOS ONE
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A simple strand-specific RNA-Seq library preparation protocol combining the Illumina TruSeq RNA and the dUTP methods.
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2012-05-15
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Marie-Laure Yaspo Hans Lehrach
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Marc Sultan Simon Dökel Vyacheslav Amstislavskiy Daniela Wuttig Holger Sültmann Marie-Laure Yaspo
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Biochemical and Biophysical Research Communications
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Transcriptome characterization by RNA-seq unravels the mechanisms of butyrate-induced epigenomic regulation in bovine cells.
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2012-05-15
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Weizhong Li
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Sitao Wu Robert W Li Cong-Jun Li
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PLOS ONE
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Transcriptome sequencing of and microarray development for a Helicoverpa zea cell line to investigate in vitro insect cell-baculovirus interactions
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2012-05-18
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Lars K. Nielsen Robin William Palfreyman Quan Nguyen
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Leslie C L Chan Steven Reid
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PLOS ONE
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RNA-seq analysis of differential gene expression in liver from lactating dairy cows divergent in negative energy balance.
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2012-05-20
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David J. Lynn Christopher J. Creevey David A Kenny
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Matthew McCabe Sinéad Waters Dermot Morris
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BMC Genomics
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Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns
|
2012-05-24
|
Anders Krogh Jun Wang Johannes Waage Joachim Weischenfeldt Bo Torben Porse Janus Schou Jakobsen Karsten Kristiansen
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Geng Tian Jing Zhao Inge Damgaard
|
Genome Biology
|
Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer
|
2012-05-25
|
Gavin Ha Daniel Lai Suet-feung Chin
|
Andrew Roth Ali Bashashati Jiarui Ding Rodrigo Goya Ryan Giuliany Jamie Rosner Arusha Oloumi Karey Shumansky Gulisa Turashvili Martin Hirst Marco A Marra Samuel Aparicio Sohrab P Shah Carlos Caldas
|
Genome Research
|
Dissect: detection and characterization of novel structural alterations in transcribed sequences
|
2012-06-01
|
Inanc Birol
|
Deniz Yorukoglu Faraz Hach Lucas Swanson Colin C Collins S Cenk Sahinalp
|
Bioinformatics
|
Trehalose-enhanced isolation of neuronal sub-types from adult mouse brain.
|
2012-06-01
|
Piero Carninci Yukihiko Noro
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Alka Saxena Akiko Wagatsuma Takenobu Kuji Atsuko Asaka-Oba Akira Watahiki Cecile Gurnot Michela Fagiolini Takao K Hensch
|
BioTechniques
|
Transcriptomic signatures of attachment, NF-κB suppression and IFN stimulation in the catfish gill following columnaris bacterial infection.
|
2012-06-02
|
Eric Peatman Shikai Liu
|
Fanyue Sun Chao Li Yanliang Jiang Zunchun Zhou Zhanjiang Liu
|
Developmental and Comparative Immunology
|
RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics
|
2012-06-08
|
John E. Lunn Björn Usadel Alisdair R Fernie Mark Stitt
|
Marc Lohse Anthony M Bolger Axel Nagel
|
Nucleic Acids Research
|
Integrated genome analysis suggests that most conserved non-coding sequences are regulatory factor binding sites
|
2012-06-08
|
Gabriel Kreiman Nicole Cloonan Sean M. Grimmond
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Martin Hemberg Jesse M Gray Scott Kuersten Michael E Greenberg
|
Nucleic Acids Research
|
Expression Profiling of a Heterogeneous Population of ncRNAs Employing a Mixed DNA/LNA Microarray.
|
2012-06-10
|
Marek Żywicki Marcel Scheideler Mathieu Rederstorff
|
Konstantinia Skreka Michael Karbiener Alexander Hüttenhofer
|
Journal of Nucleic Acids
|
Modeling gene expression using chromatin features in various cellular contexts
|
2012-06-13
|
Roderic Guigó i Serra Mark Bender Gerstein Ewan Birney Sarah Djebali Xianjun Dong Anshul Kundaje Thomas R. Gingeras
|
Melissa C Greven James B Brown Chao Cheng Zhiping Weng
|
Genome Biology
|
Identification of PTK6, via RNA sequencing analysis, as a suppressor of esophageal squamous cell carcinoma.
|
2012-06-13
|
Stephanie Ma Li Fu Xin-Yuan Guan Xin-Yuan Guan
|
Jessie Y J Bao Pak Shing Kwan Yuen Piu Chan Carol M Tong Na Zhang Amy H Y Tong Yan-Ru Qin Sai Wah Tsao Kwok Wah Chan Si Lok
|
Gastroenterology
|
Alternative splicing regulated by butyrate in bovine epithelial cells.
|
2012-06-14
|
Wen Huang Weizhong Li
|
Sitao Wu Congjun Li Robert W Li
|
PLOS ONE
|
Bellerophontes: an RNA-Seq data analysis framework for chimeric transcripts discovery based on accurate fusion model.
|
2012-06-17
|
Alberto Ferrarini Elisa Ficarra Simona Soverini Giovanni Martinelli Ilaria Iacobucci
|
Francesco Abate Andrea Acquaviva Giulia Paciello Carmelo Foti Massimo Delledonne Enrico Macii
|
Bioinformatics
|
Transcriptomic analysis of the stress response to weaning at housing in bovine leukocytes using RNA-seq technology.
|
2012-06-18
|
Sean Doyle David J. Lynn Bernadette Earley
|
Aran O'Loughlin Mark McGee Matthew McCabe
|
BMC Genomics
|
Detecting differential usage of exons from RNA-seq data
|
2012-06-21
|
Alejandro Reyes Simon Anders Wolfgang Huber
|
|
Genome Research
|
PM-Seq: Using Finite Poisson Mixture Models for RNA-Seq Data Analysis and Transcript Expression Level Quantification
|
2012-06-21
|
Zhaohui Steve Qin
|
Han Wu Yu Zhu
|
Statistics in biosciences
|
Expressed pseudogenes in the transcriptional landscape of human cancers
|
2012-06-22
|
John R. Prensner Shanker Kalyana-Sundaram Chandan Kumar-Sinha Irfan Asangani Nallasivam Palanisamy
|
Sunita Shankar Dan R Robinson Yi-Mi Wu Xuhong Cao Vishal Kothari Robert J Lonigro Matthew K Iyer Terrence Barrette Achiraman Shanmugam Saravana M Dhanasekaran Arul M Chinnaiyan
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Cell
|
RNA-Seq and human complex diseases: recent accomplishments and future perspectives.
|
2012-06-27
|
Valerio Costa
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Marianna Aprile Roberta Esposito Alfredo Ciccodicola
|
European Journal of Human Genetics
|
FusionFinder: a software tool to identify expressed gene fusion candidates from RNA-Seq data.
|
2012-06-27
|
Richard W Francis Kim Carter Denise Anderson Alex H. Beesley
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Katherine Thompson-Wicking Ursula R Kees
|
PLOS ONE
|
A systematic comparison and evaluation of high density exon arrays and RNA-seq technology used to unravel the peripheral blood transcriptome of sickle cell disease.
|
2012-06-29
|
Gregory J. Kato
|
Nalini Raghavachari Jennifer Barb Yanqin Yang Poching Liu Kimberly Woodhouse Daniel Levy Christopher J O'Donnell Peter J Munson
|
BMC Medical Genomics
|
SAVoR: a server for sequencing annotation and visualization of RNA structures
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2012-07
|
Otto Valladares Fan Li
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Paul Ryvkin Daniel M Childress Brian D Gregory Li-San Wang
|
Nucleic Acids Research
|
Digging in the RNA-seq Garbage: Evaluating the Characteristics of Unmapped RNA-seq Reads in Normal Tissues
|
2012-07
|
Federica Cavallo
|
Matteo Carrara Maddalena Arigoni Raffaele A. Calogero
|
|
Molecular and developmental contributions to divergent pigment patterns in marine and freshwater sticklebacks
|
2012-07-01
|
Catherine L Peichel
|
Anna K Greenwood Jennifer N Cech
|
Evolution & Development
|
Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions
|
2012-07-01
|
Iros Barozzi Gioacchino Natoli
|
Dev M Bhatt Amy Pandya-Jones Ann-Jay Tong Michelle M Lissner Douglas L Black Stephen T Smale
|
Cell
|
RNA-seq analysis of the C. briggsae transcriptome.
|
2012-07-06
|
Bora Uyar
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Jeffrey S C Chu Ismael A Vergara Shu Yi Chua Martin R Jones Tammy Wong David L Baillie Nansheng Chen
|
Genome Research
|
Incorporating RNA-seq data into the zebrafish Ensembl genebuild
|
2012-07-12
|
Simon White
|
John E Collins Stephen M J Searle Derek L Stemple
|
Genome Research
|
Paired-end sequencing of Fosmid libraries by Illumina.
|
2012-07-16
|
Gad Getz Chad Nusbaum Yotam Drier
|
Louise J S Williams Diana G Tabbaa Na Li Aaron M Berlin Terrance P Shea Iain Maccallum Michael S Lawrence Sarah K Young David B Jaffe Andreas Gnirke
|
Genome Research
|
Inflammatory priming predisposes mice to age-related retinal degeneration.
|
2012-07-17
|
Krzysztof Palczewski
|
Debarshi Mustafi Tadao Maeda Hideo Kohno Joseph H Nadeau
|
Journal of Clinical Investigation
|
RNA processing in the minimal organism Nanoarchaeum equitans
|
2012-07-18
|
L Randau
|
Lennart Randau
|
Genome Biology
|
Transcript profiling reveals complex auxin signalling pathway and transcription regulation involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton
|
2012-07-20
|
Daojun Yuan
|
Xiyan Yang Xianlong Zhang Fangyan Jin Yunchao Zhang Jiao Xu
|
BMC Plant Biology
|
Genomic imprinting absent in Drosophila melanogaster adult females.
|
2012-07-20
|
C Joel McManus Brenton R. Graveley
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Joseph D Coolon Kraig R Stevenson Patricia J Wittkopp
|
Cell Reports
|
Differential gene expression in tamoxifen-resistant breast cancer cells revealed by a new analytical model of RNA-Seq data
|
2012-07-23
|
Willard M. Freeman Kent Vrana
|
Kathryn J Huber-Keener Xiuping Liu Zhong Wang Yaqun Wang Song Wu Maricarmen D Planas-Silva Xingcong Ren Yan Cheng Yi Zhang Chang-Gong Liu Jin-Ming Yang Rongling Wu
|
PLOS ONE
|
Metabolic Regulation of "Ca. Methylacidiphilum Fumariolicum" SolV Cells Grown Under Different Nitrogen and Oxygen Limitations.
|
2012-07-25
|
Huub J.M. Op den Camp
|
Ahmad F Khadem Arjan Pol Adam S Wieczorek Mike S M Jetten
|
Frontiers in Microbiology
|
Effects of drought on gene expression in maize reproductive and leaf meristem tissue revealed by RNA-Seq.
|
2012-07-26
|
Akshay Kakumanu Andy Pereira
|
Madana M R Ambavaram Curtis Klumas Arjun Krishnan Utlwang Batlang Elijah Myers Ruth Grene
|
Plant Physiology
|
Identification of miRNA signatures during the differentiation of hESCs into retinal pigment epithelial cells.
|
2012-07-27
|
Guoping Fan
|
Ganlu Hu Kevin Huang Juehua Yu Sailesh Gopalakrishna-Pillai Jun Kong He Xu Zhenshan Liu Kunshan Zhang Jun Xu Yuping Luo Siguang Li Yi E Sun Linda E Iverson Zhigang Xue
|
PLOS ONE
|
Identification of novel transcripts deregulated in buccal cancer by RNA-seq.
|
2012-07-27
|
Ajai K. Tripathi Subhash J Jakhesara Chaitanya G. Joshi
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Manisha R Sajnani Amrutlal K Patel Vaibhav D Bhatt Viral B Ahir Vangipuram Shankar Siddharth Shah Tejas M Shah Prakash G Koringa
|
Gene
|
Mili and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis
|
2012-07-29
|
Anastassios Vourekas Panagiotis Alexiou Manolis Maragkakis Yohei Kirino Zissimos Mourelatos
|
Qi Zheng Brian D Gregory
|
Nature Structural & Molecular Biology
|
A mutation in the PP2C phosphatase gene in a Staphylococcus aureus USA300 clinical isolate with reduced susceptibility to vancomycin and daptomycin.
|
2012-07-30
|
Karla D Passalacqua
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Sarah W Satola Emily K Crispell Timothy D Read
|
Antimicrobial Agents and Chemotherapy
|
easyRNASeq: a bioconductor package for processing RNA-Seq data
|
2012-07-30
|
Eileen E. M. Furlong Lars M Steinmetz
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Nicolas Delhomme Ismaël Padioleau
|
Bioinformatics
|
RNASeq profiling of UTR expression during neuronal plasticity.
|
2012-07-31
|
Robert M. Flight Jeffrey C. Petruska
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Benjamin J Harrison Abdallah Eteleeb Eric C Rouchka
|
BMC Bioinformatics
|
Recurrent R-spondin fusions in colon cancer.
|
2012-08-01
|
Robert Gentleman
|
Somasekar Seshagiri Eric W Stawiski Steffen Durinck Zora Modrusan Elaine E Storm Caitlin B Conboy Subhra Chaudhuri Yinghui Guan Vasantharajan Janakiraman Bijay S Jaiswal Joseph Guillory Connie Ha Gerrit J P Dijkgraaf Jeremy Stinson Florian Gnad Melanie A Huntley Jeremiah D Degenhardt Peter M Haverty Richard Bourgon Weiru Wang Hartmut Koeppen Timothy K Starr Zemin Zhang David A Largaespada Thomas D Wu Frederic J de Sauvage
|
Nature
|
Discovery and characterization of new transcripts from RNA-seq data in mouse CD4(+) T cells.
|
2012-08-04
|
Stéphane Poulain Andrew Paul Hutchins Hodaka Fujii
|
Diego Miranda-Saavedra
|
Genomics
|
Transcriptome profiling of resistant and susceptible Cavendish banana roots following inoculation with Fusarium oxysporum f. sp. cubense tropical race 4.
|
2012-08-05
|
Altus Viljoen
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Chun-Yu Li Gui-Ming Deng Jing Yang Yan Jin Rui-Bin Kuang Cun-Wu Zuo Zhi-Cheng Lv Qiao-Song Yang Ou Sheng Yue-Rong Wei Chun-Hua Hu Tao Dong Gan-Jun Yi
|
BMC Genomics
|
Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples.
|
2012-08-08
|
Vincent Lynch
|
Günter P Wagner Koryu Kin
|
Theory in Biosciences
|
RNA-Seq provides new insights in the transcriptome responses induced by the carcinogen benzo[a]pyrene.
|
2012-08-13
|
Stan Gaj Hans Lehrach Ralf Herwig Jos Kleinjans
|
Joost van Delft Stan Gaj Matthias Lienhard Marcus W Albrecht Alexander Kirpiy Karen Brauers Sandra Claessen Daneida Lizarraga
|
Toxicological Sciences
|
Temperature during embryonic development has persistent effects on thermal acclimation capacity in zebrafish.
|
2012-08-13
|
Ian A Johnston
|
Graham R Scott
|
Proceedings of the National Academy of Sciences of the United States of America
|
Proteogenomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins.
|
2012-08-16
|
Peter A. DiMaggio Barry M Zee
|
Gary LeRoy Iouri Chepelev Mario A Blanco Keji Zhao Benjamin A Garcia
|
Genome Biology
|
Proteomics and deep sequencing comparison of seasonally active venom glands in the platypus reveals novel venom peptides and distinct expression profiles.
|
2012-08-16
|
Marilyn Renfree Anthony T. Papenfuss Emily S Wong Camilla M Whittington Glenn F King
|
David Morgenstern Ehtesham Mofiz Sara Gombert Katrina M Morris Peter Temple-Smith Wesley C Warren Katherine Belov
|
Molecular & Cellular Proteomics
|
RNA-seq transcriptome analysis of male and female zebra finch cell lines
|
2012-08-21
|
Christopher N. Balakrishnan Ya-Chi Lin Sarah E London David F. Clayton
|
Christopher N Balakrishnan Ya-Chi Lin Sarah E London David F Clayton
|
Genomics
|
Detecting transcription of ribosomal protein pseudogenes in diverse human tissues from RNA-seq data
|
2012-08-21
|
Shaojie Zhang
|
Peter Tonner Vinodh Srinivasasainagendra Degui Zhi
|
BMC Genomics
|
Research resource: RNA-Seq reveals unique features of the pancreatic β-cell transcriptome.
|
2012-08-21
|
Michael McManus Hail Kim
|
Gregory M Ku Ian W Vaughn Matthew J Hangauer Chang Myung Oh Michael S German
|
Molecular Endocrinology
|
shortran: a pipeline for small RNA-seq data analysis.
|
2012-08-22
|
Stig Uggerhøj Andersen Jens Stougaard
|
Vikas Gupta Katharina Markmann Christian N S Pedersen
|
Bioinformatics
|
Strand-specific RNA-seq reveals ordered patterns of sense and antisense transcription in Bacillus anthracis
|
2012-08-22
|
Karla D Passalacqua
|
Anjana Varadarajan Charlotte Weist Brian D Ondov Benjamin Byrd Timothy D Read Nicholas H Bergman
|
PLOS ONE
|
GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data.
|
2012-08-24
|
Yong Zhang
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Jianxing Feng Clifford A Meyer Qian Wang Jun S Liu X Shirley Liu
|
Bioinformatics
|
An injury-response mechanism conserved across kingdoms determines entry of the fungus Trichoderma atroviride into development.
|
2012-08-27
|
Miguel Hernández-Oñate Alfredo Herrera-Estrella
|
Edgardo U Esquivel-Naranjo Artemio Mendoza-Mendoza Alison Stewart
|
Proceedings of the National Academy of Sciences of the United States of America
|
A simple and novel method for RNA-seq library preparation of single cell cDNA analysis by hyperactive Tn5 transposase.
|
2012-08-28
|
Anna Terry Niall G. Campbell Charles Mein
|
Scott Brouilette Scott Kuersten Monika Bozek Kerith-Rae Dias Leena Bhaw-Rosun Yasunori Shintani Steven Coppen Chiho Ikebe Vinit Sawhney Masahiro Kaneko Nobuko Tano Hidekazu Ishida Ken Suzuki Kenta Yashiro
|
Developmental Dynamics
|
A putative role for amino acid permeases in sink-source communication of barley tissues uncovered by RNA-seq.
|
2012-08-30
|
Winfriede Weschke
|
Stefan Kohl Julien Hollmann Frank R Blattner Volodymyr Radchuk Franka Andersch Burkhard Steuernagel Thomas Schmutzer Uwe Scholz Karin Krupinska Hans Weber
|
BMC Plant Biology
|
Allele-biased expression in differentiating human neurons: implications for neuropsychiatric disorders
|
2012-08-30
|
Deyou Zheng
|
Mingyan Lin Anastasia Hrabovsky Erika Pedrosa Tao Wang Herbert M Lachman
|
PLOS ONE
|
RNA-Seq of early-infected poplar leaves by the rust pathogen Melampsora larici-populina uncovers PtSultr3;5, a fungal-induced host sulfate transporter
|
2012-08-30
|
Nicolas Rouhier Julie Poulain Benjamin Petre Sébastien Duplessis Corinne Da Silva Francis Martin Emmanuelle Morin Annegret Kohler
|
Emilie Tisserant Stéphane Hacquard Christine Delaruelle
|
PLOS ONE
|
Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs
|
2012-09
|
Roderic Guigó i Serra Sarah Djebali Rory Johnson Thomas R. Gingeras
|
Hagen Tilgner David G Knowles Carrie A Davis Sudipto Chakrabortty João Curado Michael Snyder
|
Genome Research
|
Dual RNA-seq of pathogen and host.
|
2012-09-01
|
Alexander Westermann Jörg Vogel
|
Stanislaw A Gorski
|
Nature Reviews Microbiology
|
Long noncoding RNAs are rarely translated in two human cell lines
|
2012-09-01
|
Yanbao Yu Anshul Kundaje Brian D Strahl Krzysztof Krajewski
|
Balázs Bánfai Hui Jia Jainab Khatun Emily Wood Brian Risk William E Gundling Harsha P Gunawardena Ling Xie Xian Chen Peter Bickel Morgan C Giddings James B Brown Leonard Lipovich
|
Genome Research
|
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.
|
2012-09-01
|
Andrea Tanzer Jose M Gonzalez Bronwen Aken Tim Hubbard Jennifer Harrow Felix Kokocinski Roderic Guigó i Serra Cédric Howald Thibaut Hourlier Thomas Derrien Alexandre Reymond Simon White Adam Frankish
|
Jacqueline Chrast Nathalie Walters Jan-Hinnerk Vogel Stephen Searle
|
Genome Research
|
Initial characterization of shade avoidance response suggests functional diversity between Populus phytochrome B genes.
|
2012-09-03
|
Xiaohan Yang Gerald A Tuskan Sara S Jawdy Lee Gunter Stan D Wullschleger
|
Abhijit A Karve Sara M Allen David J Weston
|
New Phytologist
|
The grapevine expression atlas reveals a deep transcriptome shift driving the entire plant into a maturation program.
|
2012-09-04
|
Silvia Dal Santo Giovanni Battista Tornielli Vittorio Murino Luca Venturini Lorenzo Farina
|
Marianna Fasoli Sara Zenoni Anita Zamboni Andrea Porceddu Manuele Bicego Alberto Ferrarini Massimo Delledonne Mario Pezzotti
|
The Plant Cell
|
A novel computational strategy to identify A-to-I RNA editing sites by RNA-Seq data: de novo detection in human spinal cord tissue
|
2012-09-05
|
Graziano Pesole Angela Gallo Ernesto Picardi
|
Federica Galeano Sara Tomaselli
|
PLOS ONE
|
Modelling and simulating generic RNA-Seq experiments with the flux simulator.
|
2012-09-07
|
Roderic Guigó i Serra Michael Sammeth
|
Thasso Griebel Benedikt Zacher Paolo Ribeca Emanuele Raineri Vincent Lacroix
|
Nucleic Acids Research
|
Comparative transcriptome analyses of deltamethrin-resistant and -susceptible Anopheles gambiae mosquitoes from Kenya by RNA-Seq
|
2012-09-07
|
Mariangela Bonnizoni Guiyun Yan
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Yaw Afrane William Augustine Dunn Francis K Atieli Goufa Zhou Daibin Zhong Jun Li Andrew Githeko
|
PLOS ONE
|
Id2a functions to limit Notch pathway activity and thereby influence the transition from proliferation to differentiation of retinoblasts during zebrafish retinogenesis.
|
2012-09-08
|
Taejoon Kwon Rosa A Uribe Jeffrey M Gross
|
|
Developmental Biology
|
A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae.
|
2012-09-10
|
Jens Nielsen Natapol Pornputtapong Linn Fagerberg Intawat Nookaew
|
Marta Papini Gionata Scalcinati Matthias Uhlén
|
Nucleic Acids Research
|
Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production.
|
2012-09-11
|
Todd P Michael
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Chongyuan Luo David J Sidote Yi Zhang Randall A Kerstetter Eric Lam
|
The Plant Journal
|
The bench scientist's guide to statistical analysis of RNA-Seq data.
|
2012-09-14
|
Craig R Yendrek
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Elizabeth A Ainsworth Jyothi Thimmapuram
|
BMC Research Notes
|
Gene expression changes in a tumor xenograft by a pyrrole-imidazole polyamide.
|
2012-09-17
|
Georgi K Marinov Peter Dervan
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Jevgenij A Raskatov Nicholas G Nickols Amanda E Hargrove Barbara Wold
|
Proceedings of the National Academy of Sciences of the United States of America
|
Heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma cells
|
2012-09-18
|
Harri Lähdesmäki Vivek Anantharaman Lakshminarayanan Aravind Tarmo Aijö John Gagnon Xing Chang
|
Micah J Benson Tarmo Aijö Utz J Pape Juha-Pekka Pursiheimo Shalini Oberdoerffer X Shirley Liu Riitta Lahesmaa Anjana Rao
|
Proceedings of the National Academy of Sciences of the United States of America
|
Functional transcriptomics of a migrating cell in Caenorhabditis elegans.
|
2012-09-18
|
Erich M Schwarz Paul W. Sternberg
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Mihoko Kato
|
Proceedings of the National Academy of Sciences of the United States of America
|
Differential Expression Analysis for RNA-Seq Data.
|
2012-09-20
|
Alok Bhattacharya
|
Rashi Gupta Isha Dewan Richa Bharti
|
ISRN bioinformatics
|
A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters
|
2012-09-20
|
Yi Zheng
|
Yun-Ru Chen Bao Liu Silin Zhong Jim Giovannoni Zhangjun Fei
|
Plant Methods
|
High-resolution transcriptome of human macrophages.
|
2012-09-21
|
Joachim Schultze Andrea Nino-Castro
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Marc Beyer Michael R Mallmann Jia Xue Andrea Staratschek-Jox Daniela Vorholt Wolfgang Krebs Daniel Sommer Jil Sander Christina Mertens Susanne V Schmidt
|
PLOS ONE
|
A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data.
|
2012-09-22
|
Hao Wu Zhijin Wu
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Chi Wang
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Biostatistics
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Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments.
|
2012-09-24
|
Axel Künstner
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Nagarjun Vijay Jelmer W Poelstra Jochen B W Wolf
|
Molecular Ecology
|
RNA-Seq Assembly - Are We There Yet?
|
2012-09-25
|
Andrea Bräutigam
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Simon Schliesky Udo Gowik Andreas P M Weber
|
Frontiers in Plant Science
|
Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3.
|
2012-09-26
|
Peggy Farnham
|
Seth Frietze Rui Wang Lijing Yao Yu Gyoung Tak Zhenqing Ye Malaina Gaddis Heather Witt Victor X Jin
|
Genome Biology
|
A next-generation sequencing approach to study the transcriptomic changes during the differentiation of physarum at the single-cell level.
|
2012-10-01
|
Israel Barrantes Jeremy Leipzig
|
Wolfgang Marwan
|
Gene Regulation and Systems Biology
|
The Snail family member Worniu is continuously required in neuroblasts to prevent Elav-induced premature differentiation
|
2012-10-01
|
Sen-Lin Lai
|
Michael R Miller Kristin J Robinson Chris Q Doe
|
Developmental Cell
|
Dual lineage-specific expression of Sox17 during mouse embryogenesis.
|
2012-10-01
|
Momoko Yoshimoto Mark A. Magnuson Elisabetta Manduchi Anne Grapin-Botton
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Eunyoung Choi Marine R C Kraus Laurence A Lemaire Sasidhar Vemula Leah A Potter Christian J Stoeckert
|
Stem Cells
|
Comprehensive genomic profiling of the lung transcriptome in emphysema and idiopathic pulmonary fibrosis using RNA-Seq.
|
2012-10-01
|
Jennifer Beane John Quackenbush Naftali Kaminski
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Rebecca L Kusko John Brothers Gang Liu Lingqi Luo Brenda Juan Guardela John Tedrow Yuriy Aleksyev Ivana V Yang Mick Correll Mark Geraci Frank Sciurba Marc Lenburg David A Schwartz Avrum Spira
|
BMC Proceedings
|
SERE: single-parameter quality control and sample comparison for RNA-Seq.
|
2012-10-03
|
Rahul Kanwar
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Stefan K Schulze Meike Gölzenleuchter Terry M Therneau Andreas S Beutler
|
BMC Genomics
|
Evaluation of different reference based annotation strategies using RNA-Seq - a case study in Drososphila pseudoobscura.
|
2012-10-03
|
Anton Suvorov
|
Nicola Palmieri Viola Nolte Carolin Kosiol Christian Schlötterer
|
PLOS ONE
|
Systems and trans-system level analysis identifies conserved iron deficiency responses in the plant lineage.
|
2012-10-05
|
David Casero Eugen Urzica Crysten E Blaby-Haas Matteo Pellegrini Sabeeha Merchant
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Hiroaki Yamasaki Scott I Hsieh Lital N Adler Steven J Karpowicz Steven G Clarke Joseph A Loo
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The Plant Cell
|
Identification of novel splice variants in horn cancer by RNA-Seq analysis in Zebu cattle.
|
2012-10-10
|
Subhash J Jakhesara Chaitanya G. Joshi Ajai K. Tripathi
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Amrutlal K Patel Vaibhav D Bhatt Manisha R Sajnani Prakash G Koringa
|
Genomics
|
New partners in regulation of gene expression: the enhancer of Trithorax and Polycomb Corto interacts with methylated ribosomal protein l12 via its chromodomain.
|
2012-10-11
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Julien Rougeot Anne Coléno-Costes Jean-Michel Gibert Frédérique Peronnet Stéphane Le Crom
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Suk Min Jang Augustin de Vanssay Tahar Bouceba Neel B Randsholt Emmanuèle Mouchel-Vielh Sébastien Bloyer
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PLOS Genetics
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Faster-X evolution of gene expression in Drosophila
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2012-10-11
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Richard P Meisel
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John H Malone Andrew G Clark
|
PLOS Genetics
|
Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads.
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2012-10-11
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Wei Li
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Tao Jiang
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Bioinformatics
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Identification of hundreds of novel UPF1 target transcripts by direct determination of whole transcriptome stability.
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2012-10-12
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Naoto Imamachi Hidenori Tani
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Kazi Abdus Salam Rena Mizutani Kenichi Ijiri Takuma Irie Tetsushi Yada Yutaka Suzuki Nobuyoshi Akimitsu
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RNA Biology
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The proteome of copper, iron, zinc, and manganese micronutrient deficiency in Chlamydomonas reinhardtii.
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2012-10-13
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Eugen Urzica David Casero Matteo Pellegrini Sabeeha Merchant
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Scott I Hsieh Madeli Castruita Davin Malasarn Jonathan Erde M Dudley Page Hiroaki Yamasaki Joseph A Loo
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Molecular & Cellular Proteomics
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High levels of gene expression explain the strong evolutionary constraint of mitochondrial protein-coding genes.
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2012-10-15
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Hans Ellegren
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Benoit Nabholz Jochen B W Wolf
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Molecular Biology and Evolution
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The biology of nematode- and IL4Rα-dependent murine macrophage polarization in vivo as defined by RNA-Seq and targeted lipidomics.
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2012-10-16
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Graham D Thomas Dominik Ruckerl Phillip D. Whitfield Mark Blaxter Judith Allen
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Benjamin H Maskrey
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Blood
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A bioinformatics approach for integrated transcriptomic and proteomic comparative analyses of model and non-sequenced anopheline vectors of human malaria parasites.
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2012-10-17
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David R. Colquhoun Jürgen Hartler Gerhard G Thallinger Jesus Martinez-Barnetche Antonis Rokas Rhoel Dinglasan
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Ceereena Ubaida Mohien Derrick K Mathias John G Gibbons Jennifer S Armistead Maria C Rodriguez Mario Henry Rodriguez Nathan J Edwards David R Graham
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Molecular & Cellular Proteomics
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Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript.
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2012-10-23
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Matteo Benelli Marco Severgnini Alberto Magi
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Chiara Pescucci Giuseppina Marseglia Francesca Torricelli
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Bioinformatics
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Molecular aspects of mucin biosynthesis and mucus formation in the bovine cervix during the periestrous period.
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2012-10-23
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Paul A McGettigan Jane A Irwin Alan Baird Brendan Loftus
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Katarzyna Pluta Colm J Reid John A Browne Tharmala Tharmalingam Anthony Corfield Alexander C O Evans Stephen D Carrington
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Physiological Genomics
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Transcriptomic profiling of the oyster pathogen Vibrio splendidus opens a window on the evolutionary dynamics of the small RNA repertoire in the Vibrio genus
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2012-10-24
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Daniel Gautheret Philippe Bouloc Annick Jacq
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Claire Toffano-Nioche An N Nguyen Claire Kuchly Alban Ott
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RNA
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STAR: ultrafast universal RNA-seq aligner
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2012-10-25
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Philippe Batut Thomas R. Gingeras
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Alexander Dobin Carrie A Davis Felix Schlesinger Jorg Drenkow Chris Zaleski Sonali Jha Mark Chaisson
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Bioinformatics
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Transcription factor Amr1 induces melanin biosynthesis and suppresses virulence in Alternaria brassicicola
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2012-10-25
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Igor V Grigoriev
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Yangrae Cho Akhil Srivastava Robin A Ohm Christopher B Lawrence Koon-Hui Wang Sharadchandra P Marahatta
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PLOS Pathogens
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RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.
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2012-10-25
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Matthew Berriman
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Jonathan D Stoltzfus Samuel Minot Thomas J Nolan James B Lok
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PLOS Neglected Tropical Diseases
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The Population Genomics of Sunflowers and Genomic Determinants of Protein Evolution Revealed by RNAseq.
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2012-10-25
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Nolan Kane Brook T Moyers Sébastien Renaut Loren H. Rieseberg
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Christopher J Grassa
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Biology
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Identification of cold-responsive genes in a New Zealand alpine stick insect using RNA-Seq.
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2012-10-27
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Richard D Newcomb Thomas R. Buckley Duckchul Park Brent J Sinclair Alice B Dennis Luke T Dunning
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Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics
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Identification of PADI2 as a potential breast cancer biomarker and therapeutic target.
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2012-10-30
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Obi Griffith Venkataraman Subramanian John L. McElwee Brian D Cherrington Louise R Howe
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Sunish Mohanan Heike C Breuer Lynne J Anguish Ashley M Palmer Corey P Causey Paul R Thompson Joe W Gray Scott A Coonrod
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BMC Cancer
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Interaction of cyclin-dependent kinase 12/CrkRS with cyclin K1 is required for the phosphorylation of the C-terminal domain of RNA polymerase II
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2012-11
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Jerry F. Tien Malachi Griffith Gregg B Morin
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S-W Grace Cheng Michael A Kuzyk Annie Moradian Taka-Aki Ichu Vicky C-D Chang Sarah E Vollett Marco A Marra
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Molecular and Cellular Biology
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Age-related changes of gene expression in the neocortex: preliminary data on RNA-Seq of the transcriptome in three functionally distinct cortical areas.
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2012-11-01
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Dean Palejev Flora M. Vaccarino
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Oksana Yu Naumova Natalia V Vlasova Maria Lee Sergei Yu Rychkov Olga N Babich Elena L Grigorenko
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Development and Psychopathology
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Resolving candidate genes of mouse skeletal muscle QTL via RNA-Seq and expression network analyses
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2012-11-05
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Andrew M Carroll Caroline Meharg David J Vandenbergh
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Arimantas Lionikas Jonathan Mj Derry Aivaras Ratkevicius David A Blizard
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BMC Genomics
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Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote
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2012-11-05
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Shikai Liu Eric Peatman Geoff Waldbieser Huseyin Kucuktas
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Yu Zhang Zunchun Zhou Geoff Waldbieser Fanyue Sun Jianguo Lu Jiaren Zhang Yanliang Jiang Hao Zhang Xiuli Wang K V Rajendran Lester Khoo Zhanjiang Liu
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BMC Genomics
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Novel BRD4-NUT fusion isoforms increase the pathogenic complexity in NUT midline carcinoma.
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2012-11-05
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Adrian K. Charles Alex H. Beesley
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K Thompson-Wicking R W Francis A Stirnweiss E Ferrari M D Welch E Baker A R Murch A M Gout K W Carter M B Phillips U R Kees
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Oncogene
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Prediction of altered 3'- UTR miRNA-binding sites from RNA-Seq data: the swine leukocyte antigen complex (SLA) as a model region
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2012-11-06
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Marie-Laure Endale Ahanda Dario Beraldi Jordi Estellé Claire Rogel-Gaillard James M Reecy
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Eric R Fritz Zhi-Liang Hu Ole Madsen Martien A M Groenen Ronan Kapetanovic David A Hume Robert R R Rowland Joan K Lunney Elisabetta Giuffra
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PLOS ONE
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Simultaneous RNA-seq analysis of a mixed transcriptome of rice and blast fungus interaction.
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2012-11-06
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Takeshi Itoh
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Yoshihiro Kawahara Youko Oono Hiroyuki Kanamori Takashi Matsumoto Eiichi Minami
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PLOS ONE
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DiffSplice: the genome-wide detection of differential splicing events with RNA-seq.
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2012-11-15
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D. Neil Hayes
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Yin Hu Yan Huang Ying Du Christian F Orellana Darshan Singh Amy R Johnson Anaïs Monroy Pei-Fen Kuan Scott M Hammond Liza Makowski Scott H Randell Derek Y Chiang Corbin Jones Yufeng Liu Jan F Prins Jinze Liu
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Nucleic Acids Research
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Methods, Challenges and Potentials of Single Cell RNA-seq.
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2012-11-16
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Daniel Hebenstreit
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Biology
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The AHL- and BDSF-dependent quorum sensing systems control specific and overlapping sets of genes in Burkholderia cenocepacia H111.
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2012-11-20
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Aurelien L Carlier Christian H Ahrens Ulrich Omasits Gabriella Pessi
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Nadine Schmid Yinyue Deng Claudio Aguilar Alexander Grunau Lian-Hui Zhang Leo Eberl
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PLOS ONE
|
Intron-centric estimation of alternative splicing from RNA-seq data.
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2012-11-21
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Roderic Guigó i Serra
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Dmitri D Pervouchine David G Knowles
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Bioinformatics
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High-throughput sequencing of the melanoma genome.
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2012-11-22
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Janet Kelso
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Manfred Kunz Michael Dannemann
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Experimental Dermatology
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A comprehensive analysis of the Manduca sexta immunotranscriptome.
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2012-11-23
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Haobo Jiang
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Ramesh T Gunaratna
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Developmental and Comparative Immunology
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Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching.
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2012-11-24
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Charles Plessy Piero Carninci
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Dave T P Tang Md Salimullah Ana Maria Suzuki Raffaella Calligaris Stefano Gustincich
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Nucleic Acids Research
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iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data
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2012-11-29
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Derek Y Chiang Michael Brudno
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Aziz M Mezlini Eric J M Smith Marc Fiume Orion Buske Gleb L Savich Sohrab Shah Sam Aparicio Anna Goldenberg
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Genome Research
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Nuclear RNA sequencing of the mouse erythroid cell transcriptome
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2012-11-29
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Chih-Yu Chen Jennifer A. Mitchell Ieuan Clay Peter Fraser
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David Umlauf Catherine A Moir Christopher H Eskiw Stefan Schoenfelder Lyubomira Chakalova Takashi Nagano
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PLOS ONE
|
The diverse applications of RNA-seq for functional genomic studies in Aspergillus fumigatus.
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2012-12-01
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Xiaofan Zhou Antonis Rokas
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John G Gibbons Anne Beauvais Jean-Paul Latgé
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Annals of the New York Academy of Sciences
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An RNA-seq-based gene expression profiling of radiation-induced tumorigenic mammary epithelial cells.
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2012-12-04
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Songnian Hu
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Lina Ma Linghu Nie Jing Liu Bing Zhang Shuhui Song Min Sun Jin Yang Yadong Yang Xiangdong Fang Yongliang Zhao Jun Yu
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Genomics Proteomics and Bioinformatics
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A histone deacetylase adjusts transcription kinetics at coding sequences during Candida albicans morphogenesis.
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2012-12-06
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Alexander Stark Denes Hnisz Karl Kuchler
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Anaïs F Bardet Clarissa J Nobile Andriy Petryshyn Walter Glaser Ulrike Schöck
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PLOS Genetics
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The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells.
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2012-12-06
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Wolf Reik Felix Krueger Bernard Thienpont Julia Arand
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Stefanie Seisenberger Simon Andrews Jörn Walter Fátima Santos Christian Popp Wendy Dean
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Molecular Cell
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RNA-Seq vs dual- and single-channel microarray data: sensitivity analysis for differential expression and clustering
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2012-12-10
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Martin Crane
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Alina Sîrbu Gráinne Kerr Heather J Ruskin
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PLOS ONE
|
Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study.
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2012-12-13
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Andrew C Perkins Timothy L. Bailey
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Lei Sun Zhihua Zhang Michael R Tallack Zhao Xu Hui Liu
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BMC Bioinformatics
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Chromatin is an ancient innovation conserved between Archaea and Eukarya.
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2012-12-13
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Corey Nislow Gary D. Bader
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Ron Ammar Dax Torti Kyle Tsui Marinella Gebbia Tanja Durbic Guri Giaever
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eLife
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RNA-Seq analysis implicates dysregulation of the immune system in schizophrenia
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2012-12-17
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Xiangning Chen
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Junzhe Xu Jingchun Sun Jingchun Chen Lily Wang Anna Li Matthew Helm Steven L Dubovsky Silviu-Alin Bacanu Zhongming Zhao
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BMC Genomics
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A specialized ABC efflux transporter GcABC-G1 confers monoterpene resistance to Grosmannia clavigera, a bark beetle-associated fungal pathogen of pine trees.
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2012-12-17
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Jörg Bohlmann
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Ye Wang Lynette Lim Scott DiGuistini Gordon Robertson Colette Breuil
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New Phytologist
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Circular RNAs are abundant, conserved, and associated with ALU repeats.
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2012-12-18
|
Norman Sharpless
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William R Jeck Jessica A Sorrentino Kai Wang Michael K Slevin Christin E Burd Jinze Liu William F Marzluff
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RNA
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HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency.
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2012-12-20
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Jeremy Luban
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Federico A Santoni Jessica Guerra
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Retrovirology
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Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice.
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2012-12-22
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Guojun Lu
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Tingting Lu Chuanrang Zhu Yunli Guo Yan Zhou Zhiyong Zhang Yan Zhao Wenjun Li Ying Lu Weihua Tang Qi Feng Bin Han
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BMC Genomics
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A comprehensive evaluation of alignment algorithms in the context of RNA-seq
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2012-12-26
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Caroline C Friedel
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Robert Lindner
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PLOS ONE
|
How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?
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2012-12-27
|
Chad Nusbaum
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Brian J Haas Melissa Chin Bruce W Birren Jonathan Livny
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BMC Genomics
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Correlates of relative resistance against low-dose rectal simian immunodeficiency virus challenges in peripheral blood mononuclear cells of vaccinated rhesus macaques.
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2012-12-27
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Sarah J. Ratcliffe
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Raj Kurupati Steve Tuyishime Andrew V Kossenkov Marina Sazanovich Larissa H Haut Marcio O Lasaro Steven E Bosinger Diane G Carnathan Mark Lewis Louise C Showe Guido Silvestri Hildegund C J Ertl
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Journal of Leukocyte Biology
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Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data
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2013
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Matthias Kretzler Gil Omenn
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Ridvan Eksi Hong-Dong Li Rajasree Menon Yuchen Wen Yuanfang Guan
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PLOS Computational Biology
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Whole-genome DNA/RNA sequencing identifies truncating mutations in RBCK1 in a novel Mendelian disease with neuromuscular and cardiac involvement
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2013
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Cecilia Kim Hakon Hakonarson
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Kai Wang Jonathan Bradfield Yunfei Guo Elina Toskala Frederick G Otieno Cuiping Hou Kelly Thomas Christopher Cardinale Gholson J Lyon Ryan Golhar
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Genome Medicine
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Molecular and cellular mechanisms of neutral lipid accumulation in diatom following nitrogen deprivation
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2013
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Hong-Ye Li
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Zhi-Kai Yang Ying-Fang Niu Yu-Han Ma Jiao Xue Meng-Han Zhang Wei-Dong Yang Jie-Sheng Liu Song-Hui Lu Yuanfang Guan
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Biotechnology for Biofuels
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"A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids"
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2013
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Jennifer Ann Harikrishna
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Mark W Davey Ranganath Gudimella Lee Wan Sin Norzulaani Khalid Johan Keulemans
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BMC Genomics
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RNA-Seq Differentiates Tumour and Host mRNA Expression Changes Induced by Treatment of Human Tumour Xenografts with the VEGFR Tyrosine Kinase Inhibitor Cediranib
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2013
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James R. Bradford
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Matthew Farren Steve J Powell Sarah Runswick Susie L Weston Helen Brown Oona Delpuech Mark Wappett Neil R Smith T Hedley Carr Jonathan R Dry Neil J Gibson Simon T Barry
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PLOS ONE
|
RNA-Seq profiling of spinal cord motor neurons from a presymptomatic SOD1 ALS mouse
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2013
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Arthur L. Horwich Justin Cotney
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Urmi Bandyopadhyay Maria Nagy Sunghee Oh Jing Leng Milind Mahajan Shrikant Mane Wayne A Fenton James P Noonan
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PLOS ONE
|
Transcriptome sequencing of tumor subpopulations reveals a spectrum of therapeutic options for squamous cell lung cancer
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2013
|
Olivier Harismendy
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Christian L Barrett Richard B Schwab HyunChul Jung Brian Crain Daniel J Goff Catriona H M Jamieson Patricia A Thistlethwaite Dennis A Carson Kelly A Frazer
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PLOS ONE
|
RNA-Seq analysis of Cocos nucifera: transcriptome sequencing and de novo assembly for subsequent functional genomics approaches
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2013
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Yaodong Yang Annaliese S Mason
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Haikuo Fan Yong Xiao Wei Xia Zhihui Xia Fei Qiao Songlin Zhao Haoru Tang
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PLOS ONE
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Integrative approach reveals composition of endoparasitoid wasp venoms
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2013
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Todd A Schlenke Nathan T Mortimer James Taylor
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Jeremy Goecks James A Mobley Gregory J Bowersock
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PLOS ONE
|
Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing
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2013
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Yinglong Chen
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Yan Wang Liang Xu Hong Shen Yiqin Gong Cecilia Limera Liwang Liu
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PLOS ONE
|
Connectivity Mapping for Candidate Therapeutics Identification Using Next Generation Sequencing RNA-Seq Data
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2013
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Philip D Dunne Darragh G McArt Shu-Dong Zhang
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Jaine K Blayney Manuel Salto-Tellez Sandra Van Schaeybroeck Peter W Hamilton
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PLOS ONE
|
Unique transcriptome patterns of the white and grey matter corroborate structural and functional heterogeneity in the human frontal lobe
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2013
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Michael Janitz Glenda Halliday
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James D Mills Tomas Kavanagh Woojin S Kim Bei Jun Chen Yoshihiro Kawahara
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PLOS ONE
|
Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy
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2013
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Majid Kazemian
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Qiong Cheng Hannah Pham Charles Blatti Susan E Celniker Scot A Wolfe Michael H Brodsky Saurabh Sinha
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PLOS Genetics
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Putative sugar transporters of the mustard leaf beetle Phaedon cochleariae: their phylogeny and role for nutrient supply in larval defensive glands
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2013
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Wilhelm Boland René R Bodemann Marco Groth
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Magdalena Stock Simone Eiserloh Antje Burse
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PLOS ONE
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MicroRNA discovery by similarity search to a database of RNA-seq profiles
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2013
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Jan Gorodkin Sachin Pundhir
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Frontiers in Genetics
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Differential analysis of gene regulation at transcript resolution with RNA-seq
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2013-01
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John L. Rinn
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Trapnell C Hendrickson DG Sauvageau M Goff L Pachter L
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Nature Biotechnology
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Interpreting personal transcriptomes: personalized mechanism-scale profiling of RNA-seq data
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2013-01-01
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Yves A. Lussier
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Alan Perez-Rathke Haiquan Li
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Pacific Symposium on Biocomputing
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Analysis of RNA-Seq data with TopHat and Cufflinks for genome-wide expression analysis of jasmonate-treated plants and plant cultures.
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2013-01-01
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Stephane Rombauts Alain Goossens
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Jacob Pollier
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Methods in Molecular Biology
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High occurrence of functional new chimeric genes in survey of rice chromosome 3 short arm genome sequences
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2013-01-01
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Rod A. Wing
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Chengjun Zhang Jun Wang Nicholas C Marowsky Manyuan Long Chuanzhu Fan
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Genome Biology and Evolution
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RNA-seq analysis of allele-specific expression, hybrid effects, and regulatory divergence in hybrids compared with their parents from natural populations.
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2013-01-01
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Loren H. Rieseberg
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Graeme D M Bell Nolan C Kane Keith L Adams
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Genome Biology and Evolution
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Transcriptome sequencing reveals the character of incomplete dosage compensation across multiple tissues in flycatchers.
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2013-01-01
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Hans Ellegren
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Severin Uebbing Axel Künstner Hannu Mäkinen
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Genome Biology and Evolution
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Genomic, RNAseq, and molecular modeling evidence suggests that the major allergen domain in insects evolved from a homodimeric origin
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2013-01-01
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Thomas A Randall Geoffrey A Mueller Lalith Perera
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Robert E London
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Genome Biology and Evolution
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Transcriptome sequencing of neonatal thymic epithelial cells.
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2013-01-01
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Claude Perreault
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Charles St-Pierre Sylvie Brochu Juan Ruiz Vanegas Maude Dumont-Lagacé Sébastien Lemieux
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Scientific Reports
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In vitro expansion of fetal neural progenitors as adherent cell lines.
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2013-01-01
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Steven M Pollard
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Methods in Molecular Biology
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Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics.
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2013-01-07
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Ching-Chia Yang Tsuyoshi Tanaka Takeshi Itoh
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Hiroaki Sakai Sung Shin Lee Hisataka Numa Jungsok Kim Yoshihiro Kawahara Hironobu Wakimoto Masao Iwamoto Takashi Abe Yuko Yamada Akira Muto Hachiro Inokuchi Toshimichi Ikemura Takashi Matsumoto Takuji Sasaki
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Plant and Cell Physiology
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RNA-Seq analysis of the parietal cortex in Alzheimer's disease reveals alternatively spliced isoforms related to lipid metabolism.
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2013-01-07
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Pingzhao Hu Michael Janitz
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James D Mills Thomas Nalpathamkalam Heidi I L Jacobs Caroline Janitz Daniele Merico
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Neuroscience Letters
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Dual functions of TAF7L in adipocyte differentiation.
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2013-01-08
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Michael Eisen Ivan Grubisic Tommy Kaplan Haiying Zhou Yan Li Zhengjian Zhang P Jeremy Wang Robert Tjian
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eLife
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MMAPPR: mutation mapping analysis pipeline for pooled RNA-seq.
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2013-01-08
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Jonathon T Hill
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Bradley L Demarest Brent W Bisgrove Bushra Gorsi Yi-Chu Su H Joseph Yost
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Genome Research
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SIBER: systematic identification of bimodally expressed genes using RNAseq data
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2013-01-09
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Kevin R. Coombes
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Pan Tong Yong Chen Xiao Su
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Bioinformatics
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Transcriptome sequencing (RNA-Seq) of human endobronchial biopsies: asthma versus controls.
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2013-01-11
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Frank Baas
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Ching Yong Yick Aeilko H Zwinderman Peter W Kunst Katrien Grünberg Thais Mauad Annemiek Dijkhuis Elisabeth H Bel René Lutter Peter J Sterk
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European Respiratory Journal
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ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution.
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2013-01-12
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Raymond Wan
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Jing-Woei Li Chi-Shing Yu Ngai Na Co Nathalie Wong Ting-Fung Chan
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Bioinformatics
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Comparative RNA-seq analysis of early-infected peach leaves by the invasive phytopathogen Xanthomonas arboricola pv. pruni.
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2013-01-14
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Joël F. Pothier A Patocchi
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Didier Socquet-Juglard Tim Kamber Danilo Christen Cesare Gessler Brion Duffy
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PLOS ONE
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Dynamic DNA methylation across diverse human cell lines and tissues
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2013-01-16
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Gregory E Crawford John A Stamatoyannopoulos
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Katherine E Varley Jason Gertz Kevin M Bowling Stephanie L Parker Timothy E Reddy Florencia Pauli-Behn Marie K Cross Brian A Williams Devin M Absher Barbara J Wold Richard M Myers
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Genome Research
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RNA-Seq data: a goldmine for organelle research.
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2013-01-18
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David Roy Smith
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Briefings in functional genomics
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Efficient and comprehensive representation of uniqueness for next-generation sequencing by minimum unique length analyses.
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2013-01-18
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Daniel Ramsköld Rickard Sandberg
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Helena Storvall
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PLOS ONE
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Analysis of RNA-Seq data reveals involvement of JAK/STAT signalling during leg regeneration in the cricket Gryllus bimaculatus.
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2013-01-23
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Taro Nakamura
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Tetsuya Bando Yoshiyasu Ishimaru Takuro Kida Yoshimasa Hamada Yuji Matsuoka Hideyo Ohuchi Sumihare Noji Taro Mito
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Development
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Conserved gene regulatory function of the carboxy-terminal domain of dictyostelid C-module-binding factor.
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2013-01-25
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Gernot Glöckner
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Anika Schmith Marco Groth Josephine Ratka Sara Gatz Thomas Spaller Oliver Siol Thomas Winckler
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Eukaryotic Cell
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Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data
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2013-01-28
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John C Marioni Jong Kyoung Kim
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Genome Biology
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Contribution of copy number variants involving nonsense-mediated mRNA decay pathway genes to neuro-developmental disorders.
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2013-01-31
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Jozef Gécz Lam S Nguyen James F. Gusella
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Hyung-Goo Kim Jill A Rosenfeld Yiping Shen Yves Lacassie Lawrence C Layman Lisa G Shaffer
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Human Molecular Genetics
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The evolutionary causes and consequences of sex-biased gene expression.
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2013-02-01
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Hans Ellegren
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John Parsch
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Nature Reviews Genetics
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Comparative study of RNA-seq- and microarray-derived coexpression networks in Arabidopsis thaliana.
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2013-02-01
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Cristian Del Fabbro
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Federico M Giorgi Francesco Licausi
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Bioinformatics
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puma 3.0: improved uncertainty propagation methods for gene and transcript expression analysis.
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2013-02-05
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Magnus Rattray
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Xuejun Liu Zhenzhu Gao Li Zhang
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BMC Bioinformatics
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Genetic screens: RNA-seq into the toolkit.
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2013-02-05
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Darren J. Burgess
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Nature Reviews Genetics
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Expression profile of ectopic olfactory receptors determined by deep sequencing.
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2013-02-06
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Hanns Hatt Günter Gisselmann
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Caroline Flegel Stavros Manteniotis Sandra Osthold Günter Gisselmann
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PLOS ONE
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A high-dimensional, deep-sequencing study of lung adenocarcinoma in female never-smokers
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2013-02-06
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Wan Kyu Kim Namshin Kim
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Sang Cheol Kim Yeonjoo Jung Jinah Park Sooyoung Cho Chaehwa Seo Jaesang Kim Pora Kim Jehwan Park Jihae Seo Jiwoong Kim Seongjin Park Insu Jang Jin Ok Yang Byungwook Lee Kyoohyoung Rho Yeonhwa Jung Juhee Keum Jinseon Lee Jungho Han Sangeun Kang Sujin Bae So-Jung Choi Sujin Kim Jong-Eun Lee Jhingook Kim Sanghyuk Lee
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PLOS ONE
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FUS regulates genes coding for RNA-binding proteins in neurons by binding to their highly conserved introns.
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2013-02-06
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Zissimos Mourelatos Manolis Maragkakis Panagiotis Alexiou
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Tadashi Nakaya Alexandra Chang
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RNA
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SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data.
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2013-02-14
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Jun Wang Wenlong Jia
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Kunlong Qiu Minghui He Pengfei Song Quan Zhou Feng Zhou Yuan Yu Dandan Zhu Michael L Nickerson Shengqing Wan Xiangke Liao Xiaoqian Zhu Shaoliang Peng Yingrui Li Guangwu Guo
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Genome Biology
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The draft genome and transcriptome of Panagrellus redivivus are shaped by the harsh demands of a free-living lifestyle
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2013-02-14
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Paul W. Sternberg
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Jagan Srinivasan Adler R Dillman Marissa G Macchietto Liisa Heikkinen Merja Lakso Kelley M Fracchia Igor Antoshechkin Ali Mortazavi Garry Wong
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Genetics
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mRNA expression, splicing and editing in the embryonic and adult mouse cerebral cortex.
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2013-02-17
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Dagmar Galter David N Hauser Mark R Cookson
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Allissa A Dillman J Raphael Gibbs Michael A Nalls Melissa K McCoy Iakov N Rudenko
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Nature Neuroscience
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EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments.
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2013-02-21
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Christina Kendziorski
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Ning Leng John A Dawson James A Thomson Victor Ruotti Anna I Rissman Bart M G Smits Jill D Haag Michael N Gould Ron M Stewart
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Bioinformatics
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Zinc deficiency impacts CO2 assimilation and disrupts copper homeostasis in Chlamydomonas reinhardtii.
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2013-02-25
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Sabeeha Merchant Matteo Pellegrini David Casero
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Davin Malasarn Janette Kropat Scott I Hsieh Giovanni Finazzi Joseph A Loo Francis-André Wollman
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Journal of Biological Chemistry
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Activity of a Py-Im polyamide targeted to the estrogen response element.
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2013-02-26
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Jerzy O Szablowski Peter Dervan
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Nicholas G Nickols Amanda E Hargrove Benjamin C Li Jevgenij A Raskatov
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Molecular Cancer Therapeutics
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Perturbations of Plasmodium Puf2 expression and RNA-seq of Puf2-deficient sporozoites reveal a critical role in maintaining RNA homeostasis and parasite transmissibility.
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2013-02-27
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Scott E. Lindner Sebastian A. Mikolajczak
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Ashley M Vaughan Wonjong Moon Brad R Joyce William J Sullivan Stefan H I Kappe
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Cellular Microbiology
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SplicingCompass: differential splicing detection using RNA-seq data.
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2013-02-28
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Roland Eils
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Moritz Aschoff Agnes Hotz-Wagenblatt Karl-Heinz Glatting Matthias Fischer Rainer König
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Bioinformatics
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Epstein - Barr virus transforming protein LMP-1 alters B cells gene expression by promoting accumulation of the oncoprotein ΔNp73α
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2013-03
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Florence Le Calvez-Kelm Birke Bartosch Evelyne Manet Hector Hernandez-Vargas
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Rosita Accardi Ikbal Fathallah Henri Gruffat Giuseppe Mariggiò Catherine Voegele James McKay Bakary S Sylla Massimo Tommasino
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PLOS Pathogens
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WNT5A inhibits metastasis and alters splicing of Cd44 in breast cancer cells.
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2013-03-06
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David K. Crossman
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Wen Jiang Elizabeth H Mitchell Philip Sohn Michael R Crowley Rosa Serra
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PLOS ONE
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RNA-seq reveals activation of both common and cytokine-specific pathways following neutrophil priming.
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2013-03-06
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Huw B Thomas Helen L Wright
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Robert J Moots Steven W Edwards
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PLOS ONE
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Regulation of viral and cellular gene expression by Kaposi's sarcoma-associated herpesvirus polyadenylated nuclear RNA.
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2013-03-06
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Cyprian Rossetto Subhash Verma Gregory S. Pari
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Margaret Tarrant-Elorza Pravinkumar Purushothaman
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Journal of Virology
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RNA-Seq analysis discloses early senescence and nucleolar dysfunction triggered by Tdp1α depletion in Medicago truncatula.
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2013-03-06
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Anca Macovei Daniela Carbonera Alma Balestrazzi
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Mattia Donà Massimo Confalonieri Andrea Minio Marco Biggiogera Armando Buttafava Elena Raimondi Massimo Delledonne Lorenzo Ventura Maria Elisa Sabatini Giorgio Giraffa
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Journal of Experimental Botany
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Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema.
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2013-03-07
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Bianca Habermann Elly M Tanaka
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Ron Stewart Cynthia Alexander Rascón Shulan Tian Jeff Nie Chris Barry Li-Fang Chu Hamisha Ardalani Ryan J Wagner Mitchell D Probasco Jennifer M Bolin Ning Leng Srikumar Sengupta Michael Volkmer James A Thomson Colin N Dewey
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PLOS Computational Biology
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Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR).
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2013-03-08
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Jasmine Jacob-Hirsch
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Oz Solomon Shirley Oren Michal Safran Naamit Deshet-Unger Pinchas Akiva Jasmine Jacob-Hirsch Karen Cesarkas Reut Kabesa Ninette Amariglio Ron Unger Gideon Rechavi Eran Eyal
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RNA
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A comparison of methods for differential expression analysis of RNA-seq data
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2013-03-09
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Charlotte Soneson
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Mauro Delorenzi
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BMC Bioinformatics
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Proteogenomic analysis of human colon carcinoma cell lines LIM1215, LIM1899, and LIM2405.
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2013-03-13
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Susan Fanayan Ling Yen Lee
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Joshua T Smith Fangfei Yan Michael Snyder William S Hancock Edouard Nice
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Journal of Proteome Research
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CathaCyc, a metabolic pathway database built from Catharanthus roseus RNA-Seq data.
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2013-03-14
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Stephane Rombauts Kirsi-Marja Oksman-Caldentey Michele Fabris Alex Van Moerkercke Jacob Pollier Johan Memelink Alain Goossens
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Gino J E Baart Ghulam Hasnain Heiko Rischer
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Plant and Cell Physiology
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Isolation of Blastomyces dermatitidis yeast from lung tissue during murine infection for in vivo transcriptional profiling
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2013-03-14
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Christina A Cuomo
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Amber J Marty Marcel Wüthrich John C Carmen Thomas D Sullivan Bruce S Klein Gregory M Gauthier
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Fungal Genetics and Biology
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TDP-43 high throughput screening analyses in neurodegeneration: advantages and pitfalls.
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2013-03-14
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Emanuele Buratti Maurizio Romano
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Francisco E Baralle
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Molecular and Cellular Neuroscience
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Interpretation, stratification and evidence for sequence variants affecting mRNA splicing in complete human genome sequences.
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2013-03-14
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Peter K. Rogan Paul I Costea
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Ben C Shirley Eliseos J Mucaki Tyson Whitehead Pelin Akan
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Genomics Proteomics and Bioinformatics
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Identification of novel exons and transcripts by comprehensive RNA-Seq of horn cancer transcriptome in Bos indicus.
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2013-03-14
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Subhash J Jakhesara Chaitanya G. Joshi
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Prakash G Koringa
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Journal of Biotechnology
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The transcript catalogue of the short-lived fish Nothobranchius furzeri provides insights into age-dependent changes of mRNA levels.
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2013-03-16
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Matthias Platzer
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Andreas Petzold Kathrin Reichwald Marco Groth Stefan Taudien Nils Hartmann Steffen Priebe Dmitry Shagin Christoph Englert
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BMC Genomics
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A multifaceted study of Pseudomonas aeruginosa shutdown by virulent podovirus LUZ19.
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2013-03-19
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Rob Lavigne
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Elke Lecoutere Jeroen Wagemans William Cenens Abram Aertsen Liliane Schoofs Bart Landuyt Jan Paeshuyse Maurice Scheer Max Schobert Pieter-Jan Ceyssens
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mBio
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Zinc-mediated RNA fragmentation allows robust transcript reassembly upon whole transcriptome RNA-Seq.
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2013-03-21
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Maxime Wery Daniel Gautheret
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Marc Descrimes Claude Thermes Antonin Morillon
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Methods
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Investigation of radiation-induced transcriptome profile of radioresistant non-small cell lung cancer A549 cells using RNA-seq
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2013-03-22
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Namshin Kim
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Hee Jung Yang Ki Moon Seong HyeSook Youn BuHyun Youn
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PLOS ONE
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Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation
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2013-03-24
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Jun Wang Junyi Wang Klaus Mayer Thomas Wicker Huanming Yang
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Jizeng Jia Shancen Zhao Xiuying Kong Yingrui Li Guangyao Zhao Weiming He Rudi Appels Matthias Pfeifer Yong Tao Xueyong Zhang Ruilian Jing Chi Zhang Youzhi Ma Lifeng Gao Chuan Gao Manuel Spannagl Dong Li Shengkai Pan Fengya Zheng Qun Hu Xianchun Xia Jianwen Li Qinsi Liang Jie Chen Caiyun Gou Hanhui Kuang Genyun He Yadan Luo Beat Keller Qiuju Xia Peng Lu Hongfeng Zou Rongzhi Zhang Junyang Xu Jinlong Gao Christopher Middleton Zhiwu Quan Guangming Liu Jian Wang Xu Liu Zhonghu He Long Mao
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Nature
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RNAseq versus genome-predicted transcriptomes: a large population of novel transcripts identified in an Illumina-454 Hydra transcriptome
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2013-03-25
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Brigitte Galliot
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Yvan Wenger
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BMC Genomics
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RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome.
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2013-03-25
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Alicia Oshlack Nadia M Davidson Craig A. Smith
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Katie L Ayers Diana Demiyah Kelly N Roeszler Frank Grützner Andrew H Sinclair
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Genome Biology
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Development of strategies for SNP detection in RNA-seq data: application to lymphoblastoid cell lines and evaluation using 1000 Genomes data
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2013-03-26
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Michael Gill Elaine M Kenny Richard Anney Derek W. Morris Aiden Corvin
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Emma M Quinn Paul Cormican Matthew Hill
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PLOS ONE
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Differential expression analysis for paired RNA-Seq data
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2013-03-27
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Ruth R Montgomery
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Lisa M Chung John P Ferguson Wei Zheng Feng Qian Vincent Bruno Hongyu Zhao
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BMC Bioinformatics
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Predicting long non-coding RNAs using RNA sequencing.
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2013-03-27
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Chris Ponting Nicholas E Ilott
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Methods
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Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.
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2013-03-28
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Jon Jerlström-Hultqvist Staffan G Svärd
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Oscar Franzén Elin Einarsson Johan Ankarklev Marcela Ferella Björn Andersson
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PLOS Computational Biology
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Gene regulation by CcpA and catabolite repression explored by RNA-Seq in Streptococcus mutans
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2013-03-28
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Adam C. Siepel Robert A Burne
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Lin Zeng Sang Chul Choi Charles G Danko Michael J Stanhope
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PLOS ONE
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Comprehensive molecular screening: from the RT-PCR to the RNA-seq.
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2013-04-01
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Rafael Rosell
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Carlota Costa Ana Giménez-Capitán Niki Karachaliou
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Translational lung cancer research
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Spatial transcriptional profile of the chick and mouse endocardial cushions identify novel regulators of endocardial EMT in vitro.
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2013-04-01
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Daniel M DeLaughter
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Daniel M DeLaughter Danos C Christodoulou Jamille Y Robinson Christine E Seidman H Scott Baldwin J G Seidman Joey V Barnett
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Journal of Molecular and Cellular Cardiology
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Frogs and estivation: transcriptional insights into metabolism and cell survival in a natural model of extended muscle disuse.
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2013-04-02
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Craig E. Franklin David I Schlipalius Paul R Ebert Rebecca L. Cramp
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Beau D Reilly
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Physiological Genomics
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New insights into Chlamydomonas reinhardtii hydrogen production processes by combined microarray/RNA-seq transcriptomics.
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2013-04-03
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Patrick May Alexander Goesmann
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Jörg Toepel Maike Illmer-Kephalides Sebastian Jaenicke Jasmin Straube Olaf Kruse
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Plant Biotechnology Journal
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Comparative RNA-Seq and microarray analysis of gene expression changes in B-cell lymphomas of Canis familiaris.
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2013-04-04
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Noel Monks
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Marie Mooney Jeffrey Bond Emily Eugster David Cherba Pamela Berlinski Steve Kamerling Keith Marotti Heather Simpson Tony Rusk Waibhav Tembe Christophe Legendre Hollie Benson Winnie Liang Craig Paul Webb
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PLOS ONE
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The transcriptome of Leishmania major in the axenic promastigote stage: transcript annotation and relative expression levels by RNA-seq.
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2013-04-04
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A Rastrojo Rosa M. Reguera
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Fernando Carrasco-Ramiro Diana Martín Antonio Crespillo Begoña Aguado Jose M Requena
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BMC Genomics
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Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro.
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2013-04-08
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Amanda J Lohan Kévin Rue-Albrecht Karsten Hokamp Brendan Loftus Eamonn Gormley David E. MacHugh Stephen V. Gordon Kate Killick
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Nicolas C Nalpas Stephen D E Park David A Magee Maria Taraktsoglou John A Browne Kevin M Conlon
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BMC Genomics
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Characterization of FUS mutations in amyotrophic lateral sclerosis using RNA-Seq.
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2013-04-08
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Marka van Blitterswijk Brad Friedman Leonard H van den Berg Jan H Veldink
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Eric T Wang Pamela J Keagle Patrick Lowe Ashley Lyn Leclerc David E Housman John E Landers
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PLOS ONE
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Functional genomics based understanding of rice endosperm development.
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2013-04-10
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Shi-Rong Zhou
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Lin-Lin Yin Hong-Wei Xue
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Current Opinion in Plant Biology
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Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo.
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2013-04-11
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Abhinav Nellore
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Alexander D Ramos Aaron Diaz Ryan N Delgado Ki-Youb Park Gabriel Gonzales-Roybal Michael C Oldham Jun S Song Daniel A Lim
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Cell Stem Cell
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Accurate detection of differential RNA processing.
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2013-04-12
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Oliver Stegle Gunnar Rätsch Karsten M Borgwardt
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Philipp Drewe Lisa Hartmann André Kahles Regina Bohnert Andreas Wachter
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Nucleic Acids Research
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Exome-based analysis for RNA epigenome sequencing data.
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2013-04-14
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Jia Meng
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Xiaodong Cui Manjeet K Rao Yidong Chen Yufei Huang
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Bioinformatics
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Glycyrrhiza uralensis transcriptome landscape and study of phytochemicals.
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2013-04-14
|
Keiichi Mochida Tetsuya Sakurai Carsten O Daub Toshiya Muranaka Kazuki Saito
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Jordan A Ramilowski Satoru Sawai Hikaru Seki Takuhiro Yoshida
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Plant and Cell Physiology
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Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size.
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2013-04-14
|
Wolfgang Huber
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Danni Yu Olga Vitek
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Bioinformatics
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Faculty of 1000 evaluation for Transcriptome Profiling of Giardia intestinalis Using Strand-specific RNA-Seq
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2013-04-16
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Christen Rune Stensvold
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C Graham Clark
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Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity
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2013-04-17
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Yohei Sasagawa Tetsutaro Hayashi Itoshi Nikaido Takeshi Imai Hiroki R Ueda
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Hiroki Danno Kenichiro D Uno
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Genome Biology
|
Sprouts of RNA epigenetics: the discovery of mammalian RNA demethylases.
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2013-04-17
|
Arne Klungland
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Guanqun Zheng John Arne Dahl Yamei Niu Ye Fu Yun-Gui Yang Chuan He
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RNA Biology
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Characterization of differential transcript abundance through time during Nematostella vectensis development.
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2013-04-19
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Sarah Tulin Joel Smith Casey W. Dunn
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Rebecca Rae Helm Stefan Siebert
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BMC Genomics
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Evolution of the eye transcriptome under constant darkness in Sinocyclocheilus cavefish
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2013-04-23
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Ingo Braasch
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Fanwei Meng Jennifer B Phillips Xiwen Lin Tom Titus Chunguang Zhang John H Postlethwait
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Molecular Biology and Evolution
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Massively parallel sequencing, aCGH, and RNA-Seq technologies provide a comprehensive molecular diagnosis of Fanconi anemia.
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2013-04-23
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Elaine Ostrander Agata Smogorzewska Arleen D. Auerbach NISC Comparative Sequencing Program
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Settara C Chandrasekharappa Francis P Lach Danielle C Kimble Aparna Kamat Jamie K Teer Frank X Donovan Elizabeth Flynn Shurjo K Sen Supawat Thongthip Erica Sanborn
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Blood
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A model based criterion for gene expression calls using RNA-seq data.
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2013-04-25
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Vincent Lynch
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Günter P Wagner Koryu Kin
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Theory in Biosciences
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Transcriptome analysis of Japanese pear (Pyrus pyrifolia Nakai) flower buds transitioning through endodormancy.
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2013-04-26
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Songling Bai
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Takanori Saito Daisuke Sakamoto Akiko Ito Hiroshi Fujii Takaya Moriguchi
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Plant and Cell Physiology
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RNAseq-based transcriptome analysis of Lactuca sativa infected by the fungal necrotroph Botrytis cinerea.
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2013-04-26
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Barbara De Coninck
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Kaat De Cremer Janick Mathys Christine Vos Lutz Froenicke Richard W Michelmore Bruno P A Cammue
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Plant, Cell and Environment
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Prediction of transcribed PIWI-interacting RNAs from CHO RNAseq data.
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2013-04-29
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Johannes Grillari Alexandra B Graf Matthias Hackl Nicole Borth
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Matthias Peter Gerstl
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Journal of Biotechnology
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RNA-Seq reveals expression signatures of genes involved in oxygen transport, protein synthesis, folding, and degradation in response to heat stress in catfish.
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2013-04-30
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Shikai Liu Eric Peatman Huseyin Kucuktas Ludmilla Kaltenboeck Luyang Sun Yu Zhang
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Xiuli Wang Fanyue Sun Jiaren Zhang Jianbin Feng Hong Liu K V Rajendran Yanliang Jiang Zhanjiang Liu
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Physiological Genomics
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Erratum: RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings
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2013-05
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Jun Wang Huanming Yang
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Shancheng Ren Zhiyu Peng Jian-Hua Mao Yongwei Yu Changjun Yin Xin Gao Zilian Cui Jibin Zhang Kang Yi Weidong Xu Chao Chen Fubo Wang Xinwu Guo Ji Lu Jun Yang Min Wei Zhijian Tian Yinghui Guan Liang Tang Chuanliang Xu Linhui Wang Xu Gao Wei Tian Jian Wang Yinghao Sun
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Cell Research
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Glucocorticoid-induced changes in gene expression of airway smooth muscle in patients with asthma.
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2013-05-01
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Frank Baas Kees Fluiter
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Ching Yong Yick Aeilko H Zwinderman Peter W Kunst Katrien Grünberg Thais Mauad Elisabeth H Bel René Lutter Peter J Sterk
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American Journal of Respiratory and Critical Care Medicine
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Transcription factors that convert adult cell identity are differentially polycomb repressed
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2013-05-01
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Sean Eddy Davis FP
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PLOS ONE
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Functional transcriptomic analysis of the role of MAB-5/Hox in Q neuroblast migration in Caenorhabditis elegans
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2013-05-04
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Stuart J Macdonald
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Joel V Tamayo Mahekta Gujar Erik A Lundquist
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BMC Genomics
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Research resource: small RNA-seq of human granulosa cells reveals miRNAs in FSHR and aromatase genes.
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2013-05-09
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Agne Velthut Madis Metsis Andres Salumets
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Jaak Simm Timo Tuuri Juha S Tapanainen
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Molecular Endocrinology
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Differences in gastric carcinoma microenvironment stratify according to EBV infection intensity: implications for possible immune adjuvant therapy.
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2013-05-09
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Melody Baddoo Michelle Lacey Erik K Flemington
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Michael J Strong Guorong Xu Joseph Coco Carl Baribault Dass S Vinay Amy L Strong Teresa A Lehman Michael B Seddon Zhen Lin Monica Concha Melody Baddoo Marybeth Ferris Kenneth F Swan Deborah E Sullivan Matthew E Burow Christopher M Taylor
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PLOS Pathogens
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In vitro-differentiated neural cell cultures progress towards donor-identical brain tissue
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2013-05-10
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Thomas G Beach
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Brooke E Hjelm Bodour Salhia Ahmet Kurdoglu Szabolcs Szelinger Rebecca A Reiman Lucia I Sue Matthew J Huentelman David W Craig
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Human Molecular Genetics
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Global detection and identification of developmental stage specific transcripts in mouse brain using subtractive cross-screening algorithm.
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2013-05-12
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Zhixiang Zuo
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Yi Lv Xiao Xu
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Genomics
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Mapping the RNA-Seq trash bin: unusual transcripts in prokaryotic transcriptome sequencing data.
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2013-05-13
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Peter F. Stadler David Langenberger
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Gero Doose Maria Alexis Rebecca Kirsch Sven Findeiß Rainer Machné Mario Mörl Steve Hoffmann
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RNA Biology
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Optimizing de novo assembly of short-read RNA-seq data for phylogenomics.
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2013-05-14
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Stephen A. Smith
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Ya Yang
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BMC Genomics
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OakContigDF159.1, a reference library for studying differential gene expression in Quercus robur during controlled biotic interactions: use for quantitative transcriptomic profiling of oak roots in ectomycorrhizal symbiosis.
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2013-05-15
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Tesfaye Wubet Martin Schädler Mika T Tarkka Stefan Scheu François Buscot
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Sylvie Herrmann Lasse Feldhahn Sabine Recht Florence Kurth Sarah Mailänder Markus Bönn Maren Neef Oguzhan Angay Michael Bacht Marcel Graf Hazel Maboreke Frank Fleischmann Thorsten E E Grams Liliane Ruess Roland Brandl Silvia D Schrey Ivo Grosse
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New Phytologist
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Complexities of gammaherpesvirus transcription revealed by microarrays and RNAseq.
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2013-05-16
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Laurie T. Krug
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Current opinion in virology
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Comparative analysis of RNA sequencing methods for degraded or low-input samples.
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2013-05-19
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Aviv Regev Rahul Satija Nathalie Pochet
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Xian Adiconis Diego Borges-Rivera David S DeLuca Michele A Busby Aaron M Berlin Andrey Sivachenko Dawn Anne Thompson Alec Wysoker Timothy Fennell Andreas Gnirke Joshua Z Levin
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Nature Methods
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Evaluation of higher plant virus resistance genes in the green alga, Chlorella variabilis NC64A, during the early phase of infection with Paramecium bursaria chlorella virus-1
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2013-05-21
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Guillaume Blanc
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Janet M Rowe David D Dunigan James R Gurnon Yuannan Xia James L Van Etten
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Virology
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Genome wide proteomics of ERBB2 and EGFR and other oncogenic pathways in inflammatory breast cancer.
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2013-05-22
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Gil Omenn Susan Fanayan
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Emma Yue Zhang Massimo Cristofanilli Fredika Robertson James M Reuben Zhaomei Mu Ronald C Beavis Hogune Im Michael Snyder Matan Hofree Trey Ideker Seul-Ki Jeong Young-Ki Paik Anna Fan Zhang Shiaw-Lin Wu William S Hancock
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Journal of Proteome Research
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Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing
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2013-05-22
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Ryan D Morin Andrew Mungall Steven Jones
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Karen Mungall Erin Pleasance Rodrigo Goya Ryan D Huff David W Scott Jiarui Ding Andrew Roth Readman Chiu Richard D Corbett Fong Chun Chan Maria Mendez-Lago Diane L Trinh Madison Bolger-Munro Greg Taylor Alireza Hadj Khodabakhshi Susana Ben-Neriah Julia Pon Barbara Meissner Bruce Woolcock Noushin Farnoud Sanja Rogic Emilia L Lim Nathalie A Johnson Sohrab Shah Christian Steidl Robert Holt Inanc Birol Richard Moore Joseph M Connors Randy D Gascoyne Marco A Marra
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Blood
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A comprehensive analysis of the effects of the deaminase AID on the transcriptome and methylome of activated B cells.
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2013-05-26
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Nina Papavasiliou Thomas Tuschl
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Eric L Fritz Brad R Rosenberg Kenneth Lay Aleksandra Mihailović F Nina Papavasiliou
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Nature Immunology
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Identification of the zebrafish maternal and paternal transcriptomes
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2013-05-29
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James Cuthbert Smith
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Steven A Harvey Ian Sealy Ross Kettleborough Fruzsina Fenyes Richard White Derek Stemple
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Development
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Transcriptome sequencing (RNA-seq) analysis of the effects of metal nanoparticle exposure on the transcriptome of Chlamydomonas reinhardtii.
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2013-05-31
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Rute F. Domingos William Zerges Kevin J Wilkinson
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Dana F Simon Charles Hauser Colin M Hutchins
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Applied and Environmental Microbiology
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Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs
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2013-06
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Michael McManus
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Matthew J Hangauer Ian W Vaughn
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PLOS Genetics
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The gene desert mammary carcinoma susceptibility locus Mcs1a regulates Nr2f1 modifying mammary epithelial cell differentiation and proliferation
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2013-06
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Christina Kendziorski
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Bart M G Smits Jill D Haag Anna I Rissman Deepak Sharma Ann Tran Alexi A Schoenborn Rachael C Baird Dan S Peiffer David Q Leinweber Matthew J Muelbl Amanda L Meilahn Mark R Eichelberg Ning Leng Manorama C John Patricia A Powers Caroline M Alexander Michael N Gould
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PLOS Genetics
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Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica
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2013-06
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Chad Nusbaum Carsten Russ Berend Snel Stephan Wawra Sucheta Tripathy Irene de Bruijn Michael F. Seidl Guido Van den Ackerveken Pieter van West Francine Govers Stan Oome Neil Horner Bernard Dumas Marcia Saraiva Julio C Vega-Arreguín Paul F Morris
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Rays H Y Jiang Brian J Haas Rodrigo Belmonte Lars Löbach James Christie Arnaud Bottin Vincent Bulone Sara M Díaz-Moreno Lin Fan Elodie Gaulin Laura J Grenville-Briggs Joshua Z Levin Marco Mammella Harold J G Meijer Stan Oome Andrew J Phillips David van Rooyen Elzbieta Rzeszutek Chris J Secombes Joost H M Stassen Sean Sykes Herbert van den Berg Sarah K Young Qiandong Zeng Javier Dieguez-Uribeondo Brett M Tyler
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PLOS Genetics
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RNA-seq analysis reveals extensive transcriptional plasticity to temperature stress in a freshwater fish species.
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2013-06-05
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Steve Smith Luciano B. Beheregaray
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Louis Bernatchez
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BMC Genomics
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Landscape of DNA virus associations across human malignant cancers: analysis of 3,775 cases using RNA-Seq
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2013-06-05
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Michelle D Williams Funda Meric-Bernstam
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Joseph D Khoury Nizar M Tannir Yunxin Chen Hui Yao Jianping Zhang Erika J Thompson TCGA Network L Jeffrey Medeiros John N Weinstein Xiaoping Su
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Journal of Virology
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A meta-analysis of the genomic and transcriptomic composition of complex life.
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2013-06-06
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John Mattick
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Ganqiang Liu Ryan J Taft
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Cell Cycle
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Discovery of diversity in xylan biosynthetic genes by transcriptional profiling of a heteroxylan containing mucilaginous tissue.
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2013-06-07
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Jacob K Jensen
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Nathan Johnson Curtis G Wilkerson
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Frontiers in Plant Science
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A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples
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2013-06-10
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Paolo Piazza Elizabeth M Batty Tanya Golubchik Kate E Dingle Paul Klenerman Daniel Wilson Eleanor Barnes
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T H Nicholas Wong Amy Trebes Karène Argoud Moustafa Attar David Buck Camilla L C Ip Madeleine Cule Rory Bowden Charis Manganis A Sarah Walker David H Wyllie Tim E A Peto Derrick W Crook
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PLOS ONE
|
Assessment of gene expression in peripheral blood using RNAseq before and after weight restoration in anorexia nervosa
|
2013-06-15
|
Cynthia M. Bulik
|
Yunjung Kim Sara E Trace James J Crowley Kimberly A Brownley Robert M Hamer David S Pisetsky Patrick F Sullivan
|
Psychiatry Research
|
Comprehensive High-Resolution Analysis of the Role of an Arabidopsis Gene Family in RNA Editing
|
2013-06-20
|
Stéphane Bentolila Maureen R. Hanson
|
Julyun Oh Robert Bukowski
|
PLOS Genetics
|
RNA-seq in the tetraploid Xenopus laevis enables genome-wide insight in a classic developmental biology model organism
|
2013-06-20
|
Erin Osborne
|
Nirav M Amin Panna Tandon Frank L Conlon
|
Methods
|
Cellular source and mechanisms of high transcriptome complexity in the mammalian testis.
|
2013-06-20
|
Anamaria Necsulea
|
Magali Soumillon Manuela Weier David Brawand Xiaolan Zhang Hongcang Gu Pauline Barthès Maria Kokkinaki Serge Nef Andreas Gnirke Martin Dym Bernard de Massy Tarjei S Mikkelsen Henrik Kaessmann
|
Cell Reports
|
ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells.
|
2013-06-21
|
Avi Ma'ayan Caroline Baroukh
|
Huilei Xu Ruth Dannenfelser Edward Y Chen Christopher M Tan Yan Kou Yujin E Kim Ihor R Lemischka
|
Database
|
Global transcriptome profiles of Camellia sinensis during cold acclimation
|
2013-06-22
|
Qiong-Yi Zhao
|
Xin-Chao Wang Chun-Lei Ma Zong-Hong Zhang Hong-Li Cao Yi-Meng Kong Chuan Yue Xin-Yuan Hao Liang Chen Jian-Qiang Ma Ji-Qiang Jin Xuan Li Ya-Jun Yang
|
BMC Genomics
|
Evaluating the impact of sequencing depth on transcriptome profiling in human adipose
|
2013-06-24
|
Jane Ferguson Muredach P. Reilly
|
Yichuan Liu Chenyi Xue Ian M Silverman Brian Gregory Mingyao Li
|
PLOS ONE
|
Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets
|
2013-06-28
|
W. Richard McCombie
|
Xiao Xu Yuanhao Zhang Jennie Williams Eric Antoniou Song Wu Wei Zhu Nicholas O Davidson Paula Denoya Ellen Li
|
BMC Bioinformatics
|
Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation.
|
2013-07-01
|
Sayan Mukherjee Uwe Ohler
|
Dina Hafez Ting Ni Jun Zhu
|
Bioinformatics
|
Classification of topological domains based on gene expression and regulation.
|
2013-07-01
|
Nadav Ahituv
|
Jingjing Zhao Hongbo Shi
|
Genome
|
RNA-Seq-based analysis of the physiologic cold shock-induced changes in Moraxella catarrhalis gene expression.
|
2013-07-02
|
Stefan Wyder Christoph Aebi
|
Violeta Spaniol
|
PLOS ONE
|
Exonuclease hDIS3L2 specifies an exosome-independent 3'-5' degradation pathway of human cytoplasmic mRNA
|
2013-07-03
|
Andrzej Dziembowski Rafał Tomecki Torben Heick Jensen Dominik Cysewski
|
Michal Lubas Christian K Damgaard
|
The EMBO Journal
|
RNaseIII and T4 polynucleotide Kinase sequence biases and solutions during RNA-seq library construction
|
2013-07-04
|
Claus O. Wilke
|
Changhoon Lee R Adron Harris Jason K Wall R Dayne Mayfield
|
Biology Direct
|
Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution
|
2013-07-05
|
Mark Bender Gerstein
|
Gang Fang Karla D Passalacqua Jason Hocking Paula Montero Llopis Nicholas H Bergman Christine Jacobs-Wagner
|
BMC Genomics
|
Identification of novel point mutations in splicing sites integrating whole-exome and RNA-seq data in myeloproliferative diseases
|
2013-07-07
|
Carlo Gambacorti-Passerini Vera Magistroni
|
Roberta Spinelli Alessandra Pirola Sara Redaelli Nitesh Sharma Hima Raman Simona Valletta Rocco Piazza
|
Molecular genetics & genomic medicine
|
Identification of genes critical for resistance to infection by West Nile virus using RNA-Seq analysis.
|
2013-07-08
|
Sebastian Kurscheid Ruth R Montgomery Erol Fikrig Mark Bender Gerstein
|
Feng Qian Lisa Chung Wei Zheng Vincent Bruno Roger P Alexander Zhong Wang Xiaomei Wang Hongyu Zhao Michael Snyder
|
Viruses
|
Clear cell renal cell carcinoma associated microRNA expression signatures identified by an integrated bioinformatics analysis.
|
2013-07-10
|
Wenying Yan
|
Jiajia Chen Daqing Zhang Wenyu Zhang Yifei Tang Lingchuan Guo Bairong Shen
|
Journal of Translational Medicine
|
Vitamin D receptor ChIP-seq in primary CD4+ cells: relationship to serum 25-hydroxyvitamin D levels and autoimmune disease
|
2013-07-12
|
Geir Kjetil Sandve Gavin Giovannoni
|
Adam E Handel Giulio Disanto Antonio J Berlanga-Taylor Giuseppe Gallone Heather Hanwell Finn Drabløs George C Ebers Sreeram V Ramagopalan
|
BMC Medicine
|
Male-biased genes in catfish as revealed by RNA-Seq analysis of the testis transcriptome.
|
2013-07-12
|
Shikai Liu Ludmilla Kaltenboeck Luyang Sun Rex Dunham
|
Fanyue Sun Xiaoyu Gao Yanliang Jiang Dayan Perera Xiuli Wang Chao Li Jiaren Zhang Zhanjiang Liu
|
PLOS ONE
|
Senescence-associated lncRNAs: senescence-associated long noncoding RNAs.
|
2013-07-14
|
Kevin G. Becker Myriam Gorospe Kotb Abdelmohsen
|
Amaresh Panda Min-Ju Kang Jason Xu Roza Selimyan Je-Hyun Yoon Jennifer L Martindale Supriyo De William H Wood
|
Aging Cell
|
Transcriptome analysis of mouse brain infected with Toxoplasma gondii.
|
2013-07-15
|
Yoshifumi Nishikawa
|
Sachi Tanaka Maki Nishimura Fumiaki Ihara Junya Yamagishi Yutaka Suzuki
|
Infection and Immunity
|
Diversity in the complexity of phosphate starvation transcriptomes among rice cultivars based on RNA-Seq profiles.
|
2013-07-16
|
Hirokazu Handa Takeshi Itoh
|
Youko Oono Yoshihiro Kawahara Takayuki Yazawa Hiroyuki Kanamori Masato Kuramata Harumi Yamagata Satomi Hosokawa Hiroshi Minami Satoru Ishikawa Jianzhong Wu Baltazar Antonio Takashi Matsumoto
|
Plant Molecular Biology
|
Proteogenomic database construction driven from large scale RNA-seq data.
|
2013-07-17
|
Vineet Bafna
|
Sunghee Woo Seong Won Cha Gennifer Merrihew Yupeng He Natalie Castellana Clark Guest Michael MacCoss
|
Journal of Proteome Research
|
CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes
|
2013-07-18
|
Jennifer Doudna Lei S Qi Jonathan Weissman Noam Stern-Ginossar
|
Luke A Gilbert Matthew H Larson Leonardo Morsut Zairan Liu Gloria A Brar Sandra E Torres Onn Brandman Evan H Whitehead Wendell A Lim
|
Cell
|
Methylmercury exposure increases lipocalin related (lpr) and decreases activated in blocked unfolded protein response (abu) genes and specific miRNAs in Caenorhabditis elegans
|
2013-07-18
|
Natalia Vanduyn
|
Martina Rudgalvyte Vuokko Aarnio Liisa Heikkinen Juhani Peltonen Merja Lakso Richard Nass Garry Wong
|
Toxicology Letters
|
Using a periclinal chimera to unravel layer-specific gene expression in plants.
|
2013-07-19
|
James Abbott
|
Ioannis Filippis Rosa Lopez-Cobollo Sarah Butcher Gerard J Bishop
|
The Plant Journal
|
Gene networks and chromatin and transcriptional regulation of the phaseolin promoter in Arabidopsis.
|
2013-07-19
|
Lakshminarayan M. Iyer
|
Sabarinath Sundaram Sunee Kertbundit Eugene V Shakirov Lakshminarayan M Iyer Miloslav Jurícek Timothy C Hall
|
The Plant Cell
|
Enhanced expression of codon optimized interferon gamma in CHO cells.
|
2013-07-19
|
Dong-Yup Lee
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Bevan Kai-Sheng Chung Faraaz N K Yusufi Mariati Yuansheng Yang
|
Journal of Biotechnology
|
GLiMMPS: robust statistical model for regulatory variation of alternative splicing using RNA-seq data.
|
2013-07-22
|
Zhi-xiang Lu
|
Keyan Zhao Juw Won Park Qing Zhou Yi Xing
|
Genome Biology
|
Replication protein A subunit 3 and the iron efficiency response in soybean.
|
2013-07-22
|
Dianne Cook
|
Sarah E Atwood Jamie A O'Rourke Gregory A Peiffer Tengfei Yin Mahbubul Majumder Chunquan Zhang Silvia R Cianzio John H Hill Steven A Whitham Randy C Shoemaker Michelle A Graham
|
Plant, Cell and Environment
|
Knockdown of CDKN1C (p57(kip2)) and PHLDA2 results in developmental changes in bovine pre-implantation embryos
|
2013-07-22
|
Francisco Peñagaricano Wen Huang
|
Ashley M Driver Jenna Kropp Hasan Khatib
|
PLOS ONE
|
Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome.
|
2013-07-22
|
Ulrich Omasits Christian H Ahrens Mark D. Robinson Christoph Dehio
|
Maxime Quebatte Daniel J Stekhoven Claudia Fortes Bernd Roschitzki
|
Genome Research
|
Pairwise comparisons of ten porcine tissues identify differential transcriptional regulation at the gene, isoform, promoter and transcription start site level.
|
2013-07-27
|
Christian Bendixen
|
Leila Farajzadeh Henrik Hornshøj Jamal Momeni Bo Thomsen Knud Larsen Jakob Hedegaard Lone Bruhn Madsen
|
Biochemical and Biophysical Research Communications
|
Basal polarization of the mucosal compartment in Flavobacterium columnare susceptible and resistant channel catfish (Ictalurus punctatus).
|
2013-07-27
|
Eric Peatman
|
Chao Li Brian C Peterson David L Straus Bradley D Farmer Benjamin H Beck
|
Molecular Immunology
|
Differential programming of B cells in AID deficient mice
|
2013-07-29
|
Bas van Steensel
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Marc A Hogenbirk Marinus R Heideman Arno Velds Paul C M van den Berk Ron M Kerkhoven Heinz Jacobs
|
PLOS ONE
|
DNA methylation, genotype and gene expression: who is driving and who is along for the ride?
|
2013-07-29
|
Meaghan J Jones Michael S Kobor
|
Anthony P Fejes
|
Genome Biology
|
Global gene expression response of a population exposed to benzene: a pilot study exploring the use of RNA-sequencing technology
|
2013-08
|
Nathaniel Rothman
|
Reuben Thomas Cliona M McHale Qing Lan Alan E Hubbard Luoping Zhang Roel Vermeulen Guilan Li Stephen M Rappaport Songnian Yin Martyn T Smith
|
Environmental and Molecular Mutagenesis
|
Computational analysis of bacterial RNA-Seq data
|
2013-08
|
Paul Sumby
|
Ryan McClure Divya Balasubramanian Yan Sun Maksym Bobrovskyy Caroline A Genco Carin K Vanderpool Brian Tjaden
|
Nucleic Acids Research
|
The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line
|
2013-08-01
|
Jay Shendure Joshua N Burton
|
Andrew Adey Jacob O Kitzman Joseph B Hiatt Alexandra P Lewis Beth K Martin Ruolan Qiu Choli Lee
|
Nature
|
Increased BCAR1 predicts poor outcomes of non-small cell lung cancer in multiple-center patients.
|
2013-08-01
|
Zhifu Sun
|
Bo Deng Wampfler Jason Ping Yang
|
Annals of Surgical Oncology
|
RNA-Seq reveals early distinctions and late convergence of gene expression between diapause and quiescence in the Asian tiger mosquito, Aedes albopictus
|
2013-08-02
|
Christine G Elsik Monica F Poelchau
|
Julie A Reynolds David L Denlinger Peter A Armbruster
|
The Journal of Experimental Biology
|
Photoreceptor phagocytosis is mediated by phosphoinositide signaling.
|
2013-08-02
|
Krzysztof Palczewski
|
Debarshi Mustafi Brian M Kevany Christel Genoud Xiaodong Bai
|
FASEB Journal
|
Simultaneous profiling of 194 distinct receptor transcripts in human cells
|
2013-08-06
|
Kevin A. Janes
|
Byong H Kang Karin J Jensen Jaime A Hatch
|
Science Signaling
|
Masculinization of the x chromosome in the pea aphid.
|
2013-08-08
|
Solenn Stoeckel Fabrice Legeai Gaël Le Trionnaire Julie Jaquiéry Nathalie Prunier-Leterme Béatrice Ségurens Julie Poulain Denis Tagu Corinne Da Silva Claude Rispe
|
Denis Roze Lucie Mieuzet Béatrice Ségurens Jean-Christophe Simon
|
PLOS Genetics
|
BlackOPs: increasing confidence in variant detection through mappability filtering.
|
2013-08-08
|
Charles M. Perou
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Christopher R Cabanski Matthew D Wilkerson Matthew Soloway Joel S Parker Jinze Liu Jan F Prins J S Marron D Neil Hayes
|
Nucleic Acids Research
|
Genome-wide transcriptional response of Trichoderma reesei to lignocellulose using RNA sequencing and comparison with Aspergillus niger
|
2013-08-09
|
Stéphane Delmas Steven T. Pullan
|
Laure Ries Sunir Malla Martin J Blythe David B Archer
|
BMC Genomics
|
Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons.
|
2013-08-12
|
Cameron Brennan David Haussler Lynda Chin
|
J Zachary Sanborn Sofie R Salama Mia Grifford Tom Mikkelsen Suresh Jhanwar Sol Katzman
|
Cancer Research
|
Developing nuclear DNA phylogenetic markers in the angiosperm genus Leucadendron (Proteaceae): a next-generation sequencing transcriptomic approach.
|
2013-08-13
|
Emmanuel J. P. Douzery
|
Jeanne Tonnabel Isabelle Olivieri Agnès Mignot Anthony Rebelo Fabienne Justy Sylvain Santoni Stéfanie Caroli Laure Sauné Olivier Bouchez
|
Molecular Phylogenetics and Evolution
|
Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp. citri provide insights into mechanisms of bacterial virulence and host range.
|
2013-08-14
|
Joao Carlos Setubal Maxuel O Andrade
|
Neha Jalan Dibyendu Kumar Fahong Yu Jeffrey B Jones James H Graham Frank F White Nian Wang
|
BMC Genomics
|
Next-generation sequencing of advanced prostate cancer treated with androgen-deprivation therapy.
|
2013-08-14
|
Owen J Sansom Chris Ponting Andreas Heger Ian Sudbery Imran Ahmad Joanne Edwards Hing Y Leung Prabhakar Rajan
|
M Eugenia M Villasevil Ernest Mui Janis Fleming Mark Davis David Sims Rhona M McMenemin Ian D Pedley
|
European Urology
|
Adaptive responses to glucose restriction enhance cell survival, antioxidant capability, and autophagy of the protozoan parasite Trichomonas vaginalis.
|
2013-08-17
|
Petrus Tang
|
Kuo-Yang Huang Yi-Ywan Margaret Chen Yi-Kai Fang Wei-Hung Cheng Chih-Chieh Cheng Yu-Chuen Chen Tiffany E Wu Fu-Man Ku Shih-Chieh Chen Rose Lin
|
Biochimica et Biophysica Acta
|
Shaping development through mechanical strain: the transcriptional basis of diet-induced phenotypic plasticity in a cichlid fish.
|
2013-08-19
|
Helen M Gunter Paolo Franchini Axel Meyer Carmelo Fruciano
|
Shaohua Fan Fan Xiong
|
Molecular Ecology
|
Mechanisms of macroevolution: polyphagous plasticity in butterfly larvae revealed by RNA-Seq.
|
2013-08-19
|
Niklas Janz Sören Nylin Maria de la Paz Celorio-Mancera
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Christopher W Wheat Heiko Vogel Lina Söderlind
|
Molecular Ecology
|
Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data.
|
2013-08-20
|
Quanhu Sheng David C Samuels
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Yan Guo Jiang Li Fei Ye Yu Shyr
|
PLOS ONE
|
A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments.
|
2013-08-21
|
Pedro Puig
|
Mikel Esnaola David Gonzalez Robert Castelo Juan R Gonzalez
|
BMC Bioinformatics
|
Whole transcriptome RNA-Seq allelic expression in human brain
|
2013-08-22
|
Wolfgang Sadee
|
Ryan M Smith Amy Webb Audrey C Papp Leslie C Newman Samuel K Handelman Adam Suhy Roshan Mascarenhas John Oberdick
|
BMC Genomics
|
Jumping and gliding rodents: mitogenomic affinities of Pedetidae and Anomaluridae deduced from an RNA-Seq approach.
|
2013-08-23
|
Knud A. Jønsson Emmanuel J. P. Douzery
|
Pierre-Henri Fabre
|
Gene
|
Profiling microRNA expression in bovine alveolar macrophages using RNA-seq.
|
2013-08-24
|
Daniel G. Bradley Peter Vegh David J. Lynn David E. MacHugh Stephen V. Gordon
|
Amir B K Foroushani David A Magee Matthew S McCabe John A Browne Nicolas C Nalpas Kevin M Conlon
|
Veterinary Immunology and Immunopathology
|
Transcriptome analysis and SNP identification in SCC of horn in (Bos indicus) Indian cattle.
|
2013-08-24
|
Subhash J Jakhesara Chaitanya G. Joshi
|
Prakash G Koringa Vaibhav D Bhatt Anand B Patel Debabrata Dash
|
Gene
|
MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples.
|
2013-08-25
|
Gunnar Rätsch
|
Jonas Behr André Kahles Yi Zhong Vipin T Sreedharan Philipp Drewe
|
Bioinformatics
|
Complete mitochondrial genome of the medicinal mushroom Ganoderma lucidum
|
2013-08-26
|
Jianhui Zhang
|
Jianqin Li Haimei Chen Xiangdong Chen Jin Lan Chang Liu
|
PLOS ONE
|
Breakpoint features of genomic rearrangements in neuroblastoma with unbalanced translocations and chromothripsis.
|
2013-08-26
|
Isabelle Janoueix-Lerosey Valérie Combaret Valentina Boeva Emmanuel Barillot Olivier Delattre
|
Stéphanie Jouannet Romain Daveau Cécile Pierre-Eugène Alex Cazes Caroline Louis-Brennetot Gudrun Schleiermacher Sandrine Ferrand Gaëlle Pierron Alban Lermine Thomas Rio Frio Virginie Raynal Gilles Vassal
|
PLOS ONE
|
Remodeling of membrane lipids in iron-starved Chlamydomonas.
|
2013-08-27
|
David Casero Sabeeha Merchant Matteo Pellegrini Eugen Urzica Sean D Gallaher Astrid Vieler Christoph Benning
|
Anne Hong-Hermesdorf M Dudley Page Janette Kropat
|
Journal of Biological Chemistry
|
Characterization and comparative analyses of muscle transcriptomes in Dorper and small-tailed Han sheep using RNA-Seq technique.
|
2013-08-30
|
Jianmin Wang
|
Chunlan Zhang Guizhi Wang Zhibin Ji Zhaohuan Liu Xiushuang Pi Cunxian Chen
|
PLOS ONE
|
SNP development from RNA-seq data in a nonmodel fish: how many individuals are needed for accurate allele frequency prediction?
|
2013-08-31
|
Enrique Macpherson
|
C Schunter J C Garza M Pascual
|
Molecular Ecology Resources
|
SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization
|
2013-08-31
|
Shintaro Katayama Juha Kere Sten Linnarsson
|
Virpi Töhönen
|
Bioinformatics
|
Editorial for “Diversity of the non-coding transcriptomes revealed by RNA-seq technologies”
|
2013-09
|
Jean-Christophe Andrau
|
Antonin Morillon
|
Methods
|
Mutually exclusive signaling signatures define the hepatic and pancreatic progenitor cell lineage divergence.
|
2013-09-01
|
Nuria Cerdá-Esteban Nancy Mah Francesca Spagnoli
|
Elisa Rodríguez-Seguel Heike Naumann Igor M Pongrac Jean-Fred Fontaine Yongbo Wang Wei Chen Miguel A Andrade-Navarro
|
Genes & Development
|
Mining RNA-seq data for infections and contaminations.
|
2013-09-03
|
Caroline C Friedel Ralf Zimmer
|
Thomas Bonfert Gergely Csaba
|
PLOS ONE
|
RNA-Seq reveals infection-related gene expression changes in Phytophthora capsici.
|
2013-09-03
|
Xiao-Ren Chen
|
Yu-Ping Xing Yan-Peng Li Yun-Hui Tong Jing-You Xu
|
PLOS ONE
|
Trametes versicolor protein YZP activates regulatory B lymphocytes - gene identification through de novo assembly and function analysis in a murine acute colitis model.
|
2013-09-03
|
Fuu Sheu
|
Yen-Chou Kuan Ying-Jou Wu Chih-Liang Hung
|
PLOS ONE
|
Short-term feed deprivation alters immune status of surface mucosa in channel catfish (Ictalurus punctatus).
|
2013-09-04
|
Eric Peatman Lisa Liu
|
Chao Li Baofeng Su Benjamin H Beck
|
PLOS ONE
|
Copper response regulator1-dependent and -independent responses of the Chlamydomonas reinhardtii transcriptome to dark anoxia.
|
2013-09-06
|
David Casero Thomas Happe Sabeeha Merchant Matteo Pellegrini Anja Hemschemeier Christoph Benning
|
Bensheng Liu
|
The Plant Cell
|
Accelerating the design of biomimetic materials by integrating RNA-seq with proteomics and materials science.
|
2013-09-08
|
Yiqi Seow Shahrouz Amini Ali Miserez
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Paul A Guerette Shawn Hoon Manfred Raida Admir Masic Fong T Wong Vincent H B Ho Kiat Whye Kong Melik C Demirel Abdon Pena-Francesch Gavin Z Tay Dawei Ding
|
Nature Biotechnology
|
Beta cell 5'-shifted isomiRs are candidate regulatory hubs in type 2 diabetes.
|
2013-09-09
|
Jeanette Baran-Gale
|
Emily E Fannin C Lisa Kurtz Praveen Sethupathy
|
PLOS ONE
|
U1 small nuclear ribonucleoprotein complex and RNA splicing alterations in Alzheimer's disease.
|
2013-09-10
|
Yuxin Li Drew R Jones Hao Wu Eric B Dammer David A Bennett
|
Bing Bai Chadwick M Hales Ping-Chung Chen Yair Gozal Jason J Fritz Xusheng Wang Qiangwei Xia Duc M Duong Craig Street Gloria Cantero Dongmei Cheng Zhiping Wu Ian Diner Craig J Heilman Howard D Rees Li Lin Keith E Szulwach Marla Gearing Elliott J Mufson Thomas J Montine Nicholas T Seyfried Thomas S Wingo Yi E Sun Peng Jin John Hanfelt Donna M Willcock Allan Levey James J Lah Junmin Peng
|
Proceedings of the National Academy of Sciences of the United States of America
|
Analysis of allele-specific expression in mouse liver by RNA-Seq: a comparison with Cis-eQTL identified using genetic linkage.
|
2013-09-11
|
Aldons Jake Lusis Eleazar Eskin Pierre-François Roux Sandrine Lagarrigue
|
Lisa Martin Farhad Hormozdiari Calvin Pan Atila van Nas Olivier Demeure Rita Cantor Anatole Ghazalpour
|
Genetics
|
Androgen receptor signaling regulates DNA repair in prostate cancers.
|
2013-09-11
|
Deyou Zheng Daniel E. Spratt Michael J Zelefsky
|
William R Polkinghorn Joel S Parker Man X Lee Elizabeth M Kass Phillip J Iaquinta Vivek K Arora Wei-Feng Yen Ling Cai Brett S Carver Yu Chen Philip A Watson Neel P Shah Sho Fujisawa Alexander G Goglia Anuradha Gopalan Haley Hieronymus John Wongvipat Peter T Scardino Maria Jasin Jayanta Chaudhuri Simon N Powell Charles L Sawyers
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Cancer Discovery
|
A combination of improved differential and global RNA-seq reveals pervasive transcription initiation and events in all stages of the life-cycle of functional RNAs in Propionibacterium acnes, a major contributor to wide-spread human disease
|
2013-09-14
|
Kenneth J McDowall
|
Yu-fei Lin David Romero A Shuang Guan Lira Mamanova
|
BMC Genomics
|
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.
|
2013-09-15
|
Ann-Christine Syvänen Michael Sammeth Tuuli Lappalainen Xavier Estivill i Pallejà Peter A.C. 't Hoen Marc Friedlander Jeroen Laros
|
Jonas Almlöf Irina Pulyakhina Seyed Yahya Anvar Henk P J Buermans Olof Karlberg Mathias Brännvall GEUVADIS Consortium Johan T den Dunnen Gert-Jan B van Ommen Ivo G Gut Roderic Guigó Emmanouil T Dermitzakis
|
Nature Biotechnology
|
Localizing transcripts to single cells suggests an important role of uncultured deltaproteobacteria in the termite gut hydrogen economy
|
2013-09-16
|
Niles A. Pierce Xinning Zhang Vikas Trivedi
|
Adam Z Rosenthal Kaitlyn S Lucey Elizabeth A Ottesen Harry M T Choi Niles A Pierce Jared R Leadbetter
|
Proceedings of the National Academy of Sciences of the United States of America
|
RNA-Seq analysis of Mycobacterium avium non-coding transcriptome
|
2013-09-16
|
Dmitriy Ignatov Timofey Skvortsov Alexander S Apt
|
Sofia Malakho Konstantin Majorov Tatyana Azhikina
|
PLOS ONE
|
DEXUS: identifying differential expression in RNA-Seq studies with unknown conditions
|
2013-09-17
|
Sepp Hochreiter Günter Klambauer Thomas Unterthiner
|
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Nucleic Acids Research
|
Analysis of the host transcriptome from demyelinating spinal cord of murine coronavirus-infected mice.
|
2013-09-18
|
Fan Li
|
Ruth Elliott Isabelle Dragomir Ming Ming W Chua Brian D Gregory Susan R Weiss
|
PLOS ONE
|
Differentiating progressive from nonprogressive T1 bladder cancer by gene expression profiling: applying RNA-sequencing analysis on archived specimens.
|
2013-09-18
|
John Quackenbush
|
Xuanhui Sharron Lin Lan Hu Kirley Sandy Mick Correll Chin-Lee Wu William Scott McDougal
|
Urologic Oncology
|
Epstein-Barr virus and human herpesvirus 6 detection in a non-Hodgkin's diffuse large B-cell lymphoma cohort by using RNA sequencing.
|
2013-09-18
|
Melody Baddoo Tina O'Grady Erik K Flemington
|
Michael J Strong Zhen Lin Guorong Xu Melody Baddoo Chris Parsons Kun Zhang Christopher M Taylor
|
Journal of Virology
|
Using transcriptomics to improve butanol tolerance of Synechocystis sp. strain PCC 6803.
|
2013-09-20
|
Jens Nielsen Mathias Uhlén Elton P. Hudson
|
Josefine Anfelt Björn Hallström
|
Applied and Environmental Microbiology
|
Accounting for technical noise in single-cell RNA-seq experiments.
|
2013-09-22
|
Simon Anders Vladimir Benes Sarah Teichmann John C Marioni Valentina Proserpio Marcus Heisler Jong Kyoung Kim
|
Philip Brennecke Aleksandra A Kołodziejczyk Xiuwei Zhang Bianka Baying
|
Nature Methods
|
Cryptic FUS-ERG fusion identified by RNA-sequencing in childhood acute myeloid leukemia.
|
2013-09-25
|
Sverre Heim Ioannis Panagopoulos
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Ludmila Gorunova Bernward Zeller Anne Tierens
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Oncology Reports
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Next-generation sequence analysis of cancer xenograft models.
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2013-09-26
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Fernando J Rossello Kara L. Britt Richard W. Tothill Luciano G. Martelotto Jason Li Luigi Marchionni
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Kieren D Marini Jeanette Falzon David M Thomas Craig D Peacock Samara Bennett Erwin Tantoso Tracey Brown Philip Chan D Neil Watkins
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PLOS ONE
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Taf7l cooperates with Trf2 to regulate spermiogenesis.
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2013-09-30
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Ke Zheng Ivan Grubisic Tommy Kaplan Robert Tjian
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Haiying Zhou Ying He P Jeremy Wang
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Proceedings of the National Academy of Sciences of the United States of America
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Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria.
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2013-09-30
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Margaret F Romine Ronald Taylor
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Bobbie-Jo M Webb Robertson Lye Meng Markillie Margrethe H Serres Bryan E Linggi Joshua T Aldrich Eric A Hill Mary S Lipton H Steven Wiley
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Integrative Biology
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Human housekeeping genes, revisited
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2013-10
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Eli Eisenberg
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Erez Y. Levanon
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Trends in Genetics
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Evaluation of the effectiveness of semen storage and sperm purification methods for spermatozoa transcript profiling
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2013-10
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Russ Hauser Zhen Chen
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Shihong Mao Robert J Goodrich Steven M Schrader Stephen A Krawetz
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Systems Biology in Reproductive Medicine
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RNA-Seq of Bacillus licheniformis: active regulatory RNA features expressed within a productive fermentation
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2013-10-01
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Heiko Liesegang Sandra Wiegand Rolf Daniel
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Sascha Dietrich Robert Hertel Johannes Bongaerts Stefan Evers Sonja Volland
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BMC Genomics
|
RNA-Seq analysis of Citrus reticulata in the early stages of Xylella fastidiosa infection reveals auxin-related genes as a defense response.
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2013-10-03
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Luciano T. Kishi
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Carolina M Rodrigues Alessandra A de Souza Marco A Takita Marcos A Machado
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BMC Genomics
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Transcriptome comparison of human neurons generated using induced pluripotent stem cells derived from dental pulp and skin fibroblasts
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2013-10-03
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Deyou Zheng John J. Foxe
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Jian Chen Mingyan Lin Erika Pedrosa Anastasia Hrabovsky Reed Carroll Herbert M Lachman
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PLOS ONE
|
Transcriptomics of the rice blast fungus Magnaporthe oryzae in response to the bacterial antagonist Lysobacter enzymogenes reveals candidate fungal defense response genes
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2013-10-03
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Bradley I. Hillman
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Sandra M Mathioni Nrupali Patel Bianca Riddick James A Sweigard Kirk J Czymmek Jeffrey L Caplan Sridhara G Kunjeti Saritha Kunjeti Vidhyavathi Raman Donald Y Kobayashi Nicole M Donofrio
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PLOS ONE
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Function of lncRNAs and approaches to lncRNA-protein interactions.
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2013-10-05
|
Hanjiang Fu
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Juanjuan Zhu Yongge Wu Xiaofei Zheng
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Science in China. Series C: Life Sciences
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In vitro grown pollen tubes of Nicotiana alata actively synthesise a fucosylated xyloglucan.
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2013-10-08
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Edwin R. Lampugnani Ed Newbigin Antony Bacic
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Isabel E Moller Andrew Cassin Daniel F Jones Poh Ling Koh Sunil Ratnayake Cherie T Beahan Sarah M Wilson
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PLOS ONE
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Soft truncation thresholding for gene set analysis of RNA-seq data: application to a vaccine study
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2013-10-09
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Gregory Poland
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Brooke L Fridley Gregory D Jenkins Diane E Grill Richard B Kennedy Ann L Oberg
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Scientific Reports
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mirCoX: a database of miRNA-mRNA expression correlations derived from RNA-seq meta-analysis.
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2013-10-09
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Mikhail G Dozmorov
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Cory B Giles Reshmi Girija-Devi Jonathan D Wren
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BMC Bioinformatics
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Towards the integration, annotation and association of historical microarray experiments with RNA-seq
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2013-10-09
|
Michael A Bauer
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Shweta S Chavan Erich A Peterson Christoph J Heuck Donald J Johann
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BMC Bioinformatics
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Host-Mycobacterium avium subsp. paratuberculosis interactome reveals a novel iron assimilation mechanism linked to nitric oxide stress during early infection.
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2013-10-10
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Srinand Sreevatsan
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Elise A Lamont Wayne W Xu
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BMC Genomics
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Histoplasma yeast and mycelial transcriptomes reveal pathogenic-phase and lineage-specific gene expression profiles.
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2013-10-10
|
Chad Rappleye
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Jessica A Edwards Chenxi Chen Megan M Kemski Jinnan Hu Thomas K Mitchell
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BMC Genomics
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Transcriptome comparison between porcine subcutaneous and intramuscular stromal vascular cells during adipogenic differentiation.
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2013-10-10
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Hongkui Wei
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Shuzhong Jiang Tongxing Song Yang Yang Jian Peng Siwen Jiang
|
PLOS ONE
|
Modeling the next generation sequencing sample processing pipeline for the purposes of classification.
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2013-10-11
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Charles D. Johnson Edward R. Dougherty
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Noushin Ghaffari Mohammadmahdi R Yousefi Ivan Ivanov
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BMC Bioinformatics
|
Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots.
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2013-10-11
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W. Richard McCombie Elena A Vidal Gabriel Krouk Milos Tanurdzic Rodrigo A Gutiérrez
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Tomás C Moyano Manpreet S Katari Gloria M Coruzzi
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BMC Genomics
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GIIRA--RNA-Seq driven gene finding incorporating ambiguous reads.
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2013-10-11
|
Bernhard Y Renard
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Franziska Zickmann Martin S Lindner
|
Bioinformatics
|
F11R is a novel monocyte prognostic biomarker for malignant glioma
|
2013-10-11
|
Xi Feng Winnie W Pong Jaebok Choi Malachi Griffith Obi Griffith Greg N. Fuller David H Gutmann
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Jason Walker Todd Wylie Vincent Magrini Jingqin Luo Ryan J Emnett Matthew L Cooper Joshua B Rubin David Piwnica-Worms Dolores Hambardzumyan John F DiPersio Elaine R Mardis
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PLOS ONE
|
SOAPfusion: a robust and effective computational fusion discovery tool for RNA-seq reads.
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2013-10-11
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Tak-Wah Lam Jun Wang Jikun Wu Zhiyu Peng
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Wenqian Zhang Songbo Huang Zengquan He Yanbing Cheng Siu-Ming Yiu
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Bioinformatics
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Profiling the molecular mechanism of fullerene cytotoxicity on tumor cells by RNA-seq.
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2013-10-12
|
Marco Gerdol Alberto Pallavicini Marianna Lucafò Gianni Sava Sabrina Pacor Maurizio Prato
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Sonia Zorzet Tatiana Da Ros
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Toxicology
|
Use of a capture-based pathogen transcript enrichment strategy for RNA-Seq analysis of the Francisella tularensis LVS transcriptome during infection of murine macrophages.
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2013-10-14
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David M Brazel
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Zachary W Bent Mary B Tran-Gyamfi Rachelle Y Hamblin Victoria A VanderNoot Steven S Branda
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PLOS ONE
|
Ribosomal protein S6 mRNA is a biomarker upregulated in multiple sclerosis, downregulated by interferon treatment, and affected by season.
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2013-10-14
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Peter M. Visscher Mark Slee Joseph E. Powell Grant W. Montgomery Fiona C McKay
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Grant P Parnell Prudence N Gatt Stephen Schibeci Malgorzata Krupa Jeannette Lechner-Scott Simon Broadley Christopher Liddle Steve Vucic Graeme J Stewart David R Booth
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Multiple Sclerosis Journal
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An RNA-seq transcriptome analysis of histone modifiers and RNA silencing genes in soybean during floral initiation process.
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2013-10-16
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Lim Chee Liew Mohan B. Singh Prem L. Bhalla
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PLOS ONE
|
Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network
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2013-10-16
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Marcel E. Dinger John Mattick Animesh Ray Shaojie Zhang
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Jian-Liang Li Joseph Mazar Cuncong Zhong Geoffrey J Faulkner Subramaniam S Govindarajan Zhan Zhang Gavin Meredith Christopher Adams Ranjan J Perera
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Scientific Reports
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A novel intra-U1 snRNP cross-regulation mechanism: alternative splicing switch links U1C and U1-70K expression.
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2013-10-17
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Ekaterina E Khrameeva
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Tanja Dorothe Rösel-Hillgärtner Lee-Hsueh Hung Patrick Le Querrec Mikhail S Gelfand Albrecht Bindereif
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PLOS Genetics
|
A KH-domain RNA-binding protein interacts with FIERY2/CTD phosphatase-like 1 and splicing factors and is important for pre-mRNA splicing in Arabidopsis.
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2013-10-17
|
Liming Xiong Shoudong Zhang
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Tao Chen Peng Cui Hao Chen Shahjahan Ali
|
PLOS Genetics
|
Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032
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2013-10-19
|
Alfred Pühler Jörn Kalinowski
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Almut Mentz Armin Neshat Katharina Pfeifer-Sancar Christian Rückert
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BMC Genomics
|
Quantitative assessment of single-cell RNA-sequencing methods.
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2013-10-20
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Barbara Treutlein Piero Dalerba
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Angela R Wu Norma F Neff Tomer Kalisky Michael E Rothenberg Francis M Mburu Gary L Mantalas Sopheak Sim Michael F Clarke Stephen R Quake
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Nature Methods
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HAMR: high-throughput annotation of modified ribonucleotides.
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2013-10-22
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Otto Valladares
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Paul Ryvkin Yuk Yee Leung Ian M Silverman Micah Childress Isabelle Dragomir Brian D Gregory Li-San Wang
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RNA
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Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe.
|
2013-10-23
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Monika Gullerova Jürg Bähler Nicholas Jarvis Proudfoot
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Margarita Schlackow Samuel Marguerat Jürg Bähler Radek Erban
|
RNA
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Parallel deep transcriptome and proteome analysis of zebrafish larvae
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2013-10-24
|
Christiaan V. Henkel Magnus Palmblad Herman P Spaink
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Ron P Dirks Annemarie H Meijer André M Deelder
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BMC Research Notes
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Integrated transcriptomic and proteomic analysis of the global response of Wolbachia to doxycycline-induced stress.
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2013-10-24
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Alistair C. Darby Dong Xia
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A Christina Gill Stuart D Armstrong Catherine S Hartley Jonathan M Wastling Benjamin L Makepeace
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The ISME Journal
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IMG 4 version of the integrated microbial genomes comparative analysis system.
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2013-10-27
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Natalia N. Ivanova Nikos C. Kyrpides Tanja Woyke Neha Varghese Konstantinos Billis Amrita Pati Marcel Huntemann Iain J. Anderson Konstantinos Mavromatis Krishna Palaniappan
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Victor M Markowitz I-Min A Chen Ken Chu Ernest Szeto Manoj Pillay Anna Ratner Jinghua Huang
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Nucleic Acids Research
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Differential expression of olfactory genes in the southern house mosquito and insights into unique odorant receptor gene isoforms.
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2013-10-28
|
Walter S Leal
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Young-Moo Choo Pingxi Xu Cherre S B da Silva Carlos Ueira-Vieira
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Proceedings of the National Academy of Sciences of the United States of America
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Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps.
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2013-10-29
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Ross C Hardison Manolis Kellis
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Ali Mortazavi Shirley Pepke Camden Jansen Georgi K Marinov Jason Ernst Richard M Myers Barbara J Wold
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Genome Research
|
A unified model for yeast transcript definition.
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2013-10-29
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Harm van Bakel Corey Nislow Carl G de Boer Quaid D Morris
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Kyle Tsui Joyce Li Jack F Greenblatt Timothy R Hughes
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Genome Research
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Inferring polymorphism-induced regulatory gene networks active in human lymphocyte cell lines by weighted linear mixed model analysis of multiple RNA-Seq datasets.
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2013-10-30
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Erik K Flemington
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Wensheng Zhang Andrea Edwards Kun Zhang
|
PLOS ONE
|
Probing bacterial metabolism during infection using high-resolution transcriptomics
|
2013-11
|
Marvin Whiteley
|
Peter Jorth Urvish Trivedi Kendra Rumbaugh
|
Journal of Bacteriology
|
An integrated model of the transcriptome of HER2-positive breast cancer.
|
2013-11-01
|
Kevin J Thompson Xiaojia Tang Krishna R Kalari Richard W. Joseph Zhifu Sun
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Brian M Necela Melissa Lau Jeanette E Eckel-Passow Jennifer M Kachergus S Keith Anderson Saurabh Baheti Jennifer M Carr Tiffany R Baker Poulami Barman Derek C Radisky Sarah A McLaughlin High-seng Chai Stephan Camille David Rossell Yan W Asmann E Aubrey Thompson Edith A Perez
|
PLOS ONE
|
Identification of molecular tumor markers in renal cell carcinomas with TFE3 protein expression by RNA sequencing.
|
2013-11-01
|
Mark Rubin
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Dorothee Pflueger Andrea Sboner Martina Storz Jasmine Roth Eva Compérat Elisabeth Bruder Peter Schraml Holger Moch
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Neoplasia
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RNA-seq-based comparative transcriptome analysis of the syngas-utilizing bacterium Clostridium ljungdahlii DSM 13528 grown autotrophically and heterotrophically.
|
2013-11-01
|
Fuli Li
|
Yang Tan Juanjuan Liu Xiaohua Chen Huajun Zheng
|
Molecular BioSystems
|
Global aspects of pacC regulation of pathogenicity genes in Colletotrichum gloeosporioides as revealed by transcriptome analysis.
|
2013-11-01
|
Michael Thon Serenella Sukno
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Noam Alkan Xiangchun Meng Gilgi Friedlander Eli Reuveni Amir Sherman Robert Fluhr Dov Prusky
|
Molecular Plant-Microbe Interactions
|
Systematic evaluation of spliced alignment programs for RNA-seq data
|
2013-11-03
|
Jennifer Harrow Roderic Guigó i Serra Tamara Steijger Pär G Engström Gregory R Grant Gunnar Rätsch Nick Goldman Paul Bertone
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Botond Sipos André Kahles Tim J Hubbard RGASP Consortium
|
Nature Methods
|
Assessment of transcript reconstruction methods for RNA-seq.
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2013-11-03
|
Tim Hubbard Jennifer Harrow Felix Kokocinski Roderic Guigó i Serra Tamara Steijger Pär G Engström Josep F. Abril Paul Bertone
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RGASP Consortium
|
Nature Methods
|
Model-based clustering for RNA-seq data.
|
2013-11-04
|
Thomas Brutnell
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Yaqing Si Peng Liu Pinghua Li
|
Bioinformatics
|
The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations
|
2013-11-04
|
Gavin Sherlock Jennifer R Wortman Diane Inglis
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Gustavo C Cerqueira Martha B Arnaud Marek S Skrzypek Gail Binkley Matt Simison Stuart R Miyasato Jonathan Binkley Joshua Orvis Prachi Shah Farrell Wymore
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Nucleic Acids Research
|
Dysregulation of synaptogenesis genes antecedes motor neuron pathology in spinal muscular atrophy.
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2013-11-04
|
Anna Maria Pinto Christopher Dengler
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Zhenxi Zhang Lili Wan Wei Wang Michael G Berg Isabela Oliva Larry N Singh Zhi Wei Gideon Dreyfuss
|
Proceedings of the National Academy of Sciences of the United States of America
|
Comparison of microarrays and RNA-seq for gene expression analyses of dose-response experiments.
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2013-11-05
|
Russell S. Thomas Michael B Black
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Bethany B Parks Linda Pluta Tzu-Ming Chu Bruce C Allen Russell D Wolfinger
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Toxicological Sciences
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Serotonergic neuron regulation informed by in vivo single-cell transcriptomics.
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2013-11-05
|
Tamas Bartfai
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Jennifer M Spaethling David Piel Hannah Dueck Peter T Buckley Jacqueline F Morris Stephen A Fisher Jaehee Lee Jai-Yoon Sul Junhyong Kim Sheryl G Beck James H Eberwine
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FASEB Journal
|
Surfing transcriptomic landscapes. A step beyond the annotation of chromosome 16 proteome.
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2013-11-05
|
Miguel Marcilla Cristina Ruiz-Romero Joan J Bech-Serra Oscar Gallardo Gorka Prieto Concha Gil Joaquín Abian Marta Mendes Irene Orera Noelia Dasilva Kerman Aloria María I Mora Manuel Fuentes José M Mato
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Víctor Segura Juan Alberto Medina-Aunon Salvador Martínez-Bartolomé Oreto Antúnez Jesús M Arizmendi Mikel Azkargorta Silvia Barceló-Batllori Jabier Beaskoetxea Francisco Blanco Mariana B Monteiro David Cáceres Francesc Canals Monserrat Carrascal José Ignacio Casal Felipe Clemente Nuria Colomé Paula Díaz Félix Elortza Patricia Fernández-Puente Severine I Gharbi Carmen González-Tejedo María Luisa Hernáez Manuel Lombardía Maria Lopez-Lucendo Eliandre Oliveira Alberto Pascual-Montano Manuel M Sánchez del Pino Daniel Tabas-Madrid Maria L Valero Vital Vialas Joan Villanueva Juan Pablo Albar Fernando J Corrales
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Journal of Proteome Research
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Modeling alternative splicing variants from RNA-Seq data with isoform graphs.
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2013-11-07
|
Gianluca Della Vedova
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Stefano Beretta Paola Bonizzoni Yuri Pirola Raffaella Rizzi
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Journal of Computational Biology
|
Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation.
|
2013-11-07
|
Alexander van Oudenaarden Wenqian Hu Jiahai Shi Harvey Lodish
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Juan R Alvarez-Dominguez Bingbing Yuan Staphany S Park Austin A Gromatzky
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Blood
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Distinct splice variants and pathway enrichment in the cell-line models of aggressive human breast cancer subtypes
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2013-11-07
|
Gil Omenn
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Rajasree Menon Hogune Im Emma Yue Zhang Shiaw-Lin Wu Rui Chen Michael Snyder William S Hancock
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Journal of Proteome Research
|
Comprehensive RNA-Seq expression analysis of sensory ganglia with a focus on ion channels and GPCRs in Trigeminal ganglia
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2013-11-08
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Hanns Hatt Günter Gisselmann
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Stavros Manteniotis Ramona Lehmann Caroline Flegel Felix Vogel Adrian Hofreuter Benjamin S P Schreiner Janine Altmüller Christian Becker Nicole Schöbel Günter Gisselmann
|
PLOS ONE
|
Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki)
|
2013-11-09
|
David Sturgill
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John H Malone Xia Sun Harold E Smith Leonard Rabinow Marie-Laure Samson Brian Oliver
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BMC Bioinformatics
|
Deletion of Asxl1 results in myelodysplasia and severe developmental defects in vivo
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2013-11-11
|
Jinfeng Liu Xinyang Zhao Eunhee Kim Omar Abdel-Wahab
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Jie Gao Mazhar Adli Anwesha Dey Thomas Trimarchi Young Rock Chung Cem Kuscu Todd Hricik Delphine Ndiaye-Lobry Lindsay M Lafave Richard Koche Alan H Shih Olga A Guryanova Sheng Li Suveg Pandey Joseph Y Shin Leon Telis Parva K Bhatt Sebastien Monette Christopher E Mason Christopher Y Park Bradley E Bernstein Iannis Aifantis Ross L Levine
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Journal of Experimental Medicine
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Efficient cellular fractionation improves RNA sequencing analysis of mature and nascent transcripts from human tissues.
|
2013-11-13
|
Adam Ameur
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Ammar Zaghlool Linnea Nyberg Jonatan Halvardson Manfred Grabherr Lucia Cavelier Lars Feuk
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BMC Biotechnology
|
Mapping genetic modifiers of survival in a mouse model of Dravet syndrome.
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2013-11-14
|
Jennifer A Kearney
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A R Miller N A Hawkins C E McCollom
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Genes, Brain and Behavior
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Early T helper cell programming of gene expression in human
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2013-11-15
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Riitta Lahesmaa
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Soile Tuomela
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Seminars in Immunology
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Resolving chromosome-centric human proteome with translating mRNA analysis: a strategic demonstration.
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2013-11-15
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Yizhi Cui Qing-Yu He Gong Zhang Tong Wang
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Jiayong Zhong Jiahui Guo Zhipeng Chen Lijuan Yang
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Journal of Proteome Research
|
Accuracy of allele frequency estimation using pooled RNA-Seq.
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2013-11-16
|
Mateusz Konczal Wieslaw Babik Jacek Radwan Paweł Koteja
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M T Stuglik
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Molecular Ecology Resources
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Proteogenomic analysis reveals unanticipated adaptations of colorectal tumor cells to deficiencies in DNA mismatch repair.
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2013-11-18
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Daniel C. Liebler
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Patrick J Halvey Xiaojing Wang Jing Wang Ajaz A Bhat Punita Dhawan Ming Li Bing Zhang Robbert J C Slebos
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Cancer Research
|
Expression of Porphyromonas gingivalis small RNA in response to hemin availability identified using microarray and RNA-seq analysis.
|
2013-11-19
|
Ann Progulske-Fox
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Priscilla Phillips Scott Grieshaber Nicole Grieshaber
|
FEMS Microbiology Letters
|
Global analysis of differentially expressed genes and proteins in the wheat callus infected by Agrobacterium tumefaciens
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2013-11-20
|
Dongwen Lv
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Xiaohong Zhou Ke Wang Chengjun Wu Jiarui Li Pei Zhao Zhishan Lin Lipu Du Yueming Yan Xingguo Ye
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PLOS ONE
|
Phenotypic and transcriptional fidelity of patient-derived colon cancer xenografts in immune-deficient mice
|
2013-11-20
|
Edus H Warren
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Jeffrey Chou Matthew P Fitzgibbon Christie-Lynn L Mortales Andrea M H Towlerton Melissa P Upton Raymond S Yeung Martin W McIntosh
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PLOS ONE
|
Global bidirectional transcription of the Epstein-Barr virus genome during reactivation.
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2013-11-20
|
Melody Baddoo Tina O'Grady Erik K Flemington
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Subing Cao Michael J Strong Monica Concha Xia Wang Sandra Splinter Bondurant Marie Adams Melody Baddoo Sudesh K Srivastav Zhen Lin Claire Fewell Qinyan Yin
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Journal of Virology
|
Genome-wide mapping of transcriptional start sites defines an extensive leaderless transcriptome in Mycobacterium tuberculosis.
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2013-11-21
|
Graham Rose Teresa Cortes Olga T Schubert Kristine B Arnvig Iñaki Comas Ruedi Aebersold
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Douglas B Young
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Cell Reports
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DUX4 binding to retroelements creates promoters that are active in FSHD muscle and testis.
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2013-11-21
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Zizhen Yao Silvère M van der Maarel
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Janet M Young Jennifer L Whiddon Bhavatharini Kasinathan Lauren Snider Linda N Geng Judit Balog Rabi Tawil Stephen J Tapscott
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PLOS Genetics
|
RNA-seq profiles of immune related genes in the staghorn coral Acropora cervicornis infected with white band disease
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2013-11-21
|
Silvia Libro
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Stefan T Kaluziak Steven V Vollmer
|
PLOS ONE
|
Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia.
|
2013-11-21
|
Víctor Quesada Núria López-Bigas Alfonso Valencia Carlos López Otín Roderic Guigó i Serra Jean Monlong Panagiotis Papasaikas Simone Ecker Guillem Clot Sarah Djebali Pedro G Ferreira Rory Johnson Daniel Rico Gonzalo Gómez-López Xose S. Puente David G. Pisano María Rozman José I Martín-Subero Dolors Colomer Elias Campo
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Pedro Jares Alejandra Martínez-Trillos Neus Villamor Abel González-Pérez David G Knowles Mónica López-Guerra Cristina Royo Maite Cazorla Magda Pinyol Marta Aymerich Marta Kulis David Tamborero Anaïs Gouin Julie Blanc Marta Gut Ivo Gut Armando López-Guillermo
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Genome Research
|
RNA-seq reveals the RNA binding proteins, Hfq and RsmA, play various roles in virulence, antibiotic production and genomic flux in Serratia sp. ATCC 39006.
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2013-11-22
|
Adam J Reid Joshua P Ramsay Laurent Gatto Lars Barquist
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Nabil M Wilf Neil R Williamson Nicholas J Croucher Svenja S Hester David Goulding Kathryn S Lilley Robert A Kingsley Gordon Dougan George Pc Salmond
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BMC Genomics
|
Assessment of myometrial transcriptome changes associated with spontaneous human labour by high-throughput RNA-seq.
|
2013-11-22
|
Jonathan D. Moore Andrew M Blanks Siobhan Quenby
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Yi-Wah Chan Hugo A van den Berg
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Experimental Physiology
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MMDiff: quantitative testing for shape changes in ChIP-Seq data sets
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2013-11-24
|
Thomas Clouaire Adrian Peter Bird
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Gabriele Schweikert Botond Cseke Guido Sanguinetti
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BMC Genomics
|
Flexible analysis of RNA-seq data using mixed effects models.
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2013-11-26
|
Ernest Turro
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William J Astle Simon Tavaré
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Bioinformatics
|
Characterization of the human ESC transcriptome by hybrid sequencing.
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2013-11-26
|
Harm van Bakel Renee Reijo Pera
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Kin Fai Au Vittorio Sebastiano Pegah Tootoonchi Afshar Jens Durruthy Durruthy Lawrence Lee Brian A Williams Eric E Schadt Jason G Underwood Wing Hung Wong
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Proceedings of the National Academy of Sciences of the United States of America
|
Transcriptional regulation of two conceptus interferon tau genes expressed in Japanese black cattle during peri-implantation period.
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2013-11-27
|
So Nakagawa
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Toshihiro Sakurai Min-Su Kim Hanako Bai Rulan Bai Junyou Li Kwan-Sik Min Atsushi Ideta Yoshito Aoyagi Kazuhiko Imakawa
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PLOS ONE
|
RNA-Seq analyses reveal CRISPR RNA processing and regulation patterns.
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2013-12-01
|
Judith Zoephel L Randau
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Judith Zoephel
|
Biochemical Society Transactions
|
An infection-relevant transcriptomic compendium for Salmonella enterica Serovar Typhimurium.
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2013-12-01
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Carsten Kröger Shabarinath Srikumar Kristian Händler Karsten Hokamp
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Aoife Colgan Sathesh K Sivasankaran Disa L Hammarlöf Rocío Canals Joe E Grissom Tyrrell Conway Jay C D Hinton
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Cell Host & Microbe
|
The transcription-splicing protein NonO/p54nrb and three NonO-interacting proteins bind to distal enhancer region and augment rhodopsin expression.
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2013-12-02
|
Anand Swaroop Matthew Brooks
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Sharda P Yadav Hong Hao Hyun-Jin Yang Marie-Audrey I Kautzmann Jacob Nellissery Bernward Klocke Martin Seifert
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Human Molecular Genetics
|
Comparative N-glycan profiling of colorectal cancer cell lines reveals unique bisecting GlcNAc and α-2,3-linked sialic acid determinants are associated with membrane proteins of the more metastatic/aggressive cell lines.
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2013-12-02
|
Morten Thaysen-Andersen Susan Fanayan Mark Baker
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Manveen K Sethi Joshua T Smith Nicolle H Packer William S Hancock
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Journal of Proteome Research
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Comparison of software packages for detecting differential expression in RNA-seq studies.
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2013-12-02
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Laura L. Elo
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Fatemeh Seyednasrollah Asta Laiho
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Briefings in Bioinformatics
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Integrated chromosome 19 transcriptomic and proteomic data sets derived from glioma cancer stem-cell lines.
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2013-12-03
|
György Marko-Varga
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Cheryl F Lichti Huiling Liu Alexander S Shavkunov Ekaterina Mostovenko Erik P Sulman Ravesanker Ezhilarasan Qianghu Wang Roger A Kroes Joseph C Moskal David Fenyö Betül Akgöl Oksuz Charles A Conrad Frederick F Lang Frode S Berven Akos Végvári Melinda Rezeli Sophia Hober Carol L Nilsson
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Journal of Proteome Research
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Joint estimation of isoform expression and isoform-specific read distribution using multisample RNA-Seq data.
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2013-12-03
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Stefano Calza
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Chen Suo Agus Salim Yudi Pawitan
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Bioinformatics
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The Clostridium small RNome that responds to stress: the paradigm and importance of toxic metabolite stress in C. acetobutylicum
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2013-12-04
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Blake Meyers
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Keerthi P Venkataramanan Shawn W Jones Kevin P McCormick Sridhara G Kunjeti Matthew T Ralston Eleftherios T Papoutsakis
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BMC Genomics
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Simultaneous transcriptional profiling of bacteria and their host cells
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2013-12-04
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Claire M. Fraser Naomi Sengamalay Marcus C. Chibucos Amol C Shetty Todd Creasy
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Michael S Humphrys Yezhou Sun Elliott F Drabek Umar Farooq Naomi Sengamalay Sandy Ott Huizhong Shou Patrik M Bavoil Anup Mahurkar Garry S A Myers
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PLOS ONE
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Vespucci: a system for building annotated databases of nascent transcripts.
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2013-12-04
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Terry Gaasterland Minna U Kaikkonen Christopher K Glass
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Karmel A Allison
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Nucleic Acids Research
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A platform independent RNA-Seq protocol for the detection of transcriptome complexity.
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2013-12-05
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Graziano Pesole Flaviana Marzano Mariano Francesco Caratozzolo Ivana Kurelac D D'Elia Anna Maria D'Erchia Flavio Licciulli Ernesto Picardi
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Claudia Calabrese Marina Mangiulli Caterina Manzari Anna Maria Paluscio Sabino Liuni Marcella Attimonelli Giuseppe Gasparre Anna Maria Porcelli Elisabetta Sbisà Apollonia Tullo
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BMC Genomics
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Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics.
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2013-12-05
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Jens Nielsen Mathias Uhlén Jenny Ottosson Takanen Cristina Al-Khalili Szigyarto Kalle von Feilitzen Linn Fagerberg Jan Mulder Mikael Huss Jochen Schwenk Jacob Odeberg Peter Nilsson Per Oksvold
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Björn M Hallström Caroline Kampf Dijana Djureinovic Masato Habuka Simin Tahmasebpoor Angelika Danielsson Karolina Edlund Anna Asplund Evelina Sjöstedt Emma Lundberg Marie Skogs Jenny Ottosson Takanen Holger Berling Hanna Tegel Cecilia Lindskog Frida Danielsson Adil Mardinoglu Asa Sivertsson Kalle von Feilitzen Mattias Forsberg Martin Zwahlen IngMarie Olsson Sanjay Navani Fredrik Ponten
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Molecular & Cellular Proteomics
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Fermentation stage-dependent adaptations of Bacillus licheniformis during enzyme production.
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2013-12-06
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Sandra Wiegand Heiko Liesegang Rolf Daniel
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Birgit Voigt Dirk Albrecht Johannes Bongaerts Stefan Evers Michael Hecker
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Microbial Cell Factories
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RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.
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2013-12-06
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Brian Scheffler Megan J Bowman Philip J Bauer
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Wonkeun Park Joshua A Udall Justin T Page Joshua Raney Don C Jones B Todd Campbell
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PLOS ONE
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Co-expression network analysis identifies Spleen Tyrosine Kinase (SYK) as a candidate oncogenic driver in a subset of small-cell lung cancer
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2013-12-09
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John K. Field
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Akshata R Udyavar Megan D Hoeksema Jonathan E Clark Yong Zou Zuojian Tang Zhiguo Li Ming Li Heidi Chen Alexander Statnikov Yu Shyr Daniel C Liebler Rosana Eisenberg Lourdes Estrada Pierre P Massion Vito Quaranta
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BMC Systems Biology
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ETV6-NTRK3 is a common chromosomal rearrangement in radiation-associated thyroid cancer.
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2013-12-10
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Tetiana Bogdanova Mark P Little
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Rebecca J Leeman-Neill Lindsey M Kelly Pengyuan Liu Alina V Brenner Viktoria N Evdokimova Maureen Hatch Liudmyla Y Zurnadzy Marina N Nikiforova Ning J Yue Miao Zhang Kiyohiko Mabuchi Mykola D Tronko Yuri E Nikiforov
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Cancer
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Next generation sequencing analysis of human platelet PolyA+ mRNAs and rRNA-depleted total RNA.
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2013-12-11
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Abdimajid Osman
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Antheia Kissopoulou Jon Jonasson Tomas L Lindahl
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PLOS ONE
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Transcriptome changes in the porcine endometrium during the preattachment phase.
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2013-12-12
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Susanne E. Ulbrich
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Anastazia Samborski Alexander Graf Stefan Krebs Barbara Kessler Myriam Reichenbach Horst-Dieter Reichenbach Stefan Bauersachs
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Biology of Reproduction
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TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes.
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2013-12-13
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Michiel Van Bel Klaas Vandepoele Yves Van de Peer
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Sebastian Proost Christophe Van Neste Dieter Deforce Yves Van de Peer
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Genome Biology
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Identification of two putative reference genes from grapevine suitable for gene expression analysis in berry and related tissues derived from RNA-Seq data
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2013-12-13
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Ariel Orellana
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Mauricio González-Agüero Miguel García-Rojas Alex Di Genova José Correa Alejandro Maass Patricio Hinrichsen
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BMC Genomics
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Transcriptome analysis of Pinus monticola primary needles by RNA-seq provides novel insight into host resistance to Cronartium ribicola.
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2013-12-16
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Jun-Jun Liu
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Rona N Sturrock Ross Benton
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BMC Genomics
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Comprehensive analysis of the Corynebacterium glutamicum transcriptome using an improved RNAseq technique
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2013-12-17
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Jörn Kalinowski
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Katharina Pfeifer-Sancar Almut Mentz Christian Rückert
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BMC Genomics
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RNA-Seq optimization with eQTL gold standards.
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2013-12-17
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Andrew B. West
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Shannon E Ellis Simone Gupta Foram N Ashar Joel S Bader Dan E Arking
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BMC Genomics
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Studying Culicoides vectors of BTV in the post-genomic era: resources, bottlenecks to progress and future directions.
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2013-12-17 2014-03-01
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Daniel Lawson Paul J Kersey
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Dana Nayduch Lee W Cohnstaedt Christopher Saski Mark Fife Simon Carpenter
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Virus Research
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Combining DGE and RNA-sequencing data to identify new polyA+ non-coding transcripts in the human genome
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2013-12-18
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Eric Rivals
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Nicolas Philippe Elias Bou Samra Anthony Boureux Alban Mancheron Florence Rufflé Qiang Bai John De Vos Thérèse Commes
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Nucleic Acids Research
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Comprehensive analysis of transcriptome variation uncovers known and novel driver events in T-cell acute lymphoblastic leukemia
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2013-12-19
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Iwona Wlodarska Gert Hulselmans Zeynep Kalender Atak Kim De Keersmaecker Peter Vandenberghe Jan Cools Stein Aerts Robin Foà
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Valentina Gianfelici Arun George Devasia Ellen Geerdens Nicole Mentens Sabina Chiaretti Kaat Durinck Anne Uyttebroeck Jacqueline Cloos Frank Speleman
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PLOS Genetics
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An overview of gene expression dynamics during early ovarian folliculogenesis: specificity of follicular compartments and bi-directional dialog.
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2013-12-19
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Sylvain Foissac
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Agnes Bonnet Cedric Cabau Olivier Bouchez Julien Sarry Nathalie Marsaud Florent Woloszyn Philippe Mulsant Beatrice Mandon-Pepin
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BMC Genomics
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Differential transcriptome analysis of glandular and filamentous trichomes in Artemisia annua
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2013-12-20
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Alain Goossens
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Sandra S A Soetaert Christophe M F Van Neste Mado L Vandewoestyne Steven R Head Filip C W Van Nieuwerburgh Dieter L D Deforce
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BMC Plant Biology
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PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution
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2013-12-20
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Xianyun Mao Jane Ferguson Muredach P. Reilly
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Yu Hu Yichuan Liu Cheng Jia Chenyi Xue Hongzhe Li Mingyao Li
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Nucleic Acids Research
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Correction: RNA-Seq-Based Analysis of the Physiologic Cold Shock-Induced Changes in Moraxella catarrhalis Gene Expression.
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2013-12-20
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Stefan Wyder
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Violeta Spaniol Christoph Aebi
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PLOS ONE
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Quantitative single-cell RNA-seq with unique molecular identifiers.
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2013-12-22
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Sten Linnarsson Peter Lönnerberg
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Saiful Islam Amit Zeisel Simon Joost Gioele La Manno Pawel Zajac Maria Kasper
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Nature Methods
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Divergent transcription is associated with promoters of transcriptional regulators.
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2013-12-23
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Marc Garibal Jean-Christophe Andrau Jean Imbert Salvatore Spicuglia
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Cyrille Lepoivre Mohamed Belhocine Aurélie Bergon Aurélien Griffon Miriam Yammine Laurent Vanhille Joaquin Zacarias-Cabeza Frederic Koch Muhammad Ahmad Maqbool Romain Fenouil Beatrice Loriod Hélène Holota Marta Gut Ivo Gut Denis Puthier
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BMC Genomics
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Lsh regulates LTR retrotransposon repression independently of Dnmt3b function.
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2013-12-24
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Colin A. Semple Tracey Davey Ian R. Adams John Greally
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Donncha S Dunican Hazel A Cruickshanks Masako Suzuki Robert J Arceci Richard R Meehan
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Genome Biology
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Blind spots of quantitative RNA-seq: the limits for assessing abundance, differential expression, and isoform switching
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2013-12-24
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Lennart Opitz
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Hubert Rehrauer Ge Tan Lina Sieverling Ralph Schlapbach
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BMC Bioinformatics
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Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors.
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2013-12-24
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Laura Elnitski Zhong Chen
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Zhenqing Ye Xun Lan Stephen Hara Benjamin Sunkel Tim H-M Huang Qianben Wang Victor X Jin
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Nucleic Acids Research
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Mycorrhizal phosphate uptake pathway in maize: vital for growth and cob development on nutrient poor agricultural and greenhouse soils.
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2013-12-26
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Jan Jansa
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Martin Willmann Nina Gerlach Benjamin Buer Aleksandra Polatajko Réka Nagy Eva Koebke René Flisch Marcel Bucher
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Frontiers in Plant Science
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Nutritional impacts on gene expression in the surface mucosa of blue catfish (Ictalurus furcatus).
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2013-12-28
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Eric Peatman
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Chao Li Benjamin H Beck
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Developmental and Comparative Immunology
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Bulk segregant RNA-seq reveals expression and positional candidate genes and allele-specific expression for disease resistance against enteric septicemia of catfish.
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2013-12-30
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Luyang Sun Shikai Liu
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Ruijia Wang Lisui Bao Jiaren Zhang Yanliang Jiang Jun Yao Lin Song Jianbin Feng Zhanjiang Liu
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BMC Genomics
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Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
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2013-12-30
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Jean-Jack M Riethoven
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Yong Ding Ning Liu Laetitia Virlouvet Michael Fromm Zoya Avramova
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BMC Plant Biology
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Transcriptomics reveal several gene expression patterns in the piezophile Desulfovibrio hydrothermalis in response to hydrostatic pressure
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2014
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Christian Tamburini
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Amira Amrani Aurélie Bergon Hélène Holota Marc Garel Bernard Ollivier Jean Imbert Alain Dolla Nathalie Pradel
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PLOS ONE
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Melanocytes in the skin--comparative whole transcriptome analysis of main skin cell types
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2014
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Viljar Jaks Ene Reimann Q24546281 Eero Vasar Sulev Kõks
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Paula Reemann Sten Ilmjärv Orm Porosaar Helgi Silm
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PLOS ONE
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Deep RNA sequencing reveals hidden features and dynamics of early gene transcription in Paramecium bursaria chlorella virus 1
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2014
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Jean-Jack M Riethoven Guillaume Blanc David D. Dunigan
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Michael Mozar Irina V Agarkova James R Gurnon Giane Yanai-Balser Janet M Rowe Yuannan Xia James L Van Etten
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PLOS ONE
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De novo assembly and characterization of the transcriptome of the toxic dinoflagellate Karenia brevis
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2014
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Lisa Campbell
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Darcie E Ryan Alan E Pepper
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BMC Genomics
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Comparative analysis and modeling of the severity of steatohepatitis in DDC-treated mouse strains
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2014
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Helmut Denk Hans Lehrach Marie-Laure Yaspo Christina Grimm Kurt Zatloukal
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Vikash Pandey Marc Sultan Karl Kashofer Meryem Ralser Vyacheslav Amstislavskiy Julia Starmann Ingrid Osprian Hendrik Hache Holger Sültmann Michael Trauner Christoph Wierling
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PLOS ONE
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Mining gene expression data for pollutants (dioxin, toluene, formaldehyde) and low dose of gamma-irradiation
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2014
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Darya Peregudova Alexey A. Dmitriev Sergey V Mylnikov Peter O Fedichev Nataliya Melnikova Anna V Kudryavtseva Mikhail V Shaposhnikov Alexey A Moskalev
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Anastasia Snezhkina Valeria Kogan Ekaterina Plyusnina Leonid Uroshlev Sergey Plusnin
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PLOS ONE
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The SLE transcriptome exhibits evidence of chronic endotoxin exposure and has widespread dysregulation of non-coding and coding RNAs
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2014
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Angela M Yu Patrícia Costa Reis Michelle A. Petri
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Lihua Shi Zhe Zhang Wei Wang Zhi Wei Ehtisham Akhter Kelly Maurer Li Song Kathleen E Sullivan
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PLOS ONE
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Establishment of highly tumorigenic human colorectal cancer cell line (CR4) with properties of putative cancer stem cells
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2014
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Iwao Ojima
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Rebecca A Rowehl Stephanie Burke Agnieszka B Bialkowska Donald W Pettet Leahana Rowehl Ellen Li Eric Antoniou Yuanhao Zhang Roberto Bergamaschi Kenneth R Shroyer Galina I Botchkina
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PLOS ONE
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RNA-sequencing analysis of HepG2 cells treated with atorvastatin
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2014
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Daniel Sachse Jens P. Berg
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Camilla Stormo Marianne K Kringen Robert Lyle Ole Kristoffer Olstad Armin P Piehler
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PLOS ONE
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The oncogenic MicroRNA Hsa-miR-155-5p targets the transcription factor ELK3 and links it to the hypoxia response
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2014
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Alain C Jung Bohdan Wasylyk
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E Douglas Robertson Christine Wasylyk Tao Ye
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PLOS ONE
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Genetics of gene expression in CNS
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2014
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Robert W. Williams
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Ashutosh K Pandey
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International Review of Neurobiology
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Towards a computational model of a methane producing archaeum
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2014
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Piyush Labhsetwar Zaida Luthey-Schulten
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Joseph R Peterson Jeremy R Ellermeier Petra R A Kohler Ankur Jain Taekjip Ha William W Metcalf
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Archaea
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Comparison between karyotyping-FISH-reverse transcription PCR and RNA-sequencing-fusion gene identification programs in the detection of KAT6A-CREBBP in acute myeloid leukemia
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2014
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Sverre Heim Ioannis Panagopoulos
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Synne Torkildsen Ludmila Gorunova Anne Tierens Geir E Tjønnfjord
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PLOS ONE
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RNA families in Epstein-Barr virus
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2014
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Joan A. Steitz
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Walter N Moss Nara Lee Genaro Pimienta
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RNA Biology
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Characterization of human pseudogene-derived non-coding RNAs for functional potential
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2014
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Deyou Zheng
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Xingyi Guo Mingyan Lin Shira Rockowitz Herbert M Lachman
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PLOS ONE
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Oqtans: a multifunctional workbench for RNA-seq data analysis
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2014
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Gunnar Rätsch
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Vipin T Sreedharan Sebastian J Schultheiss Géraldine Jean André Kahles Regina Bohnert Philipp Drewe Pramod Mudrakarta Nico Görnitz Georg Zeller
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BMC Bioinformatics
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Blood biomarkers of the late phase asthmatic response using RNA-Seq
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2014
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Louis-Philippe Boulet
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Amrit Singh Casey P Shannon Gail M Gauvreau Paul M O'Byrne J FitzGerald Scott J Tebbutt
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Allergy, Asthma & Clinical Immunology
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Emerging RNA-Seq Applications in Food Science
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2014
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Alberto Valdés Virginia García-Cañas Carolina Simó
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Clara Ibáñez
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Zinc finger transcription factors displaced SREBP proteins as the major Sterol regulators during Saccharomycotina evolution
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2014-01
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Sarah L Maguire Geraldine Butler Theodore C White Kenneth H. Wolfe Jean-Marc Nicaud Cécile Neuvéglise
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Can Wang Linda M Holland François Brunel Martin Zavrel
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PLOS Genetics
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CellFinder: a cell data repository
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2014-01
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Stefanie Seltmann Fritz Lekschas Mariana Lara Neves Harald Stachelscheid Nancy Mah Andreas Kurtz
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Jean-Fred Fontaine Miguel A Andrade-Navarro Ulf Leser
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Nucleic Acids Research
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A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells
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2014-01-01
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Michael Stratton
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Tony Ly Yasmeen Ahmad Adam Shlien Dominique Soroka Allie Mills Michael J Emanuele Angus I Lamond
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eLife
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Isl1 and Pou4f2 form a complex to regulate target genes in developing retinal ganglion cells
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2014-01-01
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Xiuqian Mu
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Renzhong Li Fuguo Wu Raili Ruonala Darshan Sapkota Zihua Hu
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PLOS ONE
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A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages.
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2014-01-01
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Danielle Thierry-Mieg Lee Lancashire Heng Luo Nan Mei Jean Thierry-Mieg
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Ying Yu James C Fuscoe Chen Zhao Chao Guo Meiwen Jia Tao Qing Desmond I Bannon Wenjun Bao Tingting Du Zhenqiang Su Wendell D Jones Carrie L Moland William S Branham Feng Qian Baitang Ning Yan Li Huixiao Hong Lei Guo Tieliu Shi Kevin Y Wang Russell D Wolfinger Yuri Nikolsky Stephen J Walker Penelope Duerksen-Hughes Christopher E Mason Weida Tong Leming Shi Charles Wang
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Nature Communications
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Correlating histone modification patterns with gene expression data during hematopoiesis.
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2014-01-01
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Gangqing Hu
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Keji Zhao
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Methods in Molecular Biology
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Domestic dogs and cancer research: a breed-based genomics approach.
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2014-01-01
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Elaine Ostrander
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Brian W Davis
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ILAR Journal
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Topographical transcriptome mapping of the mouse medial ganglionic eminence by spatially resolved RNA-seq.
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2014-01-01
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Sten Linnarsson Peter Lönnerberg Sabrina Zechel
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Pawel Zajac Carlos F Ibáñez
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Genome Biology
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RNA-Seq reveals novel transcriptional reorganization in human alcoholic brain.
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2014-01-01
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Sean P Farris
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R Dayne Mayfield
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International Review of Neurobiology
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Discovery of Protein-lncRNA Interactions by Integrating Large-Scale CLIP-Seq and RNA-Seq Datasets
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2014-01-01
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Liang-Hu Qu
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Jun-Hao Li Shun Liu Ling-Ling Zheng Jie Wu Wen-Ju Sun Ze-Lin Wang Hui Zhou Jian-Hua Yang
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Frontiers in Bioengineering and Biotechnology
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Next-generation sequencing applied to flower development: RNA-seq.
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2014-01-01
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Yuling Jiao
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Jun He
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Methods in Molecular Biology
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Riboswitch discovery by combining RNA-seq and genome-wide identification of transcriptional start sites.
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2014-01-01
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Isabelle Rosinski-Chupin
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Olga Soutourina Isabelle Martin-Verstraete
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Methods in Enzymology
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Plant and fungal gene expression in mycorrhizal protocorms of the orchid Serapias vomeracea colonized by Tulasnella calospora.
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2014-01-01
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Fabiano Sillo Silvia Perotto Raffaella Balestrini
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Luca Nerva Mariangela Girlanda
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Plant Signaling and Behavior
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Shared transcription factors contribute to distinct cell fates
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2014-01-01
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Berthold Göttgens
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Felicia S L Ng Fernando J Calero-Nieto
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Transcription
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Transcriptomic changes in brain development.
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2014-01-01
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Mark R Cookson
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Allissa A Dillman
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International Review of Neurobiology
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RNA-Seq and Network Analysis Revealed Interacting Pathways in TGF-β-Treated Lung Cancer Cell Lines.
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2014-01-01
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Youping Deng
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Yan Li Omid Rouhi Hankui Chen Rolando Ramirez Jeffrey A Borgia
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Cancer Informatics
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Developmental analysis of spliceosomal snRNA isoform expression.
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2014-01-01
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Zhipeng Lu
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A Gregory Matera
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G3
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Deep sequencing of small chromatin-associated RNA: bioinformatic analysis.
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2014-01-01
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Sarah Diermeier Gernot Längst
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Methods in Molecular Biology
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Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells.
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2014-01-01
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Daniel Ramsköld Rickard Sandberg Qiaolin Deng Björn Reinius
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Science
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edgeR for differential RNA-seq and ChIP-seq analysis: an application to stem cell biology.
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2014-01-01
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Mark D. Robinson
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Olga Nikolayeva
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Methods in Molecular Biology
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Quantitative transcriptome analysis using RNA-seq.
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2014-01-01
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Andrea Bräutigam
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Canan Külahoglu
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Methods in Molecular Biology
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Full-length RNA-seq from single cells using Smart-seq2.
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2014-01-02
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Omid R Faridani Rickard Sandberg
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Simone Picelli Asa K Björklund Gösta Winberg Sven Sagasser
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Nature Protocols
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Variable suites of non-effector genes are co-regulated in the type III secretion virulence regulon across the Pseudomonas syringae phylogeny.
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2014-01-02
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Marc T Nishimura Jeff H. Chang David A. Baltrus
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Tatiana S Mucyn Scott Yourstone Abigail L Lind Surojit Biswas Jason S Cumbie Corbin D Jones Jeffery L Dangl Sarah R Grant
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PLOS Pathogens
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RNA-Seq analysis of the toxicant-induced transcriptome of the marine diatom, Ceratoneis closterium.
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2014-01-04
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Philippe Moncuquet
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Sharon E Hook Hannah L Osborn Francesca Gissi Natalie A Twine Marc R Wilkins Merrin S Adams
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Marine Genomics
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Differential expression analysis of RNA-seq data at single-base resolution
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2014-01-06
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Kasper D. Hansen Jeffrey T. Leek
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Alyssa C Frazee Sarven Sabunciyan Rafael A Irizarry
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Biostatistics
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A unique missense allele of BAF155, a core BAF chromatin remodeling complex protein, causes neural tube closure defects in mice.
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2014-01-09
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Dawn E Watkins-Chow William J Pavan Lee Niswander
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Laura Harmacek Jianfu Chen Kenneth L Jones J Michael Salbaum
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Developmental Neurobiology
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The histone-H3K4-specific demethylase KDM5B binds to its substrate and product through distinct PHD fingers.
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2014-01-09
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Brian D Strahl Scott B Rothbart
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Brianna J Klein Lianhua Piao Yuanxin Xi Hector Rincon-Arano Danni Peng Hong Wen Connie Larson Xi Zhang Xia Zheng Michael A Cortazar Pedro V Peña Anthony Mangan David L Bentley Mark Groudine Wei Li Xiaobing Shi Tatiana G Kutateladze
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Cell Reports
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Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis.
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2014-01-11
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Georg Zeller Gunnar Rätsch
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Vipin T Sreedharan Sebastian J Schultheiss Géraldine Jean André Kahles Regina Bohnert Philipp Drewe Pramod Mudrakarta Nico Görnitz
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Bioinformatics
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Differential protein occupancy profiling of the mRNA transcriptome.
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2014-01-13
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Markus Landthaler
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Markus Schueler Mathias Munschauer Lea Haarup Gregersen Ana Finzel Alexander Loewer Wei Chen Christoph Dieterich
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Genome Biology
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Production of RNA for transcriptomic analysis from mouse spinal cord motor neuron cell bodies by laser capture microdissection.
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2014-01-13
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Arthur L. Horwich
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Urmi Bandyopadhyay Wayne A Fenton Maria Nagy
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Journal of Visualized Experiments
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GuavaH: a compendium of host genomic data in HIV biology and disease.
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2014-01-15
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Paul J. McLaren Angela Ciuffi Jacques Fellay
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István Bartha Amalio Telenti
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Retrovirology
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Transciptome analysis of the gill and swimbladder of Takifugu rubripes by RNA-Seq.
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2014-01-16
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Shikai Liu
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Jun Cui Bing Zhang Hongdi Wang Hongjuan Sun Shuhui Song Xuemei Qiu Yang Liu Xiuli Wang Zhiqiang Jiang Zhanjiang Liu
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PLOS ONE
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Transcriptome analysis of psoriasis in a large case-control sample: RNA-seq provides insights into disease mechanisms
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2014-01-17
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A Johnston Lam C. Tsoi
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Bingshan Li William R Swindell Johann E Gudjonsson Trilokraj Tejasvi Jun Ding Philip E Stuart Xianying Xing James J Kochkodan John J Voorhees Hyun M Kang Rajan P Nair Goncalo R Abecasis James T Elder
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Journal of Investigative Dermatology
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The development of a high density linkage map for black tiger shrimp (Penaeus monodon) based on cSNPs.
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2014-01-17
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Matthew Baranski Nicholas A. Robinson
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Gopalapillay Gopikrishna Vinaya Kumar Katneni Mudagandur S Shekhar Jayakani Shanmugakarthik Sarangapani Jothivel Chavali Gopal Pitchaiyappan Ravichandran Matthew Kent Mariann Arnyasi Alphis G Ponniah
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PLOS ONE
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Transcriptome analysis of alternative splicing events regulated by SRSF10 reveals position-dependent splicing modulation.
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2014-01-17
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Wenwu Wu James L. Manley
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Xuexia Zhou Huang Li Yuanming Cheng Ning Wei Jie Zong Xiaoyan Feng Zhiqin Xie Dai Chen Hui Wang Ying Feng
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Nucleic Acids Research
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A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis
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2014-01-17
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Lior Pachter Harold Pimentel Narla Mohandas Xiuli An
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Marilyn Parra Sherry Gee Dana Ghanem Jie Li John G Conboy
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Nucleic Acids Research
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Set5 and Set1 cooperate to repress gene expression at telomeres and retrotransposons.
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2014-01-17
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Sean R Collins Devin A King Ashby Morrison Or Gozani
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Glòria Mas Martín Erin M Green Pablo E Garcia-Nieto Richard Alexander Nevan J Krogan
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Epigenetics
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ALEA: a toolbox for allele-specific epigenomics analysis.
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2014-01-21
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Mohammad M Karimi Torsten Möller Matthew C. Lorincz
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Hamid Younesy Alireza Heravi-Moussavi Jeffrey B Cheng Joseph F Costello Steven J M Jones
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Bioinformatics
|
RNA-Seq analysis provides insights for understanding photoautotrophic polyhydroxyalkanoate production in recombinant Synechocystis Sp.
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2014-01-22
|
Kumar Sudesh
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Nyok-Sean Lau Choon Pin Foong Yukio Kurihara Kumar Sudesh Minami Matsui
|
PLOS ONE
|
RNA-Seq transcriptome analysis of Spirodela dormancy without reproduction.
|
2014-01-23
|
Wenqin Wang Joachim Messing
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Yongrui Wu
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BMC Genomics
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glbase: a framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data.
|
2014-01-24
|
Andrew Paul Hutchins
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Ralf Jauch Mateusz Dyla Diego Miranda-Saavedra
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Cell regeneration (London, England)
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A comparison of RNA-seq and exon arrays for whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat.
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2014-01-28
|
Christine Orengo James R Perkins Matthias Kohl Stephen B McMahon
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Ana Antunes-Martins Margarita Calvo John Grist Werner Rust Ramona Schmid Tobias Hildebrandt David L H Bennett
|
Molecular Pain
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The RNA-binding protein hnRNPLL induces a T cell alternative splicing program delineated by differential intron retention in polyadenylated RNA.
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2014-01-29
|
Anselm Enders
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Vicky Cho Yan Mei Arleen Sanny Stephanie Chan Edward M Bertram Andy Tan Christopher C Goodnow T Daniel Andrews
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Genome Biology
|
RNA-seq analysis of host and viral gene expression highlights interaction between varicella zoster virus and keratinocyte differentiation.
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2014-01-30
|
Judith Breuer Paul Kellam
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Meleri Jones Inga R Dry Dan Frampton Manuraj Singh Ravinder K Kanda Michael B Yee Michael Hollinshead Paul R Kinchington Edel A O'Toole
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PLOS Pathogens
|
bwtool: a tool for bigWig files.
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2014-01-30
|
Miguel Beato del Rosal
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Andy Pohl
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Bioinformatics
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A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events
|
2014-01-31
|
Matthew Meyerson Mara Rosenberg Marcin Imielinski Juliann Chmielecki Gad Getz Gordon Saksena
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Angela N Brooks Peter S Choi Luc de Waal Tanaz Sharifnia Chandra Sekhar Pedamallu Andrey Sivachenko Michael S Lawrence David S DeLuca
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PLOS ONE
|
Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types.
|
2014-02-01
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Naama Elefant Hadas Keren-Shaul Franziska Paul Alexander Mildner Steffen Jung
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Diego Adhemar Jaitin Ephraim Kenigsberg Hadas Keren-Shaul Naama Elefant Irina Zaretsky Nadav Cohen Amos Tanay Ido Amit
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Science
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SOX9: a stem cell transcriptional regulator of secreted niche signaling factors.
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2014-02-01
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Deyou Zheng Elaine Fuchs Maria Genander
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Meelis Kadaja Brice E Keyes Mingyan Lin H Amalia Pasolli Lisa Polak Nicole Stokes
|
Genes & Development
|
Faculty of 1000 evaluation for Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells
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2014-02-02
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Marc S. Williams
|
|
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voom: Precision weights unlock linear model analysis tools for RNA-seq read counts.
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2014-02-03
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Gordon K Smyth
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Charity W Law Yunshun Chen Wei Shi
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Genome Biology
|
Ultra deep sequencing of Listeria monocytogenes sRNA transcriptome revealed new antisense RNAs.
|
2014-02-03
|
Ramakanth Madhugiri Stefanie Widder Thomas Rattei
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Sebastian Behrens Gopala Krishna Mannala Xiaoxing Qing Nathalie Kefer Mobarak Abu Mraheil Torsten Hain
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PLOS ONE
|
The Cryptococcus neoformans transcriptome at the site of human meningitis.
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2014-02-04
|
Yuan Chen David R. Boulware
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Dena L Toffaletti Jennifer L Tenor Anastasia P Litvintseva Charles Fang Thomas G Mitchell Tami R McDonald Kirsten Nielsen Tihana Bicanic John R Perfect
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mBio
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Tissue-specific RNA-Seq in human evoked inflammation identifies blood and adipose LincRNA signatures of cardiometabolic diseases.
|
2014-02-06
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Rachel L Ballantyne Muredach P. Reilly
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Yichuan Liu Jane F Ferguson Chenyi Xue Ian M Silverman Sager J Gosai Jacquelyn Serfecz Michael P Morley Brian D Gregory Mingyao Li
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Arteriosclerosis, Thrombosis, and Vascular Biology
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RNA-seq reveals transcriptomic shock involving transposable elements reactivation in hybrids of young lake whitefish species.
|
2014-02-06
|
Sébastien Renaut Louis Bernatchez
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Anne-Marie Dion-Côté Eric Normandeau
|
Molecular Biology and Evolution
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Secondary cell wall composition and candidate gene expression in developing willow (Salix purpurea) stems.
|
2014-02-07
|
Keywan Hassani-Pak Angela Karp Huw Dylan Jones
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Yongfang Wan Cristina Gritsch Theodora Tryfona Mike J Ray Ambrose Andongabo Paul Dupree Peter R Shewry Rowan A C Mitchell
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Planta
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Dormancy within Staphylococcus epidermidis biofilms: a transcriptomic analysis by RNA-seq.
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2014-02-07
|
Rui Vitorino Gerald B Pier Manuel Vilanova
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Virginia Carvalhais Angela França Filipe Cerca Nuno Cerca
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Applied Microbiology and Biotechnology
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Analysis of 52 Rab GTPases from channel catfish and their involvement in immune responses after bacterial infections.
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2014-02-07
|
Luyang Sun Shikai Liu Yu Zhang
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Ruijia Wang Chao Li Lisui Bao Jianbin Feng Zhanjiang Liu
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Developmental and Comparative Immunology
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ALS-associated mutation FUS-R521C causes DNA damage and RNA splicing defects.
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2014-02-10
|
Erik D. Roberson James Shorter Eric J Huang
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Haiyan Qiu Sebum Lee Yulei Shang Wen-Yuan Wang Kin Fai Au Sherry Kamiya Sami J Barmada Steven Finkbeiner Hansen Lui Caitlin E Carlton Amy A Tang Michael C Oldham Hejia Wang Anthony J Filiano Warren G Tourtellotte Bin Chen Li-Huei Tsai
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Journal of Clinical Investigation
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SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads.
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2014-02-13
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Gane Ka-Shu Wong Ruibang Luo Tak-Wah Lam Jun Wang
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Yinlong Xie Gengxiong Wu Jingbo Tang Jordan Patterson Shanlin Liu Weihua Huang Guangzhu He Shengchang Gu Shengkang Li Xin Zhou Yingrui Li Xun Xu
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Bioinformatics
|
Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia.
|
2014-02-13
|
Ana Conesa Corey Nislow Eduardo Larriba José Martín-Nieto Luis V Lopez-Llorca
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María D L A Jaime José Carbonell-Caballero Joaquín Dopazo
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Fungal Genetics and Biology
|
Condition-specific target prediction from motifs and expression.
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2014-02-14
|
Martin Vingron
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Guofeng Meng
|
Bioinformatics
|
Dynamic recruitment of amino acid transporters to the insect/symbiont interface.
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2014-02-16
|
John P. McCutcheon Rebecca P. Duncan Filip Husník
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James T Van Leuven Donald G Gilbert Liliana M Dávalos Alex C C Wilson
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Molecular Ecology
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SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing.
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2014-02-17
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Xi Wang Murray J Cairns
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Bioinformatics
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Interaction of vitamin D with membrane-based signaling pathways
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2014-02-18
|
María Jesús Larriba
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José Manuel González-Sancho Félix Bonilla Alberto Muñoz
|
Frontiers in Physiology
|
Ammonium induces differential expression of methane and nitrogen metabolism-related genes in Methylocystis sp. strain SC2.
|
2014-02-18
|
Werner Liesack
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Bomba Dam Somasri Dam Yongkyu Kim
|
Environmental Microbiology
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Transcriptomic analysis reveals key regulators of mammogenesis and the pregnancy-lactation cycle.
|
2014-02-19
|
Songnian Hu
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YuanYuan Zhou Wei Gong JingFa Xiao JiaYan Wu LinLin Pan XiaoNuan Li XuMin Wang WeiWei Wang Jun Yu
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Science in China. Series C: Life Sciences
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Insight into insulin secretion from transcriptome and genetic analysis of insulin-producing cells of Drosophila
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2014-02-20
|
Luis A Milla Wenxiu Ma Maria L Spletter
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Jian Cao Julie Ni Vanessa Shiu Sangbin Park Sheng Tang Jun Zhang Xing Wei Seung K Kim Matthew P Scott
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Genetics
|
Improving reliability and absolute quantification of human brain microarray data by filtering and scaling probes using RNA-Seq.
|
2014-02-24
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Jeremy A Miller Vilas Menon Jeff Goldy Ajamete Kaykas Chang-Kyu Lee Kimberly A Smith Elaine H Shen John W Phillips Ed S Lein Mike J Hawrylycz
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BMC Genomics
|
Context-selective death of acute myeloid leukemia cells triggered by the novel hybrid retinoid-HDAC inhibitor MC2392.
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2014-02-24
|
Dante Rotili Yves Collette Angela Nebbioso Antonello Mai Hugues de Thé Mariarosaria Conte Sergio Valente Lucia Altucci Julien Ablain Vincenzo Carafa
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Floriana De Bellis Francesca Petraglia Filomena Matarese Kees-Jan Françoijs Rèmy Castellano Armelle Goubard Amit Mandoli Joost H A Martens Hendrik G Stunnenberg
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Cancer Research
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RNA CoMPASS: a dual approach for pathogen and host transcriptome analysis of RNA-seq datasets
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2014-02-25
|
Erik K Flemington
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Guorong Xu Michael J Strong Michelle R Lacey Carl Baribault Christopher M Taylor
|
PLOS ONE
|
Transcriptomic profiling of differential responses to drought in two freshwater mussel species, the giant floater Pyganodon grandis and the pondhorn Uniomerus tetralasmus.
|
2014-02-25
|
Eric Peatman
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Yupeng Luo Chao Li Andrew Gascho Landis Guiling Wang James Stoeckel
|
PLOS ONE
|
FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions.
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2014-02-25
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Carlos Torroja Francesco Mazzarotto Enrique Lara-Pezzi Alberto Gatto
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Stuart A Cook Paul J R Barton Fátima Sánchez-Cabo
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Nucleic Acids Research
|
AnaLysis of Expression on human chromosome 21, ALE-HSA21: a pilot integrated web resource.
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2014-02-25
|
Claudia Angelini Valerio Costa Maria Rosaria Ambrosio
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Margherita Scarpato Roberta Esposito Daniela Evangelista Marianna Aprile Alfredo Ciccodicola
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Database
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SnapShot-Seq: a method for extracting genome-wide, in vivo mRNA dynamics from a single total RNA sample
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2014-02-26
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Nimrod Miller Sarah A Boswell Yong-Chao Ma Nicole Cloonan Sean M. Grimmond
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Jesse M Gray David A Harmin Thomas E Mullen Joseph J Ling Scott Kuersten Steven A McCarroll Michael Springer
|
PLOS ONE
|
Identification and initial functional characterization of a human vascular cell-enriched long noncoding RNA.
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2014-02-27
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Deyou Zheng
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Robert D Bell Xiaochun Long Mingyan Lin Jan H Bergmann Vivek Nanda Sarah L Cowan Qian Zhou Yu Han David L Spector Joseph M Miano
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Arteriosclerosis, Thrombosis, and Vascular Biology
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Metabolic reprogramming during purine stress in the protozoan pathogen Leishmania donovani
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2014-02-27
|
Jessica L Martin Vladislav A Petyuk Kristin E Burnum Richard D. Smith
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Phillip A Yates Radika Soysa Joshua F Alfaro Feng Yang Karl K Weitz David G Camp Phillip A Wilmarth Larry L David Gowthaman Ramasamy Peter J Myler Nicola S Carter
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PLOS Pathogens
|
The path to triacylglyceride obesity in the sta6 strain of Chlamydomonas reinhardtii.
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2014-02-28
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Sean D Gallaher Taylor L Weiss David Casero Shannon L Johnson Matteo Pellegrini Sabeeha Merchant Ursula Goodenough
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Ian Blaby Carrie Goodson Jae-Hyeok Lee Robyn Roth Jannette Rusch Manmilan Singh James G Umen Tuya Wulan
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Eukaryotic Cell
|
Transcriptome analysis of Listeria monocytogenes exposed to biocide stress reveals a multi-system response involving cell wall synthesis, sugar uptake, and motility
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2014-02-28
|
Stephan Schmitz-Esser Edward M Fox Aidan Coffey
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Aidan Casey Edward M Fox Aidan Coffey Olivia McAuliffe Kieran Jordan
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Frontiers in Microbiology
|
ChIP-Seq and RNA-Seq reveal an AmrZ-mediated mechanism for cyclic di-GMP synthesis and biofilm development by Pseudomonas aeruginosa
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2014-03-01
|
Yasuhiko Irie Peter White
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Christopher J. Jones David Newsom Benjamin Kelly Laura K. Jennings Binjie Xu Dominique H. Limoli Joe J. Harrison Matthew R. Parsek Daniel J. Wozniak
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PLOS Pathogens
|
The IncRNAs PCGEM1 and PRNCR1 are not implicated in castration resistant prostate cancer.
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2014-03-01
|
Elai Davicioni
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John R Prensner Anirban Sahu Matthew K Iyer Rohit Malik Benjamin Chandler Irfan A Asangani Anton Poliakov Ismael A Vergara Mohammed Alshalalfa Robert B Jenkins Felix Y Feng Arul M Chinnaiyan
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Oncotarget
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Transcriptome profiling of human hippocampus dentate gyrus granule cells in mental illness
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2014-03-04
|
Eric Haugen
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R Kohen A Dobra J H Tracy
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Translational Psychiatry
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Differential transcriptomic analysis by RNA-Seq of GSNO-responsive genes between Arabidopsis roots and leaves.
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2014-03-04
|
Juan C Begara-Morales Francisco J. Corpas
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Beatriz Sánchez-Calvo Francisco Luque María O Leyva-Pérez Marina Leterrier Juan B Barroso
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Plant and Cell Physiology
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Relaxed functional constraints on triplicate α-globin gene in the bank vole suggest a different evolutionary history from other rodents.
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2014-03-05
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Jeremy Searle Petr Kotlík
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S Marková
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Heredity
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The human testis-specific proteome defined by transcriptomics and antibody-based profiling.
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2014-03-05
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Linn Fagerberg Mathias Uhlén
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D Djureinovic B Hallström A Danielsson C Lindskog F Pontén
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Molecular Human Reproduction
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Overexpression of molecular chaperone genes in nucleomorph genomes.
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2014-03-06
|
Patrick J. Keeling
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Yoshihisa Hirakawa Shigekatsu Suzuki John M Archibald Ken-ichiro Ishida
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Molecular Biology and Evolution
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Faculty of 1000 evaluation for SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads
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2014-03-06
|
Steven Salzberg
|
|
|
Variation in RNA-Seq transcriptome profiles of peripheral whole blood from healthy individuals with and without globin depletion.
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2014-03-07
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Casey P. Shannon Robert Balshaw
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Heesun Shin Nick Fishbane Jian Ruan Mi Zhou Janet E Wilson-McManus Raymond T Ng Bruce M McManus Scott J Tebbutt PROOF Centre of Excellence Team
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PLOS ONE
|
Vicinal: a method for the determination of ncRNA ends using chimeric reads from RNA-seq experiments.
|
2014-03-12
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Zhipeng Lu
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A Gregory Matera
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Nucleic Acids Research
|
RNA- and antibody-based profiling of the human proteome with focus on chromosome 19.
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2014-03-12
|
Linn Fagerberg Mathias Uhlén Per Oksvold
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Charlotte Stadler Åsa Sivertsson Martin Zwahlen Björn M Hallström Emma Lundberg
|
Journal of Proteome Research
|
Sensitive and specific detection of EML4-ALK rearrangements in non-small cell lung cancer (NSCLC) specimens by multiplex amplicon RNA massive parallel sequencing.
|
2014-03-13
|
Hans-Ulrich Schildhaus Sabine Merkelbach-Bruse
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Evgeny A Moskalev Judith Frohnauer Arno Dimmler Thomas Schubert Carsten Boltze Helmut König Florian Fuchs Horia Sirbu Ralf J Rieker Abbas Agaimy Arndt Hartmann Florian Haller
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Lung Cancer
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Lacking alignments? The next-generation sequencing mapper segemehl revisited.
|
2014-03-13
|
Peter F. Stadler
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Christian Otto Steve Hoffmann
|
Bioinformatics
|
Identification of novel point mutations in splicing sites integrating whole-exome and RNA-seq data in myeloproliferative diseases.
|
2014-03-13
|
Carlo Gambacorti-Passerini
|
Roberta Spinelli Alessandra Pirola Sara Redaelli Nitesh Sharma Hima Raman Simona Valletta Vera Magistroni Rocco Piazza
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Molecular genetics & genomic medicine
|
Identification of candidate genes involved in coronary artery calcification by transcriptome sequencing of cell lines.
|
2014-03-14
|
NISC Comparative Sequencing Program Leslie G Biesecker Eric D. Green James C Mullikin
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Shurjo K Sen Jennifer J Barb Praveen F Cherukuri David S Accame Abdel G Elkahloun Larry N Singh Shih-Queen Lee-Lin Frank D Kolodgie Qi Cheng XiaoQing Zhao Marcus Y Chen Andrew E Arai Peter J Munson
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BMC Genomics
|
RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence.
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2014-03-18
|
Hans J Nauwynck
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Bouabid Badaoui Teresa Rutigliano Anna Anselmo Merijn Vanhee Elisabetta Giuffra Sara Botti
|
PLOS ONE
|
The human liver-specific proteome defined by transcriptomics and antibody-based profiling.
|
2014-03-19
|
Jens Nielsen Linn Fagerberg Mathias Uhlén
|
Caroline Kampf Adil Mardinoglu Björn M Hallström Karolina Edlund Emma Lundberg Fredrik Pontén
|
FASEB Journal
|
SNP discovery from transcriptome of the swimbladder of Takifugu rubripes
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2014-03-20
|
Shikai Liu
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Jun Cui Hongdi Wang Lifu Zhu Xuemei Qiu Zhiqiang Jiang Xiuli Wang Zhanjiang Liu
|
PLOS ONE
|
The highly conserved MraZ protein is a transcriptional regulator in Escherichia coli.
|
2014-03-21
|
Jesus M Eraso Ronald Taylor
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Lye M Markillie Hugh D Mitchell Galya Orr William Margolin
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Journal of Bacteriology
|
Genomics of CpG methylation in developing and developed zebrafish
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2014-03-21
|
David M McGaughey
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Hatice Ozel Abaan Ryan M Miller Peter A Kropp Lawrence C Brody
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G3
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The characteristic direction: a geometrical approach to identify differentially expressed genes.
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2014-03-21
|
Avi Ma'ayan
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Neil R Clark Kevin S Hu Axel S Feldmann Yan Kou Edward Y Chen Qiaonan Duan
|
BMC Bioinformatics
|
From root to fruit: RNA-Seq analysis shows that arbuscular mycorrhizal symbiosis may affect tomato fruit metabolism
|
2014-03-21
|
Matteo Chialva Paola Bonfante
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Inès Zouari Alessandra Salvioli Mara Novero Laura Miozzi Gian Carlo Tenore Paolo Bagnaresi
|
BMC Genomics
|
spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.
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2014-03-23
|
Albin Sandelin Kristoffer Vitting-Seerup Johannes Waage Bo Torben Porse
|
|
BMC Bioinformatics
|
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.
|
2014-03-23
|
John L. Rinn
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Cole Trapnell Davide Cacchiarelli Jonna Grimsby Prapti Pokharel Shuqiang Li Michael Morse Niall J Lennon Kenneth J Livak Tarjei S Mikkelsen
|
Nature Biotechnology
|
RNA-seq analysis identifies an intricate regulatory network controlling cluster root development in white lupin
|
2014-03-25
|
Oliver Berkowitz James Whelan
|
David Secco Huixia Shou
|
BMC Genomics
|
RNA sequencing reveals upregulation of RUNX1-RUNX1T1 gene signatures in clear cell renal cell carcinoma
|
2014-03-25
|
Jianfeng Xu
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Zuquan Xiong Hongjie Yu Yan Ding Chenchen Feng Hanming Wei Sha Tao Dan Huang Siqun Lilly Zheng Jielin Sun Zujun Fang
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BioMed Research International
|
De novo transcriptome analysis of Hevea brasiliensis tissues by RNA-seq and screening for molecular markers
|
2014-03-26
|
Luiz Gonzaga Paula de Almeida Dominique Garcia Daniel Guariz Pinheiro Antonio Figueira Luiz L Coutinho
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Leonardo Rippel Salgado Daniela Martins Koop Ronan Rivallan Vincent Le Guen Marisa Fabiana Nicolás Viviani Ribeiro Rocha Milena Magalhães Alexandra Lehmkuhl Gerber Júlio Cézar de Mattos Cascardo AnaTereza Ribeiro de Vasconcelos Wilson Araújo Silva
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BMC Genomics
|
De novo transcriptome assembly reveals sex-specific selection acting on evolving neo-sex chromosomes in Drosophila miranda.
|
2014-03-27
|
Doris Bachtrog
|
Vera B Kaiser
|
BMC Genomics
|
RNA-Seq reveals infection-induced gene expression changes in the snail intermediate host of the carcinogenic liver fluke, Opisthorchis viverrini.
|
2014-03-27
|
Thewarach Laha Smarn Tesana
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Sattrachai Prasopdee Javier Sotillo Jutharat Kulsantiwong Matthew J Nolan Alex Loukas Cinzia Cantacessi
|
PLOS Neglected Tropical Diseases
|
Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing.
|
2014-03-27
|
Hideya Kawaji Masayoshi Itoh Piero Carninci Yoshihide Hayashizaki
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Marina Lizio Mutsumi Kanamori-Katayama Ai Kaiho Hiromi Nishiyori-Sueki Jay W Shin Miki Kojima-Ishiyama Mitsuoki Kawano Mitsuyoshi Murata Noriko Ninomiya-Fukuda Sachi Ishikawa-Kato Sayaka Nagao-Sato Shohei Noma Alistair R R Forrest FANTOM Consortium
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Genome Research
|
Transcriptome analysis of the gill of Takifugu rubripes using Illumina sequencing for discovery of SNPs.
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2014-03-27
|
Shikai Liu
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Jun Cui Hongdi Wang Xuemei Qiu Zhiqiang Jiang Xiuli Wang
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Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics
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RNA-seq dependent transcriptional analysis unveils gene expression profile in the intestine of sea cucumber Apostichopus japonicus during aestivation.
|
2014-03-27
|
Kenneth B. Storey
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Ye Zhao Hongsheng Yang Muyan Chen
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Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics
|
HDAC-regulated myomiRs control BAF60 variant exchange and direct the functional phenotype of fibro-adipogenic progenitors in dystrophic muscles.
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2014-03-28
|
Janet Rossant Gianmaria Frigè Lorenzo Giordani Alberto Termanini Chiara Mozzetta Giovanna Borsellino
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Valentina Saccone Silvia Consalvi Iros Barozzi Martina Sandoná Tammy Ryan Agustin Rojas-Muñoz Luca Madaro Pasquale Fasanaro Marco De Bardi Xin Sun Benoit G Bruneau Mark Mercola Saverio Minucci Pier Lorenzo Puri
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Genes & Development
|
Differential meta-analysis of RNA-seq data from multiple studies
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2014-03-29
|
Florence Jaffrézic
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Andrea Rau Guillemette Marot Florence Jaffrézic
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BMC Bioinformatics
|
The Period protein homolog LIN-42 negatively regulates microRNA biogenesis in C. elegans.
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2014-03-31
|
Amy E Pasquinelli Priscilla M Van Wynsberghe
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Emily F Finnegan Thomas Stark Evan P Angelus Kathryn E Homan Gene W Yeo
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Developmental Biology
|
Small regulatory RNAs in Archaea.
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2014-03-31
|
L Randau Jörg Soppa
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Julia Babski Lisa-Katharina Maier Ruth Heyer Katharina Jaschinski Daniela Prasse Dominik Jäger Ruth A Schmitz Anita Marchfelder
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RNA Biology
|
RNA-seq identifies clinically relevant fusion genes in leukemia including a novel MEF2D/CSF1R fusion responsive to imatinib.
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2014-04
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Henrik Lilljebjörn Hans Ehrencrona Thoas Fioretos
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H Ågerstam C Orsmark-Pietras M Rissler L Nilsson J Richter
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Leukemia
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Odorant and gustatory receptors in the tsetse fly Glossina morsitans morsitans
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2014-04
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Daniel K. Masiga Paul O. Mireji Alan Christoffels
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George F O Obiero Steven R G Nyanjom Hugh M Robertson
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PLOS Neglected Tropical Diseases
|
PRADA: pipeline for RNA sequencing data analysis
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2014-04-01
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Gad Getz
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Wandaliz Torres-García Siyuan Zheng Andrey Sivachenko Rahulsimham Vegesna Qianghu Wang Rong Yao Michael F Berger John N Weinstein Roel G W Verhaak
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Bioinformatics
|
RNA sequencing and proteogenomics reveal the importance of leaderless mRNAs in the radiation-tolerant bacterium Deinococcus deserti.
|
2014-04-01
|
Arjan de Groot Laurence Blanchard David Vallenet David Pignol Jean Armengaud
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David Roche Bernard Fernandez Monika Ludanyi Stéphane Cruveiller
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Genome Biology and Evolution
|
Genome-wide transcriptomic responses of the seagrasses Zostera marina and Nanozostera noltii under a simulated heatwave confirm functional types.
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2014-04-03
|
Erich Bornberg-Bauer Susanne U Franssen
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Jenny Gu Gidon Winters Ann-Kathrin Huylmans Isabell Wienpahl Maximiliane Sparwel James A Coyer Jeanine L Olsen Thorsten B H Reusch
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Marine Genomics
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LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq.
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2014-04-07
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Daniel C. Jeffares Graeme C Smith Charalampos Rallis Jürg Bähler
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Danny A Bitton Charalampos Rallis Graeme C Smith Yuan Y C Chen Sandra Codlin Samuel Marguerat Jürg Bähler
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Genome Research
|
ZBED6 modulates the transcription of myogenic genes in mouse myoblast cells
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2014-04-08
|
Lin Jiang Ola Wallerman Göran Andersson Leif Andersson
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Shady Younis Carl-Johan Rubin Elizabeth R Gilbert Elisabeth Sundström Awaisa Ghazal Xiaolan Zhang Li Wang Tarjei S Mikkelsen
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PLOS ONE
|
Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-Seq and ESTs.
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2014-04-10
|
Gordon G Simpson Nicholas Schurch Christian Cole Sara J Brown Geoffrey J. Barton
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Alexander Sherstnev Junfang Song Céline Duc Kate G Storey W H Irwin McLean
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PLOS ONE
|
Post-translational decrease in respiratory chain proteins in the Polg mutator mouse brain.
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2014-04-10
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David N Hauser Mark R Cookson
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Allissa A Dillman Jinhui Ding Yan Li
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PLOS ONE
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Widespread use of non-productive alternative splice sites in Saccharomyces cerevisiae
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2014-04-10
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Matteo Pellegrini
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Tadashi Kawashima Stephen Douglass Jason Gabunilas Guillaume F Chanfreau
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PLOS Genetics
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Mining of public sequencing databases supports a non-dietary origin for putative foreign miRNAs: underestimated effects of contamination in NGS.
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2014-04-11
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Juan Pablo Tosar Alfonso Cayota
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Carlos Rovira Hugo Naya
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RNA
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Comparison of transcriptional profiles of Clostridium thermocellum grown on cellobiose and pretreated yellow poplar using RNA-Seq.
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2014-04-11
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Michael E Himmel
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Hui Wei Yan Fu Lauren Magnusson John O Baker Pin-Ching Maness Qi Xu Shihui Yang Andrew Bowersox Igor Bogorad Wei Wang Melvin P Tucker Shi-You Ding
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Frontiers in Microbiology
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Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq
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2014-04-13
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Doug Brownfield Barbara Treutlein
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Angela R Wu Norma F Neff Gary L Mantalas F Hernan Espinoza Tushar J Desai Mark A Krasnow Stephen R Quake
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Nature
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VDR primary targets by genome-wide transcriptional profiling.
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2014-04-13
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Graziano Pesole Matteo Pallocca
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Frauke Goeman Francesca De Nicola Paolo D'Onorio De Meo Berardino Elmi Tiziana Castrignanò Sabrina Strano Giovanni Blandino Maurizio Fanciulli Paola Muti
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The Journal of Steroid Biochemistry and Molecular Biology
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Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans.
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2014-04-14
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Gavin Sherlock Jonathan Weissman
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Dale Muzzey
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Genome Research
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Heat shock alters the expression of schizophrenia and autism candidate genes in an induced pluripotent stem cell model of the human telencephalon
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2014-04-15
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Deyou Zheng
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Mingyan Lin Dejian Zhao Anastasia Hrabovsky Erika Pedrosa Herbert M Lachman
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PLOS ONE
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Comparative genomic and transcriptomic analysis of wangiella dermatitidis, a major cause of phaeohyphomycosis and a model black yeast human pathogen
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2014-04-16
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Christina A Cuomo
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Zehua Chen Diego A Martinez Sharvari Gujja Sean M Sykes Qiandong Zeng Paul J Szaniszlo Zheng Wang
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G3
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Transcriptome profiling to identify genes involved in pathogenicity of Valsa mali on apple tree.
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2014-04-16
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Zhiyuan Yin
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Xiwang Ke Na Song Qingqing Dai Ralf T Voegele Yangyang Liu Haiying Wang Xiaoning Gao Zhensheng Kang Lili Huang
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Fungal Genetics and Biology
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Structure and Function of Steroid Receptor RNA Activator Protein, the Proposed Partner of SRA Noncoding RNA
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2014-04-17
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Thomas Cech
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David B McKay Linghe Xi Kristen K B Barthel
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Journal of Molecular Biology
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Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation.
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2014-04-17
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Alexander Idnurm Jason E. Stajich Christina A Cuomo Yuan Chen Gautam Chatterjee Kate L Ormerod Yen-Ping Hsueh James Fraser Tristan Rossignol Kaustuv Sanyal Guilhem Janbon Yong-Sun Bahn Steven Jones Piotr A Mieczkowski Caroline Proux Vikas Yadav Cécile Neuvéglise Joseph Heitman
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Damien Paulet Edmond J Byrnes Nandita Mullapudi Chung-Chau Hon R Blake Billmyre François Brunel Weidong Chen Eve W L Chow Jean-Yves Coppée Anna Floyd-Averette Claude Gaillardin Kimberly J Gerik Jonathan Goldberg Sara Gonzalez-Hilarion Sharvari Gujja Joyce L Hamlin Giuseppe Ianiri Chinnappa D Kodira Lukasz Kozubowski Woei Lam Marco Marra Larry D Mesner Frédérique Moyrand Kirsten Nielsen Jacqueline E Schein Sheng Sun Carolin Wollschlaeger Ian A Wood Qiandong Zeng Carol S Newlon John R Perfect Jennifer K Lodge James W Kronstad Fred S Dietrich
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PLOS Genetics
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IKKα restoration via EZH2 suppression induces nasopharyngeal carcinoma differentiation.
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2014-04-17
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Eric W-F Lam
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Min Yan Yan Zhang Bin He Jin Xiang Zi-feng Wang Fei-meng Zheng Jie Xu Ming-yuan Chen Yu-liang Zhu Hai-jun Wen Xiang-bo Wan Cai-feng Yue Na Yang Wei Zhang Jia-liang Zhang Jing Wang Yang Wang Lian-hong Li Yi-xin Zeng Mien-Chie Hung Quentin Liu
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Nature Communications
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Colorectal cancer cell lines are representative models of the main molecular subtypes of primary cancer.
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2014-04-22
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Diego Arango Walter Bodmer Oliver Sieber Robert N Jorissen Daniel D Buchanan John M Mariadason
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Dmitri Mouradov Clare Sloggett Christopher G Love Shan Li Antony W Burgess Robert L Strausberg Samuel Wormald Liam O'Connor Jennifer L Wilding David Bicknell Ian P M Tomlinson
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Cancer Research
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RNA sequencing shows transcriptomic changes in rectosigmoid mucosa in patients with irritable bowel syndrome-diarrhea: a pilot case-control study.
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2014-04-24
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Michael Camilleri
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Paula Carlson Andres Acosta Irene Busciglio Asha A Nair Simon J Gibbons Gianrico Farrugia Eric W Klee
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American Journal of Physiology - Gastrointestinal and Liver Physiology
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Insights into the trypanosome-host interactions revealed through transcriptomic analysis of parasitized tsetse fly salivary glands.
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2014-04-24
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Michelle B O'Neill Thiago Luiz Alves e Silva Erich L Telleria Serap Aksoy
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Joshua B Benoit Xin Zhao Amy F Savage Sandesh Regmi
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PLOS Neglected Tropical Diseases
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A novel highly divergent protein family identified from a viviparous insect by RNA-seq analysis: a potential target for tsetse fly-specific abortifacients.
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2014-04-24
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Geoffrey Attardo Aaron A Baumann Qirui Zhang Paul O. Mireji Serap Aksoy José M. Ribeiro
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Joshua B Benoit Veronika Michalkova Tyler B Krause Jana Bohova Peter Takáč David L Denlinger
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PLOS Genetics
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A gene expression atlas of early craniofacial development
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2014-04-26
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Phillip Dexheimer
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Eric W Brunskill Andrew S Potter Andrew Distasio Andrew Plassard Bruce J Aronow S Steven Potter
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Developmental Biology
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The cytochrome P450 genes of channel catfish: their involvement in disease defense responses as revealed by meta-analysis of RNA-Seq data sets.
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2014-04-27
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David Robert Nelson Geoff Waldbieser Luyang Sun Shikai Liu Yu Zhang
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Jiaren Zhang Jun Yao Ruijia Wang Yanliang Jiang Jianbin Feng Nannan Liu Geoff Waldbieser Zhanjiang Liu
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Biochimica et Biophysica Acta
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An improved genome release (version Mt4.0) for the model legume Medicago truncatula.
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2014-04-27
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Haibao Tang Vivek Krishnakumar Laurent Gentzbittel Kevin L. Childs
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Shelby Bidwell Benjamin Rosen Agnes Chan Shiguo Zhou Mark Yandell Heidrun Gundlach Klaus F X Mayer David C Schwartz Christopher D Town
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BMC Genomics
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Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival.
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2014-04-29
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Spencer D. Martin Brad H Nelson Robert A Holt
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Scott D Brown Rene L Warren Ewan A Gibb John J Spinelli
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Genome Research
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Microfluidic single-cell whole-transcriptome sequencing.
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2014-04-29
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Liang Zhao Yanyi Huang
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Aaron M Streets Xiannian Zhang Chen Cao Yuhong Pang Xinglong Wu Liang Xiong Lu Yang Yusi Fu Fuchou Tang
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Proceedings of the National Academy of Sciences of the United States of America
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Longer Reads Do Not Significantly Improve RNA-seq Results.
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2014-05-01
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Sagar Chhangawala
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Gabe Rudy Po-Yen Wu Scott Tighe May D. Wang Don A. Baldwin George Grills Christopher E. Mason Jeffrey Rosenfeld
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Journal of Biomolecular Techniques
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From genome to function by studying eQTLs.
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2014-05-04
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Lude Franke
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Harm-Jan Westra
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Biochimica et Biophysica Acta
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Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis.
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2014-05-05
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Gregory B. Gloor
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Andrew D Fernandes Jennifer Ns Reid Jean M Macklaim Thomas A McMurrough David R Edgell
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Microbiome
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A new class of protein cancer biomarker candidates: differentially expressed splice variants of ERBB2 (HER2/neu) and ERBB1 (EGFR) in breast cancer cell lines
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2014-05-05
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Gil Omenn
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Yuanfang Guan Rajasree Menon
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Journal of Proteomics
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Characterization of a genetic mouse model of lung cancer: a promise to identify Non-Small Cell Lung Cancer therapeutic targets and biomarkers.
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2014-05-06
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Matteo Carrara Dario Livio Longo Elena Quaglino Manuela Iezzi Silvio Bicciato Raffaele A. Calogero Federica Cavallo Lorena Landuzzi
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Federica Riccardo Maddalena Arigoni Genny Buson Elisa Zago Alessandra Fiore Simona Nuzzo Patrizia Nanni
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BMC Genomics
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Genome sequencing and comparative genomics of the broad host-range pathogen Rhizoctonia solani AG8.
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2014-05-08
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Jana Sperschneider James K Hane Jonathan P Anderson Karam B. Singh
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Angela H Williams
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PLOS Genetics
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lncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs.
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2014-05-09
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Wan Kyu Kim
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Charny Park Namhee Yu Ikjung Choi Sanghyuk Lee
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Bioinformatics
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De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum.
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2014-05-12
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Paul J Kersey Arnaud Kerhornou Sushma Naithani Dan Bolser Gerard Lazo
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Samuel E Fox Matthew Geniza Mamatha Hanumappa Chris Sullivan Justin Preece Vijay K Tiwari Justin Elser Jeffrey M Leonard Abigail Sage Cathy Gresham Fiona McCarthy Pankaj Jaiswal
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PLOS ONE
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Facile functional analysis of insect odorant receptors expressed in the fruit fly: validation with receptors from taxonomically distant and closely related species.
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2014-05-13
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Walter S Leal
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Carlos Ueira-Vieira Deborah A Kimbrell Washington J de Carvalho
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Cellular and Molecular Life Sciences
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Identification of a radiation sensitivity gene expression profile in primary fibroblasts derived from patients who developed radiotherapy-induced fibrosis.
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2014-05-13
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Jason Li
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Helen B Forrester Trevor Leong Michael J McKay Carl N Sprung
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Radiotherapy and Oncology
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Expression profiling of the wheat pathogen Zymoseptoria tritici reveals genomic patterns of transcription and host-specific regulatory programs
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2014-05-14
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Tiffany Hsu Ronny Kellner Eva H Stukenbrock
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Amitava Bhattacharyya Stephan Poppe Rachel B Brem
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Genome Biology and Evolution
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Network topology-based detection of differential gene regulation and regulatory switches in cell metabolism and signaling
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2014-05-16
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Roland Eils Rosario M. Piro
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Stefan Wiesberg Gunnar Schramm Nico Rebel Marcus Oswald Gerhard Reinelt Rainer König
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BMC Systems Biology
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Dual RNA-seq transcriptional analysis of wheat roots colonized by Azospirillum brasilense reveals up-regulation of nutrient acquisition and cell cycle genes.
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2014-05-16
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Glaucio Valdameri Helisson Faoro Lucélia Donatti Leda S Chubatsu
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Doumit Camilios-Neto Paloma Bonato Roseli Wassem Michelle Z Tadra-Sfeir Liziane C C Brusamarello-Santos Vinicius A Weiss Fábio O Pedrosa Emanuel M Souza
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BMC Genomics
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Estimates of allele-specific expression in Drosophila with a single genome sequence and RNA-seq data.
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2014-05-19
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Francis M Jiggins
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Andrew Quinn Punita Juneja
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Bioinformatics
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RNA sequencing analysis of the gametophyte transcriptome from the liverwort, Marchantia polymorpha.
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2014-05-19
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Mohan B. Singh Prem L. Bhalla
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Niharika Sharma Chol-Hee Jung
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PLOS ONE
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Production, gene structure and characterization of two orthologs of leptin and a leptin receptor in tilapia.
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2014-05-20
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Tomer Ventura Berta Levavi-Sivan
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Michal Shpilman Lian Hollander-Cohen Arieh Gertler
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General and Comparative Endocrinology
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A dynamic regulatory network explains ParaHox gene control of gut patterning in the sea urchin.
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2014-05-21
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Maria Ina Arnone
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Rossella Annunziata
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Development
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Dual RNA-seq of parasite and host reveals gene expression dynamics during filarial worm-mosquito interactions
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2014-05-22
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George F Mayhew Matthew T Aliota
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Young-Jun Choi Sara M Erickson Bruce M Christensen
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PLOS Neglected Tropical Diseases
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Transcriptome of Atoh7 retinal progenitor cells identifies new Atoh7-dependent regulatory genes for retinal ganglion cell formation.
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2014-05-22
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Xiuqian Mu
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Zhiguang Gao Chai-An Mao Ping Pan William H Klein
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Developmental Neurobiology
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A SUF Fe-S cluster biogenesis system in the mitochondrion-related organelles of the anaerobic protist Pygsuia.
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2014-05-22
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Laura Eme Matthew W. Brown Mark van der Giezen Courtney W Stairs Graham Dellaire
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Cornelis Mutsaers Edward Susko Darren M Soanes Andrew J Roger
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Current Biology
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Oak root response to ectomycorrhizal symbiosis establishment: RNA-Seq derived transcript identification and expression profiling
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2014-05-23
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Bruno M Vieira Octávio S. Paulo Filipa Monteiro Lisete Sousa Mónica Sebastiana Rui Manuel Tavares Andreia Figueiredo
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Teresa Lino-Neto Maria Salomé Pais
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PLOS ONE
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Sequential combination of karyotyping and RNA-sequencing in the search for cancer-specific fusion genes.
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2014-05-23
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Sverre Heim Ioannis Panagopoulos
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Jim Thorsen Ludmila Gorunova Francesca Micci
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International Journal of Biochemistry & Cell Biology
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Selective and flexible depletion of problematic sequences from RNA-seq libraries at the cDNA stage.
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2014-05-26
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Thomas Preiss
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Stuart K Archer Nikolay E Shirokikh
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BMC Genomics
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DUX4-induced gene expression is the major molecular signature in FSHD skeletal muscle
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2014-05-26
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Silvère M van der Maarel
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Zizhen Yao Lauren Snider Judit Balog Richard J L F Lemmers Rabi Tawil Stephen J Tapscott
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Human Molecular Genetics
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Time-resolved gene expression profiling during reprogramming of C/EBPα-pulsed B cells into iPS cells
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2014-05-27
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Bruno Di Stefano
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Samuel Collombet Thomas Graf
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Scientific Data
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Transcription of nuclear organellar DNA in a model plant system.
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2014-05-27
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David L. Adelson
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Dong Wang Zhipeng Qu Jian-Kang Zhu Jeremy N Timmis
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Genome Biology and Evolution
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The PhoP-dependent ncRNA Mcr7 modulates the TAT secretion system in Mycobacterium tuberculosis.
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2014-05-29
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Luis Solans Jesús Gonzalo-Asensio Claudia Sala Carlos Martín
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Andrej Benjak Swapna Uplekar Jacques Rougemont Christophe Guilhot Wladimir Malaga Stewart T Cole
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PLOS Pathogens
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SHP2 regulates chondrocyte terminal differentiation, growth plate architecture and skeletal cell fates
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2014-05-29
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Margot Bowen
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Ugur M Ayturk Kyle C Kurek Wentian Yang Matthew L Warman
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PLOS Genetics
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RNA-seq: impact of RNA degradation on transcript quantification.
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2014-05-30
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Irene Gallego Romero
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Athma A Pai Jenny Tung Yoav Gilad
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BMC Biology
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Down-regulation of AUXIN RESPONSE FACTORS 6 and 8 by microRNA 167 leads to floral development defects and female sterility in tomato
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2014-06
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Jason Reed
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Ning Liu Shan Wu Jason Van Houten Ying Wang Biao Ding Zhangjun Fei Thomas H Clarke Esther van der Knaap
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Journal of Experimental Botany
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Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation.
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2014-06-01
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Harri Lähdesmäki Zhi Chen Vincent Butty Tarmo Äijö
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Verna Salo Subhash Tripathi Christopher B Burge Riitta Lahesmaa
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Bioinformatics
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Differential RNA-seq: the approach behind and the biological insight gained.
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2014-06-01
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Cynthia Sharma Jörg Vogel
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Current Opinion in Microbiology
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Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling.
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2014-06-02
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Charles M. Perou
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Wei Zhao Xiaping He Katherine A Hoadley Joel S Parker David Neil Hayes
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BMC Genomics
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Genome-wide identification of long intergenic noncoding RNA genes and their potential association with domestication in pigs.
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2014-06-02
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David M. Irwin
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Zhong-Yin Zhou Ai-Min Li Adeniyi C Adeola Yan-Hu Liu Hai-Bing Xie Ya-Ping Zhang
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Genome Biology and Evolution
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Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series.
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2014-06-03
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Ana Conesa Sonia Tarazona María José Nueda
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Bioinformatics
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The combination of transcriptomics and informatics identifies pathways targeted by miR-204 during neurogenesis and axon guidance.
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2014-06-03
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Remo Sanges David A van Heel Elia Stupka Raquel Marco-Ferreres Ivan Conte Dejan Lazarevic Paola Bovolenta Sandro Banfi
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Stefania Merella Jose Manuel Garcia-Manteiga Chiara Migliore Sabrina Carrella Raffaella Avellino Nathan Paul Davidson Warren Emmett Nicholas Bockett Germana Meroni
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Nucleic Acids Research
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RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri.
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2014-06-06
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Nicholas Thomson
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Marta Vergara-Irigaray Maria C Fookes Christoph M Tang
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BMC Genomics
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Transcriptome sequencing revealed the transcriptional organization at ribosome-mediated attenuation sites in Corynebacterium glutamicum and identified a novel attenuator involved in aromatic amino acid biosynthesis.
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2014-06-06
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Jörn Kalinowski
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Armin Neshat Almut Mentz Christian Rückert
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Journal of Biotechnology
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Comparative transcriptional analysis of asexual and sexual morphs reveals possible mechanisms in reproductive polyphenism of the cotton aphid.
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2014-06-10
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Wei Guo
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Li-Jun Liu Hong-Yuan Zheng Feng Jiang Shu-Tang Zhou
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PLOS ONE
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Variable escape from X-chromosome inactivation: identifying factors that tip the scales towards expression
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2014-06-10 2014-08-01
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Allison M Cotton Carolyn J. Brown
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Samantha B Peeters
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BioEssays
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An optimized method for the extraction of bacterial mRNA from plant roots infected with Escherichia coli O157:H7.
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2014-06-10
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Robert W Jackson Nicola Holden
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Ashleigh Holmes Louise Birse
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Frontiers in Microbiology
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ARH-seq: identification of differential splicing in RNA-seq data
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2014-06-11
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Marie-Laure Yaspo Hans Lehrach Ralf Herwig
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Axel Rasche Matthias Lienhard Marie-Laure Yaspo
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Nucleic Acids Research
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Single-cell RNA-seq reveals dynamic paracrine control of cellular variation.
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2014-06-11
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Nir Friedman Aviv Regev Rahul Satija Nir Hacohen Schraga Schwartz Raktima Raychowdhury Alex K. Shalek
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Joe Shuga John J Trombetta Dave Gennert Diana Lu Peilin Chen Rona S Gertner Jellert T Gaublomme Nir Yosef Brian Fowler Suzanne Weaver Jing Wang Xiaohui Wang Ruihua Ding Raktima Raychowdhury Hongkun Park Andrew P May
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Nature
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Comparison of REST cistromes across human cell types reveals common and context-specific functions
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2014-06-12
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Elaine Fuchs Deyou Zheng
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Shira Rockowitz Wen-Hui Lien Erika Pedrosa Gang Wei Mingyan Lin Keji Zhao Herbert M Lachman
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PLOS Computational Biology
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A novel functional role for MMSET in RNA processing based on the link between the REIIBP isoform and its interaction with the SMN complex
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2014-06-12
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Fabio Mirabella Andrew Thompson C Pawlyn Christopher P Wardell Brian A. Walker
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Alexander Murison Lauren I Aronson Sarah J Hanrahan Jacqueline H L Fok Martin F Kaiser Faith E Davies Gareth J Morgan
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PLOS ONE
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Annotation of long non-coding RNAs expressed in collaborative cross founder mice in response to respiratory virus infection reveals a new class of interferon-stimulated transcripts
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2014-06-12
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Ralph S Baric Yoshihiro Kawaoka
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Laurence Josset Nicolas Tchitchek Lisa E Gralinski Martin T Ferris Amie J Eisfeld Richard R Green Matthew J Thomas Jennifer Tisoncik-Go Gary P Schroth Fernando Pardo Manuel de Villena Mark T Heise Xinxia Peng Michael G Katze
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RNA Biology
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A transcription factor network specifying inhibitory versus excitatory neurons in the dorsal spinal cord.
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2014-06-12
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Diogo S. Castro
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Mark D Borromeo David M Meredith Joshua C Chang Kuang-Chi Tung Francois Guillemot Jane E Johnson
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Development
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RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.
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2014-06-13
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Jessica Lasky-Su
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Blanca E Himes Xiaofeng Jiang Peter Wagner Ruoxi Hu Qiyu Wang Barbara Klanderman Reid M Whitaker Qingling Duan Christina Nikolos William Jester Martin Johnson Reynold A Panettieri Kelan G Tantisira Scott T Weiss Quan Lu
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PLOS ONE
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The Aux/IAA gene rum1 involved in seminal and lateral root formation controls vascular patterning in maize (Zea mays L.) primary roots.
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2014-06-13
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Nina Opitz Frank Hochholdinger Cheng-Ting Yeh
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Yanxiang Zhang Anja Paschold Caroline Marcon Sanzhen Liu Huanhuan Tai Josefine Nestler Christa Lanz Patrick S Schnable
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Journal of Experimental Botany
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miR-PREFeR: an accurate, fast and easy-to-use plant miRNA prediction tool using small RNA-Seq data.
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2014-06-14
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Jikai Lei
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Yanni Sun
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Bioinformatics
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An integrative method to normalize RNA-Seq data.
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2014-06-14
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Klopp Christophe
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Cyril Filloux Meersseman Cédric Philippe Romain Forestier Lionel Rocha Dominique Maftah Abderrahman Petit Daniel
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BMC Bioinformatics
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Mapping of HPV transcripts in four human cervical lesions using RNAseq suggests quantitative rearrangements during carcinogenic progression.
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2014-06-14
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Michael Poidinger
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Jinmiao Chen Yuezhen Xue Thimothy Lim Sung Hock Chew Chai Ling Pang Jean-Pierre Abastado Françoise Thierry
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Virology
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A chemical potentiator of copper-accumulation used to investigate the iron-regulons of Saccharomyces cerevisiae.
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2014-06-15
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Ehmke Pohl Nigel Robinson
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Andrew W Foster Samantha J Dainty Carl J Patterson Hannah Blackburn Clare Wilson Corinna R Hess Julian C Rutherford Laura Quaranta Andy Corran
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Molecular Microbiology
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Transcriptomic landscape of prophase I sunflower male meiocytes.
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2014-06-16
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Octavio Martínez
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Nathalia M V Flórez-Zapata M H Reyes-Valdés Fernando Hernandez-Godínez
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Frontiers in Plant Science
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Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum
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2014-06-17
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W. Richard McCombie Clícia Grativol Felipe Rodrigues da Silva
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Michael Regulski Marcelo Bertalan Adhemar Zerlotini Neto Renato Vicentini Laurent Farinelli Adriana Silva Hemerly Robert A Martienssen Paulo Cavalcanti Gomes Ferreira
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The Plant Journal
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RNA-Seq analysis implicates detoxification pathways in ovine mycotoxin resistance
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2014-06-17
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Jinbi Zhang
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Zengxiang Pan Stephanie Moloney Allan Sheppard
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PLOS ONE
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The Chlamydomonas genome project: a decade on.
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2014-06-17
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David Goodstein Jane Grimwood Crysten E Blaby-Haas Sabeeha Merchant
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Ian K Blaby Nicolas Tourasse Erik F Y Hom David Lopez Munevver Aksoy Arthur Grossman James Umen Susan Dutcher Mary Porter Stephen King George B Witman Mario Stanke Elizabeth H Harris Jane Grimwood Jeremy Schmutz Olivier Vallon Simon Prochnik
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Trends in Plant Science
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Adolescent mouse takes on an active transcriptomic expression during postnatal cerebral development
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2014-06-18
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Songnian Hu
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Wei Xu Chengqi Xin Qiang Lin Feng Ding Wei Gong Yuanyuan Zhou Jun Yu Peng Cui
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Genomics Proteomics and Bioinformatics
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Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing.
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2014-06-19
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Dominique Rocha Daniel Gautheret
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Coline Billerey Mekki Boussaha Diane Esquerré Emmanuelle Rebours Anis Djari Cédric Meersseman Christophe Klopp
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BMC Genomics
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RNA-Seq for the identification of novel Mediator transcripts in endothelial progenitor cells.
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2014-06-19
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Valerio Costa Concetta Schiano Claudio Napoli Monica Rienzo Amelia Casamassimi
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Margherita Scarpato Vincenzo Grimaldi Alfredo Ciccodicola
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Gene
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Epigenetic regulation by chromatin activation mark H3K4me3 in primate progenitor cells within adult neurogenic niche
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2014-06-20
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Richard Sandstrom Eric Haugen
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Michael R Foret Douglas A Grow Christopher T Rhodes Astrid E Cardona Clyde F Phelix Yufeng Wang Mitchel S Berger Chin-Hsing Annie Lin
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Scientific Reports
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A systems biology approach to the analysis of subset-specific responses to lipopolysaccharide in dendritic cells.
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2014-06-20
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Elena Shklovskaya Barbara Fazekas De St Groth
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David G Hancock Thomas V Guy Reza Falsafi Chris D Fjell William Ritchie Robert E W Hancock
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PLOS ONE
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Genomic characterization of acute leukemias.
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2014-06-20
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Robin Foà
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Sabina Chiaretti Valentina Gianfelici Giulia Ceglie
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Medical Principles and Practice
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RNA-binding protein RBM20 represses splicing to orchestrate cardiac pre-mRNA processing.
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2014-06-24
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Markus Landthaler Nikolaus Rajewsky Marvin Jens Martin Liss Michael H Radke Matthias Heinig Michael Gotthardt Eleonora Adami
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Henrike Maatz Sebastian Schafer Marieluise Kirchner Carola Rintisch Vita Dauksaite Matthias Selbach Paul J R Barton Stuart A Cook Norbert Hubner
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Journal of Clinical Investigation
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Comprehensive analysis of the whole transcriptomes from two different pig breeds using RNA-Seq method.
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2014-06-24
|
Artur Gurgul Maria Oczkowicz Katarzyna Ropka-Molik Katarzyna Piórkowska
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Kacper Zukowski Robert Eckert
|
Animal Genetics
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A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.
|
2014-06-25
|
Richard Emes Joanna Moreton Stephen Dunham
|
|
Frontiers in Genetics
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A comparison of transcriptional patterns and mycological phenotypes following infection of Fusarium graminearum by four mycoviruses
|
2014-06-25
|
Kyunghun Min
|
Kyung-Mi Lee Won Kyong Cho Jisuk Yu Moonil Son Hoseong Choi Yin-Won Lee Kook-Hyung Kim
|
PLOS ONE
|
A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package.
|
2014-06-27
|
Jia Meng
|
Zhiliang Lu Hui Liu Lin Zhang Shaowu Zhang Yidong Chen Manjeet K Rao Yufei Huang
|
Methods
|
Profile of whole blood gene expression following immune stimulation in a wild passerine
|
2014-06-27
|
Peeter Hõrak Reidar Andreson
|
Richard Meitern Peeter Hõrak
|
BMC Genomics
|
Response of the hepatic transcriptome to aflatoxin B1 in domestic turkey (Meleagris gallopavo).
|
2014-06-30
|
Melissa S Monson
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Robert E Settlage Kevin W McMahon Kristelle M Mendoza Sumit Rawal Hani S El-Nezami Roger A Coulombe Kent M Reed
|
PLOS ONE
|
Building the sugarcane genome for biotechnology and identifying evolutionary trends.
|
2014-06-30
|
Hélène Bergès Monalisa Sampaio Carneiro Claudio Benicio Cardoso-Silva Carlos T Hotta Cushla Jane Metcalfe Glaucia Mendes Souza Changsoo Kim Alessandro Varani Marie-Anne Van Sluys Anete Pereira Souza
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Nathalia de Setta Cláudia Barros Monteiro-Vitorello Guilherme Marcelo Queiroga Cruz Luiz Eduardo Del Bem Renato Vicentini Fábio Tebaldi Silveira Nogueira Roberta Alvares Campos Sideny Lima Nunes Paula Cristina Gasperazzo Turrini Andreia Prata Vieira Edgar Andrés Ochoa Cruz Tatiana Caroline Silveira Corrêa Sonia Vautrin Adilson Silva da Trindade Mariane de Mendonça Vilela Carolina Gimiliani Lembke Paloma Mieko Sato Rodrigo Fandino de Andrade Milton Yutaka Nishiyama Katia Castanho Scortecci Antônio Augusto Franco Garcia Andrew H Paterson Angélique D'Hont Michel Vincentz João Paulo Kitajima
|
BMC Genomics
|
Requirements for Pseudomonas aeruginosa acute burn and chronic surgical wound infection
|
2014-07
|
Marvin Whiteley
|
Keith H Turner Jake Everett Urvish Trivedi Kendra P Rumbaugh
|
PLOS Genetics
|
The coding and noncoding architecture of the Caulobacter crescentus genome
|
2014-07
|
Bo Zhou Jared M Schrader Sean Crosson Jonathan Weissman
|
Gene-Wei Li Keren Lasker W Seth Childers Brandon Williams Tao Long Harley H McAdams Lucy Shapiro
|
PLOS Genetics
|
Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing
|
2014-07-01
|
Aviv Regev Rahul Satija Alex K. Shalek
|
John J. Trombetta David Gennert Diana Lu
|
Current protocols in molecular biology
|
Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data.
|
2014-07-01
|
Jingyi Jessica Li Steven E. Brenner
|
Haiyan Huang Peter J Bickel
|
Genome Research
|
SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models.
|
2014-07-01
|
Christoph W. Sensen
|
Ian Reid Nicholas O'Toole Omar Zabaneh Reza Nourzadeh Mahmoud Dahdouli Mostafa Abdellateef Paul M K Gordon Jung Soh Gregory Butler Adrian Tsang
|
BMC Bioinformatics
|
IMAGE GUIDED RNA-SEQ REVEALS SUBTYPE-SPECIFIC PATTERNS AT THE INFILTRATIVE MARGINS OF GLIOBLASTOMA.
|
2014-07-01
|
Michael B Sisti
|
Peter Canoll Peter Sims Brian Gil David Pisapia Hani Malone Hannah Goldstein Liang Lei Adam Sonabend Jonathan Yun Jorge Samanamud Jennifer Sims Andrew Teich Sameer Sheth Guy McKhann Jeffrey Bruce
|
Neuro-Oncology
|
Corrigendum: Differential expression analysis of RNA-seq data at single-base resolution.
|
2014-07-01
|
Kasper D. Hansen Jeffrey T. Leek
|
Frazee AC Sabunciyan S Irizarry RA
|
Biostatistics
|
Comprehensive high-throughput RNA sequencing analysis reveals contamination of multiple nasopharyngeal carcinoma cell lines with HeLa cell genomes.
|
2014-07-02
|
Melody Baddoo Asuka Nanbo
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Michael J Strong Melody Baddoo Miao Xu Adriane Puetter Zhen Lin
|
Journal of Virology
|
Novel bioinformatics method for identification of genome-wide non-canonical spliced regions using RNA-Seq data.
|
2014-07-03
|
Gil Omenn
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Yongsheng Bai Justin Hassler Ahdad Ziyar Philip Li Zachary Wright Rajasree Menon James D Cavalcoli Randal J Kaufman Maureen A Sartor
|
PLOS ONE
|
Status of duckweed genomics and transcriptomics.
|
2014-07-04
|
Wenqin Wang
|
J Messing
|
Plant Biology
|
Exploring the stability of long intergenic non-coding RNA in K562 cells by comparative studies of RNA-Seq datasets
|
2014-07-05
|
Jing Tu
|
Lei Wang Dequan Zhou Yan Wang Zuhong Lu
|
Biology Direct
|
Large-scale transcriptional response to hypoxia in Aspergillus fumigatus observed using RNAseq identifies a novel hypoxia regulated ncRNA.
|
2014-07-05
|
Suman B Pakala Vinita S Joardar Bridget M Barker Nikhat Zafar
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Liliana Losada Suchitra Pakala Stephanie Mounaud Natalie Fedorova William C Nierman Robert A Cramer
|
Mycopathologia
|
Enhanced whole genome sequence and annotation of Clostridium stercorarium DSM8532T using RNA-seq transcriptomics and high-throughput proteomics.
|
2014-07-07
|
Gerhard G Thallinger Richard Sparling Bernard Henrissat
|
John J Schellenberg Tobin J Verbeke Peter McQueen Oleg V Krokhin Xiangli Zhang Graham Alvare Brian Fristensky John A Wilkins David B Levin
|
BMC Genomics
|
De novo transcriptome sequencing and sequence analysis of the malaria vector Anopheles sinensis (Diptera: Culicidae).
|
2014-07-07
|
Liang Qiao
|
Bin Chen Yu-Juan Zhang Zhengbo He Wanshun Li Fengling Si Yao Tang Qiyi He Zhentian Yan Wenbo Fu Yanfei Che
|
Parasites & Vectors
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Comparative Analysis of Glycogene Expression in Different Mouse Tissues Using RNA-Seq Data
|
2014-07-09
|
Vivekanand Jha Ahmad Firoz Sanjay Kumar Singh
|
Adeel Malik Amjad Ali
|
International Journal of Genomics
|
Occupancy of tissue-specific cis-regulatory modules by Otx2 and TLE/Groucho for embryonic head specification.
|
2014-07-09
|
Yuuri Yasuoka Yoshikazu Haramoto Makoto Asashima
|
Yutaka Suzuki Shuji Takahashi Haruka Someya Norihiro Sudou Ken W Cho Sumio Sugano Masanori Taira
|
Nature Communications
|
Analysis of the transcriptome and immune function of monocytes during IFNα-based therapy in chronic HCV revealed induction of TLR7 responsiveness.
|
2014-07-09
|
Andre Boonstra Wilfred F J van IJcken
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Jun Hou Zwier M A Groothuismink Ludi Koning Robert Roomer Kim Kreefft Bi-Sheng Liu Harry L A Janssen Robert J de Knegt
|
Antiviral Research
|
Apomictic and sexual germline development differ with respect to cell cycle, transcriptional, hormonal and epigenetic regulation.
|
2014-07-10
|
Christian Sailer Ueli Grossniklaus
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Anja Schmidt Marc W Schmid Ulrich C Klostermeier Weihong Qi Daniela Guthörl Manuel Waller Philip Rosenstiel Ueli Grossniklaus
|
PLOS Genetics
|
Expression pattern of immunoglobulin superfamily members in the silkworm, Bombyx mori.
|
2014-07-11
|
Moli Huang
|
Lei He Guangli Cao Renyu Xue Xiaolong Hu Chengliang Gong
|
Gene
|
A memory-efficient algorithm to obtain splicing graphs and de novo expression estimates from de Bruijn graphs of RNA-Seq data
|
2014-07-14
|
Aaron M. Tarone
|
Sing-Hoi Sze
|
BMC Genomics
|
Reference genes for RT-qPCR studies in Corynebacterium pseudotuberculosis identified through analysis of RNA-seq data.
|
2014-07-15
|
Bruno Bastos
|
Daiane M Carvalho Pablo H de Sá Thiago L P Castro Rodrigo D Carvalho Anne Pinto Danilo J P Gil Priscilla Bagano Lilia F M Costa Roberto Meyer Artur Silva Vasco Azevedo Rommel T J Ramos Luis G C Pacheco
|
Antonie van Leeuwenhoek
|
Roothairless5, which functions in maize (Zea mays L.) root hair initiation and elongation encodes a monocot-specific NADPH oxidase.
|
2014-07-15
|
Frank Hochholdinger
|
Josefine Nestler Sanzhen Liu Tsui-Jung Wen Anja Paschold Caroline Marcon Ho Man Tang Delin Li Li Li Robert B Meeley Hajime Sakai Wesley Bruce Patrick S Schnable
|
The Plant Journal
|
Whole transcriptome RNA-seq analysis: tumorigenesis and metastasis of melanoma.
|
2014-07-15
|
Songnian Hu
|
Hua Zhao Yongjun Li Shaobin Wang Yadong Yang Junyun Wang Xiuyan Ruan Yaran Yang Kan Cai Bing Zhang Peng Cui Jiangwei Yan Yongliang Zhao Edward K Wakeland Quanzhen Li Xiangdong Fang
|
Gene
|
SigFuge: single gene clustering of RNA-seq reveals differential isoform usage among cancer samples
|
2014-07-16
|
Charles M. Perou Liza Makowski Patrick K Kimes
|
Christopher R Cabanski Matthew D Wilkerson Ni Zhao Amy R Johnson Christopher A Maher Yufeng Liu J S Marron D Neil Hayes
|
Nucleic Acids Research
|
Differential gene expression in the respiratory tree of the sea cucumber Apostichopus japonicus during aestivation.
|
2014-07-16
|
Kenneth B. Storey
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Ye Zhao Hongsheng Yang Muyan Chen
|
Marine Genomics
|
Polyphosphate accumulation is driven by transcriptome alterations that lead to near-synchronous and near-equivalent uptake of inorganic cations in an arbuscular mycorrhizal fungus.
|
2014-07-16
|
Katsuharu Saito Tatsuhiro Ezawa
|
Yusuke Kikuchi Nowaki Hijikata Kaede Yokoyama Ryo Ohtomo Yoshihiro Handa Masayoshi Kawaguchi
|
New Phytologist
|
Bioinformatic exploration of RIO protein kinases of parasitic and free-living nematodes.
|
2014-07-17
|
Pasi K. Korhonen Neil D. Young Andreas Hofmann Robin B. Gasser Aaron R Jex Paul W. Sternberg
|
Bert Breugelmans Stefano Mangiola Peter R Boag
|
International Journal for Parasitology
|
Developmental heterogeneity of cardiac fibroblasts does not predict pathological proliferation and activation.
|
2014-07-18
|
Kristy Red-Horse
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Shah R Ali Sara Ranjbarvaziri Mahmood Talkhabi Peng Zhao Ali Subat Armin Hojjat Paniz Kamran Antonia M S Müller Katharina S Volz Zhaoyi Tang Kristy Red-Horse Reza Ardehali
|
Circulation Research
|
Gene expression profiling of laser microdissected airway smooth muscle tissue in asthma and atopy.
|
2014-07-19
|
Frank Baas
|
C Y Yick A H Zwinderman P W Kunst K Grünberg T Mauad S Chowdhury E H Bel R Lutter P J Sterk
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Allergy
|
Genome-wide characterization of light-regulated genes in Neurospora crassa.
|
2014-07-21
|
Jeremy Zucker Erin Bredeweg Matthew S. Sachs
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Cheng Wu Fei Yang Kristina M Smith Matthew Peterson Rigzin Dekhang Ying Zhang Chandrashekara Mallappa Xiaoying Zhou Anna Lyubetskaya Jeffrey P Townsend James E Galagan Michael Freitag Jay C Dunlap Deborah Bell-Pedersen
|
G3
|
Sequence, structural and expression divergence of duplicate genes in the bovine genome.
|
2014-07-23
|
Graham Plastow Paul Stothard
|
Xiaoping Liao Hua Bao Yan Meng Stephen Moore
|
PLOS ONE
|
Hierarchical molecular events driven by oocyte-specific factors lead to rapid and extensive reprogramming
|
2014-07-24
|
Charles R Bradshaw Richard P Halley-Stott Vincent Pasque Kei Miyamoto John Gurdon
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Jerome Jullien George E Allen Nigel J Garrett Hiroshi Kimura Keita Ohsumi
|
Molecular Cell
|
A new dataset of spermatogenic vs. oogenic transcriptomes in the nematode Caenorhabditis elegans.
|
2014-07-24
|
Marco A Ortiz Judith Kimble
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Daniel Noble Elena P Sorokin
|
G3
|
Transcriptome Analysis of the Human Striatum in Tourette Syndrome.
|
2014-07-24
|
Gianfilippo Coppola Dean Palejev Flora M. Vaccarino Nenad Sestan
|
Jessica B Lennington Yuko Kataoka-Sasaki Thomas V Fernandez Yifan Li Anita Huttner Mihovil Pletikos Nenad Sestan James F Leckman
|
Biological Psychiatry
|
iRegulon: from a gene list to a gene regulatory network using large motif and track collections.
|
2014-07-24
|
Zeynep Kalender Atak Delphine Potier Stein Aerts Jean-Christophe Marine Bram Van de Sande Gert Hulselmans Marina N Sanchez
|
Rekin's Janky Annelien Verfaillie Hana Imrichová Laura Standaert Valerie Christiaens Koen Herten Dmitry Svetlichnyy Mark Fiers
|
PLOS Computational Biology
|
Characterization of long non-coding RNA transcriptome in clear-cell renal cell carcinoma by next-generation deep sequencing.
|
2014-07-25
|
Olivier Cussenot
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Gabriel G Malouf Jianping Zhang Ying Yuan Eva Compérat Morgan Rouprêt Yunxin Chen Erika J Thompson Nizar M Tannir John N Weinstein Vicente Valero David Khayat Jean-Philippe Spano Xiaoping Su
|
Molecular Oncology
|
RNA-seq of the aging brain in the short-lived fish N. furzeri - conserved pathways and novel genes associated with neurogenesis.
|
2014-07-25
|
Eva Terzibasi Tozzini Francesco Spallotta Mario Baumgart Michela Ori Marco Groth Alessandro Cellerino Carlo Gaetano Matthias Platzer
|
Steffen Priebe Aurora Savino Giovanna Testa Andreas Dix Roberto Ripa Reinhard Guthke
|
Aging Cell
|
Utility of RNA-seq and GPMDB protein observation frequency for improving the sensitivity of protein identification by tandem MS
|
2014-07-28
|
Alexey I Nesvizhskii
|
Avinash K Shanmugam Anastasia K Yocum
|
Journal of Proteome Research
|
Genomes and transcriptomes of partners in plant-fungal-interactions between canola (Brassica napus) and two Leptosphaeria species.
|
2014-07-28
|
Jonathan Grandaubert Angela P Van de Wouw Barbara Jane Howlett
|
Rohan G T Lowe Andrew Cassin Bethany L Clark Thierry Rouxel
|
PLOS ONE
|
Transcriptome analysis reveals the same 17 S-locus F-box genes in two haplotypes of the self-incompatibility locus of Petunia inflata.
|
2014-07-28
|
Joshua P. Der Justin S Williams
|
Claude W dePamphilis Teh-Hui Kao
|
The Plant Cell
|
Genetic organization of interphase chromosome bands and interbands in Drosophila melanogaster
|
2014-07-29
|
Vladimir N. Babenko
|
Igor F Zhimulev Tatyana Yu Zykova Fyodor P Goncharov Varvara A Khoroshko Olga V Demakova Valeriy F Semeshin Galina V Pokholkova Lidiya V Boldyreva Darya S Demidova Sergey A Demakov Elena S Belyaeva
|
PLOS ONE
|
Molecular targets of chromatin repressive mark H3K9me3 in primate progenitor cells within adult neurogenic niches.
|
2014-07-30
|
Richard Sandstrom
|
Michael R Foret Christopher T Rhodes Yufeng Wang Mitchel S Berger Chin-Hsing Annie Lin
|
Frontiers in Genetics
|
Rbfox2-coordinated alternative splicing of Mef2d and Rock2 controls myoblast fusion during myogenesis.
|
2014-07-31
|
Zheng Xia Jernej Ule Ravi K. Singh Auinash Kalsotra
|
Christopher S Bland Marissa A Scavuzzo Tomaz Curk Wei Li Thomas A Cooper
|
Molecular Cell
|
Discovery of novel transcripts and gametophytic functions via RNA-seq analysis of maize gametophytic transcriptomes.
|
2014-07-31
|
Scott A. Givan
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Antony M Chettoor Rex A Cole Clayton T Coker Erica Unger-Wallace Zuzana Vejlupkova Erik Vollbrecht John E Fowler Matthew Ms Evans
|
Genome Biology
|
Single-cell RNA-seq: advances and future challenges
|
2014-08 2014-08-01
|
Jörg Vogel Alexander Westermann
|
Antoine-Emmanuel Saliba Stanislaw A. Gorski
|
Nucleic Acids Research
|
Temporally and spatially restricted gene expression profiling
|
2014-08-01
|
Alexandra Tallafuss
|
Philip Washbourne John Postlethwait
|
Current Genomics
|
Characterization of distinct classes of differential gene expression in osteoblast cultures from non-syndromic craniosynostosis bone
|
2014-08-01
|
Rene Olivares-Navarrete
|
Monica L Rojas-Peña Sharon Hyzy Dalia Arafat Zvi Schwartz Barbara D Boyan Joseph Williams Greg Gibson
|
Journal of genomics
|
c-Jun promotes cell migration and drives expression of the motility factor ENPP2 in soft tissue sarcomas
|
2014-08-01
|
Massimo Loda
|
Stefano Sioletic Jeffrey Czaplinski Lan Hu Jonathan A Fletcher Christopher D M Fletcher Andrew J Wagner George D Demetri Ewa T Sicinska Eric L Snyder
|
The Journal of Pathology
|
In vivo mRNA profiling of uropathogenic Escherichia coli from diverse phylogroups reveals common and group-specific gene expression profiles
|
2014-08-05
|
Susanne Häussler Sarah Pohl Denitsa Eckweiler
|
Piotr Bielecki Uthayakumar Muthukumarasamy Agata Bielecka Ansgar Schanz Ute Niemeyer Tonio Oumeraci Nils von Neuhoff Jean-Marc Ghigo
|
mBio
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Transcriptomic profiling revealed an important role of cell wall remodeling and ethylene signaling pathway during salt acclimation in Arabidopsis.
|
2014-08-05
|
Changle Ma
|
Xiaoyan Shen Zenglan Wang Xiaofeng Song Jiajia Xu Chunyun Jiang Yanxiu Zhao Hui Zhang
|
Plant Molecular Biology
|
Reduction of systematic bias in transcriptome data from human peripheral blood mononuclear cells for transportation and biobanking.
|
2014-08-07
|
Hideki Ohmomo
|
Tsuyoshi Hachiya Yu Shiwa Ryohei Furukawa Kanako Ono Shigeki Ito Yoji Ishida Mamoru Satoh Jiro Hitomi Kenji Sobue Atsushi Shimizu
|
PLOS ONE
|
MBASED: allele-specific expression detection in cancer tissues and cell lines.
|
2014-08-07
|
Jinfeng Liu
|
Oleg Mayba Houston N Gilbert Peter M Haverty Suchit Jhunjhunwala Zhaoshi Jiang Colin Watanabe Zemin Zhang
|
Genome Biology
|
Influence of RNA extraction methods and library selection schemes on RNA-seq data.
|
2014-08-11
|
Marie-Laure Yaspo Hans Lehrach
|
Marc Sultan Vyacheslav Amstislavskiy Thomas Risch Moritz Schuette Simon Dökel Meryem Ralser Daniela Balzereit Marie-Laure Yaspo
|
BMC Genomics
|
MRI-localized biopsies reveal subtype-specific differences in molecular and cellular composition at the margins of glioblastoma.
|
2014-08-11
|
Michael B Sisti
|
Brian J Gill David J Pisapia Hani R Malone Hannah Goldstein Liang Lei Adam Sonabend Jonathan Yun Jorge Samanamud Jennifer S Sims Matei Banu Athanassios Dovas Andrew F Teich Sameer A Sheth Guy M McKhann Jeffrey N Bruce Peter A Sims Peter Canoll
|
Proceedings of the National Academy of Sciences of the United States of America
|
SERPINB3/B4 contributes to early inflammation and barrier dysfunction in an experimental murine model of atopic dermatitis.
|
2014-08-11
|
Gurjit Khurana Hershey
|
Umasundari Sivaprasad Kayla G Kinker Mark B Ericksen Mark Lindsey Aaron M Gibson Stacey A Bass Nicolas S Hershey Jingyuan Deng Mario Medvedovic
|
Journal of Investigative Dermatology
|
A comparative study of techniques for differential expression analysis on RNA-Seq data.
|
2014-08-13
|
Naomi R. Wray Zong Hong Zhang Qiong-Yi Zhao Janette Edson Denis C Bauer
|
Dhanisha J Jhaveri Vikki M Marshall Ramesh K Narayanan Gregory J Robinson Andreas E Lundberg Perry F Bartlett
|
PLOS ONE
|
Interferon gene expression signature in rheumatoid arthritis neutrophils correlates with a good response to TNFi therapy.
|
2014-08-13
|
Helen L Wright
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Huw B Thomas Robert J Moots Steven W Edwards
|
Rheumatology
|
Functional expression of dental plaque microbiota.
|
2014-08-14
|
Andrew I. Su Tobias Meißner
|
Scott N Peterson Erik Snesrud Ana C Ong Nicholas J Schork Walter A Bretz
|
Frontiers in cellular and infection microbiology
|
Discovering functional modules by topic modeling RNA-Seq based toxicogenomic data.
|
2014-08-14
|
Binsheng Gong
|
Ke Yu Mikyung Lee Zhichao Liu Joshua Xu Roger Perkins Weida Tong
|
Chemical Research in Toxicology
|
Itch-associated peptides: RNA-Seq and bioinformatic analysis of natriuretic precursor peptide B and gastrin releasing peptide in dorsal root and trigeminal ganglia, and the spinal cord.
|
2014-08-14
|
Danielle Thierry-Mieg Jean Thierry-Mieg
|
Samridhi C Goswami Santosh Mishra Mark A Hoon Andrew J Mannes Michael J Iadarola
|
Molecular Pain
|
De novo transcriptome assembly and comparative analysis of differentially expressed genes in Prunus dulcis Mill. in response to freezing stress.
|
2014-08-14
|
Arghavan Alisoltani
|
Sadegh Mousavi Behrouz Shiran Hossein Fallahi Esameil Ebrahimie Ali Imani Saadollah Houshmand
|
PLOS ONE
|
RNA-Rocket: An RNA-Seq Analysis Resource for Infectious Disease Research
|
2014-08-14
|
Leslie Birgit Vosshall Michael McClelland Cristina Aurrecoechea
|
Andrew S. Warren Brian Brunk Prerak Desai Scott Emrich Gloria I. Giraldo-Calderón Omar Harb Deborah Hix Daniel Lawson Dustin Machi Chunhong Mao Eric Nordberg Maulik Shukla Alice R. Wattam Rebecca Will Hyun Seung Yoo Bruno Sobral
|
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Insights into the epigenomic landscape of the human malaria vector Anopheles gambiae
|
2014-08-15
|
Elena Gómez-Díaz Fabrice Chandre
|
Ana Rivero Victor G Corces
|
Frontiers in Genetics
|
Genetic and pharmacological reactivation of the mammalian inactive X chromosome.
|
2014-08-18
|
Sanchita Bhatnagar
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Xiaochun Zhu Jianhong Ou Ling Lin Lynn Chamberlain Lihua J Zhu Narendra Wajapeyee Michael R Green
|
Proceedings of the National Academy of Sciences of the United States of America
|
H3S28 phosphorylation is a hallmark of the transcriptional response to cellular stress.
|
2014-08-18
|
Karl Mechtler
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Anna Sawicka Dominik Hartl Malgorzata Goiser Oliver Pusch Roman R Stocsits Ido M Tamir Christian Seiser
|
Genome Research
|
Dynamic changes in the Streptococcus pneumoniae transcriptome during transition from biofilm formation to invasive disease upon influenza A virus infection.
|
2014-08-18
|
Yong Kong Anders P. Hakansson
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Melinda M Pettigrew Laura R Marks Janneane F Gent Hazeline Roche-Hakansson
|
Infection and Immunity
|
Detecting translational regulation by change point analysis of ribosome profiling data sets
|
2014-08-21
|
Anze Zupanic Daryl P Shanley John C. Mathers
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Catherine Meplan Sushma N Grellscheid Tom B L Kirkwood John E Hesketh
|
RNA
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A multi-resource data integration approach: identification of candidate genes regulating cell proliferation during neocortical development.
|
2014-08-21
|
Florian Freudenberg Richard S. Nowakowski Cynthia Vied Alexandre A S F Raposo David Feng
|
Yuting Wang
|
Frontiers in Neuroscience
|
Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations
|
2014-08-22
|
Pratik D. Jagtap
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Gloria M Sheynkman James E Johnson Michael R Shortreed Getiria Onsongo Brian L Frey Timothy J Griffin Lloyd M Smith
|
BMC Genomics
|
MicroRNA and mRNA cargo of extracellular vesicles from porcine adipose tissue-derived mesenchymal stem cells.
|
2014-08-23
|
Lilach O. Lerman
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Alfonso Eirin Scott M Riester Xiang-Yang Zhu Hui Tang Jared M Evans Daniel O'Brien Andre J van Wijnen
|
Gene
|
RNA-seq transcriptome profiling reveals that Medicago truncatula nodules acclimate N₂ fixation before emerging P deficiency reaches the nodules.
|
2014-08-23
|
Gabriela Salinas-Riester Claudia Pommerenke
|
Ricardo A Cabeza Rebecca Liese Annika Lingner Ilsabe von Stieglitz Janice Neumann Klaus Dittert Joachim Schulze
|
Journal of Experimental Botany
|
Normalization of RNA-seq data using factor analysis of control genes or samples
|
2014-08-24
|
Davide Risso
|
John Ngai Terence P Speed Sandrine Dudoit
|
Nature Biotechnology
|
The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance
|
2014-08-24
|
Danielle Thierry-Mieg Michele Filosi Roberto Visintainer Florian Caiment Samantha Riccadonna Marco Chierici Lee Lancashire Binsheng Gong Davide Albanese Jean Thierry-Mieg Giuseppe Jurman Jos Kleinjans
|
Charles Wang Pierre R Bushel Joshua Xu Hong Fang Huixiao Hong Jie Shen Zhenqiang Su Joe Meehan Xiaojin Li Lu Yang Haiqing Li Paweł P Łabaj David P Kreil Dalila Megherbi Stan Gaj Joost van Delft Andreas Scherer Viswanath Devanarayan Jian Wang Yong Yang Hui-Rong Qian Marina Bessarabova Yuri Nikolsky Cesare Furlanello Ke K Zhang Jianying Li Jui-Hua Hsieh Daniel L Svoboda James C Fuscoe Youping Deng Leming Shi Richard S Paules Scott S Auerbach Weida Tong
|
Nature Biotechnology
|
RNA-seq Transcriptional Profiling of Peripheral Blood Leukocytes from Cattle Infected with Mycobacterium bovis.
|
2014-08-26
|
Kévin Rue-Albrecht Karsten Hokamp Eamonn Gormley David E. MacHugh Stephen V. Gordon Kate Killick
|
Kirsten E McLoughlin Nicolas C Nalpas John A Browne David A Magee Stephen D E Park Kieran G Meade Cliona O'Farrelly
|
Frontiers in Immunology
|
Deletion of aryl hydrocarbon receptor AHR in mice leads to subretinal accumulation of microglia and RPE atrophy.
|
2014-08-26
|
Anand Swaroop Soo-Young Kim Wai T. Wong Robert N. Fariss Matthew Brooks Emily Chew
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Hyun-Jin Yang Yi-Sheng Chang Jung-Woong Kim Rivka A Rachel Tiziana Cogliati Haohua Qian
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Investigative Ophthalmology & Visual Science
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Transcriptomic profiling of rat liver samples in a comprehensive study design by RNA-Seq.
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2014-08-26
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Danielle Thierry-Mieg Jean Thierry-Mieg
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Binsheng Gong Charles Wang Zhenqiang Su Huixiao Hong Leming Shi Scott S Auerbach Weida Tong Joshua Xu
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Scientific Data
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Cross-platform ultradeep transcriptomic profiling of human reference RNA samples by RNA-Seq.
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2014-08-26
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Danielle Thierry-Mieg Jean Thierry-Mieg
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Joshua Xu Zhenqiang Su Huixiao Hong David P Kreil Christopher E Mason Weida Tong Leming Shi
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Scientific Data
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RVboost: RNA-seq variants prioritization using a boosting method
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2014-08-27
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Andrew L Feldman
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Chen Wang Jaime I Davila Saurabh Baheti Aditya V Bhagwate Xue Wang Jean-Pierre A Kocher Susan L Slager Anne J Novak James R Cerhan E Aubrey Thompson Yan W Asmann
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Bioinformatics
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RNA-Seq analysis reveals a six-gene SoxR regulon in Streptomyces coelicolor
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2014-08-27
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Joshua Shapiro Nawar Naseer
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Monica Chander
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PLOS ONE
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Identification of sRNAs expressed by the human pathogen Neisseria gonorrhoeae under disparate growth conditions.
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2014-08-28
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Ryan S McClure
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Brian Tjaden Caroline Genco
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Frontiers in Microbiology
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Ionotropic GABA and glycine receptor subunit composition in human pluripotent stem cell-derived excitatory cortical neurones.
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2014-08-28
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Owen Dando Peter C Kind David J Wyllie Giles E. Hardingham Siddharthan Chandran
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Owain T James Matthew R Livesey Jing Qiu Bilada Bilican Ghazal Haghi Rinku Rajan Karen Burr
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The Journal of Physiology
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DNA copy number evolution in Drosophila cell lines
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2014-08-28
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Maurizio Gatti Brenton R. Graveley Teresa M Przytycka
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Hangnoh Lee C Joel McManus Dong-Yeon Cho Matthew Eaton Fioranna Renda Maria Patrizia Somma Lucy Cherbas Gemma May Sara Powell Dayu Zhang Lijun Zhan Alissa Resch Justen Andrews Susan E Celniker Peter Cherbas Brian Oliver David MacAlpine
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Genome Biology
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Identification of differentially expressed genes during development of the zebrafish pineal complex using RNA sequencing.
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2014-08-28
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Q85220273
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Joshua T Gamse
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Developmental Biology
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Assessing the clinical use of clear cell renal cell carcinoma molecular subtypes identified by RNA expression analysis.
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2014-08-28
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Richard W. Joseph Thai Huu Ho
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Jeanette E Eckel-Passow Daniel A Igel Daniel J Serie John C Cheville Alexander S Parker
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Urologic Oncology
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RNA sequencing analysis of the broad-host-range strain Sinorhizobium fredii NGR234 identifies a large set of genes linked to quorum sensing-dependent regulation in the background of a traI and ngrI deletion mutant
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2014-09
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Lei Li Konrad Förstner Wolfgang R Streit
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Dagmar Krysciak Jessica Grote Mariita Rodriguez Orbegoso Christian Utpatel Christel Schmeisser Hari B Krishnan
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Applied and Environmental Microbiology
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Using heterogeneity of the patient-derived xenograft model to identify the chemoresistant population in ovarian cancer
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2014-09-01
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Britt K. Erickson David A Schneider
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Zachary C Dobbin Ashwini A Katre Adam D Steg Monjri M Shah Ronald D Alvarez Michael G Conner Dongquan Chen Charles N Landen
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Oncotarget
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miR-155 induced transcriptome changes in the MCF-7 breast cancer cell line leads to enhanced mitogen activated protein kinase signaling
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2014-09-01
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Melody Baddoo Erik K Flemington
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Elizabeth C Martin Adrienne E Krebs Hope E Burks Steven Elliott Melody Baddoo Bridgette M Collins-Burow Matthew E Burow
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Genes & Cancer
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Genome-wide interrogation of longitudinal FEV1 in children with asthma
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2014-09-01
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Hae Kyung Im Nancy J Cox
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Kehua Wu Eric R Gamazon Hae Kyung Im Paul Geeleher Steven R White Julian Solway George L Clemmer Scott T Weiss Kelan G Tantisira Mark J Ratain R Stephanie Huang
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American Journal of Respiratory and Critical Care Medicine
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Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function.
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2014-09-01
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Gregory E Crawford
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James A Browne Rui Yang Lingyun Song Shih-Hsing Leir Ann Harris
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Molecular Human Reproduction
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The devil in the details of RNA-seq
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2014-09-01
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Anton Kratz Piero Carninci
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Nature Biotechnology
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Genome-wide distribution of Auts2 binding localizes with active neurodevelopmental genes.
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2014-09-02
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Ramon Y Birnbaum Nadav Ahituv
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N Oksenberg G D E Haliburton W L Eckalbar I Oren S Nishizaki K Murphy K S Pollard
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Translational Psychiatry
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RNA-seq reveals aurora kinase-driven mTOR pathway activation in patients with sarcomatoid metastatic renal cell carcinoma.
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2014-09-02
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Tommy Tong Jeremy O Jones
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Sumanta K Pal Miaoling He Huiqing Wu Xueli Liu Clayton Lau Jin-Hui Wang Charles Warden Xiwei Wu Sabina Signoretti Toni K Choueiri Jose A Karam
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Molecular Cancer Research
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Transcriptomic dissection of the rice-Burkholderia glumae interaction.
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2014-09-03
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Teresia J Buza Peng Deng Daniel G. Peterson
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Zenaida V Magbanua Mark Arick Chuan-Yu Hsu Kurt C Showmaker Philippe Chouvarine Shien Lu
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BMC Genomics
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Transcriptional profiles of bovine in vivo pre-implantation development.
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2014-09-04
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Junhong Luo
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Zongliang Jiang Jiangwen Sun Hong Dong Xinbao Zheng Craig Obergfell Yong Tang Jinbo Bi Rachel O'Neill Yijun Ruan Jingbo Chen Xiuchun Cindy Tian
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BMC Genomics
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Whole transcriptome sequencing reveals extensive unspliced mRNA in metastatic castration-resistant prostate cancer.
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2014-09-04
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Adam G Sowalsky
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Zheng Xia Liguo Wang Hao Zhao Shaoyong Chen Glenn J Bubley Steven P Balk Wei Li
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Molecular Cancer Research
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Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer.
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2014-09-04
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Elisa Ficarra Lasorella A Iavarone A Raul Rabadan
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Francesco Abate Sakellarios Zairis Andrea Acquaviva Chris H Wiggins Veronique Frattini Giorgio Inghirami
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BMC Systems Biology
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Caught in the act: RNA-Seq provides novel insights into mRNA degradation.
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2014-09-04
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Jörg Stülke
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Jan Gerwig
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Molecular Microbiology
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Transcriptome profiling of spinal muscular atrophy motor neurons derived from mouse embryonic stem cells
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2014-09-05
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Matthew E R Butchbach
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Miho Maeda Ashlee W Harris Brewster F Kingham Casey J Lumpkin Lynn M Opdenaker Suzanne M McCahan Wenlan Wang
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PLOS ONE
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Progressive increase in mtDNA 3243A>G heteroplasmy causes abrupt transcriptional reprogramming.
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2014-09-05
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Paweł Golik
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Martin Picard Jiangwen Zhang Saege Hancock Olga Derbeneva Ryan Golhar Sean O'Hearn Shawn Levy Prasanth Potluri Maria Lvova Antonio Davila Chun Shi Lin Juan Carlos Perin Eric F Rappaport Hakon Hakonarson Ian A Trounce Vincent Procaccio Douglas C Wallace
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Proceedings of the National Academy of Sciences of the United States of America
|
Transcriptome profiling of Vitis amurensis, an extremely cold-tolerant Chinese wild Vitis species, reveals candidate genes and events that potentially connected to cold stress.
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2014-09-05
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Weirong Xu
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Ruimin Li Ningbo Zhang Fuli Ma Yuntong Jiao Zhenping Wang
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Plant Molecular Biology
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Genome-wide binding and transcriptome analysis of human farnesoid X receptor in primary human hepatocytes.
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2014-09-08
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Yaping Fang
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Le Zhan Hui-Xin Liu Bo Kong Yuqi He Xiao-Bo Zhong Jianwen Fang Yu-Jui Yvonne Wan Grace L Guo
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PLOS ONE
|
The sialotranscriptome of Amblyomma triste, Amblyomma parvum and Amblyomma cajennense ticks, uncovered by 454-based RNA-seq.
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2014-09-08
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Luiz Gustavo Gardinassi José M. Ribeiro Beatriz R Ferreira C L Mafra Matias Pablo Juan Szabó Sandra Regina Maruyama
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Gustavo Rocha Garcia Elen Anatriello Higo Nasser Santanna Moreira Maria Marlene Martins Isabel Kinney Ferreira de Miranda-Santos
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Parasites & Vectors
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RNA-Seq analysis of the multipartite genome of Rhizobium etli CE3 shows different replicon contributions under heat and saline shock.
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2014-09-08
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Q85275267 Santiago Castillo-Ramírez
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Maria Luisa Tabche Alfredo Mendoza-Vargas Miguel A Ramírez-Romero Guillermo Dávila
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BMC Genomics
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Expression of antisense small RNAs in response to stress in Pseudomonas aeruginosa.
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2014-09-11
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Søren Molin Rasmus L Marvig
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María Gómez-Lozano Monica V L Tulstrup
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BMC Genomics
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Transcriptome characteristics of filamentous fungi deduced using high-throughput analytical technologies.
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2014-09-11
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Lucía Ramírez
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Martha Lucía Meijueiro Francisco Santoyo Antonio G Pisabarro
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Briefings in functional genomics
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GSAASeqSP: a toolset for gene set association analysis of RNA-Seq data
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2014-09-12
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Terrence S. Furey
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Qing Xiong Sayan Mukherjee
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Scientific Reports
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Transcriptomic analysis identifies gene networks regulated by estrogen receptor α (ERα) and ERβ that control distinct effects of different botanical estrogens
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2014-09-12
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Zeynep Madak-Erdogan
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Ping Gong Jilong Li Jianlin Cheng C Michael Greenlief William Helferich John A Katzenellenbogen Benita S Katzenellenbogen
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Nuclear Receptor Signaling
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TELP, a sensitive and versatile library construction method for next-generation sequencing
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2014-09-15
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Feng Xu
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Xu Peng Jingyi Wu Reinhard Brunmeir Sun-Yee Kim Qiongyi Zhang Chunming Ding Weiping Han Wei Xie
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Nucleic Acids Research
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Onecut1 and Onecut2 redundantly regulate early retinal cell fates during development.
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2014-09-16
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Xiuqian Mu
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Darshan Sapkota Hemabindu Chintala Fuguo Wu Steven J Fliesler Zihua Hu
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Proceedings of the National Academy of Sciences of the United States of America
|
Using normalization to resolve RNA-Seq biases caused by amplification from minimal input.
|
2014-09-16
|
Christiaan V. Henkel Finn-Arne Weltzien
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Eirill Ager-Wick Trude M Haug
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Physiological Genomics
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Understanding gene regulatory mechanisms by integrating ChIP-seq and RNA-seq data: statistical solutions to biological problems.
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2014-09-17
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Claudia Angelini Valerio Costa
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|
Frontiers in cell and developmental biology
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Optimization of extraction of circulating RNAs from plasma--enabling small RNA sequencing
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2014-09-17
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Bettina Haase Benedikt Kirchner Michael W Pfaffl
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Melanie Spornraft Vladimir Benes Irmgard Riedmaier
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PLOS ONE
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SOX9 regulates multiple genes in chondrocytes, including genes encoding ECM proteins, ECM modification enzymes, receptors, and transporters.
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2014-09-17
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Yue Lu
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Chun-do Oh Shoudan Liang Yuko Mori-Akiyama Di Chen Benoit de Crombrugghe Hideyo Yasuda
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PLOS ONE
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Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis.
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2014-09-18
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Francesca Finotello
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Barbara Di Camillo
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Briefings in functional genomics
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Clonal variation in interferon response determines the outcome of oncolytic virotherapy in mouse CT26 colon carcinoma model.
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2014-09-18
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Seppo Ylä-Herttuala Minna Niittykoski
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J J Ruotsalainen M U Kaikkonen M W Martikainen C G Lemay J Cox N S De Silva A Kus T J Falls J-S Diallo F Le Boeuf J C Bell A E Hinkkanen M J Vähä-Koskela
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Gene Therapy
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Nontemplated nucleotide additions distinguish the small RNA composition in cells from exosomes.
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2014-09-18
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Bauke Ylstra Michael Hackenberg Nicoletta Zini Jaap M Middeldorp
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Danijela Koppers-Lalic Irene V Bijnsdorp Monique A J van Eijndhoven Payman Sadek Daud Sie Renee X de Menezes Thomas Würdinger Gerrit A Meijer D Michiel Pegtel
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Cell Reports
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Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli.
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2014-09-18
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Kenneth J McDowall
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Justin E Clarke Louise Kime David Romero A
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Nucleic Acids Research
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A comprehensive transcriptomic analysis of infant and adult mouse ovary.
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2014-09-20
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Songnian Hu
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Linlin Pan Wei Gong Yuanyuan Zhou Xiaonuan Li Jun Yu
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Genomics Proteomics and Bioinformatics
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Rule-based integration of RNA-Seq analyses tools for identification of novel transcripts.
|
2014-09-22
|
Avik Datta
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Harshal Inamdar Sunitha Manjari K Rajendra Joshi
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Journal of Bioinformatics and Computational Biology
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Error estimates for the analysis of differential expression from RNA-seq count data.
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2014-09-23
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Conrad J Burden
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Sumaira E Qureshi Susan R Wilson
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PeerJ
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Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi.
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2014-09-23
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Robert M. Waterhouse Gareth L. Maslen Daniel Lawson
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Xiaofang Jiang Ashley Peery A Brantley Hall Atashi Sharma Xiao-Guang Chen Aleksey Komissarov Michelle M Riehle Yogesh Shouche Maria V Sharakhova Nazzy Pakpour Peter Arensburger Victoria L M Davidson Karin Eiglmeier Scott Emrich Phillip George Ryan C Kennedy Shrinivasrao P Mane Chioma Oringanje Yumin Qi Robert Settlage Marta Tojo Jose M C Tubio Maria F Unger Bo Wang Kenneth D Vernick Jose M C Ribeiro Anthony A James Kristin Michel Michael A Riehle Shirley Luckhart Igor V Sharakhov Zhijian Tu
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Genome Biology
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Rare occurrence of EGFRvIII deletion in head and neck squamous cell carcinoma.
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2014-09-23
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Arun Khattri Zhixiang Zuo Everett E Vokes
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Johannes Brägelmann Michaela K Keck Mohamed El Dinali Christopher D Brown Thomas Stricker Anish Munagala Ezra E W Cohen Mark W Lingen Kevin P White Tanguy Y Seiwert
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Oral Oncology
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CO2 exposure at pressure impacts metabolism and stress responses in the model sulfate-reducing bacterium Desulfovibrio vulgaris strain Hildenborough.
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2014-09-25
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Matthew J. Marshall
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Michael J Wilkins David W Hoyt Paul A Alderson Andrew E Plymale L Meng Markillie Abby E Tucker Eric D Walter Bryan E Linggi Alice C Dohnalkova Ron C Taylor
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Frontiers in Microbiology
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Transcriptome profile analysis reveals specific signatures of pollutants in Atlantic eels.
|
2014-09-26
|
Louis Bernatchez Hélène Budzinski
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Lucie Baillon Fabien Pierron Raphaël Coudret Eric Normendeau Antoine Caron Laurent Peluhet Pierre Labadie Gilles Durrieu Jérôme Sarraco Pierre Elie Patrice Couture Magalie Baudrimont
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Ecotoxicology
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Maize and millet transcription factors annotated using comparative genomic and transcriptomic data.
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2014-09-27
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Chun-Ping Yu Wen-Hsiung Li
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Jinn-Jy Lin Yao-Ming Chang Sean Chun-Chang Chen
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BMC Genomics
|
Open-access synthetic spike-in mRNA-seq data for cancer gene fusions.
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2014-09-30
|
Valérie Montel
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Waibhav D Tembe Stephanie J K Pond Christophe Legendre Han-Yu Chuang Winnie S Liang Nancy E Kim Shukmei Wong Timothy K McDaniel David W Craig John D Carpten
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BMC Genomics
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Tracking difference in gene expression in a time-course experiment using gene set enrichment analysis.
|
2014-09-30
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Tsuyoshi Tanaka
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Pui Shan Wong Michihiro Tanaka Yoshihiko Sunaga Masayoshi Tanaka Takeaki Taniguchi Tomoko Yoshino Wataru Fujibuchi Sachiyo Aburatani
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PLOS ONE
|
Weak base pairing in both seed and 3' regions reduces RNAi off-targets and enhances si/shRNA designs.
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2014-09-30
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Martin Kampmann
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Shuo Gu Yue Zhang Lan Jin Yong Huang Feijie Zhang Michael C Bassik Mark A Kay
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Nucleic Acids Research
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RNA-Seq gene profiling--a systematic empirical comparison.
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2014-09-30
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Nuno A. Fonseca Alvis Brazma John C Marioni
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PLOS ONE
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Global transcriptome analysis of Al-induced genes in an Al-accumulating species, common buckwheat (Fagopyrum esculentum Moench).
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2014-09-30
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Naoki Yamaji
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Kengo Yokosho Jian Feng Ma
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Plant and Cell Physiology
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A comparison of sperm RNA-seq methods
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2014-10
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Russ Hauser
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Shihong Mao Edward Sendler Robert J Goodrich Stephen A Krawetz
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Systems Biology in Reproductive Medicine
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Genome-wide discovery of drug-dependent human liver regulatory elements
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2014-10
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Marcelo Rizzatti Luizon Nadav Ahituv
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Robin P Smith Walter L Eckalbar Kari M Morrissey Thomas J Hoffmann Xuefeng Sun Stacy L Jones Shelley Force Aldred Anuradha Ramamoorthy Zeruesenay Desta Yunlong Liu Todd C Skaar Nathan D Trinklein Kathleen M Giacomini
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PLOS Genetics
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Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta.
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2014-10-01
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Reedik Mägi Andres Metspalu Ene Reimann Kristiina Rull Jaak Vilo Lili Milani Andres Salumets Triin Viltrop Maire Peters Sulev Kõks
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Tauno Metsalu Airi Tiirats Balaji Rajashekar Ganesh Acharya Purusotam Basnet Kadri Haller-Kikkatalo
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Epigenetics
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How deep is enough in single-cell RNA-seq?
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2014-10-01
|
Yanyi Huang
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Aaron M Streets
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Nature Biotechnology
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RNA-seq analysis of the rat placentation site reveals maternal obesity-associated changes in placental and offspring thyroid hormone signaling.
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2014-10-05
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Kartik Shankar
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J Saben P Kang Y Zhong K M Thakali H Gomez-Acevedo S J Borengasser A Andres T M Badger
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Placenta
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Detection of very long antisense transcripts by whole transcriptome RNA-Seq analysis of Listeria monocytogenes by semiconductor sequencing technology.
|
2014-10-06
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Stefanie Wehner Ramakanth Madhugiri
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Gopala K Mannala Xiaoxing Qing Trinad Chakraborty Mobarak A Mraheil Torsten Hain Manja Marz
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PLOS ONE
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Role for LSM genes in the regulation of circadian rhythms.
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2014-10-06
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Lauren J. Francey
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Soledad Perez-Santángelo Estefanía Mancini Ruben Gustavo Schlaen Ariel Chernomoretz John B Hogenesch Marcelo J Yanovsky
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Proceedings of the National Academy of Sciences of the United States of America
|
Genome-wide identification and tissue-specific expression analysis of UDP-glycosyltransferases genes confirm their abundance in Cicer arietinum (Chickpea) genome
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2014-10-07
|
Vimal Rawat
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Ranu Sharma C G Suresh
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PLOS ONE
|
Comparative transcriptomics and metabolomics in a rhesus macaque drug administration study.
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2014-10-08
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Jessica C Kissinger Jeremy Debarry Karan Uppal
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Kevin J Lee Weiwei Yin Dalia Arafat Yan Tang ViLinh Tran Monica Cabrera-Mora Stacey Lapp Alberto Moreno Esmeralda Meyer Suman Pakala Vishal Nayak Dean P Jones Mary Galinski Mark P Styczynski Greg Gibson
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Frontiers in cell and developmental biology
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Gene expression plasticity resulting from parental leaf damage in Mimulus guttatus.
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2014-10-08
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Lena Hileman
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Jack M Colicchio Patrick J Monnahan John K Kelly
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New Phytologist
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Argonaute-1 binds transcriptional enhancers and controls constitutive and alternative splicing in human cells.
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2014-10-13
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Eduardo Eyras Eneritz Agirre Matías Blaustein Gwendal Dujardin Federico Pelisch Juan Valcárcel Reinhard Georg Lührmann Alberto Kornblihtt
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Mariano Alló Sergey Bessonov Paola Bertucci Luciana Gómez Acuña Valeria Buggiano Nicolás Bellora Babita Singh Ezequiel Petrillo Belén Miñana Berta Pozzi Elías Bechara Dmitry E Agafonov Anabella Srebrow
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Proceedings of the National Academy of Sciences of the United States of America
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trieFinder: an efficient program for annotating Digital Gene Expression (DGE) tags.
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2014-10-13
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Matthew C LaFave Shawn M. Burgess
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Gabriel Renaud Jin Liang Tyra G Wolfsberg
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BMC Bioinformatics
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Characterization of two regulators of the TNF-α signaling pathway in Apostichopus japonicus: LPS-induced TNF-α factor and baculoviral inhibitor of apoptosis repeat-containing 2.
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2014-10-13
|
Chenghua Li
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Xiumei Zhang Pengjuan Zhang Ye Li Chunhua Jin Weiwei Zhang
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Developmental and Comparative Immunology
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RNA-seq reveals the pan-transcriptomic impact of attenuating the gliotoxin self-protection mechanism in Aspergillus fumigatus
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2014-10-14
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David A Fitzpatrick Gary W Jones Thomas M Keane Sean Doyle
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Grainne O'Keeffe Stephen Hammel Rebecca A Owens
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BMC Genomics
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Quality Control for RNA-Seq (QuaCRS): An Integrated Quality Control Pipeline.
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2014-10-15
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James S Blachly
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Karl W Kroll Nima E Mokaram Alexander R Pelletier David E Frankhouser Maximillian S Westphal Paige A Stump Cameron L Stump Ralf Bundschuh Pearlly Yan
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Cancer Informatics
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Rcount: simple and flexible RNA-Seq read counting.
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2014-10-15
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Ueli Grossniklaus
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Marc W Schmid Ueli Grossniklaus
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Bioinformatics
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Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis.
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2014-10-15
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Ross C Hardison Christapher S Morrissey Mitchell J Weiss
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Weisheng Wu Cheryl A Keller Tejaswini Mishra Maxim Pimkin Gerd A Blobel
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Genome Research
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Defining the genome-wide role of CRE1 during carbon catabolite repression in Trichoderma reesei using RNA-Seq analysis.
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2014-10-18
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Rafael Silva-Rocha
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Amanda Cristina Campos Antoniêto Lílian dos Santos Castro Gabriela Felix Persinoti Roberto Nascimento Silva
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Fungal Genetics and Biology
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Transcriptomic portrait of human Mesenchymal Stromal/Stem Cells isolated from bone marrow and placenta.
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2014-10-19
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Javier De Las Rivas Fermin Sanchez-Guijo
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Beatriz Roson-Burgo Consuelo Del Cañizo
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BMC Genomics
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Comparative proteomic and transcriptomic profile of Staphylococcus epidermidis biofilms grown in glucose-enriched medium.
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2014-10-19
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Gerald B Pier Manuel Vilanova Nuno Cerca Rui Vitorino
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Virginia Carvalhais Angela França
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Talanta
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CHD8 regulates neurodevelopmental pathways associated with autism spectrum disorder in neural progenitors
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2014-10-21
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Nicholas Katsanis Manolis Kellis Stephen J Haggarty Serkan Erdin Michael E. Talkowski Marta Biagioli Christelle Golzio James F. Gusella
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Aarathi Sugathan Ian Blumenthal Poornima Manavalan Ashok Ragavendran Harrison Brand Diane Lucente Judith Miles Steven D Sheridan Alexei Stortchevoi
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Proceedings of the National Academy of Sciences of the United States of America
|
Differential expression of endogenous plant cell wall degrading enzyme genes in the stick insect (Phasmatodea) midgut.
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2014-10-21
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Lynn Kimsey
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Matan Shelomi W Cameron Jasper Joel Atallah Brian R Johnson
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BMC Genomics
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Gene expression associated with intersterility in Heterobasidion.
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2014-10-22
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Mårten Lind Malin Elfstrand Magnus Karlsson Jan Stenlid
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M A Van der Nest Å Olson K Dalman M Brandström-Durling B D Wingfield
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Fungal Genetics and Biology
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Gene expression patterns and sequence polymorphisms associated with mosquito resistance to Bacillus thuringiensis israelensis toxins
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2014-10-23
|
Aurélie Bonin Stéphane Reynaud Laurence Despres Jean-Philippe David Guillaume Tetreau
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Renaud Stalinski Margot Paris Vincent Navratil
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BMC Genomics
|
Expression profile of Caenorhabditis elegans mutant for the Werner syndrome gene ortholog reveals the impact of vitamin C on development to increase life span.
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2014-10-27
|
Martin J. Simard
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Alexandra Dallaire Sophie Proulx Michel Lebel
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BMC Genomics
|
Large-scale coding sequence change underlies the evolution of postdevelopmental novelty in honey bees.
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2014-10-28
|
Timothy A Linksvayer
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William Cameron Jasper Timothy A Linksvayer Joel Atallah Daniel Friedman Joanna C Chiu Brian R Johnson
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Molecular Biology and Evolution
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The multidrug resistance 1 gene Abcb1 in brain and placenta: comparative analysis in human and guinea pig
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2014-10-29
|
Gustavo Turecki Matthew Suderman
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Jane J Pappas Sophie Petropoulos Majid Iqbal Vasilis Moisiadis Stephen G Matthews Moshe Szyf
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PLOS ONE
|
In vivo proximity labeling for the detection of protein-protein and protein-RNA interactions.
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2014-10-29
|
Roberto Bonasio Michiel Vermeulen
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David B Beck Varun Narendra William J Drury Ryan Casey Pascal W T C Jansen Zuo-Fei Yuan Benjamin A Garcia
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Journal of Proteome Research
|
Transcriptional adaptations during long-term persistence of Staphylococcus aureus in the airways of a cystic fibrosis patient.
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2014-10-29
|
Boyke Bunk Barbara C. Kahl Alexander Mellmann Cathrin Spröer
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Nadine Windmüller Anika Witten Desirée Block
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International Journal of Medical Microbiology
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Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential.
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2014-10-31
|
Igor V Grigoriev
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Jennifer M Hurley Arko Dasgupta Jillian M Emerson Xiaoying Zhou Carol S Ringelberg Nicole Knabe Anna M Lipzen Erika A Lindquist Christopher G Daum Kerrie W Barry Kristina M Smith James E Galagan Deborah Bell-Pedersen Michael Freitag Chao Cheng Jennifer J Loros Jay C Dunlap
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Proceedings of the National Academy of Sciences of the United States of America
|
GeneFriends: a human RNA-seq-based gene and transcript co-expression database
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2014-10-31
|
Thomas Craig
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Sipko van Dam João Pedro de Magalhães
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Nucleic Acids Research
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BCOR-CCNB3 fusions are frequent in undifferentiated sarcomas of male children.
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2014-10-31
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Stephen F Sarabia Alexander J. Lazar
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Tricia L Peters Vijetha Kumar Sumanth Polikepahad Frank Y Lin Yu Liang Wei-Lien Wang HarshaVardhan Doddapaneni Hsu Chao Donna M Muzny David A Wheeler M Fatih Okcu Sharon E Plon M John Hicks Dolores López-Terrada D Williams Parsons Angshumoy Roy
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Modern Pathology
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Widespread intron retention in mammals functionally tunes transcriptomes
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2014-11
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Ulrich Braunschweig Thomas Gonatopoulos-Pournatzis Babak Alipanahi Nuno L Barbosa-Morais Manuel Irimia
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Qun Pan Emil N Nachman Brendan Frey Benjamin J Blencowe
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Genome Research
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Several fusion genes identified by whole transcriptome sequencing in a spindle cell sarcoma with rearrangements of chromosome arm 12q and MDM2 amplification
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2014-11
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Sverre Heim Ioannis Panagopoulos
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Bodil Bjerkehagen Ludmila Gorunova Jeanne-Marie Berner Kjetil Boye
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International Journal of Oncology
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Tissue-specific mtDNA abundance from exome data and its correlation with mitochondrial transcription, mass and respiratory activity.
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2014-11-01
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Carmela Gissi Graziano Pesole Matteo Chiara Anna Maria D'Erchia Ernesto Picardi Anna Atlante
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Gemma Gadaleta Giulio Pavesi Caterina De Virgilio Caterina Manzari Francesca Mastropasqua Gian Marco Prazzoli David Horner Aurelio Reyes Elisabetta Sbisà Apollonia Tullo
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Mitochondrion
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Whole transcriptome analysis for T cell receptor-affinity and IRF4-regulated clonal expansion of T cells
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2014-11-01
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Gordon K Smyth
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Wei Shi Kevin Man Stephen L Nutt Axel Kallies
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Genomics Data
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Increasing gene discovery and coverage using RNA-seq of globin RNA reduced porcine blood samples.
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2014-11-04
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Paul Stothard
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Igseo Choi Hua Bao Arun Kommadath Afshin Hosseini Xu Sun Yan Meng Graham S Plastow Christopher K Tuggle James M Reecy Eric Fritz-Waters Samuel M Abrams Joan K Lunney Le Luo Guan
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BMC Genomics
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DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data.
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2014-11-05
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Shin Kawano
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Ayako Suzuki Hiroyuki Wakaguri Riu Yamashita Katsuya Tsuchihara Sumio Sugano Yutaka Suzuki Kenta Nakai
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Nucleic Acids Research
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Transcriptomic analysis across nasal, temporal, and macular regions of human neural retina and RPE/choroid by RNA-Seq
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2014-11-05
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Alex H Wagner Adam P. DeLuca Arlene Drack Budd A. Tucker Todd E. Scheetz Robert F. Mullins Edwin M. Stone
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S Scott Whitmore Shemin Zeng Terry A Braun
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Experimental Eye Research
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The landscape of microRNA, Piwi-interacting RNA, and circular RNA in human saliva.
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2014-11-06
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Xianzhi Lin Feng Li Xinshu Xiao
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Jae Hoon Bahn Qing Zhang Tak-Ming Chan Yong Kim David T W Wong
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Clinical Chemistry
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Biochemical and molecular changes associated with heteroxylan biosynthesis in Neolamarckia cadamba (Rubiaceae) during xylogenesis
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2014-11-07
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Antony Bacic
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Xianhai Zhao Kunxi Ouyang Siming Gan Wei Zeng Lili Song Shuai Zhao Juncheng Li Monika S Doblin Xiao-Yang Chen Alan Marchant Xiaomei Deng Ai-Min Wu
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Frontiers in Plant Science
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Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state
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2014-11-07
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Christopher J. Lengner Rudolf Jaenisch
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Yarden Katz Feifei Li Nicole J Lambert Ethan S Sokol Wai-Leong Tam Albert W Cheng Edoardo M Airoldi Piyush B Gupta Zhengquan Yu Christopher B Burge
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eLife
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Nasonia vitripennis venom causes targeted gene expression changes in its fly host.
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2014-11-10
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Aisha L Siebert
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Ellen O Martinson David Wheeler Jeremy Wright Mrinalini John H Werren
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Molecular Ecology
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COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems.
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2014-11-11
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Yasunobu Okamura Shu Tadaka
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Yuichi Aoki Takeshi Obayashi Satoshi Ito Takafumi Narise Kengo Kinoshita
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Nucleic Acids Research
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Suppression of the FOXM1 transcriptional programme via novel small molecule inhibition
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2014-11-12
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Christopher Lowe Michael V Gormally Ajit Jadhav
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Thomas S Dexheimer Giovanni Marsico Deborah A Sanders Dijana Matak-Vinković Sam Michael Ganesha Rai David J Maloney Anton Simeonov Shankar Balasubramanian
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Nature Communications
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The putative Leishmania telomerase RNA (LeishTER) undergoes trans-splicing and contains a conserved template sequence
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2014-11-12
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Marcelo Santos da Silva
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Elton J R Vasconcelos Vinícius S Nunes Marcela Segatto Peter J Myler Maria Isabel N Cano
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PLOS ONE
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Investigating the molecular underpinnings underlying morphology and changes in carbon partitioning during tension wood formation in Eucalyptus.
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2014-11-12
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Shawn D Mansfield
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Eshchar Mizrachi Victoria J Maloney Janine Silberbauer Charles A Hefer Dave K Berger Alexander A Myburg
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New Phytologist
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Functional diversity of carbohydrate-active enzymes enabling a bacterium to ferment plant biomass.
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2014-11-13
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Jean Weissenbach Andrew C Tolonen Adriana Alberti
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Magali Boutard Tristan Cerisy Pierre-Yves Nogue Marcel Salanoubat
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PLOS Genetics
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RNA-seq analysis of Quercus pubescens Leaves: de novo transcriptome assembly, annotation and functional markers development.
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2014-11-13
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Alessio Fini Federico Sebastiani Cecilia Brunetti Massimiliano Tattini
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Sara Torre Silvia Fineschi Francesco Ferrini
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PLOS ONE
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De-regulation of gene expression and alternative splicing affects distinct cellular pathways in the aging hippocampus.
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2014-11-13
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Stefan Bonn Roman Stilling
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Eva Benito Michael Gertig Jonas Barth Vincenzo Capece Susanne Burkhardt Andre Fischer
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Frontiers in Cellular Neuroscience
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Transcriptomic and physiological insights into the robustness of long filamentous cells of Methanosaeta harundinacea, prevalent in upflow anaerobic sludge blanket granules.
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2014-11-14
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Songnian Hu
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Liguang Zhou Haiying Yu Guomin Ai Bo Zhang Xiuzhu Dong
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Applied and Environmental Microbiology
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Detection theory in identification of RNA-DNA sequence differences using RNA-sequencing.
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2014-11-14
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Gregory R Grant
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Jonathan M Toung Nicholas Lahens John B Hogenesch
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PLOS ONE
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Construction and assessment of individualized proteogenomic databases for large-scale analysis of nonsynonymous single nucleotide variants.
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2014-11-17
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Boris Macek
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Karsten Krug Sasa Popic Alejandro Carpy Christoph Taumer
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Proteomics
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Genome-wide analysis of the omega-3 fatty acid desaturase gene family in Gossypium
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2014-11-18
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Daniel Ilut
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Olga P Yurchenko Sunjung Park Jay J Inmon Jon C Millhollon Zach Liechty Justin T Page Matthew A Jenks Kent D Chapman Joshua A Udall Michael A Gore John M Dyer
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BMC Plant Biology
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Omics profiles used to evaluate the gene expression of Exiguobacterium antarcticum B7 during cold adaptation.
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2014-11-18
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Vivian H. Pellizari Adriano M C Pimenta
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Hivana P M B Dall'Agnol Rafael A Baraúna Pablo H C G de Sá Rommel T J Ramos Felipe Nóbrega Catarina I P Nunes Diego A das Graças Adriana R Carneiro Daniel M Santos Marta S P Carepo Vasco Azevedo Maria P C Schneider Artur Silva
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BMC Genomics
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IsoSCM: improved and alternative 3' UTR annotation using multiple change-point inference.
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2014-11-18
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Pedro Miura Piero Sanfilippo Eric C Lai
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Sol Shenker
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RNA
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Expression of human skin-specific genes defined by transcriptomics and antibody-based profiling
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2014-11-19
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Mathias Uhlén Linn Fagerberg
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Per-Henrik D Edqvist Björn M Hallström Angelika Danielsson Karolina Edlund Fredrik Pontén
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Journal of Histochemistry & Cytochemistry
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Aberrant expression of miR-218 and miR-204 in human mesial temporal lobe epilepsy and hippocampal sclerosis-convergence on axonal guidance.
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2014-11-19
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Anne Yael Nossent Kees Fluiter A Sabers Lisbeth Birk Møller Asli Silahtaroglu Rikke S Møller Niels Tommerup Eleonora Aronica
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Sanne S Kaalund Morten T Venø Mads Bak Henning Laursen Flemming Madsen Helle Broholm Bjørn Quistorff Peter Uldall Sakari Kauppinen Jørgen Kjems Zeynep Tümer
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Epilepsia
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ChiTaRS 2.1--an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts
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2014-11-20
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Alfonso Valencia Alessandro Gorohovski Milana Frenkel-Morgenstern
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Dunja Vucenovic Lorena Maestre
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Nucleic Acids Research
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DB-AT: a 2015 update to the Full-parasites database brings a multitude of new transcriptomic data for apicomplexan parasites.
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2014-11-20
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Tabea G Kischka Marcin Jąkalski Ikuo Igarashi Xuenan Xuan Yoshifumi Nishikawa
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Hiroyuki Wakaguri Shin-ichiro Kawazu Makoto Matsubayashi Fumiya Kawahara Naotoshi Tsuji Shinuo Cao Fujiko Sunaga Kazuhiro Okubo Josef Tuda Arthur E Mongan Yuki Eshita Ryuichiro Maeda Wojciech Makałowski Yutaka Suzuki Junya Yamagishi
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Nucleic Acids Research
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The TCF C-clamp DNA binding domain expands the Wnt transcriptome via alternative target recognition.
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2014-11-20
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Pierre Baldi
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Nate P Hoverter Michael D Zeller Miriam M McQuade Angela Garibaldi Anke Busch Elizabeth M Selwan Klemens J Hertel Marian L Waterman
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Nucleic Acids Research
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The mechanisms of genome-wide target gene regulation by TCF7L2 in liver cells
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2014-11-20
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Ralph A DeFronzo
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Luke Norton Xi Chen Marcel Fourcaudot Nikhil K Acharya Sami Heikkinen
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Nucleic Acids Research
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Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing.
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2014-11-24
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Sten Linnarsson Peter Lönnerberg Jens Hjerling-Leffler Patrik Ernfors
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Dmitry Usoskin Alessandro Furlan Saiful Islam Hind Abdo Daohua Lou Jesper Haeggström Olga Kharchenko Peter V Kharchenko
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Nature Neuroscience
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Promiscuous mRNA splicing under the control of AIRE in medullary thymic epithelial cells.
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2014-11-25
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Rhodri Ceredig
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Peter Keane Cathal Seoighe
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Bioinformatics
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Identification of Salt-Stress-Induced Genes from the RNA-Seq Data of Reaumuria trigyna Using Differential-Display Reverse Transcription PCR.
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2014-11-26
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Shu-Biao Wu
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Zhen-Hua Dang Qi Qi Hui-Rong Zhang Hao-Yu Li Ying-Chun Wang
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International Journal of Genomics
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Natural genetic variation impacts expression levels of coding, non-coding, and antisense transcripts in fission yeast
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2014-11-28
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Jürg Bähler María Rodríguez-López Francesc X. Marsellach Christopher T. Workman
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Mathieu Clément-Ziza Sandra Codlin Manos A Papadakis Susanne Reinhardt Stuart Martin Samuel Marguerat Alexander Schmidt Eunhye Lee Jürg Bähler Andreas Beyer
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Molecular Systems Biology
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The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease
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2014-12
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Kerstin Lindblad-Toh Jessica Alföldi Federica Di Palma Marcia Lara Thibaut Hourlier Adam C. Siepel Christophe Dessimoz Jason Turner-Maier David Brawand Kevin Gori Bronwen Aken John F Engelhardt Yoshihiro Kawaoka
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Xinxia Peng Amie J Eisfeld Scott R Tyler Jennifer Tisoncik-Go G Lynn Law Nives Skunca Masato Hatta David J Gasper Sara M Kelly Jean Chang Matthew J Thomas Jeremy Johnson Aaron M Berlin Pamela Russell Ross Swofford Jason Turner-Maier Sarah Young Steve Searle Xingshen Sun Yaling Yi M Suresh Terrence M Tumpey Samantha M Wisely Bruce W Birren Robert E Palermo Michael G Katze
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Nature Biotechnology
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Development of novel filtering criteria to analyze RNA-sequencing data obtained from the murine ocular lens during embryogenesis
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2014-12-01
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Melinda K Duncan Shawn W Polson
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Abby L Manthey Anne M Terrell Salil A Lachke
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Genomics Data
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Transcriptome profiling of Set5 and Set1 methyltransferases: Tools for visualization of gene expression.
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2014-12-01
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Devin A King Ashby Morrison
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Glòria Mas Martín Pablo E Garcia-Nieto
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Genomics Data
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Genotet: An Interactive Web-based Visual Exploration Framework to Support Validation of Gene Regulatory Networks.
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2014-12-01
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Christoph Hafemeister
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Bowen Yu Harish Doraiswamy Xi Chen Emily Miraldi Mario Luis Arrieta-Ortiz Christoph Hafemeister Aviv Madar Richard Bonneau Cláudio T Silva
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IEEE Transactions on Visualization and Computer Graphics
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Identifying direct targets of transcription factor Rfx2 that coordinate ciliogenesis and cell movement
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2014-12-01
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Taejoon Kwon
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Mei-I Chung Rakhi Gupta Julie C Baker John B Wallingford
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Genomics Data
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Transcriptome structure variability in Saccharomyces cerevisiae strains determined with a newly developed assembly software.
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2014-12-01
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Laura Treu Stefano Campanaro
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Alessandro Sardu
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BMC Genomics
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Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress.
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2014-12-02
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Nedeljka N. Rosic Chon-Kit Kenneth Chan Sophie Dove David Edwards Ove Hoegh-Guldberg
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Paulina Kaniewska Edmund Yew Siang Ling
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BMC Genomics
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An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era
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2014-12-03
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Lee Lancashire
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Zhenqiang Su Hong Fang Huixiao Hong Leming Shi Wenqian Zhang Wenwei Zhang Yanyan Zhang Zirui Dong Marina Bessarabova Xi Yang Baitang Ning Binsheng Gong Joe Meehan Joshua Xu Weigong Ge Roger Perkins Matthias Fischer Weida Tong
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Genome Biology
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Impact of the genetic background on the composition of the chicken plasma MiRNome in response to a stress
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2014-12-04
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Marie-Laure Endale Ahanda
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Tatiana Zerjal Sophie Dhorne-Pollet Andrea Rau Amanda Cooksey Elisabetta Giuffra
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PLOS ONE
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QuASAR: quantitative allele-specific analysis of reads.
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2014-12-04
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Xiaoquan Wen Francesca Luca Roger Pique-Regi
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Chris T Harvey Gregory A Moyerbrailean Gordon O Davis
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Bioinformatics
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rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data
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2014-12-05 2014-12-23
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Zhi-xiang Lu Michael D. Henry
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Shihao Shen Juw Won Park Lan Lin Ying Nian Wu Qing Zhou Yi Xing Michael D. Henry
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Proceedings of the National Academy of Sciences of the United States of America
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RNA-seq analysis of oil palm under cold stress reveals a different C-repeat binding factor (CBF) mediated gene expression pattern in Elaeis guineensis compared to other species.
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2014-12-05
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Yaodong Yang Annaliese S Mason
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Xintao Lei Yong Xiao Wei Xia Zilong Ma Ming Peng
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PLOS ONE
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SNPlice: variants that modulate Intron retention from RNA-sequencing data.
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2014-12-06
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Kamran Kowsari
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Prakriti Mudvari Mercedeh Movassagh Ali Seyfi Maria Kokkinaki Nathan J Edwards Nady Golestaneh Anelia Horvath
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Bioinformatics
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Direct and indirect consequences on gene expression of a thyroid hormone receptor alpha 1 mutation restricted to Sertoli cells.
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2014-12-08
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Gabriel Livera
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Fabrice Chatonnet Betty Fumel Sophie FouchÉCourt Frédéric Flamant
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Molecular Reproduction and Development
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Dynamic changes in the cardiac methylome during postnatal development.
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2014-12-09
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Mark Ziemann James E Hudson Enzo R Porrello Assam El-osta
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Choon Boon Sim Antony Kaspi K N Harikrishnan Jenny Ooi Ishant Khurana Lisa Chang
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FASEB Journal
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MCMC implementation of the optimal Bayesian classifier for non-Gaussian models: model-based RNA-Seq classification.
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2014-12-10
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Edward R. Dougherty
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Jason M Knight Ivan Ivanov
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BMC Bioinformatics
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An epigenomic roadmap to induced pluripotency reveals DNA methylation as a reprogramming modulator.
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2014-12-10
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Thomas Bleazard Thomas Preiss Nicole Cloonan Andras Nagy Sean M. Grimmond
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Dong-Sung Lee Jong-Yeon Shin Peter D Tonge Mira C Puri Seungbok Lee Hansoo Park Won-Chul Lee Samer M I Hussein Ji-Young Yun Jihye Kim Mira Li David Wood Jennifer L Clancy Rowland Mosbergen Jae-Hyuk Yi Kap-Seok Yang Hyungtae Kim Hwanseok Rhee Christine A Wells Ian M Rogers Jeong-Sun Seo
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Nature Communications
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RNA-seq analysis of broiler liver transcriptome reveals novel responses to high ambient temperature.
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2014-12-10
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Carl J Schmidt
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Derrick J Coble Damarius Fleming Michael E Persia Chris M Ashwell Max F Rothschild Susan J Lamont
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BMC Genomics
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High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies
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2014-12-11
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Aviv Regev Nir Hacohen Raktima Raychowdhury Nir Friedman
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Michal Rabani Raktima Raychowdhury Marko Jovanovic Michael Rooney Deborah J Stumpo Andrea Pauli Alexander F Schier Perry J Blackshear Ido Amit
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Cell
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UPF2, a nonsense-mediated mRNA decay factor, is required for prepubertal Sertoli cell development and male fertility by ensuring fidelity of the transcriptome.
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2014-12-11
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Wei Yan Shuiqiao Yuan Jianqiang Bao Bo Torben Porse
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Chong Tang
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Development
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Whole exome sequencing of a single osteosarcoma case--integrative analysis with whole transcriptome RNA-seq data.
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2014-12-11
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Sulev Kõks
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Ene Reimann Xuan Dung Ho Katre Maasalu Aare Märtson
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Human genomics
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The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data
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2014-12-16
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Richard Weinshilboum Kevin J Thompson Xiaojia Tang Krishna R Kalari
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Saurabh Baheti Khader Shameer Quin Wills Nifang Niu Ilona N Holcomb Stephane C Boutet Ramesh Ramakrishnan Jennifer M Kachergus Jean-Pierre A Kocher Liewei Wang E Aubrey Thompson
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Nucleic Acids Research
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Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems.
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2014-12-16
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Julie Dickerson
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Ruolin Liu Ann E Loraine
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BMC Bioinformatics
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Advances in translational bioinformatics facilitate revealing the landscape of complex disease mechanisms
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2014-12-16
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Youping Deng
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Jack Y Yang A Dunker Jun S Liu Xiang Qin Hamid R Arabnia William Yang Andrzej Niemierko Zhongxue Chen Zuojie Luo Liangjiang Wang Yunlong Liu Dong Xu Weida Tong Mary Yang
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BMC Bioinformatics
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Identification of genes and pathways involved in kidney renal clear cell carcinoma
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2014-12-16
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Youping Deng
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William Yang Kenji Yoshigoe Xiang Qin Jun S Liu Jack Y Yang Andrzej Niemierko Yunlong Liu A Dunker Zhongxue Chen Liangjiang Wang Dong Xu Hamid R Arabnia Weida Tong Mary Yang
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BMC Bioinformatics
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Regulation of the KNOX-GA gene module induces heterophyllic alteration in North American lake cress.
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2014-12-16
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Hitoshi Sakakibara Seisuke Kimura
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Hokuto Nakayama Naomi Nakayama Sumer Seiki Mikiko Kojima Neelima Sinha
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The Plant Cell
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Recurrent PRDM10 gene fusions in undifferentiated pleomorphic sarcoma.
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2014-12-16
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Fredrik Mertens
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Jakob Hofvander Johnbosco Tayebwa Jenny Nilsson Linda Magnusson Otte Brosjö Olle Larsson Fredrik Vult von Steyern Nils Mandahl Christopher D M Fletcher
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Clinical Cancer Research
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Evaluation and validation of a robust single cell RNA-amplification protocol through transcriptional profiling of enriched lung cancer initiating cells.
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2014-12-17
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Luca Roz Giulia Bertolini Louise Carter Massimo Moro Crispin J. Miller Fiona Blackhall Caroline Dive
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Dominic G Rothwell Yaoyong Li Mahmood Ayub Catriona Tate Gillian Newton Yvonne Hey Suzanne Faulkner Stuart Pepper Ged Brady
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BMC Genomics
|
Identification of a candidate prognostic gene signature by transcriptome analysis of matched pre- and post-treatment prostatic biopsies from patients with advanced prostate cancer.
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2014-12-18
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Chris Ponting Andreas Heger Jacqueline Stockley Ian Sudbery Hing Y Leung Prabhakar Rajan
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Janis T Fleming Ann Hedley Gabriela Kalna David Sims Craig N Robson Rhona M McMenemin Ian D Pedley
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BMC Cancer
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Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference.
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2014-12-18
|
Delphine Potier Kristofer Davie Stein Aerts Gert Hulselmans
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Marina Naval Sanchez Lotte Haagen Vân Anh Huynh-Thu Duygu Koldere Arzu Celik Pierre Geurts Valerie Christiaens
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Cell Reports
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RNA-seq analysis reveals significant transcriptome changes in turbot (Scophthalmus maximus) suffering severe enteromyxosis.
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2014-12-19
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Paolo Ronza Ana Paula Losada Peter W Harrison Belén G Pardo Ariadna Sitjà-Bobadilla Paulino Martínez
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Diego Robledo Roberto Bermúdez María José Redondo María Isabel Quiroga
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BMC Genomics
|
Genome-wide analysis of the human p53 transcriptional network unveils a lncRNA tumour suppressor signature.
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2014-12-19
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Maite Huarte Alejandro Athie Francesco P Marchese
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Yolanda Sánchez Victor Segura Oskar Marín-Béjar Jovanna González Luis Bujanda Shuling Guo Ander Matheu
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Nature Communications
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plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants.
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2014-12-23
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Peter F. Stadler David Langenberger
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Deblina Patra Mario Fasold Gerhard Steger Ivo Grosse
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Frontiers in Plant Science
|
A note on an exon-based strategy to identify differentially expressed genes in RNA-seq experiments.
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2014-12-26
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Laura L. Elo
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Asta Laiho
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PLOS ONE
|
RNA-seq profiling of small numbers of Drosophila neurons.
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2014-12-26
|
Michael Rosbash E Nagoshi Xiao Chen
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Katharine Abruzzi Abby Zadina
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Methods in Enzymology
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Considerations for RNA-seq analysis of circadian rhythms.
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2014-12-26
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Gregory R Grant
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Jiajia Li John B Hogenesch Michael E Hughes
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Methods in Enzymology
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Identification of RNA polymerase III-transcribed Alu loci by computational screening of RNA-Seq data.
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2014-12-29
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Silvia Fustinoni Giorgio Dieci Davide Carnevali Matteo Pellegrini Anastasia Conti
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Nucleic Acids Research
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Comparisons of de novo transcriptome assemblers in diploid and polyploid species using peanut (Arachis spp.) RNA-Seq data.
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2014-12-31
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Ratan Chopra
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Gloria Burow Andrew Farmer Joann Mudge Charles E Simpson Mark D Burow
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PLOS ONE
|
Subgroup-elimination transcriptomics identifies signaling proteins that define subclasses of TRPV1-positive neurons and a novel paracrine circuit.
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2014-12-31
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Tim Hucho
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Jörg Isensee Carsten Wenzel Rene Buschow Robert Weissmann Andreas W Kuss
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PLOS ONE
|
Β-catenin-dependent control of positional information along the AP body axis in planarians involves a teashirt family member.
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2014-12-31
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Gilbert Weidinger
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Hanna Reuter Martin März Matthias C Vogg David Eccles Laura Grífol-Boldú Daniel Wehner Suthira Owlarn Teresa Adell Kerstin Bartscherer
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Cell Reports
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Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties
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2015
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Eshita Mutt Pritha Ghosh Oommen K Mathew
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Atul K Upadhyay Anita R Chacko A Gandhimathi K Harini Agnel P Joseph Adwait G Joshi Snehal D Karpe Swati Kaushik Nagesh Kuravadi Chandana S Lingu J Mahita Ramya Malarini Sony Malhotra Manoharan Malini Mahantesha Naika Sathyanarayanan Nitish Shaik Naseer Pasha Upadhyayula S Raghavender Anantharamanan Rajamani S Shilpa Prashant N Shingate Heikham Russiachand Singh Anshul Sukhwal Margaret S Sunitha Manojkumar Sumathi S Ramaswamy Malali Gowda Ramanathan Sowdhamini
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BMC Plant Biology
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ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines
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2015
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Fabian Amman Florian Eggenhofer
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Michael T Wolfinger Jörg Fallmann
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F1000Research
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Ixodes scapularis and Ixodes ricinus tick cell lines respond to infection with tick-borne encephalitis virus: transcriptomic and proteomic analysis
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2015
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Margarita Villar José de la Fuente John Fazakerley Mick Watson Hana Tykalová Lesley Bell-Sakyi
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Sabine Weisheit Marina Popara Julia Loecherbach Daniel Růžek Libor Grubhoffer
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Parasites & Vectors
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Dynamics in Transcriptomics: Advancements in RNA-seq Time Course and Downstream Analysis
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2015
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Daniel Spies Constance Ciaudo
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Computational and Structural Biotechnology Journal
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Remodeling of the Nuclear Envelope and Lamina during Bovine Preimplantation Development and Its Functional Implications
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2015
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Valeri Zakhartchenko Eckhard Wolf Volker J Schmid
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Jens Popken Alexander Graf Stefan Krebs Helmut Blum Axel Strauss Tuna Guengoer Thomas Cremer
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PLOS ONE
|
Genes expressed in grapevine leaves reveal latent wood infection by the fungal pathogen Neofusicoccum parvum
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2015
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Andrew J McElrone Grant Cramer
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Stefan Czemmel Erin R Galarneau Renaud Travadon Kendra Baumgartner
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PLOS ONE
|
Whole transcriptome analysis using next-generation sequencing of sterile-cultured Eisenia andrei for immune system research
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2015
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Tetsuya Sakurai
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Yoshikazu Mikami Atsushi Fukushima Takao Kuwada-Kusunose Taiichi Kitano Yusuke Komiyama Takashi Iwase Kazuo Komiyama
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PLOS ONE
|
Transcriptomic Characterization of Innate and Acquired Immune Responses in Red-Legged Partridges (Alectoris rufa): A Resource for Immunoecology and Robustness Selection
|
2015
|
Natalia Sevane
|
Javier Cañon Ignacio Gil Susana Dunner
|
PLOS ONE
|
Size of the Ovulatory Follicle Dictates Spatial Differences in the Oviductal Transcriptome in Cattle
|
2015
|
Fernando S Mesquita Luiz L Coutinho
|
Angela María Gonella-Diaza Sónia Cristina da Silva Andrade Mariana Sponchiado Guilherme Pugliesi Veerle Van Hoeck Ricardo de Francisco Strefezzi Gustavo R Gasparin Mario Binelli
|
PLOS ONE
|
Comparative Analysis of Muscle Transcriptome between Pig Genotypes Identifies Genes and Regulatory Mechanisms Associated to Growth, Fatness and Metabolism
|
2015
|
Rita Benítez Ana Isabel Rey Cristina Ovilo
|
Miriam Ayuso Almudena Fernández Yolanda Núñez Beatriz Isabel Carmen Barragán Ana Isabel Fernández Juan F Medrano Ángela Cánovas Antonio González-Bulnes Clemente López-Bote
|
PLOS ONE
|
From Insect to Man: Photorhabdus Sheds Light on the Emergence of Human Pathogenicity
|
2015
|
Helge Bode Nicholas J Tobias Michael L. Beeton Richard ffrench-Constant
|
Geraldine Mulley Paul Wilkinson Isabella Vlisidou Nina Ockendon-Powell Alexia Hapeshi Friederike I Nollmann Jean van den Elsen Nicholas R Waterfield
|
PLOS ONE
|
Decreased SMAD4 expression is associated with induction of epithelial-to-mesenchymal transition and cetuximab resistance in head and neck squamous cell carcinoma.
|
2015
|
Ruchira Ranaweera Elana J. Fertig
|
Haixia Cheng Hiroyuki Ozawa Hiromitsu Hatakeyama Jason D Howard Jimena Perez Michael Considine Manjusha Thakar Gabriel Krigsfeld Christine H Chung
|
Cancer Biology and Therapy
|
A cell-based systems biology assessment of human blood to monitor immune responses after influenza vaccination
|
2015
|
Nripesh Prasad Parimal Samir Sebastian Joyce Shawn Levy Q52577914
|
Kristen L Hoek Leigh M Howard Xinnan Niu Allison Galassie Qi Liu Tara M Allos Kyle A Floyd Yan Guo Yu Shyr Andrew J Link
|
PLOS ONE
|
Activin-A and Bmp4 levels modulate cell type specification during CHIR-induced cardiomyogenesis
|
2015
|
Karl Stamm
|
Min-Su Kim Audrey Horst Steven Blinka Donna Mahnke James Schuman Rebekah Gundry Aoy Tomita-Mitchell John Lough
|
PLOS ONE
|
mRNA profiling reveals determinants of trastuzumab efficiency in HER2-positive breast cancer
|
2015
|
Manuel Nietert Gabriela Salinas-Riester Silvia von der Heyde
|
Steve Wagner Alexander Czerny Fabian Ludewig Dorit Arlt Tim Beißbarth
|
PLOS ONE
|
The exosome component Rrp6 is required for RNA polymerase II termination at specific targets of the Nrd1-Nab3 pathway
|
2015
|
Amber L. Mosley
|
Melanie J Fox Hongyu Gao Whitney R Smith-Kinnaman Yunlong Liu
|
PLOS Genetics
|
A Genome-Wide Association Study for Culm Cellulose Content in Barley Reveals Candidate Genes Co-Expressed with Members of the CELLULOSE SYNTHASE A Gene Family
|
2015
|
Diane Mather Rachel A Burton Brian Steffenson Kanwarpal S Dhugga Robbie Waugh
|
Kelly Houston Beata Sznajder Antoni J Rafalski Jillian Taylor Geoffrey B Fincher
|
PLOS ONE
|
Differential Expression Analysis by RNA-Seq Reveals Perturbations in the Platelet mRNA Transcriptome Triggered by Pathogen Reduction Systems
|
2015
|
Abdimajid Osman Patrick Provost Adam Ameur
|
Walter E Hitzler
|
PLOS ONE
|
Asparagus Spears as a Model to Study Heteroxylan Biosynthesis during Secondary Wall Development
|
2015
|
Kelsey L. Picard Wei Zeng Edwin R. Lampugnani Antony Bacic
|
Lili Song Aimin Wu Roshan Cheetamun Cherie Beahan Andrew Cassin Andrew Lonsdale Monika S Doblin
|
PLOS ONE
|
Global Gene Expression Profiling through the Complete Life Cycle of Trypanosoma vivax
|
2015
|
Matthew Berriman Mandy Sanders Sophie Goyard Andrew P Jackson Dong Xia Paola Minoprio
|
Bernardo J Foth Jonathan M Wastling
|
PLOS Neglected Tropical Diseases
|
Gene Expression Ratios Lead to Accurate and Translatable Predictors of DR5 Agonism across Multiple Tumor Lineages
|
2015
|
John Monahan
|
Anupama Reddy Joseph D Growney Nick S Wilson Caroline M Emery Jennifer A Johnson Rebecca Ward Kelli A Monaco Joshua Korn Mark D Stump Felipa A Mapa Christopher J Wilson Janine Steiger Jebediah Ledell Richard J Rickles Vic E Myer Seth A Ettenberg Robert Schlegel William R Sellers Heather A Huet Joseph Lehár
|
PLOS ONE
|
RNA-Seq Analysis of Human Trigeminal and Dorsal Root Ganglia with a Focus on Chemoreceptors
|
2015
|
Janine Altmüller Hanns Hatt Günter Gisselmann
|
Caroline Flegel Nicole Schöbel Christian Becker Andrea Tannapfel Günter Gisselmann
|
PLOS ONE
|
Whole Body Melanoma Transcriptome Response in Medaka
|
2015
|
Manfred Schartl
|
Yingjia Shen Katja Maurus Ron Walter Chad Tomlinson Richard K Wilson John Postlethwait Wesley C Warren
|
PLOS ONE
|
OperomeDB: A Database of Condition-Specific Transcription Units in Prokaryotic Genomes
|
2015
|
Sarath Chandra Janga
|
Kashish Chetal Sarath Chandra Janga
|
BioMed Research International
|
Genome-wide transcriptional analysis suggests hydrogenase- and nitrogenase-mediated hydrogen production in Clostridium butyricum CWBI 1009
|
2015
|
Annick Wilmotte
|
Magdalena Calusinska Christopher Hamilton Pieter Monsieurs Gregory Mathy Natalie Leys Fabrice Franck Bernard Joris Philippe Thonart Serge Hiligsmann
|
Biotechnology for Biofuels
|
Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data
|
2015
|
Detlef Weigel Korbinian Schneeberger Vimal Rawat
|
Ahmed Abdelsamad Björn Pietzenuk Danelle K Seymour Daniel Koenig Ales Pecinka
|
PLOS ONE
|
Using RNA-Seq Data to Evaluate Reference Genes Suitable for Gene Expression Studies in Soybean
|
2015
|
Hon-Ming Lam
|
Aldrin Kay-Yuen Yim Johanna Wing-Hang Wong Yee-Shan Ku Hao Qin Ting-Fung Chan
|
PLOS ONE
|
274: Next generation sequencing (RNA-seq) of the human decidual and placental villous transcriptomes in intra-amniotic infection (IAI) induced preterm birth (PTB)
|
2015-01
|
Antonis Rokas
|
William Ackerman Irina Buhimschi Haley Eidem David Rinker Kara Rood Guomao Zhao Taryn Summerfield Mark Landon Catalin Buhimschi
|
American Journal of Obstetrics and Gynecology
|
Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli
|
2015-01-01
|
Thorsten Bischler Alexander Herbig Cynthia Sharma Konrad Förstner
|
Maureen K Thomason Sara K Eisenbart Aixia Zhang Kay Nieselt Gisela Storz
|
Journal of Bacteriology
|
A pan-cancer analysis of prognostic genes.
|
2015-01-01
|
Stefan Bekiranov Wei-Min Chen Anindya Dutta
|
Jordan Anaya Brian Reon Stefan Bekiranov
|
PeerJ
|
The transcription factor Nerfin-1 prevents reversion of neurons into neural stem cells
|
2015-01-01
|
Anthony T. Papenfuss Chen-Fang Weng Louise Y. Cheng
|
Francesca Froldi Milan Szuperak Wei Shi
|
Genes & Development
|
Quantifying entire transcriptomes by aligned RNA-seq data.
|
2015-01-01
|
Raffaele A. Calogero
|
Francesca Zolezzi
|
Methods in Molecular Biology
|
Exploring the RNA editing potential of RNA-Seq data by ExpEdit.
|
2015-01-01
|
Graziano Pesole Anna Maria D'Erchia Ernesto Picardi
|
Mattia D'Antonio Tiziana Castrignanò
|
Methods in Molecular Biology
|
Integrated whole transcriptome and DNA methylation analysis identifies gene networks specific to late-onset Alzheimer's disease.
|
2015-01-01
|
Margaret A. Pericak-Vance
|
Crystal E Humphries Martin A Kohli Lubov Nathanson Patrice Whitehead Gary Beecham Eden Martin Deborah C Mash John Gilbert
|
Journal of Alzheimer's Disease
|
Translating Ribosome Affinity Purification (TRAP) followed by RNA sequencing technology (TRAP-SEQ) for quantitative assessment of plant translatomes.
|
2015-01-01
|
María Eugenia Zanetti
|
Mauricio A Reynoso Piyada Juntawong Marcos Lancia Flavio A Blanco Julia Bailey-Serres
|
Methods in Molecular Biology
|
Nuclear transcriptome profiling of induced pluripotent stem cells and embryonic stem cells identify non-coding loci resistant to reprogramming
|
2015-01-01
|
Piero Carninci
|
Alexandre Fort Daisuke Yamada Kosuke Hashimoto Haruhiko Koseki
|
Cell Cycle
|
Plasticity of DNA methylation in a nerve injury model of pain.
|
2015-01-01
|
Julie M. Cunningham
|
Meike Gölzenleuchter Rahul Kanwar Manal Zaibak Fadi Al Saiegh Theresa Hartung Jana Klukas Regenia L Smalley Maria E Figueroa Gary P Schroth Terry M Therneau Michaela S Banck Andreas S Beutler
|
Epigenetics
|
Interferon regulatory factor 1 and histone H4 acetylation in systemic lupus erythematosus.
|
2015-01-01
|
Michelle A. Petri
|
Yiu Tak Leung Lihua Shi Kelly Maurer Li Song Zhe Zhang Kathleen E Sullivan
|
Epigenetics
|
Identification of secretaglobin Scgb2a1 as a target for developmental reprogramming by BPA in the rat prostate
|
2015-01-01
|
Kurunthachalam Kannan
|
Rebecca Lee Yean Wong Quan Wang Lindsey S Treviño Maarten C Bosland Jing Chen Mario Medvedovic Gail S Prins Shuk-Mei Ho Cheryl Lyn Walker
|
Epigenetics
|
Characterization of the Olfactory Receptors Expressed in Human Spermatozoa
|
2015-01-01
|
Hanns Hatt Günter Gisselmann
|
Caroline Flegel Felix Vogel Adrian Hofreuter Benjamin S P Schreiner Sandra Osthold Sophie Veitinger Christian Becker Norbert H Brockmeyer Michael Muschol Gunther Wennemuth Janine Altmüller Günter Gisselmann
|
Frontiers in molecular biosciences
|
MicroRNA profiling of the bovine alveolar macrophage response to Mycobacterium bovis infection suggests pathogen survival is enhanced by microRNA regulation of endocytosis and lysosome trafficking.
|
2015-01-01
|
Kenneth Bryan Daniel G. Bradley David J. Lynn David E. MacHugh Stephen V. Gordon
|
Peter Vegh David A Magee Nicolas C Nalpas Matthew S McCabe John A Browne Kevin M Conlon
|
Tuberculosis
|
Noncoding regions of C. elegans mRNA undergo selective adenosine to inosine deamination and contain a small number of editing sites per transcript.
|
2015-01-01
|
Michael C Washburn
|
Emily C Wheeler Francois Major Douglas B Rusch Heather A Hundley
|
RNA Biology
|
Investigating CRISPR RNA Biogenesis and Function Using RNA-seq.
|
2015-01-01
|
Jörg Vogel Cynthia Sharma Gaurav Dugar Nadja Heidrich
|
|
Methods in Molecular Biology
|
Integrative genome-wide analysis of the determinants of RNA splicing in kidney renal clear cell carcinoma.
|
2015-01-01
|
Oliver Stegle Cyriac Kandoth Nikolaus Schultz
|
Kjong-Van Lehmann André Kahles William Lee Gunnar Rätsch
|
Pacific Symposium on Biocomputing
|
Analysis of alternative splicing events in custom gene datasets by AStalavista.
|
2015-01-01
|
Sylvain Foissac Michael Sammeth
|
|
Methods in Molecular Biology
|
Computer-assisted annotation of small RNA transcriptomes.
|
2015-01-01
|
Grant W Hennig Wei Yan
|
Nicole Ortogero Dickson Luong
|
Methods in Molecular Biology
|
First insights into the giant panda (Ailuropoda melanoleuca) blood transcriptome: a resource for novel gene loci and immunogenetics.
|
2015-01-02
|
Bisong Yue
|
Lianming Du Wujiao Li Zhenxin Fan Fujun Shen Mingyu Yang Zili Wang Zuoyi Jian Rong Hou Xiuyue Zhang
|
Molecular Ecology Resources
|
Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data.
|
2015-01-05
|
Åslaug Helland Lynnette Fernandez-Cuesta Joachim H Clement Martin Peifer Stefan Haas Gavin Wright Peter Nürnberg Steinar Solberg Martin Vingron Elisabeth Brambilla
|
Ruping Sun Roopika Menon Julie George Susanne Lorenz Leonardo A Meza-Zepeda Dennis Plenker Johannes M Heuckmann Frauke Leenders Thomas Zander Ilona Dahmen Mirjam Koker Jakob Schöttle Roland T Ullrich Christian Becker Henrik Seidel Diana Böhm Friederike Göke Sascha Ansén Prudence A Russell Zoe Wainer Benjamin Solomon Iver Petersen Jörg Sänger Odd-Terje Brustugun Marius Lund-Iversen Reinhard Buettner Jürgen Wolf Sven Perner Roman K Thomas
|
Genome Biology
|
Characterization of human cyclin-dependent kinase 12 (CDK12) and CDK13 complexes in C-terminal domain phosphorylation, gene transcription, and RNA processing
|
2015-01-05
|
Laurence Florens Michael P. Washburn
|
Kaiwei Liang Xin Gao Joshua M Gilmore Edwin Smith Ali Shilatifard
|
Molecular and Cellular Biology
|
rbamtools: an R interface to samtools enabling fast accumulative tabulation of splicing events over multiple RNA-seq samples.
|
2015-01-05
|
Wolfgang Kaisers
|
Wolfgang Kaisers Heiner Schaal Holger Schwender
|
Bioinformatics
|
iRNA-seq: computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data
|
2015-01-06
|
Susanne Mandrup Bjørk Ditlev Larsen Søren Fisker Schmidt
|
Jesper Grud Skat Madsen Anne Loft Ronni Nielsen
|
Nucleic Acids Research
|
Astrovirus VA1/HMO-C: an increasingly recognized neurotropic pathogen in immunocompromised patients
|
2015-01-07
|
Vincent Plagnol Divya Shah Sofia Morfopoulou Julianne R Brown Judith Breuer Waseem Qasim
|
Jonathan Hubb Warren A Emmett Winnie Ip Tony Brooks Simon M L Paine Glenn Anderson Alex Virasami C Y William Tong Duncan A Clark Thomas S Jacques Mike Hubank
|
Clinical Infectious Diseases
|
RNA-Rocket: an RNA-Seq analysis resource for infectious disease research
|
2015-01-07
|
Andrew Warren Omar S. Harb Daniel Lawson Leslie Birgit Vosshall Michael McClelland Cristina Aurrecoechea
|
Brian Brunk Prerak Desai Scott Emrich Gloria I Giraldo-Calderón Deborah Hix Dustin Machi Chunhong Mao Eric Nordberg Maulik Shukla Alice R Wattam Rebecca Will Hyun Seung Yoo Bruno Sobral
|
Bioinformatics
|
Systems biology with high-throughput sequencing reveals genetic mechanisms underlying the metabolic syndrome in the Lyon hypertensive rat.
|
2015-01-08
|
Man Chun John Ma Anne E Kwitek
|
Jinkai Wang Amanda K Mennie Janette M Pettus Yang Xu Lan Lin Matthew G Traxler Jessica Jakoubek Santosh S Atanur Timothy J Aitman Yi Xing
|
Circulation: Cardiovascular Genetics
|
Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli.
|
2015-01-12
|
Xiaoliang Sunney Xie
|
Huiyi Chen Katsuyuki Shiroguchi Hao Ge
|
Molecular Systems Biology
|
Defining the transcriptomic landscape of Candida glabrata by RNA-Seq.
|
2015-01-13
|
Oliver Kurzai Reinhard Guthke
|
Jörg Linde Seána Duggan Michael Weber Fabian Horn Patricia Sieber Daniela Hellwig Konstantin Riege Manja Marz Ronny Martin
|
Nucleic Acids Research
|
Deep sequencing of the murine olfactory receptor neuron transcriptome.
|
2015-01-15
|
Hanns Hatt Günter Gisselmann Christian H. Wetzel Eva M. Neuhaus
|
Ninthujah Kanageswaran Marilen Demond Maximilian Nagel Benjamin S P Schreiner Sabrina Baumgart Paul Scholz Janine Altmüller Christian Becker Julia F Doerner Heike Conrad Sonja Oberland Günter Gisselmann
|
PLOS ONE
|
Reprogramming of Yersinia from virulent to persistent mode revealed by complex in vivo RNA-seq analysis.
|
2015-01-15
|
Kemal Avican Mikael Huss
|
Anna Fahlgren Ann Kathrin Heroven Michael Beckstette Petra Dersch Maria Fällman
|
PLOS Pathogens
|
Blocking miRNA Biogenesis in Adult Forebrain Neurons Enhances Seizure Susceptibility, Fear Memory, and Food Intake by Increasing Neuronal Responsiveness.
|
2015-01-16
|
Angel Barco
|
Anna Fiorenza Jose P Lopez-Atalaya Victor Rovira Marilyn Scandaglia Emilio Geijo-Barrientos
|
Cerebral Cortex
|
Partial dosage compensation in Strepsiptera, a sister group of beetles.
|
2015-01-18
|
Doris Bachtrog
|
Shivani Mahajan
|
Genome Biology and Evolution
|
Integrated modeling of protein-coding genes in the Manduca sexta genome using RNA-Seq data from the biochemical model insect.
|
2015-01-20
|
Xiaolong Cao Haobo Jiang
|
|
Insect Biochemistry and Molecular Biology
|
Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation in Caenorhabditis elegans intestine and muscles.
|
2015-01-20
|
Marco Mangone
|
Stephen M Blazie Cody Babb Henry Wilky Alan Rawls Jin G Park
|
BMC Biology
|
Combining RNA and protein profiling data with network interactions identifies genes associated with spermatogenesis in mouse and human.
|
2015-01-21
|
Bernard Jégou Fatima Smagulova Soazik P Jamin Fabrice G Petit Emmanuelle Becker Frédéric Chalmel Michael Primig
|
Christine Kervarrec Chunxiang Hao Bernard Jégou
|
Biology of Reproduction
|
Claudin multigene family in channel catfish and their expression profiles in response to bacterial infection and hypoxia as revealed by meta-analysis of RNA-Seq datasets.
|
2015-01-21
|
Luyang Sun Shikai Liu
|
Lisui Bao Yun Li Jianbin Feng Zhanjiang Liu
|
Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics
|
Quantitative visualization of alternative exon expression from RNA-seq data.
|
2015-01-22
|
Schraga Schwartz Jill P. Mesirov Helga Thorvaldsdóttir
|
Yarden Katz Eric T Wang Jacob Silterra Bang Wong Helga Thorvaldsdóttir James T Robinson Edoardo M Airoldi Christopher B Burge
|
Bioinformatics
|
RNA-Seq reveals a role for NFAT-signaling in human retinal microvascular endothelial cells treated with TNFα.
|
2015-01-24
|
Colin A Bretz
|
Sara R Savage John S Penn
|
PLOS ONE
|
Blocking yersiniabactin import attenuates extraintestinal pathogenic Escherichia coli in cystitis and pyelonephritis and represents a novel target to prevent urinary tract infection.
|
2015-01-26
|
Harry L T Mobley
|
Ariel R Brumbaugh Sara N Smith Sargurunathan Subashchandrabose Stephanie D Himpsl Tracy H Hazen David A Rasko
|
Infection and Immunity
|
The long intergenic noncoding RNA landscape of human lymphocytes highlights the regulation of T cell differentiation by linc-MAF-4.
|
2015-01-26
|
Sergio Abrignani Massimiliano Pagani
|
Valeria Ranzani Grazisa Rossetti Ilaria Panzeri Alberto Arrigoni Raoul Jp Bonnal Serena Curti Paola Gruarin Elena Provasi Elisa Sugliano Maurizio Marconi Raffaele De Francesco Jens Geginat Beatrice Bodega
|
Nature Immunology
|
Next-Generation Sequencing Reveals Low-Dose Effects of Cationic Dendrimers in Primary Human Bronchial Epithelial Cells
|
2015-01-27
|
Pekka Kohonen Hanna L. Karlsson Bengt Fadeel Neus Feliu Yuning Zhang
|
Neus Feliu Jie Ji Lena Palmberg Andreas Nyström
|
ACS Nano
|
Age dependent changes in the LPS induced transcriptome of bovine dermal fibroblasts occurs without major changes in the methylome
|
2015-01-27
|
Stephanie McKay
|
Benjamin B Green David E Kerr
|
BMC Genomics
|
Computational and analytical challenges in single-cell transcriptomics.
|
2015-01-28
|
Sarah Teichmann John C Marioni Oliver Stegle
|
|
Nature Reviews Genetics
|
The transcriptional stress response of Candida albicans to weak organic acids.
|
2015-01-29
|
Norman Pavelka Michael Poidinger
|
Fabien Cottier Alrina Shin Min Tan Jinmiao Chen Josephine Lum Francesca Zolezzi
|
G3
|
The avian transcriptome response to malaria infection
|
2015-01-29
|
Olof Hellgren Gediminas Valkiūnas Elin Videvall Vaidas Palinauskas
|
Charlie K Cornwallis
|
Molecular Biology and Evolution
|
Saccharomyces cerevisiae transcriptional reprograming due to bacterial contamination during industrial scale bioethanol production.
|
2015-01-30
|
Melline F Noronha Luciana S Mofatto Juan Lucas Argueso Piotr A Mieczkowski
|
Osmar V Carvalho-Netto Marcelo F Carazzolle Paulo J P L Teixeira Luige A L Calderón Gonçalo A G Pereira
|
Microbial Cell Factories
|
RNA-seq SSRs and small RNA-seq SSRs: new approaches in cancer biomarker discovery.
|
2015-01-30
|
Arghavan Alisoltani
|
Arghavan Alisoltani Hossein Fallahi Behrouz Shiran Anousheh Alisoltani Esmaeil Ebrahimie
|
Gene
|
RNA-Seq analysis of rye-grass transcriptomic response to an herbicide inhibiting acetolactate-synthase identifies transcripts linked to non-target-site-based resistance.
|
2015-01-31
|
Jérôme Gouzy
|
Arnaud Duhoux Sébastien Carrère Ludovic Bonin Christophe Délye
|
Plant Molecular Biology
|
Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data.
|
2015-02-01
|
Federico Comoglio
|
Cem Sievers Renato Paro
|
BMC Bioinformatics
|
Fertility and genomics: comparison of gene expression in contrasting reproductive tissues of female cattle.
|
2015-02-01
|
Trudee Fair Niamh Forde John R. Roche
|
P A McGettigan J A Browne S D Carrington M A Crowe B J Loftus A Lohan P Lonergan K Pluta S Mamo A Murphy S W Walsh C J Creevey B Earley S Keady D A Kenny D Matthews M McCabe D Morris A O'Loughlin S Waters M G Diskin A C O Evans
|
Reproduction, Fertility and Development
|
The role of TP53 in miRNA loading onto AGO2 and in remodelling the miRNA-mRNA interaction network.
|
2015-02-01
|
Teresa Colombo Valerio Fulci
|
Jonathan Krell Justin Stebbing Adam Enver Frampton Claudia Carissimi Victoria Harding Alexander De Giorgio Giuseppe Macino Leandro Castellano
|
The Lancet
|
Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers.
|
2015-02-02
|
Laura Clarke Paul Flicek Xabier Agirre Michael I Robson Marien Pascual Avik Datta Renée Beekman David Richardson Giancarlo Castellano Juan R Rodriguez-Madoz José I Martín-Subero Norma C. Gutiérrez José M García-Verdugo Elias Campo Simon Heath Felipe Prosper Eric C Schirmer Reiner Siebert
|
Marta Kulis Victor Segura Anke Bergmann Anna Esteve Angelika Merkel Emanuele Raineri Lidia Agueda Julie Blanc Nuria Russiñol Ana C Queirós Edurne San José-Enériz Fang Fang Elisabeth Guruceaga Joost H A Martens Marta Gut Maria J Calasanz Jesús F San Miguel Ari Melnick Hendrik G Stunnenberg Ivo G Gut
|
Genome Research
|
Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling.
|
2015-02-02
|
Jens Nielsen Mathias Uhlén
|
Pouyan Ghaffari Adil Mardinoglu Anna Asplund Saeed Shoaie Caroline Kampf
|
Scientific Reports
|
The genomic landscape of phaeochromocytoma.
|
2015-02-02
|
Stephen B. Fox Richard W. Tothill Rodney J. Hicks Aidan Flynn Jason Li Grant McArthur Roderick J Clifton-Bligh
|
Diana Benn Bruce Robinson Alison H Trainer Paul James Annette Hogg Kelly Waldeck Joshy George Anthony J Gill
|
The Journal of Pathology
|
Analysis of the Bovine Monocyte-Derived Macrophage Response to Mycobacterium avium Subspecies Paratuberculosis Infection Using RNA-seq.
|
2015-02-04
|
Karsten Hokamp David E. MacHugh Kate Killick
|
Maura E Casey Kieran G Meade Nicolas C Nalpas Maria Taraktsoglou John A Browne Stephen D E Park Eamonn Gormley David A Magee
|
Frontiers in Immunology
|
Comparison of larval and adult Drosophila astrocytes reveals stage-specific gene expression profiles
|
2015-02-04
|
Yanmei Huang
|
Fanny S Ng F Rob Jackson
|
G3
|
Integrating transcriptomics and proteomics to show that tanshinone IIA suppresses cell growth by blocking glucose metabolism in gastric cancer cells.
|
2015-02-05
|
Chia-Lang Hsu Hsuan-Cheng Huang Hsueh-Fen Juan
|
Li-Ling Lin Chieh-Ren Hsia
|
BMC Genomics
|
Computational prediction of molecular pathogen-host interactions based on dual transcriptome data.
|
2015-02-06
|
Reinhard Guthke
|
Sylvie Schulze Sebastian G Henkel Dominik Driesch Jörg Linde
|
Frontiers in Microbiology
|
Vision from next generation sequencing: multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease
|
2015-02-07
|
Anand Swaroop Rinki Ratnapriya
|
Hyun-Jin Yang Tiziana Cogliati Jung-Woong Kim
|
Progress in Retinal and Eye Research
|
Regulatory small RNAs from the 3' regions of bacterial mRNAs.
|
2015-02-09
|
Jörg Vogel Masatoshi Miyakoshi Yanjie Chao
|
|
Current Opinion in Microbiology
|
Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome.
|
2015-02-10
|
Catherine Feuillet Etienne Paux Frédéric Choulet Adriana Alberti
|
Lise Pingault Natasha Glover Patrick Wincker
|
Genome Biology
|
Rapid changes in gene expression direct rapid shifts in intestinal form and function in the Burmese python after feeding.
|
2015-02-10
|
David D. Pollock
|
Audra L Andrew Daren C Card Robert P Ruggiero Drew R Schield Richard H Adams Stephen M Secor Todd A Castoe
|
Physiological Genomics
|
Bridger: a new framework for de novo transcriptome assembly using RNA-seq data.
|
2015-02-11
|
Cody Ashby
|
Zheng Chang Guojun Li Juntao Liu Yu Zhang Deli Liu Carole L Cramer Xiuzhen Huang
|
Genome Biology
|
Distinct Transcriptomic Features are Associated with Transitional and Mature B-Cell Populations in the Mouse Spleen.
|
2015-02-11
|
Daria Salyakina Jean-Christophe Renauld
|
Eden Kleiman Magali De Heusch Kristen L Hoek Joan M Llanes Iris Castro Jacqueline A Wright Emily S Clark Derek M Dykxhoorn Enrico Capobianco Akiko Takeda Wasif N Khan
|
Frontiers in Immunology
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Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues.
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2015-02-12
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Je Hyuk Lee George M. Church
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Evan R Daugharthy Jonathan Scheiman Reza Kalhor Thomas C Ferrante Richard Terry Brian M Turczyk Joyce L Yang Ho Suk Lee John Aach Kun Zhang
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Nature Protocols
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The herbicide linuron inhibits cholesterol biosynthesis and induces cellular stress responses in brown trout.
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2015-02-12
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Eduarda M. Santos Tamsyn M Uren Webster
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Mandy H Perry
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Environmental Science & Technology
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The evolutionary panorama of organ-specifically expressed or repressed orthologous genes in nine vertebrate species.
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2015-02-13
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Zhan Zhou
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Libing Shen Gangbiao Liu Yangyun Zou Zhixi Su Xun Gu
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PLOS ONE
|
Asexual expansion of Toxoplasma gondii merozoites is distinct from tachyzoites and entails expression of non-overlapping gene families to attach, invade, and replicate within feline enterocytes.
|
2015-02-13
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Peter Deplazes
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Adrian B Hehl Walter U Basso Christoph Lippuner Chandra Ramakrishnan Michal Okoniewski Robert A Walker Michael E Grigg Nicholas C Smith
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BMC Genomics
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SplicingTypesAnno: annotating and quantifying alternative splicing events for RNA-Seq data.
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2015-02-14
|
Gaurav Sablok
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Xiaoyong Sun Fenghua Zuo Yuanbin Ru Jiqiang Guo Xiaoyan Yan
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Computer Methods and Programs in Biomedicine
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Transcriptome analysis of thermophilic methylotrophic Bacillus methanolicus MGA3 using RNA-sequencing provides detailed insights into its previously uncharted transcriptional landscape
|
2015-02-14
|
Jörn Kalinowski
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Marta Irla Armin Neshat Trygve Brautaset Christian Rückert Volker F Wendisch
|
BMC Genomics
|
Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli.
|
2015-02-14
|
Vânia Pobre Cecília Maria Arraiano
|
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BMC Genomics
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Differential RNA-seq of Vibrio cholerae identifies the VqmR small RNA as a regulator of biofilm formation
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2015-02-17
|
Cynthia Sharma Kai Papenfort Bonnie Bassler Konrad Förstner
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Jian-Ping Cong
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Proceedings of the National Academy of Sciences of the United States of America
|
DNA methylation-based subtype prediction for pediatric acute lymphoblastic leukemia.
|
2015-02-17
|
Ann-Christine Syvänen Christofer L. Bäcklin Ann Nordgren Jonas Abrahamsson Trond Flægstad Kjeld Schmiegelow Rolf Larsson
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Jessica Nordlund Vasilios Zachariadis Lucia Cavelier Johan Dahlberg Ingegerd Öfverholm Gisela Barbany Elin Övernäs Mats M Heyman Ólafur G Jónsson Jukka Kanerva Josefine Palle Mats G Gustafsson Gudmar Lönnerholm Erik Forestier
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Clinical epigenetics
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Aging-like changes in the transcriptome of irradiated microglia
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2015-02-17
|
Matthew D Li Steven A. Sloan
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Terry C Burns Sunny Kumar Alexander A Morgan Theo D Palmer
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Glia
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Molecular characterization and transcriptome analysis of orange head Chinese cabbage (Brassica rapa L. ssp. pekinensis).
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2015-02-17
|
Barry J Pogson
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Junxiang Zhang Hui Yuan Zhangjun Fei Lugang Zhang Li Li
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Planta
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StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
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2015-02-18
|
Steven Salzberg Mihaela Pertea
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Geo M Pertea Corina M Antonescu Tsung-Cheng Chang Joshua T Mendell
|
Nature Biotechnology
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RNA Seq analysis of the Eimeria tenella gametocyte transcriptome reveals clues about the molecular basis for sexual reproduction and oocyst biogenesis
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2015-02-18
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Peter Deplazes
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Robert A Walker Philippa A Sharman Catherine M Miller Christoph Lippuner Michal Okoniewski Ramon M Eichenberger Chandra Ramakrishnan Fabien Brossier Adrian B Hehl Nicholas C Smith
|
BMC Genomics
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Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq.
|
2015-02-19
|
Sten Linnarsson Peter Lönnerberg Jens Hjerling-Leffler Gioele La Manno Hermany Munguba Charlotte Rolny Gonçalo Castelo-Branco Christer Betsholtz
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Amit Zeisel Ana B Muñoz-Manchado Simone Codeluppi Anna Juréus Sueli Marques Liqun He
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Science
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Flexible expressed region analysis for RNA-seq with derfinder
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2015-02-19
|
Michael I Love Leonardo Collado-Torres Jeffrey T. Leek Ben Langmead Abhinav Nellore
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Alyssa C Frazee Christopher Wilks Rafael A Irizarry Andrew E Jaffe
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The lncRNA DRAIC/PCAT29 Locus Constitutes a Tumor-Suppressive Nexus.
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2015-02-20
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Anindya Dutta Jordan Anaya
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Kouhei Sakurai Brian J Reon
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Molecular Cancer Research
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Inferring bona fide transfrags in RNA-Seq derived-transcriptome assemblies of non-model organisms.
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2015-02-21
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Peter van Heusden Uljana Hesse Alan Christoffels
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Stanley Kimbung Mbandi
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BMC Bioinformatics
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A phylogenetic backbone for Bivalvia: an RNA-seq approach
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2015-02-22
|
Casey W. Dunn Sónia C S Andrade Rüdiger Bieler Gonzalo Giribet John D. Taylor
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Vanessa L González Timothy M Collins Paula M Mikkelsen
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Proceedings of the Royal Society B
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A transcriptome derived female-specific marker from the invasive Western mosquitofish (Gambusia affinis).
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2015-02-23
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Manfred Schartl Shinichi Nakagawa
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Dunja K Lamatsch Sofia Adolfsson Alistair M Senior Guntram Christiansen Maria Pichler Yuichi Ozaki Linnea Smeds
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PLOS ONE
|
Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs.
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2015-02-23
|
John Mattick Peter M Clark Aristeidis G Telonis Yohei Kirino Michelle Lally Karen E Knudsen Isidore Rigoutsos George A. Calin Michael J. Keating
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Eric Londin Phillipe Loher Kevin Quann Yi Jing Eleftheria Hatzimichael Shozo Honda Bharat Ramratnam Clay E S Comstock Leonard Gomella George L Spaeth Lisa Hark L Jay Katz Agnieszka Witkiewicz Abdolmohamad Rostami Sergio A Jimenez Michael A Hollingsworth Jen Jen Yeh Chad A Shaw Steven E McKenzie Paul Bray Peter T Nelson Simona Zupo Katrien Van Roosbroeck Charles Yeo Masaya Jimbo Joseph Cozzitorto Jonathan R Brody Kathleen Delgrosso Paolo Fortina
|
Proceedings of the National Academy of Sciences of the United States of America
|
Polyribosomal RNA-Seq reveals the decreased complexity and diversity of the Arabidopsis translatome.
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2015-02-23
|
Vivek Krishnakumar
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Xingtan Zhang Benjamin D Rosen Haibao Tang Christopher D Town
|
PLOS ONE
|
RNA-seq analysis of the response of the halophyte, Mesembryanthemum crystallinum (ice plant) to high salinity.
|
2015-02-23
|
Hironaka Tsukagoshi Sumie Ishiguro
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Takamasa Suzuki Kouki Nishikawa Sakae Agarie Tetsuya Higashiyama
|
PLOS ONE
|
Overlapping and unique signatures in the proteomic and transcriptomic responses of the nematode Caenorhabditis elegans toward pathogenic Bacillus thuringiensis.
|
2015-02-23
|
Andreas Tholey
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Wentao Yang Katja Dierking Daniela Esser Matthias Leippe Philip Rosenstiel Hinrich Schulenburg
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Developmental and Comparative Immunology
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Guidance for RNA-seq co-expression network construction and analysis: safety in numbers.
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2015-02-24
|
Jesse Gillis
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S Ballouz W Verleyen
|
Bioinformatics
|
RNAseq reveals weed-induced PIF3-like as a candidate target to manipulate weed stress response in soybean.
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2015-02-25
|
Brian Scheffler Ronald Pierik
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David P Horvath Stephanie A Hansen Janet P Moriles-Miller Changhui Yan David E Clay Sharon A Clay
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New Phytologist
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RNA-Seq: Improving Our Understanding of Retinal Biology and Disease.
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2015-02-26
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Eric A Pierce
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Michael H Farkas Elizabeth D Au Maria E Sousa
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Cold Spring Harbor Perspectives in Medicine
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Exon Skipping Is Correlated with Exon Circularization.
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2015-02-26
|
Steven Kelly Argyris Papantonis
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Chris Greenman Peter R Cook
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Journal of Molecular Biology
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The landscape of long noncoding RNAs in the human transcriptome
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2015-03
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John R. Prensner
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Matthew K Iyer Yashar S Niknafs Rohit Malik Udit Singhal Anirban Sahu Yasuyuki Hosono Terrence R Barrette Joseph R Evans Shuang Zhao Anton Poliakov Xuhong Cao Saravana M Dhanasekaran Yi-Mi Wu Dan R Robinson David G Beer Felix Y Feng Hariharan K Iyer Arul M Chinnaiyan
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Nature Genetics
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Open pipelines for integrated tumor genome profiles reveal differences between pancreatic cancer tumors and cell lines
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2015-03
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James Taylor
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Jeremy Goecks Bassel F El-Rayes Shishir K Maithel H Jean Khoury Michael R Rossi
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Cancer Medicine
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Simultaneous generation of many RNA-seq libraries in a single reaction
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2015-03-02
|
Georgia Giannoukos Jenny Chen Alper Kucukural
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Alexander A Shishkin Dawn Ciulla Michele Busby Christine Surka Roby P Bhattacharyya Robert F Rudy Milesh M Patel Nathaniel Novod Deborah T Hung Andreas Gnirke Manuel Garber Mitchell Guttman Jonathan Livny
|
Nature Methods
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Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators.
|
2015-03-03
|
Steven A. Sloan
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Qinghong Yan Sebastien M Weyn-Vanhentenryck Jie Wu Ye Zhang Kenian Chen Jia Qian Wu Ben A Barres Chaolin Zhang
|
Proceedings of the National Academy of Sciences of the United States of America
|
Systems approach for exploring the intricate associations between sweetness, color and aroma in melon fruits
|
2015-03-03
|
Shiri Freilich
|
Shery Lev Itay Gonda Eli Reuveni Vitaly Portnoy Elad Oren Marc Lohse Navot Galpaz Einat Bar Galil Tzuri Guy Wissotsky Ayala Meir Joseph Burger Yaakov Tadmor Arthur Schaffer Zhangjun Fei James Giovannoni Efraim Lewinsohn Nurit Katzir
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BMC Plant Biology
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Discovery of putative small non-coding RNAs from the obligate intracellular bacterium Wolbachia pipientis.
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2015-03-04
|
Jean Popovici Jonathan M Keith
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Megan Woolfit Manjula Algama Elizabeth A McGraw
|
PLOS ONE
|
Activation of an endogenous retrovirus-associated long non-coding RNA in human adenocarcinoma.
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2015-03-05
|
Gregg B Morin
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Ewan A Gibb René L Warren Gavin W Wilson Scott D Brown Gordon A Robertson Robert A Holt
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Genome Medicine
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PATZ1 Is a DNA Damage-Responsive Transcription Factor That Inhibits p53 Function.
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2015-03-09
|
Wilfried Ellmeier Rengul Cetin-Atalay
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Nazli Keskin Emre Deniz Jitka Eryilmaz Manolya Un Tugce Batur Tulin Ersahin Shinya Sakaguchi Batu Erman
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Molecular and Cellular Biology
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Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing.
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2015-03-09
|
Lars K. Nielsen Anton J. Enright John Mattick Marcel E. Dinger Kim-Anh Lê Cao Tommaso Leonardi Giovanni Bussotti Michael B. Clark Joanna Crawford Gethin Thomas
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Tim R Mercer Katelin R Haynes Marion E Brunck Kim-Anh Lê Cao Wendy Y Chen Ryan J Taft
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Nature Methods
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Conditional-ready mouse embryonic stem cell derived macrophages enable the study of essential genes in macrophage function
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2015-03-10
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Oliver Billker
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A T Y Yeung C Hale J Xia P H Tate D Goulding J A Keane S Mukhopadhyay L Forrester W C Skarnes R E W Hancock G Dougan
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Scientific Reports
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DNA methylation dynamics at imprinted genes during bovine pre-implantation embryo development.
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2015-03-10
|
Niamh Forde Alan M O'Doherty Trudee Fair
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David A Magee Lynee C O'Shea Marijke E Beltman Solomon Mamo
|
BMC Developmental Biology
|
Nuclear genomic signals of the 'microturbellarian' roots of platyhelminth evolutionary innovation
|
2015-03-12
|
Andreas Hejnol Gonzalo Giribet
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Christopher E Laumer
|
eLife
|
Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum
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2015-03-12
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Qin Ma
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Wen-Chi Chou Shihui Yang Sha Cao Dawn M Klingeman Steven D Brown Ying Xu
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Nucleic Acids Research
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RNA-seq analysis of Macrobrachium rosenbergii hepatopancreas in response to Vibrio parahaemolyticus infection.
|
2015-03-14
|
Jun Wang
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Rama Rao Ya Bing Zhu Tahereh Alinejad Suma Tiruvayipati Kwai Lin Thong Subha Bhassu
|
Gut Pathogens
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Modifying effects of vitamin E on chlorpyrifos toxicity in atlantic salmon
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2015-03-16
|
Pål A. Olsvik
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Marc H G Berntssen Liv Søfteland
|
PLOS ONE
|
Cyclic GMP balance is critical for malaria parasite transmission from the mosquito to the mammalian host
|
2015-03-17
|
Sebastian A. Mikolajczak
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Viswanathan Lakshmanan Matthew E Fishbaugher Bob Morrison Michael Baldwin Michael Macarulay Ashley M Vaughan Stefan H I Kappe
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mBio
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Transcriptomic profiling of linolenic acid-responsive genes in ROS signaling from RNA-seq data in Arabidopsis.
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2015-03-17
|
Juan C Begara-Morales Francisco J. Corpas
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Capilla Mata-Pérez Beatriz Sánchez-Calvo Francisco Luque Jaime Jiménez-Ruiz María N Padilla Jesús Fierro-Risco Raquel Valderrama Ana Fernández-Ocaña Juan B Barroso
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Frontiers in Plant Science
|
Neuronal identity genes regulated by super-enhancers are preferentially down-regulated in the striatum of Huntington's disease mice.
|
2015-03-17
|
Irwin Davidson Christian Neri
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Mayada Achour Stéphanie Le Gras Céline Keime Frédéric Parmentier François-Xavier Lejeune Anne-Laurence Boutillier Karine Merienne
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Human Molecular Genetics
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Goodness-of-fit tests and model diagnostics for negative binomial regression of RNA sequencing data
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2015-03-18
|
Gu Mi
|
Yanming Di Daniel W Schafer
|
PLOS ONE
|
Escape from X inactivation varies in mouse tissues.
|
2015-03-18
|
Jay Shendure
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Joel B Berletch Wenxiu Ma Fan Yang William S Noble Christine M Disteche Xinxian Deng
|
PLOS Genetics
|
Immunoglobulin transcript sequence and somatic hypermutation computation from unselected RNA-seq reads in chronic lymphocytic leukemia.
|
2015-03-18
|
Albert de la Chapelle John C Byrd
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James S Blachly Amy S Ruppert Weiqiang Zhao Susan Long Joseph Flynn Ian Flinn Jeffrey Jones Kami Maddocks Leslie Andritsos Emanuela M Ghia Laura Z Rassenti Thomas J Kipps
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Proceedings of the National Academy of Sciences of the United States of America
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A comparative study of RNA-seq analysis strategies.
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2015-03-18
|
Ernest Turro Alexandra M. Lewin
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Jürgen Jänes Fengyuan Hu
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Briefings in Bioinformatics
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Gene expression dosage regulation in an allopolyploid fish
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2015-03-19
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Maria Manuela Coelho Manfred Schartl
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I Matos M P Machado
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PLOS ONE
|
The transcriptome of equine peripheral blood mononuclear cells.
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2015-03-19
|
Alicja Pacholewska
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Michaela Drögemüller Jolanta Klukowska-Rötzler Simone Lanz Eman Hamza Emmanouil T Dermitzakis Eliane Marti Vincent Gerber Tosso Leeb Vidhya Jagannathan
|
PLOS ONE
|
Preclinical activity of combined HDAC and KDM1A inhibition in glioblastoma.
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2015-03-19
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Michelle Craig Barton
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Melissa M Singh Blake Johnson Avinashnarayan Venkatarayan Elsa R Flores Jianping Zhang Xiaoping Su Frederick Lang Joya Chandra
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Neuro-Oncology
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GLI2 inhibition abrogates human leukemia stem cell dormancy.
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2015-03-21
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John McPherson Tannishtha Reya
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Anil Sadarangani Gabriel Pineda Kathleen M Lennon Hye-Jung Chun Alice Shih Annelie E Schairer Angela C Court Daniel J Goff Sacha L Prashad Ifat Geron Russell Wall Richard A Moore Minya Pu Lei Bao Amy Jackson-Fisher Michael Munchhof Todd VanArsdale Sheldon R Morris Mark D Minden Karen Messer Hanna K A Mikkola Marco A Marra Thomas J Hudson Catriona H M Jamieson
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Journal of Translational Medicine
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Alternative polyadenylation allows differential negative feedback of human miRNA miR-579 on its host gene ZFR.
|
2015-03-23
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Ludwig Christian Hinske Anamaria Aranha Camargo Lucila Ohno-Machado
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Pedro A F Galante Elisabeth Limbeck Patrick Möhnle Raphael B Parmigiani Simone Kreth
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PLOS ONE
|
SplicePie: a novel analytical approach for the detection of alternative, non-sequential and recursive splicing.
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2015-03-23
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Annemieke Aartsma-Rus Peter A.C. 't Hoen Jeroen Laros
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Irina Pulyakhina Isabella Gazzoli Nisha Verwey Johan T den Dunnen
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Nucleic Acids Research
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A cytochrome P450, OsDSS1, is involved in growth and drought stress responses in rice (Oryza sativa L.).
|
2015-03-24
|
Hideo Matsumura
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Muluneh Tamiru Jerwin R Undan Hiroki Takagi Akira Abe Kakoto Yoshida Jesusa Q Undan Satoshi Natsume Aiko Uemura Hiromasa Saitoh Naoya Urasaki Takao Yokota Ryohei Terauchi
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Plant Molecular Biology
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The RNAi machinery controls distinct responses to environmental signals in the basal fungus Mucor circinelloides.
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2015-03-25
|
Victoriano Garre Simon Moxon
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Francisco E Nicolás Ana Vila María D Cascales Santiago Torres-Martínez Rosa M Ruiz-Vázquez
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BMC Genomics
|
Discovery of molecular markers to discriminate corneal endothelial cells in the human body.
|
2015-03-25
|
Masahito Yoshihara Hideya Kawaji Masayoshi Itoh Kohji Nishida Yoshihide Hayashizaki
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Hiroko Ohmiya Susumu Hara Satoshi Kawasaki FANTOM consortium Motokazu Tsujikawa
|
PLOS ONE
|
Correction: Reprogramming of Yersinia from virulent to persistent mode revealed by complex in vivo RNA-seq analysis.
|
2015-03-25
|
PLOS Pathogens Staff
|
|
PLOS Pathogens
|
Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols.
|
2015-03-26
|
Michael Eisen Peter A Combs
|
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PeerJ
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SplAdder: Identification, quantification and testing of alternative splicing events from RNA-Seq data
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2015-03-26
|
Gunnar Rätsch
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Andre Kahles Cheng Soon Ong Yi Zhong
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Assessing allele-specific expression across multiple tissues from RNA-seq read data
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2015-03-27
|
Tuuli Lappalainen Matti Pirinen Mark McCarthy Peter Donnelly
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Noah A Zaitlen GTEx Consortium Emmanouil T Dermitzakis Manuel A Rivas
|
Bioinformatics
|
Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels
|
2015-03-27
|
Cisca Wijmenga Daria V. Zhernakova Kristin Abbott Patrick Deelen Jingyuan Fu Marc Jan Bonder Morris A Swertz
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Mark de Haan Marijke van der Sijde Juha Karjalainen K Joeri van der Velde Richard J Sinke Lude Franke
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Genome Medicine
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Folate receptor-α (FOLR1) expression and function in triple negative tumors
|
2015-03-27
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Krishna R Kalari Karla V Ballman Zhifu Sun
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Brian M Necela Jennifer A Crozier Cathy A Andorfer Laura Lewis-Tuffin Jennifer M Kachergus Xochiquetzal J Geiger Daniel J Serie Alvaro Moreno-Aspitia Daniel J O'Shannessy Julia D Maltzman Ann E McCullough Barbara A Pockaj Heather E Cunliffe E Aubrey Thompson Edith A Perez
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PLOS ONE
|
Functional characterization of BC039389-GATM and KLK4-KRSP1 chimeric read-through transcripts which are up-regulated in renal cell cancer
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2015-03-27
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Mark Rubin
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Dorothee Pflueger Christiane Mittmann Silvia Dehler Holger Moch Peter Schraml
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BMC Genomics
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BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis.
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2015-03-28
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Yang Pan
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Quan Wan Hayley Dingerdissen Yu Fan Naila Gulzar Tsung-Jung Wu Cheng Yan Haichen Zhang Raja Mazumder
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Database
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The Listeria monocytogenes strain 10403S BioCyc database.
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2015-03-28
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Teresa M Bergholz Kathryn J Boor Martin Wiedmann
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Renato H Orsi
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Database
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Linear mRNA amplification approach for RNAseq from limited amount of RNA.
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2015-03-28
|
Maria A Nagai Dirce Carraro Helena Brentani Renata Pasqualini
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Elisa Napolitano Ferreira Gustavo de Campos Molina Renato David Puga Antônio Hugo José Froes Marques Campos Gustavo Cardoso Guimarães Diana Noronha Nunes Wadih Arap Emmanuel Dias-Neto Ricardo R Brentani
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Gene
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UV irradiation responses in Giardia intestinalis.
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2015-03-28
|
Karin Troell Staffan G Svärd
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Elin Einarsson
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Experimental Parasitology
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Long intervening non-coding RNA 00320 is human brain-specific and highly expressed in the cortical white matter.
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2015-03-29
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Glenda Halliday Eleonora Aronica
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James D Mills Jieqiong Chen Woojin S Kim Paul D Waters Avanita S Prabowo Michael Janitz
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Neurogenetics
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Assessing the consistency of public human tissue RNA-seq data sets.
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2015-03-30
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David Gomez-Cabrero Mikael Huss
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Frida Danielsson Tojo James
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Briefings in Bioinformatics
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The Solanum commersonii Genome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives
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2015-04
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Toni Gabaldón Riccardo Aiese Cigliano Walter Sanseverino Salvador Capella-Gutierrez Riccardo Aversano James M Bradeen Alessandra Dal Molin
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Felice Contaldi Maria Raffaella Ercolano Valentina Grosso Massimo Iorizzo Filippo Tatino Luciano Xumerle Carla Avanzato Alberto Ferrarini Massimo Delledonne Luigi Frusciante Domenico Carputo
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The Plant Cell
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Methyl-CpG Binding Protein 2 Regulates Microglia and Macrophage Gene Expression in Response to Inflammatory Stimuli.
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2015-04-01
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Jonathan Kipnis Tajie H. Harris Stephen D Turner Steffen Jung Igor Smirnov
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James C Cronk Noël C Derecki Emily Ji Yang Xu Aaron E Lampano Wendy Baker Geoffrey T Norris Ioana Marin Nathan Coddington Yochai Wolf Alan Aderem Alexander L Klibanov Vladimir Litvak
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Immunity
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p53 Enables metabolic fitness and self-renewal of nephron progenitor cells
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2015-04-01
|
Melody Baddoo Yumei Feng
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Yuwen Li Jiao Liu Wencheng Li Aaron Brown Melody Baddoo Marilyn Li Thomas Carroll Leif Oxburgh Zubaida Saifudeen
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Development
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A pooled shRNA screen for regulators of primary mammary stem and progenitor cells identifies roles for Asap1 and Prox1.
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2015-04-03
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Ross A. Dickins Matthew E Ritchie Geoffrey J. Lindeman Gordon K Smyth
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Julie M Sheridan Sarah A Best Kun Jiang Tamara J Beck François Vaillant Kevin Liu Jane E Visvader
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BMC Cancer
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EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments.
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2015-04-05
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Christina Kendziorski
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Ning Leng Yuan Li Brian E McIntosh Bao Kim Nguyen Bret Duffin Shulan Tian James A Thomson Colin N Dewey Ron Stewart
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Bioinformatics
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Regulation of early T-lineage gene expression and developmental progression by the progenitor cell transcription factor PU.1.
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2015-04-06
|
Stephen L. Nutt Ellen V. Rothenberg
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Ameya Champhekar Sagar S Damle George Freedman Sebastian Carotta
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Genes & Development
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Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum.
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2015-04-06
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Alexias Safi Gregory E Crawford
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Christopher L Frank Fang Liu Ranjula Wijayatunge Lingyun Song Matthew T Biegler Marty G Yang Christopher M Vockley Charles A Gersbach Anne E West
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Nature Neuroscience
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The level of residual dispersion variation and the power of differential expression tests for RNA-Seq data
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2015-04-07
|
Gu Mi
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Yanming Di
|
PLOS ONE
|
The immune signaling pathways of Manduca sexta
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2015-04-07
|
Haobo Jiang
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Xiaolong Cao Yan He Yingxia Hu Yang Wang Yun-Ru Chen Bart Bryant Rollie J Clem Lawrence M Schwartz Gary Blissard
|
Insect Biochemistry and Molecular Biology
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Characterization of the transcriptome of nascent hair cells and identification of direct targets of the Atoh1 transcription factor
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2015-04-08
|
Andrew K. Groves Huda Zoghbi
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Tiantian Cai Hsin-I Jen Hyojin Kang Tiemo J Klisch
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Journal of Neuroscience
|
Genome-wide analysis of the family 1 glycosyltransferases in cotton.
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2015-04-08
|
Juan Huang
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Juan Huang Chaoyou Pang Shuli Fan Meizhen Song Jiwen Yu Hengling Wei Qifeng Ma Libei Li Chi Zhang Shuxun Yu
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Molecular Genetics and Genomics
|
Purification and Transcriptomic Analysis of Mouse Fetal Leydig Cells Reveals Candidate Genes for Specification of Gonadal Steroidogenic Cells.
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2015-04-08
|
Alicia Oshlack Josephine Bowles Kathryn S McClelland Vincent R Harley Peter Koopman
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Katrina Bell Christian Larney Andrew H Sinclair
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Biology of Reproduction
|
New basal cell carcinoma susceptibility loci.
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2015-04-09
|
Laufey Tryggvadottir Unnur Þorsteinsdóttir Hrefna Johannsdottir Anne Tjønneland Gudmar Thorleifsson Thorunn Rafnar Y Gilaberte Hreinn Stefansson Eduardo Nagore Rajiv Kumar Ulla Vogel Kim Overvad Augustine Kong Peter Rudnai Patrick Sulem Daniel F Gudbjartsson Kári Stefánsson
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Simon N Stacey Hannes Helgason Sigurjon A Gudjonsson Florian Zink Asgeir Sigurdsson Birte Kehr Julius Gudmundsson Bardur Sigurgeirsson Kristrun R Benediktsdottir Kristin Thorisdottir Rafn Ragnarsson Victoria Fuentelsaz Cristina Corredera Matilde Grasa Dolores Planelles Onofre Sanmartin Eugene Gurzau Kvetoslava Koppova Bjørn A Nexø Jon G Jonasson Anna M Kristinsdottir Gisli Masson Olafur T Magnusson Bjarni V Halldorsson José I Mayordomo Jon H Olafsson
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Nature Communications
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New signaling pathways govern the host response to C. albicans infection in various niches.
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2015-04-09
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Jacques Ravel Jennifer Schwartz Amol C Shetty Claire M. Fraser
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Yaoping Liu L Latey Bradford Wenjie Xu Qyunh T Phan Priti Kumari Anup Mahurkar Aaron P Mitchell Scott G Filler Vincent M Bruno
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Genome Research
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Allelic Imbalance Is a Prevalent and Tissue-Specific Feature of the Mouse Transcriptome.
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2015-04-09
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Bernhard Payer David Colognori Ruslan I Sadreyev
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Stefan F Pinter Brian J Beliveau Eda Yildirim Chao-Ting Wu Jeannie T Lee
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Genetics
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Decreased expression of endogenous feline leukemia virus in cat lymphomas: a case control study.
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2015-04-10
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Reinhard Ertl Fritz Sedlazeck Regina Hofmann-Lehmann
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Milica Krunic Benedikt Hagen Arndt von Haeseler Dieter Klein
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BMC Veterinary Research
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High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin.
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2015-04-13
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Kaia Achim Daria Gavriouchkina Luis R. Saraiva John C Marioni
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Jean-Baptiste Pettit Tomas Larsson Detlev Arendt
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Nature Biotechnology
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Spatial reconstruction of single-cell gene expression data.
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2015-04-13
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Aviv Regev Rahul Satija Jeffrey A Farrell
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David Gennert Alexander F Schier
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Nature Biotechnology
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Identification of non-coding RNAs associated with telomeres using a combination of enChIP and RNA sequencing
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2015-04-13
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Hodaka Fujii Daisuke Okuzaki
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Toshitsugu Fujita Miyuki Yuno Rieko Ohki
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PLOS ONE
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Asymmetric transcript discovery by RNA-seq in C. elegans blastomeres identifies neg-1, a gene important for anterior morphogenesis.
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2015-04-13
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Erin Osborne Bob Goldstein
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Jay C Zhang Adam D Werts Jason D Lieb
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PLOS Genetics
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Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum.
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2015-04-13
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Gad Shaulsky
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Rafael David Rosengarten Balaji Santhanam Danny Fuller Mariko Katoh-Kurasawa William F Loomis Blaz Zupan
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BMC Genomics
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ChIP-Seq and RNA-Seq analyses identify components of the Wnt and Fgf signaling pathways as Prep1 target genes in mouse embryonic stem cells.
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2015-04-13
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Miguel Torres Hans-Jörg Warnatz Marie-Laure Yaspo
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Audrey Laurent Manuela Calabrese Marie-Laure Yaspo Vsevolod Tkachuk Francesco Blasi Dmitry Penkov
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PLOS ONE
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A serine-arginine-rich (SR) splicing factor modulates alternative splicing of over a thousand genes in Toxoplasma gondii.
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2015-04-13
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Giel G van Dooren Stuart A Ralph
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Lee M Yeoh Christopher D Goodman Nathan E Hall Geoffrey I McFadden
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Nucleic Acids Research
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RNA-Seq analysis of the wild barley (H. spontaneum) leaf transcriptome under salt stress.
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2015-04-13
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Ahmed Bahieldin
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Ahmed Atef Jamal S M Sabir Nour O Gadalla Sherif Edris Ahmed M Alzohairy Nezar A Radhwan Mohammed N Baeshen Ahmed M Ramadan Hala F Eissa Sabah M Hassan Nabih A Baeshen Osama Abuzinadah Magdy A Al-Kordy Fotouh M El-Domyati Robert K Jansen
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Comptes Rendus Biologies
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Evaluation of two statistical methods provides insights into the complex patterns of alternative polyadenylation site switching
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2015-04-14
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Yonggui Fu Jie Li
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Rui Li Leiming You Anlong Xu Shengfeng Huang
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PLOS ONE
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NMD3 regulates both mRNA and rRNA nuclear export in African trypanosomes via an XPOI-linked pathway.
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2015-04-14
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Paul Capewell Isabel Roditi Alasdair Ivens
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Melanie Bühlmann Pegine Walrad Eva Rico Arunasalam Naguleswaran Keith R Matthews
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Nucleic Acids Research
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Identification of candidate mimicry proteins involved in parasite-driven phenotypic changes
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2015-04-15
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Nadia Aubin-Horth Mahesh Panchal Iain Barber
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Francois Olivier Hebert Luke Phelps Irene Samonte Stephan Grambauer Martin Kalbe Christian R Landry
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Parasites & Vectors
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Antagonistic regulation of mRNA expression and splicing by CELF and MBNL proteins.
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2015-04-16
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Amanda J Ward Jimena Giudice
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Eric T Wang Jennifer M Cherone Thomas T Wang Daniel J Treacy Nicole J Lambert Peter Freese Tanvi Saxena Thomas A Cooper Christopher B Burge
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Genome Research
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Widespread exon skipping triggers degradation by nuclear RNA surveillance in fission yeast
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2015-04-16
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Jürg Bähler
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Danny A Bitton Sophie R Atkinson Charalampos Rallis Graeme C Smith David A Ellis Yuan Y C Chen Michal Malecki Sandra Codlin Jean-François Lemay Cristina Cotobal François Bachand Samuel Marguerat Juan Mata Jürg Bähler
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Genome Research
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SF3B1 association with chromatin determines splicing outcomes.
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2015-04-16
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Arnab Datta
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Nir Kfir Galit Lev-Maor Ohad Glaich Adi Alajem Siu K Sze Eran Meshorer Gil Ast
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Cell Reports
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First description of small proteins encoded by spRNAs in Methanosarcina mazei strain Gö1.
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2015-04-16
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Ruth Schmitz-Streit Dörte Becher
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Daniela Prasse Jens Thomsen Rebecca De Santis Jan Muntel
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Biochimie
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PGTools: A Software Suite for Proteogenomic Data Analysis and Visualization.
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2015-04-17
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Sean M. Grimmond Nicola J Waddell Anil K Madugundu
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Shivashankar H Nagaraj Scott Wood Alun Jones Ramya A Mandyam Katia Nones John V Pearson
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Journal of Proteome Research
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ContextMap 2: fast and accurate context-based RNA-seq mapping
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2015-04-17
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Ralf Zimmer
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Thomas Bonfert Evelyn Kirner Gergely Csaba Caroline C Friedel
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BMC Bioinformatics
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High throughput profiling of the cotton bollworm Helicoverpa armigera immunotranscriptome during the fungal and bacterial infections
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2015-04-18
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Haobo Jiang
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Guang-Hua Xiong Long-Sheng Xing Zhe Lin Tusar T Saha Chengshu Wang Zhen Zou
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BMC Genomics
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Transcriptomics-based analysis using RNA-Seq of the coconut (Cocos nucifera) leaf in response to yellow decline phytoplasma infection.
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2015-04-18
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Mark Ziemann
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Naghmeh Nejat David M Cahill Ganesan Vadamalai James Rookes Neda Naderali
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Molecular Genetics and Genomics
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Transcriptome analysis reveals the host response to Schmallenberg virus in bovine cells and antagonistic effects of the NSs protein
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2015-04-19
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Alain Kohl
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Anne-Lie Blomström Quan Gu Gerald Barry Gavin Wilkie Jessica K Skelton Margaret Baird Melanie McFarlane Esther Schnettler Richard M Elliott Massimo Palmarini
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BMC Genomics
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A RNA-Seq Analysis of the Rat Supraoptic Nucleus Transcriptome: Effects of Salt Loading on Gene Expression.
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2015-04-21
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David Murphy
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Kory R Johnson C C T Hindmarch Yasmmyn D Salinas YiJun Shi Michael Greenwood See Ziau Hoe Harold Gainer
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PLOS ONE
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Functional and mechanistic studies of XPC DNA-repair complex as transcriptional coactivator in embryonic stem cells.
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2015-04-21
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Robert Tjian Claudia Cattoglio
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Elisa T Zhang Ivan Grubisic Kunitoshi Chiba Yick W Fong
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Proceedings of the National Academy of Sciences of the United States of America
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edgeRun: an R package for sensitive, functionally relevant differential expression discovery using an unconditional exact test.
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2015-04-21
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Winston Hide Rory Kirchner
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Emmanuel Dimont Jiantao Shi
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Bioinformatics
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From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data.
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2015-04-22
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Thomas P Mawhinney
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Jilong Li Jie Hou Lin Sun Jordan Maximillian Wilkins Yuan Lu Chad E Niederhuth Benjamin Ryan Merideth Valeri V Mossine C Michael Greenlief John C Walker William R Folk Mark Hannink Dennis B Lubahn James A Birchler Jianlin Cheng
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PLOS ONE
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Hepatitis D Virus Infection of Mice Expressing Human Sodium Taurocholate Co-transporting Polypeptide
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2015-04-22
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Wenhui Li Jianhua Sui
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Wenhui He Bijie Ren Fengfeng Mao Zhiyi Jing Yunfei Li Yang Liu Bo Peng Huan Yan Yonghe Qi Yinyan Sun Ju-Tao Guo Fengchao Wang
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PLOS Pathogens
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Integrated RNA-Seq and sRNA-Seq Analysis Identifies Chilling and Freezing Responsive Key Molecular Players and Pathways in Tea Plant (Camellia sinensis).
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2015-04-22
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Chao Zheng
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Lei Zhao Yu Wang Jiazhi Shen Yinfei Zhang Sisi Jia Yusheng Li Zhaotang Ding
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PLOS ONE
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Functional analysis and transcriptomic profiling of iPSC-derived macrophages and their application in modeling Mendelian disease.
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2015-04-22
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Muredach P. Reilly
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Hanrui Zhang Chenyi Xue Rhia Shah Kate Bermingham Christine C Hinkle Wenjun Li Amrith Rodrigues Jennifer Tabita-Martinez John S Millar Marina Cuchel Evanthia E Pashos Ying Liu Ruilan Yan Wenli Yang Sager J Gosai Daniel VanDorn Stella T Chou Brian D Gregory Edward E Morrisey Mingyao Li Daniel J Rader
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Circulation Research
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Individual genome sequencing identified a novel enhancer element in exon 7 of the CSFR1 gene by shift of expressed allele ratios.
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2015-04-22
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Ekaterina E Khrameeva S Zhenilo
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S Tsygankova N Zhigalova A Mazur E Prokhortchouk
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Gene
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ZNF804A Transcriptional Networks in Differentiating Neurons Derived from Induced Pluripotent Stem Cells of Human Origin
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2015-04-23
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Deyou Zheng
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Jian Chen Mingyan Lin Anastasia Hrabovsky Erika Pedrosa Jason Dean Swati Jain Herbert M Lachman
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PLOS ONE
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De Novo Reconstruction of Adipose Tissue Transcriptomes Reveals Long Non-coding RNA Regulators of Brown Adipocyte Development.
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2015-04-23
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Nikolai Slavov Harvey Lodish
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Juan R Alvarez-Dominguez Zhiqiang Bai Dan Xu Bingbing Yuan Kinyui Alice Lo Myeong Jin Yoon Yen Ching Lim Marko Knoll Shuai Chen Chen Peng Lei Sun
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Cell Metabolism
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Imprinted expression in cystic embryoid bodies shows an embryonic and not an extra-embryonic pattern
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2015-04-24
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Christoph Bock Sylvia Knapp Josef M Penninger Tomasz Kuliński Paul Datlinger
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M Rita T Casari Philipp M Guenzl Daniel Wenzel Daniel Andergassen Anastasiya Hladik Matthias Farlik H-Christian Theussl Denise P Barlow Quanah J Hudson
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Developmental Biology
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PtaRHE1, a Populus tremula × Populus alba RING-H2 protein of the ATL family, has a regulatory role in secondary phloem fibre development.
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2015-04-25
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Wout Boerjan Annegret Kohler
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Fabien Baldacci-Cresp Jihad Moussawi Jean-Charles Leplé Rebecca Van Acker Julie Candiracci Laure Twyffels Antanas V Spokevicius Gerd Bossinger Françoise Laurans Nicole Brunel Marjorie Vermeersch Mondher El Jaziri Marie Baucher
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The Plant Journal
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Tet3 regulates synaptic transmission and homeostatic plasticity via DNA oxidation and repair
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2015-04-27
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Guo-Li Ming Hongjun Song Daniel Geschwind
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Huimei Yu Yijing Su Jaehoon Shin Chun Zhong Junjie U Guo Yi-Lan Weng Fuying Gao Giovanni Coppola
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Nature Neuroscience
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High-performance probes for light and electron microscopy
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2015-04-27
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Gerald M. Rubin Megan E Williams Erik B. Bloss Brian P. English
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Sarada Viswanathan Timothy J Stasevich Colenso M Speer Aljoscha Nern Barret D Pfeiffer Bryan M Hooks Wei-Ping Li Teresa Tian Gilbert L Henry John J Macklin Ronak Patel Charles R Gerfen Xiaowei Zhuang Yalin Wang Loren L Looger
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Nature Methods
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Polyester: simulating RNA-seq datasets with differential transcript expression.
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2015-04-28
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Jeffrey T. Leek Andrew E Jaffe Ben Langmead
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Alyssa C Frazee
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Bioinformatics
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New Noncoding Lytic Transcripts Derived from the Epstein-Barr Virus Latency Origin of Replication, oriP, Are Hyperedited, Bind the Paraspeckle Protein, NONO/p54nrb, and Support Viral Lytic Transcription.
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2015-04-29
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Melody Baddoo Michael J Strong Tina O'Grady Erik K Flemington
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Subing Cao Walter Moss Monica Concha Xia Wang Yi Yu Melody Baddoo Kun Zhang Claire Fewell Zhen Lin Yan Dong
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Journal of Virology
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Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses.
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2015-04-29
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Gordon K Smyth
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Ruijie Liu Aliaksei Z Holik Shian Su Natasha Jansz Kelan Chen Huei San Leong Marnie E Blewitt Marie-Liesse Asselin-Labat Matthew E Ritchie
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Nucleic Acids Research
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Oviduct-Embryo Interactions in Cattle: Two-Way Traffic or a One-Way Street?
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2015-04-29
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Niamh Forde Thomas E. Spencer Alfonso Gutierrez-Adan Gregory W Burns V Maillo Peadar Ó Gaora D Rizos
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Urban Besenfelder Vitezslav Havlicek Patrick Lonergan
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Biology of Reproduction
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Coronary Artery Disease Associated Transcription Factor TCF21 Regulates Smooth Muscle Precursor Cells That Contribute to the Fibrous Cap
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2015-05
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Thomas Quertermous Sylvia T Nurnberg Ivan Carcamo-Oribe Michelle D Tallquist Lars Maegdefessel Ulf Hedin
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Karen Cheng Azad Raiesdana Ramendra Kundu Clint L Miller Juyong B Kim Komal Arora Yiqin Xiong Nikhil Tellakula Vivek Nanda Nikitha Murthy William A Boisvert Ljubica Perisic Silvia Aldi Milos Pjanic Gary K Owens
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PLOS Genetics
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Mutant U2AF1 Expression Alters Hematopoiesis and Pre-mRNA Splicing In Vivo.
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2015-05-01
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Sean D McGrath Malachi Griffith Timothy A. Graubert Catrina Fronick
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Cara Lunn Shirai James N Ley Brian S White Sanghyun Kim Justin Tibbitts Jin Shao Matthew Ndonwi Brian Wadugu Eric J Duncavage Theresa Okeyo-Owuor Tuoen Liu Vincent Magrini Robert S Fulton Michelle O'Laughlin Matthew J Walter
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Cancer Cell
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Integrative Analysis of Normal Long Intergenic Non-Coding RNAs in Prostate Cancer.
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2015-05-01
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Saurabh Gupta
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Pushpinder Bawa Sajna Zackaria Mohit Verma R Srivatsan Bibha Chaudhary Subhashini Srinivasan
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PLOS ONE
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Perturbations of heart development and function in cardiomyocytes from human embryonic stem cells with trisomy 21.
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2015-05-01
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Stylianos Antonarakis Outi Hovatta Laura Sartiani Marisa Jaconi Biljana Dumevska
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Alexis Bosman Audrey Letourneau Martina Del Lungo Flavio Ronzoni Rostyslav Kuziakiv Virpi Tohonen Marco Zucchelli Federico Santoni Michel Guipponi Outi Hovatta
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Stem Cells
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Telomere dysfunction drives aberrant hematopoietic differentiation and myelodysplastic syndrome.
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2015-05-01
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Marianna D'Anca Matteo Marchesini Paola Storti Simona Colla Marcos Estecio Nicola Giuliani Lynda Chin Hagop Kantarjian Guillermo Garcia-Manero
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Derrick Sek Tong Ong Yamini Ogoti Nipun A Mistry Karen Clise-Dwyer Sonny A Ang Andrea Viale Kathryn Ruisaard Irene Ganan Gomez Christopher A Bristow David C Weksberg Yan Wing Ho Baoli Hu Giannicola Genovese Piergiorgio Pettazzoni Asha S Multani Shan Jiang Sujun Hua Michael C Ryan Alessandro Carugo Luigi Nezi Yue Wei Hui Yang Li Zhang Sarah Gaddis Ting Gong James W Horner Timothy P Heffernan Philip Jones Laurence J N Cooper Han Liang Y Alan Wang Carlos Bueso-Ramos Ronald A DePinho
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Cancer Cell
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regionReport: Interactive reports for region-level and feature-level genomic analyses.
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2015-05-01
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Leonardo Collado-Torres Andrew E Jaffe Jeffrey T. Leek
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F1000Research
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A bioinformatics approach to distinguish plant parasite and host transcriptomes in interface tissue by classifying RNA-Seq reads.
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2015-05-03
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Tomoaki Sakamoto
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Daisuke Ikeue Christian Schudoma Wenna Zhang Yoshiyuki Ogata Tetsuya Kurata Takeshi Furuhashi Friedrich Kragler Koh Aoki
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Plant Methods
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Bariatric Surgery Induces Disruption in Inflammatory Signaling Pathways Mediated by Immune Cells in Adipose Tissue: A RNA-Seq Study
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2015-05-04
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Yuna Blum Karine Clément
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Christine Poitou Claire Perret François Mathieu Vinh Truong Hervé Durand Rohia Alili Nadjim Chelghoum Véronique Pelloux Judith Aron-Wisnewsky Adriana Torcivia Jean-Luc Bouillot Brian W Parks Ewa Ninio Laurence Tiret
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PLOS ONE
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The Transcriptome and Terpene Profile of Eucalyptus grandis Reveals Mechanisms of Defense Against the Insect Pest, Leptocybe invasa.
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2015-05-05
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Bernard Slippers
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Caryn N Oates Carsten Külheim Alexander A Myburg Sanushka Naidoo
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Plant and Cell Physiology
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Identification of genes involved in the phosphate metabolism in Cryptococcus neoformans.
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2015-05-05
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Yu Kanesaki
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Akio Toh-e Misako Ohkusu Hao-Man Li Kiminori Shimizu Azusa Takahashi-Nakaguchi Toru Gonoi Susumu Kawamoto Hirofumi Yoshikawa Masafumi Nishizawa
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Fungal Genetics and Biology
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MIsoMine: a genome-scale high-resolution data portal of expression, function and networks at the splice isoform level in the mouse
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2015-05-07
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Gil Omenn
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Hong-Dong Li Yuanfang Guan
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Database
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Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species.
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2015-05-07
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Igor Ulitsky
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Hadas Hezroni David Koppstein Matthew G Schwartz Alexandra Avrutin David P Bartel
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Cell Reports
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Rail-RNA: Scalable analysis of RNA-seq splicing and coverage
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2015-05-07
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Jeffrey T. Leek Ben Langmead Abhinav Nellore
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Leonardo Collado-Torres Andrew E Jaffe José Alquicira-Hernández Jacob Pritt James Morton
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Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea.
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2015-05-08
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Gustavo Rodriguez-Esteban Emili Salo Josep F. Abril
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Alejandro González-Sastre José Ignacio Rojo-Laguna
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BMC Genomics
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Combining GWAS and RNA-Seq Approaches for Detection of the Causal Mutation for Hereditary Junctional Epidermolysis Bullosa in Sheep.
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2015-05-08
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Gwenola Tosser-Klopp Julio Benavides Gwenola Tosser-Klopp Juan J Arranz Valentín Pérez
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Aroa Suárez-Vega Beatriz Gutiérrez-Gil Christophe Klopp Stephen J Keennel
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PLOS ONE
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Gene expression associated with white syndromes in a reef building coral, Acropora hyacinthus.
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2015-05-09
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Mikhail Matz
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Rachel M Wright Galina V Aglyamova Eli Meyer
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BMC Genomics
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Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data.
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2015-05-12
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Angelika N Christ Nicole Cloonan Sean M. Grimmond
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David L A Wood Katia Nones Anita Steptoe Ivon Harliwong Felicity Newell Timothy J C Bruxner David Miller
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PLOS ONE
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Probe Region Expression Estimation for RNA-Seq Data for Improved Microarray Comparability.
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2015-05-12
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Antti Honkela
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Karolis Uziela Antti Honkela
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PLOS ONE
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Contrasting host-pathogen interactions and genome evolution in two generalist and specialist microsporidian pathogens of mosquitoes.
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2015-05-13
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Christina A Cuomo Hiten D. Madhani James J. Becnel
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Christopher A Desjardins Neil D Sanscrainte Jonathan M Goldberg David Heiman Sarah Young Qiandong Zeng
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Nature Communications
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Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data.
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2015-05-14
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Frank Emmert-Streib
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Ricardo de Matos Simoes Sabine Dalleau Kate E Williamson
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BMC Systems Biology
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GermlncRNA: a unique catalogue of long non-coding RNAs and associated regulations in male germ cell development.
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2015-05-17
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Tin-Lap Lee
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Alfred Chun-Shui Luk Huayan Gao Sizhe Xiao Jinyue Liao Daxi Wang Jiajie Tu Owen M Rennert Wai-Yee Chan
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Database
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Splice variants and regulatory networks associated with host resistance to the intestinal worm Cooperia oncophora in cattle.
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2015-05-18
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Steven G Schroeder Weizhong Li Cong-Jun Li
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Robert W Li Sitao Wu
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Veterinary Parasitology
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Ratios of Four STAT3 Splice Variants in Human Eosinophils and Diffuse Large B Cell Lymphoma Cells
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2015-05-18
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Stephane Esnault
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Keren B Turton Douglas S Annis Lixin Rui Deane F Mosher
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PLOS ONE
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Genome-wide analysis links NFATC2 with asparaginase hypersensitivity.
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2015-05-18
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Seth Karol Laura B Ramsey Charles G. Mullighan Ching-Hon Pui Stephen P Hunger
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Christian A Fernandez Colton Smith Wenjian Yang Chunxu Qu Eric Larsen W Paul Bowman Chengcheng Liu Tamara Chang Mignon L Loh Elizabeth A Raetz Naomi J Winick William L Carroll Sima Jeha William E Evans Meenakshi Devidas Mary V Relling
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Blood
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Chlamydomonas reinhardtii cells adjust the metabolism to maintain viability in response to atrazine stress.
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2015-05-19
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Marta Esperanza Marta Seoane Concepción Herrero Carmen Rioboo Ángeles Cid
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Aquatic Toxicology
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Effect of ovarian hormones on the healthy equine uterus: a global gene expression analysis.
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2015-05-20
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Neil D. Young Natali Krekeler
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Christina D Marth Lisa Y Glenton Drew M Noden Glenn F Browning
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Reproduction, Fertility and Development
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Diffusion maps for high-dimensional single-cell analysis of differentiation data.
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2015-05-21
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Q85197310 Florian Buettner Fabian J. Theis
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Laleh Haghverdi
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Bioinformatics
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Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations
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2015-05-21
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Chris Ponting Caroline Oedekoven Fernando J Calero-Nieto Florian Buettner Iain C Macaulay David Kent Fabian J. Theis Anthony R Green Berthold Göttgens Carlos Caldas
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Nicola K Wilson Mona Shehata Manuel Sánchez Castillo Evangelia Diamanti Reiner Schulte Thierry Voet John Stingl
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Cell Stem Cell
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Effects of Tris(1,3-dichloro-2-propyl) Phosphate (TDCPP) in Tetrahymena Thermophila: Targeting the Ribosome.
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2015-05-21
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John P Giesy
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Jing Li Liqin Yu Guangyu Li Chunsheng Liu
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Scientific Reports
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Alzheimer disease (AD) specific transcription, DNA methylation and splicing in twenty AD associated loci
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2015-05-21
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Margaret A. Pericak-Vance
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Crystal Humphries Martin A Kohli Patrice Whitehead Deborah C Mash John Gilbert
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Molecular and Cellular Neuroscience
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TRUFA: A User-Friendly Web Server for de novo RNA-seq Analysis Using Cluster Computing.
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2015-05-24
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Julio Rozas Rafael Zardoya
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Etienne Kornobis Luis Cabellos Fernando Aguilar Cristina Frías-López Jesús Marco
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Evolutionary Bioinformatics
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RNA-seq Transcriptional Profiling of an Arbuscular Mycorrhiza Provides Insights into Regulated and Coordinated Gene Expression in Lotus japonicus and Rhizophagus irregularis.
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2015-05-25
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Masayoshi Kawaguchi
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Yoshihiro Handa Hiroyo Nishide Naoya Takeda Yutaka Suzuki Katsuharu Saito
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Plant and Cell Physiology
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A Comprehensive Analysis of Codon Usage Patterns in Blunt Snout Bream (Megalobrama amblycephala) Based on RNA-Seq Data
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2015-05-26
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Shaokui Yi
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Xiaoke Duan Xianwu Guo Weimin Wang
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International Journal of Molecular Sciences
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Systematic transcriptome analysis reveals tumor-specific isoforms for ovarian cancer diagnosis and therapy
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2015-05-26
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Christopher DeBoever Frazer KA
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Christian L Barrett Kristen Jepsen Cheryl C Saenz Dennis A Carson
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Proceedings of the National Academy of Sciences of the United States of America
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nagnag: Identification and quantification of NAGNAG alternative splicing using RNA-Seq data.
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2015-05-27
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Gaurav Sablok
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Xiaoyan Yan Gang Feng Jiaxin Ma Hongwei Zhao Xiaoyong Sun
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FEBS Letters
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Cellular microRNA miR-26a suppresses replication of porcine reproductive and respiratory syndrome virus by activating innate antiviral immunity.
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2015-05-27
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Yuhai Bi
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Xiaojuan Jia Jing Li Qing Xie Hanchun Yang Wenjun Liu
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Scientific Reports
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Towards Elucidating Carnosic Acid Biosynthesis in Lamiaceae: Functional Characterization of the Three First Steps of the Pathway in Salvia fruticosa and Rosmarinus officinalis
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2015-05-28
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Q85232174 Irini Pateraki Fani Chatzopoulou Albert Ferrer Alain Tissier Sotirios Kampranis Angelos K Kanellis
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Dimitra Papaefthimiou Kathleen Brückner Ric C H de Vos Constantinos A Tsoleridis Dimitra Katsarou Antigoni Papanikolaou Eleni Dimitriadou Stefanos Kostas David Manzano Ulschan Scheler Antonios M Makris
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PLOS ONE
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Identification of regulatory network hubs that control lipid metabolism in Chlamydomonas reinhardtii
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2015-05-28
|
Leslie M. Hicks
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Mahmoud Gargouri Jeong-Jin Park F Omar Holguin Min-Jeong Kim Hongxia Wang Rahul R Deshpande Yair Shachar-Hill David R Gang
|
Journal of Experimental Botany
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Tracking global gene expression responses in T cell differentiation.
|
2015-05-28
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Vincent Piras Kumar Selvarajoo
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Oriane Simeoni Masaru Tomita
|
Gene
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Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators
|
2015-05-29
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Alexias Safi Gregory E Crawford
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Lauren R Polstein Pablo Perez-Pinera D Dewran Kocak Christopher M Vockley Peggy Bledsoe Lingyun Song Timothy E Reddy Charles A Gersbach
|
Genome Research
|
Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus agalactiae
|
2015-05-30
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Isabelle Rosinski-Chupin Patrick Trieu-Cuot Philippe Bouloc Marie-Agnès Dillies Marie-Frédérique Lartigue
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Elisabeth Sauvage Odile Sismeiro Adrien Villain Violette Da Cunha Marie-Elise Caliot Philippe Glaser
|
BMC Genomics
|
Functionally defined therapeutic targets in diffuse intrinsic pontine glioma
|
2015-06
|
Wenchao Sun Jacques Grill Michelle Monje Javad Nazarian Maryam Fouladi Cynthia Hawkins
|
Catherine S Grasso Yujie Tang Nathalene Truffaux Noah E Berlow Lining Liu Marie-Anne Debily Michael J Quist Lara E Davis Elaine C Huang Pamelyn J Woo Anitha Ponnuswami Spenser Chen Tessa B Johung Mari Kogiso Yuchen Du Lin Qi Yulun Huang Marianne Hütt-Cabezas Katherine E Warren Ludivine Le Dret Paul S Meltzer Hua Mao Martha Quezado Dannis G van Vuurden Jinu Abraham Matthew N Svalina Nicholas Wang Marta M Alonso Eric H Raabe Esther Hulleman Paul T Spellman Xiao-Nan Li Charles Keller Ranadip Pal
|
Nature Medicine
|
3USS: a web server for detecting alternative 3'UTRs from RNA-seq experiments
|
2015-06-01
|
Anna Tramontano
|
Loredana Le Pera Mariagiovanna Mazzapioda
|
Bioinformatics
|
FourCSeq: analysis of 4C sequencing data.
|
2015-06-01
|
Yad Ghavi-Helm Wolfgang Huber Simon Anders Eileen E. M. Furlong
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Felix A Klein Tibor Pakozdi
|
Bioinformatics
|
FunPat: function-based pattern analysis on RNA-seq time series data.
|
2015-06-01
|
Francesca Finotello Tiziana Sanavia
|
Barbara Di Camillo
|
BMC Genomics
|
Condensin-driven remodelling of X chromosome topology during dosage compensation.
|
2015-06-01
|
Rachel Patton McCord
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Emily Crane Qian Bian Bryan R Lajoie Bayly S Wheeler Edward J Ralston Satoru Uzawa Job Dekker Barbara J Meyer
|
Nature
|
Dynamics of GATA1 binding and expression response in a GATA1-induced erythroid differentiation system
|
2015-06-01
|
Ross C Hardison Christapher S Morrissey Mitchell J Weiss
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Deepti Jain Tejaswini Mishra Belinda M Giardine Cheryl A Keller Susan Magargee Christine M Dorman Maria Long
|
Genomics Data
|
RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application.
|
2015-06-01
|
Matteo Pallocca Anna Maria D'Erchia Ernesto Picardi Raffaele A. Calogero
|
Mattia D'Antonio Paolo D'Onorio De Meo Tiziana Castrignanò Graziano Pesole
|
BMC Genomics
|
Elucidating steroid alkaloid biosynthesis in Veratrum californicum: production of verazine in Sf9 cells.
|
2015-06-01
|
Gane Ka-Shu Wong Megan M Augustin
|
Dan R Ruzicka Ashutosh K Shukla Jörg M Augustin Courtney M Starks Mark O'Neil-Johnson Michael R McKain Bradley S Evans Matt D Barrett Ann Smithson Michael K Deyholos Patrick P Edger J Chris Pires James H Leebens-Mack David A Mann Toni M Kutchan
|
The Plant Journal
|
Detecting disease genes of non-small lung cancer based on consistently differential interactions.
|
2015-06-01
|
Xiaoping Liu Tao Zeng
|
Qianqian Shi William Wang Luonan Chen
|
Cancer and Metastasis Reviews
|
Immune cell profiling to guide therapeutic decisions in rheumatic diseases
|
2015-06-02
|
Deepak A Rao Soumya Raychaudhuri
|
Joerg Ermann Nikola C Teslovich Michael B Brenner
|
Nature Reviews Rheumatology
|
RNA-Seq analysis of isolated satellite cells in Prmt5 deficient mice.
|
2015-06-03
|
Carsten T Kuenne Mario Looso Thomas Braun
|
Stefan Guenther Ting Zhang Marcus Krueger Yonggang Zhou Johnny Kim
|
Genomics Data
|
CD24(+) cells fuel rapid tumor growth and display high metastatic capacity
|
2015-06-04
|
Derek LeRoith
|
Ran Rostoker Sagi Abelson Inna Genkin Sarit Ben-Shmuel Ravi Sachidanandam Eyal J Scheinman Keren Bitton-Worms Zila Shen Orr Avishay Caspi Maty Tzukerman
|
Breast Cancer Research
|
Defective pollen wall contributes to male sterility in the male sterile line 1355A of cotton.
|
2015-06-05
|
Ling Min Longfu Zhu Daojun Yuan Xianlong Zhang
|
Yuanlong Wu Zancheng Wu Li Yang Xiyan Yang Xiaoping Guo
|
Scientific Reports
|
The generation of macrophages with anti-inflammatory activity in the absence of STAT6 signaling.
|
2015-06-05
|
Najib El-sayed
|
Bryan D Fleming Prabha Chandrasekaran Laura A L Dillon Elizabeth Dalby Rahul Suresh Arup Sarkar David M Mosser
|
Journal of Leukocyte Biology
|
Scalable microfluidics for single-cell RNA printing and sequencing.
|
2015-06-06
|
Dana Pe'er Peter A Sims
|
Sayantan Bose Zhenmao Wan Ambrose Carr Abbas H Rizvi Gregory Vieira Dana Pe'er
|
Genome Biology
|
Flagellin Is Required for Host Cell Invasion and Normal Salmonella Pathogenicity Island 1 Expression by Salmonella enterica Serovar Paratyphi A
|
2015-06-08
|
Michael McClelland
|
Dana Elhadad Prerak Desai Galia Rahav Ohad Gal-Mor
|
Infection and Immunity
|
Infiltration of chitin by protein coacervates defines the squid beak mechanical gradient.
|
2015-06-08
|
Ali Miserez
|
YerPeng Tan Shawn Hoon Paul A Guerette Wei Wei Ali Ghadban Cai Hao J Herbert Waite
|
Nature Chemical Biology
|
hnRNP U protein is required for normal pre-mRNA splicing and postnatal heart development and function
|
2015-06-09
|
Rhonda Bassel-Duby Tom Maniatis Junqiang Ye Lindsey J. Macpherson
|
Nadine Beetz Sean O'Keeffe Juan Carlos Tapia Weisheng V. Chen Eric N. Olson
|
Proceedings of the National Academy of Sciences of the United States of America
|
From Glacier to Sauna: RNA-Seq of the Human Pathogen Black Fungus Exophiala dermatitidis under Varying Temperature Conditions Exhibits Common and Novel Fungal Response
|
2015-06-10
|
Barbara Blasi Hakim Tafer
|
Donatella Tesei Katja Sterflinger
|
PLOS ONE
|
Molecular characterization of two novel molecular chaperones in bacterial-challenged Apostichopus japonicus.
|
2015-06-10
|
Chenghua Li
|
Haihong Wang Yina Shao Weiwei Zhang Zhimeng Lv Chunhua Jin
|
Gene
|
RNA-Seq analysis of isolate- and growth phase-specific differences in the global transcriptomes of enteropathogenic Escherichia coli prototype isolates
|
2015-06-12
|
Sean C Daugherty
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Tracy H Hazen Amol Shetty Anup A Mahurkar Owen White James B Kaper David A Rasko
|
Frontiers in Microbiology
|
The Impact of Normalization Methods on RNA-Seq Data Analysis.
|
2015-06-15
|
Marek Figlerowicz
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J Zyprych-Walczak A Szabelska L Handschuh K Górczak K Klamecka I Siatkowski
|
BioMed Research International
|
Combined Targeted DNA Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using UNCseq and NGScopy, and RNA Sequencing Using UNCqeR for the Detection of Genetic Aberrations in NSCLC.
|
2015-06-15
|
Norman Sharpless Nirali M Patel Vonn Walter
|
Xiaobei Zhao Anyou Wang David A Eberhard Michele C Hayward Ashley H Salazar Heejoon Jo Matthew G Soloway Matthew D Wilkerson Joel S Parker Xiaoying Yin Guosheng Zhang Marni B Siegel Gary B Rosson H Shelton Earp Margaret L Gulley Karen E Weck D Neil Hayes Stergios J Moschos
|
PLOS ONE
|
Suppressing Sorbitol Synthesis Substantially Alters the Global Expression Profile of Stress Response Genes in Apple (Malus domestica) Leaves.
|
2015-06-15
|
Yi Zheng Abhaya Dandekar
|
Ting Wu Yi Wang Zhangjun Fei Kenong Xu Zhenhai Han Lailiang Cheng
|
Plant and Cell Physiology
|
Differential RNA-seq (dRNA-seq) for annotation of transcriptional start sites and small RNAs in Helicobacter pylori.
|
2015-06-16
|
Cynthia Sharma
|
Thorsten Bischler Hock Siew Tan Kay Nieselt
|
Methods
|
RNASequel: accurate and repeat tolerant realignment of RNA-seq reads.
|
2015-06-16
|
Lincoln Stein
|
Gavin W Wilson
|
Nucleic Acids Research
|
YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut.
|
2015-06-17
|
Abhaya Dandekar
|
Sandeep Chakraborty Monica Britton Jill Wegrzyn Timothy Butterfield Pedro José Martínez-García Russell L Reagan Basuthkar J Rao Charles A Leslie Mallikarjuna Aradhaya David Neale Keith Woeste
|
F1000Research
|
RNA-seq analysis of an apical meristem time series reveals a critical point in Arabidopsis thaliana flower initiation
|
2015-06-18
|
Anna V Klepikova Sergey E. Dmitriev
|
Maria D Logacheva Aleksey A Penin
|
BMC Genomics
|
RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications.
|
2015-06-18
|
Gane Ka-Shu Wong Udo Gowik
|
Ming-Ju Amy Lyu Steve Kelly Sarah Covshoff Julia Mallmann Peter Westhoff Julian M Hibberd Matt Stata Rowan F Sage Haorong Lu Xiaofeng Wei Xin-Guang Zhu
|
BMC Evolutionary Biology
|
Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens
|
2015-06-19
|
Dario Cantu
|
Abraham Morales-Cruz Katherine C H Amrine Barbara Blanco-Ulate Daniel P Lawrence Renaud Travadon Philippe E Rolshausen Kendra Baumgartner
|
BMC Genomics
|
PAT-seq: a method to study the integration of 3'-UTR dynamics with gene expression in the eukaryotic transcriptome.
|
2015-06-19
|
Thomas Preiss Traude H. Beilharz David Powell Ana Traven Torsten Seemann
|
Paul F Harrison Jennifer L Clancy Peter R Boag
|
RNA
|
Benchmarking Transcriptome Quantification Methods for Duplicated Genes in Xenopus laevis.
|
2015-06-19
|
Taejoon Kwon
|
|
Cytogenetics and Genome Research
|
RNA-Seq analysis of resistant and susceptible potato varieties during the early stages of potato virus Y infection.
|
2015-06-20
|
Jeff H. Chang
|
Aymeric Goyer Launa Hamlin James M Crosslin Alex Buchanan
|
BMC Genomics
|
Marrying microfluidics and microwells for parallel, high-throughput single-cell genomics.
|
2015-06-20
|
Alex K. Shalek
|
Marc H Wadsworth Travis K Hughes
|
Genome Biology
|
Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data.
|
2015-06-22
|
Bonnie Berger
|
Sean Simmons Jian Peng Jadwiga Bienkowska
|
Journal of Computational Biology
|
ArcA Controls Metabolism, Chemotaxis, and Motility Contributing to the Pathogenicity of Avian Pathogenic Escherichia coli.
|
2015-06-22
|
Eve Syrkin Wurtele Dan Nettleton
|
Fengwei Jiang Chunxia An Yinli Bao Xuefeng Zhao Robert L Jernigan Andrew Lithio Ling Li Lisa K Nolan Chengping Lu Ganwu Li
|
Infection and Immunity
|
RNA Seq profiling reveals a novel expression pattern of TGF-β target genes in human blood eosinophils.
|
2015-06-22
|
Stephane Esnault
|
Zhong-Jian Shen Jie Hu Igor Dozmorov James S Malter
|
Immunology Letters
|
RNA-seq Reveals Complicated Transcriptomic Responses to Drought Stress in a Nonmodel Tropic Plant, Bombax ceiba L.
|
2015-06-23
|
Yuan Chen Liuyang Wang
|
Zhili Zhou Huancheng Ma Kevin Lin Youjie Zhao Zhi Xiong Bin Tian
|
Evolutionary Bioinformatics
|
An integrated RNA-Seq and network study reveals a complex regulation process of rice embryo during seed germination.
|
2015-06-23
|
Songnian Hu
|
Ting Wei Zilong He XinYu Tan Xue Liu Xiao Yuan Yingfeng Luo
|
Biochemical and Biophysical Research Communications
|
Systematically evaluating interfaces for RNA-seq analysis from a life scientist perspective.
|
2015-06-23
|
Alicia Poplawski Federico Marini
|
Moritz Hess Tanja Zeller Johanna Mazur Harald Binder
|
Briefings in Bioinformatics
|
How Many Genes Are Expressed in a Transcriptome? Estimation and Results for RNA-Seq.
|
2015-06-24
|
Luis Fernando García-Ortega Octavio Martínez
|
|
PLOS ONE
|
Gene expression analysis of skin grafts and cultured keratinocytes using synthetic RNA normalization reveals insights into differentiation and growth control.
|
2015-06-25
|
Juha Kere Eeva-Mari Jouhilahti Sten Linnarsson Peter Lönnerberg Tiina Skoog Shintaro Katayama Esko Kankuri
|
H Annika Siitonen Kristo Nuutila Mari H Tervaniemi Jyrki Vuola Anna Johnsson Outi Elomaa
|
BMC Genomics
|
Comparison of RNA-seq and microarray-based models for clinical endpoint prediction.
|
2015-06-25
|
Benedikt Brors Danielle Thierry-Mieg Falk Hertwig Weihong Xu Marco Chierici Lee Lancashire Richard G Grundy Heng Luo Davide Albanese Martin Peifer Jean Thierry-Mieg Jun Wang Zhiyu Peng Jo Vandesompele
|
Wenqian Zhang Ying Yu Wenwei Zhang Jian Wang Cesare Furlanello Viswanath Devanarayan Jie Cheng Youping Deng Barbara Hero Huixiao Hong Meiwen Jia Li Li Simon M Lin Yuri Nikolsky André Oberthuer Tao Qing Zhenqiang Su Ruth Volland Charles Wang May D Wang Junmei Ai Shahab Asgharzadeh Smadar Avigad Wenjun Bao Marina Bessarabova Murray H Brilliant Tzu-Ming Chu Jibin Zhang Min Max He Scott Hebbring Howard L Kaufman Samir Lababidi Yan Li Xin X Lu Xiwen Ma Baitang Ning Rosa Noguera John H Phan Frederik Roels Carolina Rosswog Susan Shao Jie Shen Jessica Theissen Gian Paolo Tonini Po-Yen Wu Wenzhong Xiao Joshua Xu Jiekun Xuan Yong Yang Zhan Ye Zirui Dong Ke K Zhang Ye Yin Chen Zhao Yuanting Zheng Russell D Wolfinger Tieliu Shi Linda H Malkas Frank Berthold Weida Tong Leming Shi Matthias Fischer
|
Genome Biology
|
AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana.
|
2015-06-25
|
Eduardo Eyras Allan B. James Yamile Marquez Maria Kalyna Hugh G. Nimmo Andrea Barta
|
Runxuan Zhang Cristiane P G Calixto Nikoleta A Tzioutziou Craig G Simpson Wenbin Guo Rob Patro John W S Brown
|
New Phytologist
|
Correction: A RNA-Seq Analysis of the Rat Supraoptic Nucleus Transcriptome: Effects of Salt Loading on Gene Expression.
|
2015-06-25
|
David Murphy
|
Kory R Johnson C C T Hindmarch Yasmmyn D Salinas YiJun Shi Michael Greenwood See Ziau Hoe Harold Gainer
|
PLOS ONE
|
Intratumoral morphologic and molecular heterogeneity of rhabdoid renal cell carcinoma: challenges for personalized therapy.
|
2015-06-26
|
Lalit Patel
|
Rajesh R Singh Paari Murugan Horatiu Voicu Suk-Young Yoo Tadeusz Majewski Meenakshi Mehrotra Khalida Wani Nizar Tannir Jose A Karam Eric Jonasch Christopher G Wood Chad J Creighton L Jeffrey Medeiros Russell R Broaddus Pheroze Tamboli Keith A Baggerly Kenneth D Aldape Bogdan Czerniak Rajyalakshmi Luthra Kanishka Sircar
|
Modern Pathology
|
Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium.
|
2015-06-27
|
Hideya Kawaji Mathias Uhlén Nancy Y Yu Linn Fagerberg Piero Carninci Yoshihide Hayashizaki
|
Björn M Hallström Fredrik Ponten Alistair R R Forrest Fantom Consortium Carsten O Daub
|
Nucleic Acids Research
|
Sex hormone-dependent tRNA halves enhance cell proliferation in breast and prostate cancers.
|
2015-06-29
|
Yohei Kirino
|
Shozo Honda Phillipe Loher Megumi Shigematsu Juan P Palazzo Ryusuke Suzuki Issei Imoto Isidore Rigoutsos
|
Proceedings of the National Academy of Sciences of the United States of America
|
Gene fusion detection in formalin-fixed paraffin-embedded benign fibrous histiocytomas using fluorescence in situ hybridization and RNA sequencing.
|
2015-06-29
|
David Gisselsson Fredrik Mertens
|
Charles Walther Jakob Hofvander Jenny Nilsson Linda Magnusson Henryk A Domanski Johnbosco Tayebwa Leona A Doyle Christopher D M Fletcher
|
Laboratory Investigation
|
A nested parallel experiment demonstrates differences in intensity-dependence between RNA-seq and microarrays.
|
2015-06-30
|
John D. Storey
|
David G Robinson Jean Y Wang
|
Nucleic Acids Research
|
Phylogenetic analysis and expression profiling of the pattern recognition receptors: Insights into molecular recognition of invading pathogens in Manduca sexta
|
2015-07
|
Xiaolong Cao Haobo Jiang
|
Xiufeng Zhang Yan He Ramesh T Gunaratna Yun-ru Chen Gary Blissard Michael R Kanost
|
Insect Biochemistry and Molecular Biology
|
Isoform-level brain expression profiling of the spermidine/spermine N1-Acetyltransferase1 (SAT1) gene in major depression and suicide
|
2015-07
|
Victoria Arango Peter L Nagy
|
Spiro P Pantazatos Stuart J Andrews Jane Dunning-Broadbent Jiuhong Pang Yung-Yu Huang J John Mann
|
Neurobiology of Disease
|
The Discovery, Distribution, and Evolution of Viruses Associated with Drosophila melanogaster
|
2015-07
|
Giada Ferrari Fergal M Waldron Jewelna Osei-Poku Elizabeth H Bayne Ben Longdon Amy H Buck Darren J. Obbard
|
Claire L Webster Shaun Robertson Daisy Crowson Juan F Quintana Jean-Michel Brouqui Brian P Lazzaro Penelope R Haddrill
|
PLOS Biology
|
Computational assignment of cell-cycle stage from single-cell transcriptome data.
|
2015-07-01
|
Sarah Teichmann Valentina Proserpio Kedar N Natarajan Antonio Scialdone Florian Buettner Luis R. Saraiva Oliver Stegle John C Marioni
|
|
Methods
|
The 3'-5' exoribonuclease Dis3 regulates the expression of specific microRNAs in Drosophila wing imaginal discs.
|
2015-07-01
|
Christopher Jones Sandra Cristina Viegas Cecília Maria Arraiano
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Benjamin P Towler Patricia Apura Joseph A Waldron Sarah K Smalley Sarah F Newbury
|
RNA Biology
|
Gene and miRNA expression changes in squamous cell carcinoma of larynx and hypopharynx.
|
2015-07-01
|
Prachi Jain
|
Jayalakshmi Nair Udita Chandola Vinayak Palve N R Harsha Vardhan Ram Bhupal Reddy Vikram D Kekatpure Amritha Suresh Moni Abraham Kuriakose Binay Panda
|
Genes & Cancer
|
Positional RNA-Seq identifies candidate genes for phenotypic engineering of sexual traits.
|
2015-07-03
|
Peter Ladurner Eugene Berezikov
|
Roberto Arbore Kiyono Sekii Christian Beisel Lukas Schärer
|
Frontiers in Zoology
|
Quantitative and functional interrogation of parent-of-origin allelic expression biases in the brain.
|
2015-07-03
|
Catherine Dulac
|
Julio D Perez Nimrod D Rubinstein Daniel E Fernandez Stephen W Santoro Leigh A Needleman Olivia Ho-Shing John J Choi Mariela Zirlinger Shau-Kwaun Chen Jun S Liu
|
eLife
|
"Pocket-sized RNA-Seq": A Method to Capture New Mature microRNA Produced from a Genomic Region of Interest.
|
2015-07-03
|
Florent Hube
|
Claire Francastel
|
Non-coding RNA
|
Age-Related Gene Expression Differences in Monocytes from Human Neonates, Young Adults, and Older Adults.
|
2015-07-06
|
Tobias Kollmann
|
Michelle M Lissner Brandon J Thomas Kathleen Wee Ann-Jay Tong Stephen T Smale
|
PLOS ONE
|
Transcriptomic Responses of the Heart and Brain to Anoxia in the Western Painted Turtle.
|
2015-07-06
|
Cyriac Kandoth
|
Sarah W Keenan Craig A Hill Leslie T Buck Daniel E Warren
|
PLOS ONE
|
Cytoplasmic LSM-1 protein regulates stress responses through the insulin/IGF-1 signaling pathway in Caenorhabditis elegans
|
2015-07-06
|
Denis Dupuy Eric Cornes J Cerón
|
Montserrat Porta-De-La-Riva David Aristizábal-Corrales Ana María Brokate-Llanos Francisco Javier García-Rodríguez Iris Ertl Mònica Díaz Laura Fontrodona Kadri Reis Robert Johnsen David Baillie Manuel J Muñoz Mihail Sarov
|
RNA
|
Transcriptomic profiling of gene expression and RNA processing during Leishmania major differentiation.
|
2015-07-06
|
Najib El-sayed
|
Laura A L Dillon Kwame Okrah V Keith Hughitt Rahul Suresh Yuan Li Maria Cecilia Fernandes A Trey Belew Hector Corrada Bravo David M Mosser
|
Nucleic Acids Research
|
Biphasic components of sarcomatoid clear cell renal cell carcinomas are molecularly similar to each other, but distinct from, non-sarcomatoid renal carcinomas
|
2015-07-07
|
Lalit Patel
|
Kanishka Sircar Suk-Young Yoo Tadeusz Majewski Khalida Wani Horatiu Voicu Wandaliz Torres-Garcia Roel G W Verhaak Nizar Tannir Jose A Karam Eric Jonasch Christopher G Wood Pheroze Tamboli Keith A Baggerly Kenneth D Aldape Bogdan Czerniak
|
The journal of pathology. Clinical research
|
Transcriptional landscape of trans-kingdom communication between Candida albicans and Streptococcus gordonii.
|
2015-07-07
|
Sophie Shaw Howard F. Jenkinson Angela H Nobbs
|
L C Dutton K H Paszkiewicz R J Silverman P R Splatt R J Lamont M Ramsdale
|
Molecular Oral Microbiology
|
Tungsten-induced carcinogenesis in human bronchial epithelial cells.
|
2015-07-08
|
Steven Shen Maria Antonietta Zoroddu Massimiliano Peana
|
Freda Laulicht Jason Brocato Laura Cartularo Joshua Vaughan Feng Wu Thomas Kluz Hong Sun Betul Akgol Oksuz Serenella Medici Max Costa
|
Toxicology and Applied Pharmacology
|
Impact of feed additives on surface mucosal health and columnaris susceptibility in channel catfish fingerlings, Ictalurus punctatus.
|
2015-07-08
|
Eric Peatman Wilawan Thongda
|
Honggang Zhao Chao Li Benjamin H Beck Ran Zhang Wilawan Thongda D Allen Davis
|
Fish and Shellfish Immunology
|
Revealing Missing Human Protein Isoforms Based on Ab Initio Prediction, RNA-seq and Proteomics
|
2015-07-09
|
Parvathy Venugopal Bergithe E Oftedal Zhiqiang Hu Chaochun Wei David L. Adelson Hamish S. Scott
|
Guangrong Qin Guangyong Zheng Xixia Chu Lu Xie Milena Babic Christopher N Hahn Bing Zhang Xiaojing Wang Nan Li
|
Scientific Reports
|
Evolutionary Divergence of Gene and Protein Expression in the Brains of Humans and Chimpanzees.
|
2015-07-10
|
Chet C. Sherwood
|
Amy L Bauernfeind Erik J Soderblom Meredith E Turner M Arthur Moseley John J Ely Patrick R Hof Gregory A Wray Courtney C Babbitt
|
Genome Biology and Evolution
|
Drosophila anti-nematode and antibacterial immune regulators revealed by RNA-Seq
|
2015-07-11
|
Upasana Shokal Julio Cesar Castillo Todd Creasy
|
Priti Kumari Amol Shetty Luke J Tallon Ioannis Eleftherianos
|
BMC Genomics
|
Differential and coherent processing patterns from small RNAs
|
2015-07-13
|
Jan Gorodkin Sachin Pundhir
|
|
Scientific Reports
|
Microbes & neurodevelopment--Absence of microbiota during early life increases activity-related transcriptional pathways in the amygdala.
|
2015-07-13
|
Roman Stilling Feargal J Ryan Marcus J Claesson Gerard Clarke Timothy G. Dinan John F. Cryan
|
Alan E Hoban Fergus Shanahan
|
Brain, Behavior, and Immunity
|
Opposing roles of STAT1 and STAT3 in IL-21 function in CD4+ T cells
|
2015-07-13
|
Majid Kazemian
|
Chi-Keung Wan Allison B Andraski Rosanne Spolski Peng Li Jangsuk Oh Leigh Samsel Phillip A Swanson Dorian B McGavern Elizabeth P Sampaio Alexandra F Freeman Joshua D Milner Steven M Holland Warren J Leonard
|
Proceedings of the National Academy of Sciences of the United States of America
|
Physiology and immunology of mucosal barriers in catfish (Ictalurus spp.)
|
2015-07-15
|
Eric Peatman
|
Miles Lange Honggang Zhao Benjamin H Beck
|
Tissue Barriers
|
Leveraging transcript quantification for fast computation of alternative splicing profiles.
|
2015-07-15
|
Eduardo Eyras
|
Gael P Alamancos Amadís Pagès Juan L Trincado Nicolás Bellora
|
RNA
|
Correction: De novo Transcriptome Analysis of Portunus trituberculatus Ovary and Testis by RNA-Seq: Identification of Genes Involved in Gonadal Development.
|
2015-07-15
|
PLOS ONE staff
|
|
PLOS ONE
|
Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package
|
2015-07-16
|
María José Nueda Antonio Di Pietro
|
Sonia Tarazona Pedro Furió-Tarí David Turrà Alberto Ferrer Ana Conesa
|
Nucleic Acids Research
|
Widespread Inducible Transcription Downstream of Human Genes.
|
2015-07-16
|
Joan A. Steitz
|
Anna Vilborg Maria C Passarelli Therese A Yario Kazimierz T Tycowski
|
Molecular Cell
|
Expression of an estrogen-regulated variant transcript of the peroxisomal branched chain fatty acid oxidase ACOX2 in breast carcinomas
|
2015-07-17
|
Anne-Lise Børresen-Dale Surendra Kumar Vessela Kristensen Bjørn Naume
|
Sunniva Stordal Bjørklund Michael Seiler Grethe I Grenaker Alnæs Yao Ming John Kerrigan Ravi Sachidanandam Gyan Bhanot Shridar Ganesan
|
BMC Cancer
|
A nonlethal sampling method to obtain, generate and assemble whole blood transcriptomes from small, wild mammals.
|
2015-07-17
|
Emma C. Teeling Sébastien J. Puechmaille Michaël Bekaert
|
Zixia Huang Aurore Gallot Nga T Lao Nicole M Foley David Jebb
|
Molecular Ecology Resources
|
Genome-wide association analysis on normal hearing function identifies PCDH20 and SLC28A3 as candidates for hearing function and loss.
|
2015-07-17
|
Dragana Vuckovic Sally J. Dawson Giorgia Girotto Anne Viljanen Taina Rantanen Marina Ciullo Diego Vozzi Teresa Nutile Ginevra Biino Anu Loukola
|
Deborah I Scheffer Anna Morgan Mariateresa Di Stazio Maria P Concas Lisa Nolan Aileen Bahl Adrian Davis David P Corey Mario Pirastu Paolo Gasparini
|
Human Molecular Genetics
|
Integrative analyses of RNA editing, alternative splicing, and expression of young genes in human brain transcriptome by deep RNA sequencing.
|
2015-07-17
|
David M. Irwin
|
Dong-Dong Wu Ling-Qun Ye Yan Li Yan-Bo Sun Yi Shao Chunyan Chen Zhu Zhu Li Zhong Lu Wang Yong E Zhang Ya-Ping Zhang
|
Journal of molecular cell biology
|
QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments
|
2015-07-19
|
James C Mullikin
|
Stephen W Hartley
|
BMC Bioinformatics
|
How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets
|
2015-07-21
|
Shane G. Poplawski Lucia Peixoto Davide Risso Ted Abel
|
Mathieu E Wimmer Terence P Speed Marcelo A Wood
|
Nucleic Acids Research
|
Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data.
|
2015-07-21
|
Tomasz Kuliński
|
Daniel Andergassen Christoph P Dotter Philipp M Guenzl Philipp C Bammer Denise P Barlow Florian M Pauler Quanah J Hudson
|
Nucleic Acids Research
|
Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data.
|
2015-07-23
|
Mihaela Zavolan Andreas R Gruber Foivos Gypas Alexander Kanitz
|
Georges Martin
|
Genome Biology
|
Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment.
|
2015-07-23
|
Geoffrey J. Barton Gordon G Simpson Nicholas Schurch Christian Cole Tom Owen-Hughes Karim Gharbi Mark Blaxter
|
Marek Gierliński Pietà Schofield Alexander Sherstnev Vijender Singh Nicola Wrobel
|
Bioinformatics
|
TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets.
|
2015-07-23
|
Oliver H Tam
|
Ying Jin Eric Paniagua Molly Hammell
|
Bioinformatics
|
TANRIC: An Interactive Open Platform to Explore the Function of lncRNAs in Cancer.
|
2015-07-24
|
Lingxiang Liu Jun Li Leng Han
|
Paul Roebuck Lixia Diao Yuan Yuan John N Weinstein Han Liang
|
Cancer Research
|
Experimental validation of methods for differential gene expression analysis and sample pooling in RNA-seq.
|
2015-07-25
|
Per Qvist Anto P. Rajkumar Mette Nyegaard Ole Mors
|
Ross Lazarus Francesco Lescai Jia Ju Anders D Børglum Qibin Li Jane H Christensen
|
BMC Genomics
|
Identifying new sex-linked genes through BAC sequencing in the dioecious plant Silene latifolia.
|
2015-07-25
|
Alex Widmer Nicolas Blavet Niklaus Zemp Jos Käfer
|
H Blavet A Muyle R Cegan C Deschamps S Mousset S Aubourg R Bergero D Charlesworth R Hobza G A B Marais
|
BMC Genomics
|
Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17 Human Proteome Project.
|
2015-07-28
|
Gil Omenn
|
Hong-Dong Li Rajasree Menon Brandon Govindarajoo Bharat Panwar Yang Zhang Yuanfang Guan
|
Journal of Proteome Research
|
Transcriptional profiling of macrophages derived from monocytes and iPS cells identifies a conserved response to LPS and novel alternative transcription
|
2015-07-30
|
Siamon Gordon
|
Kaur Alasoo Fernando O Martinez Christine Hale Fiona Powrie Gordon Dougan Subhankar Mukhopadhyay Daniel J Gaffney
|
Scientific Reports
|
Transcriptome Dynamics of Developing Photoreceptors in Three-Dimensional Retina Cultures Recapitulates Temporal Sequence of Human Cone and Rod Differentiation Revealing Cell Surface Markers and Gene Networks
|
2015-07-31
|
Anand Swaroop Kohei Homma Jizhong Zou Matthew Brooks
|
Rossukon Kaewkhaw Koray Dogan Kaya Vijender Chaitankar Mahendra Rao
|
Stem Cells
|
DNA hypomethylation-mediated activation of Cancer/Testis Antigen 45 (CT45) genes is associated with disease progression and reduced survival in epithelial ovarian cancer.
|
2015-08-01
|
Kunle Odunsi
|
Wa Zhang Carter J Barger Petra A Link Paulette Mhawech-Fauceglia Austin Miller Stacey N Akers Adam R Karpf
|
Epigenetics
|
Analysis of the Human Prostate-Specific Proteome Defined by Transcriptomics and Antibody-Based Profiling Identifies TMEM79 and ACOXL as Two Putative, Diagnostic Markers in Prostate Cancer
|
2015-08-03
|
Mathias Uhlén Linn Fagerberg William M Gallagher Karin Jirström
|
Gillian O'Hurley Christer Busch Björn M Hallström Charlotte Stadler Anna Tolf Emma Lundberg Jochen M Schwenk Anders Bjartell Fredrik Pontén
|
PLOS ONE
|
Similarities in Gene Expression Profiles during In Vitro Aging of Primary Human Embryonic Lung and Foreskin Fibroblasts.
|
2015-08-03
|
Peter Hemmerich Reinhard Guthke
|
Shiva Marthandan Steffen Priebe Mario Baumgart Marco Groth Alessandro Cellerino Stephan Diekmann
|
BioMed Research International
|
Dynamics of gene silencing during X inactivation using allele-specific RNA-seq.
|
2015-08-03
|
Tahsin Stefan Barakat Hendrik Marks Wouter de Laat Austin Smith
|
Hindrik H D Kerstens Erik Splinter René A M Dirks Guido van Mierlo Onkar Joshi Shuang-Yin Wang Tomas Babak Cornelis A Albers Tüzer Kalkan Alice Jouneau Joost Gribnau Hendrik G Stunnenberg
|
Genome Biology
|
RNA-seq reveals the critical role of OtpR in regulating Brucella melitensis metabolism and virulence under acidic stress.
|
2015-08-05
|
Yongqun He
|
Wenxiao Liu Hao Dong Jing Li Qixing Ou Yujin Lv Xiaolei Wang Zuoshuang Xiang Qingmin Wu
|
Scientific Reports
|
Transcriptome response to heat stress in a chicken hepatocellular carcinoma cell line.
|
2015-08-05
|
Carl J Schmidt
|
Liang Sun Susan J Lamont Amanda M Cooksey Fiona McCarthy Catalina O Tudor K Vijay-Shanker Rachael M DeRita Max Rothschild Chris Ashwell Michael E Persia
|
Cell Stress & Chaperones
|
RNASeq in C. elegans Following Manganese Exposure.
|
2015-08-06
|
Michael Aschner
|
Nancy L Parmalee Shahina B Maqbool Bin Ye Brent Calder Aaron B Bowman
|
Current protocols in toxicology / editorial board, Mahin D. Maines (editor-in-chief) ... [et al.]
|
Comprehensive assembly of novel transcripts from unmapped human RNA-Seq data and their association with cancer
|
2015-08-07
|
Majid Kazemian
|
Min Ren Jian-Xin Lin Wei Liao Rosanne Spolski Warren J Leonard
|
Molecular Systems Biology
|
An RNA-Seq-based reference transcriptome for Citrus.
|
2015-08-11
|
Terol J
|
Francisco Tadeo Daniel Ventimilla Manuel Talon
|
Plant Biotechnology Journal
|
ROTS: reproducible RNA-seq biomarker detector-prognostic markers for clear cell renal cell cancer.
|
2015-08-11
|
Laura L. Elo Panu M Jaakkola
|
Fatemeh Seyednasrollah Krista Rantanen
|
Nucleic Acids Research
|
Transcriptome profiling of larvae of the marine medaka Oryzias melastigma by Illumina RNA-seq.
|
2015-08-11
|
Jae-Seong Lee
|
Bo-Mi Kim Beom-Soon Choi Hui-Soo Kim Jae-Sung Rhee Doris W T Au Rudolf S S Wu Ik-Young Choi
|
Marine Genomics
|
Galaxy Integrated Omics: Web-based Standards-Compliant Workflows for Proteomics Informed by Transcriptomics.
|
2015-08-12
|
Jun Fan Fawaz Ghali David A. Matthews Andrew Jones
|
Shyamasree Saha Gary Barker Kate J Heesom Conrad Bessant
|
Molecular & Cellular Proteomics
|
Host and non-host roots in rice: cellular and molecular approaches reveal differential responses to arbuscular mycorrhizal fungi.
|
2015-08-13
|
Paola Bonfante
|
Valentina Fiorilli Marta Vallino Chiara Biselli Antonella Faccio Paolo Bagnaresi
|
Frontiers in Plant Science
|
Comparative RNA-seq analysis of the Tritrichomonas foetus PIG30/1 isolate from pigs reveals close association with Tritrichomonas foetus BP-4 isolate 'bovine genotype'.
|
2015-08-14
|
Ana Conesa
|
Victoria Morin-Adeline Kai Mueller Jan Šlapeta
|
Veterinary Parasitology
|
The identification and characterization of novel transcripts from RNA-seq data.
|
2015-08-17
|
Stefanie Dimmeler Tyler Weirick Shizuka Uchida
|
Giuseppe Militello Raphael Müller David John
|
Briefings in Bioinformatics
|
Lost in Translation: Pitfalls in Deciphering Plant Alternative Splicing Transcripts.
|
2015-08-18
|
Andrea Barta Yamile Marquez Maria Kalyna Geoffrey Michael Gadd
|
John W S Brown Craig G Simpson
|
The Plant Cell
|
The mRNA expression of soluble urokinase plasminogen activator surface receptor in human adipose tissue is positively correlated with body mass index.
|
2015-08-18
|
Kok Gan Chan
|
Hien Fuh Ng Kin Fah Chin Yun Fong Ngeow
|
Genome
|
Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis.
|
2015-08-19
|
Guo-Li Ming Hongjun Song Daniel A Berg David Nauen
|
Jaehoon Shin Yunhua Zhu Joseph Y Shin Juan Song Michael A Bonaguidi Grigori Enikolopov Kimberly M Christian
|
Cell Stem Cell
|
Assembly and Analysis of Differential Transcriptome Responses of Hevea brasiliensis on Interaction with Microcyclus ulei.
|
2015-08-19
|
Ibonne Aydee García Romero Dolly Montoya Castaño Silvia Restrepo
|
Uriel Alonso Hurtado Páez Fabio Ancizar Aristizábal Gutiérrez
|
PLOS ONE
|
Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development.
|
2015-08-19
|
Dmitry A Ovchinnikov Deanne M. Taylor Ernst J. Wolvetang
|
Yu Hasegawa Laurence de Torrenté Jessica C Mar
|
PLOS Genetics
|
Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms
|
2015-08-19
|
Mihaela Pertea Steven Salzberg
|
Tsung-Cheng Chang Sungyul Lee Joshua T Mendell
|
Genome Research
|
Regulation of alternative splicing in Drosophila by 56 RNA binding proteins.
|
2015-08-20
|
Steven E. Brenner Brenton R. Graveley
|
Angela N Brooks Michael O Duff Gemma May Li Yang Mohan Bolisetty Jane Landolin Ken Wan Jeremy Sandler Benjamin W Booth Susan E Celniker
|
Genome Research
|
Defining the three cell lineages of the human blastocyst by single-cell RNA-seq.
|
2015-08-20
|
Tim Xiaoming Hu Ignacio del Valle Kay Elder Paul Robson
|
Paul Blakeley Norah M E Fogarty Sissy E Wamaitha Philip Snell Leila Christie Kathy K Niakan
|
Development
|
Full-length de novo assembly of RNA-seq data in pea (Pisum sativum L.) provides a gene expression atlas and gives insights into root nodulation in this species.
|
2015-08-22
|
Jérôme Gouzy Pascal Gamas Corinne Da Silva
|
Susete Alves-Carvalho Grégoire Aubert Sébastien Carrère Corinne Cruaud Anne-Lise Brochot Françoise Jacquin Anthony Klein Chantal Martin Karen Boucherot Jonathan Kreplak Sandra Moreau Patrick Wincker Judith Burstin
|
The Plant Journal
|
Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments
|
2015-08-24
|
Christina Kendziorski
|
Ning Leng Li-Fang Chu Chris Barry Yuan Li Jeea Choi Xiaomao Li Peng Jiang Ron M Stewart James A Thomson
|
Nature Methods
|
Novel insights into the molecular events linking to cell death induced by tetracycline in the amitochondriate protozoan Trichomonas vaginalis.
|
2015-08-24
|
Po-Jung Huang Petrus Tang
|
Kuo-Yang Huang Fu-Man Ku Wei-Hung Cheng Chi-Ching Lee Lichieh Julie Chu Chih-Chieh Cheng Yi-Kai Fang Hsueh-Hsia Wu
|
Antimicrobial Agents and Chemotherapy
|
Time-Course RNA-Seq Analysis Reveals Transcriptional Changes in Rice Plants Triggered by Rice stripe virus Infection.
|
2015-08-25
|
Jin Kyo Jung
|
Won Kyong Cho Sen Lian Sang-Min Kim Bo Yoon Seo Kook-Hyung Kim
|
PLOS ONE
|
Identification of miRNAs in Bovine Endometrium through RNAseq and Prediction of Regulated Pathways.
|
2015-08-25
|
Soroush Sharbati
|
S E Palma-Vera R Einspanier
|
Reproduction in Domestic Animals
|
MetaRNA-Seq: An Interactive Tool to Browse and Annotate Metadata from RNA-Seq Studies.
|
2015-08-25
|
Karsten Suhre Anja M Billing Anna Halama
|
Pankaj Kumar Shahina Hayat Manish Gupta Noha A Yousri Gregory M Smith
|
BioMed Research International
|
Fast and accurate approximate inference of transcript expression from RNA-seq data.
|
2015-08-26
|
Antti Honkela
|
James Hensman Panagiotis Papastamoulis Peter Glaus Antti Honkela Magnus Rattray
|
Bioinformatics
|
Stimulation of Innate and Adaptive Immunity by Using Filamentous Bacteriophage fd Targeted to DEC-205
|
2015-08-26
|
Piergiuseppe De Berardinis
|
Luciana D'Apice Valerio Costa Rossella Sartorius Maria Trovato Marianna Aprile
|
Journal of Immunology Research
|
Altered Exosomal RNA Profiles in Bronchoalveolar Lavage from Lung Transplants with Acute Rejection
|
2015-08-26
|
Aric Gregson David Sayah
|
Aki Hoji Patil Injean Steven T Poynter Claudia Briones Vyacheslav Palchevskiy S Sam Weigt Michael Y Shino Ariss Derhovanessian Rajan Saggar David Ross Abbas Ardehali Joseph P Lynch John A Belperio
|
American Journal of Respiratory and Critical Care Medicine
|
Genome-wide RNA-Seq of Human Motor Neurons Implicates Selective ER Stress Activation in Spinal Muscular Atrophy.
|
2015-08-26
|
Natalia Rodríguez-Muela Shi-Yan Ng Lee L Rubin John L. Rinn
|
Boon Seng Soh David G Hendrickson Feodor Price
|
Cell Stem Cell
|
RNAseq analysis of Aspergillus fumigatus in blood reveals a just wait and see resting stage behavior
|
2015-08-27
|
Ana Conesa Sven Krappmann Gerhard H Braus
|
Henriette Irmer Sonia Tarazona Christoph Sasse Patrick Olbermann Jürgen Loeffler
|
BMC Genomics
|
The coelomic epithelium transcriptome from a clonal sea star, Coscinasterias muricata.
|
2015-08-27
|
Josep F. Abril Pedro Martinez
|
Jonatan L Gabre Helen Nilsson Sköld Olga Ortega-Martinez
|
Marine Genomics
|
RNA-Seq analysis of urea nutrition responsive transcriptome of Oryza sativa elite indica cultivar RP Bio 226.
|
2015-08-28
|
K Ulaganathan
|
Mettu Madhavi Reddy
|
Genomics Data
|
Chromatin features, RNA polymerase II and the comparative expression of lens genes encoding crystallins, transcription factors, and autophagy mediators
|
2015-08-28
|
Deyou Zheng Ales Cvekl
|
Jian Sun Shira Rockowitz Daniel Chauss Ping Wang Marc Kantorow
|
Molecular Vision
|
Concordance between RNA-sequencing data and DNA microarray data in transcriptome analysis of proliferative and quiescent fibroblasts
|
2015-09
|
Brett Trost Anthony Kusalik
|
Catherine A Moir Zoe E Gillespie Jennifer A Mitchell Christopher H Eskiw
|
Royal Society Open Science
|
Relationships within Cladobranchia (Gastropoda: Nudibranchia) based on RNA-Seq data: an initial investigation
|
2015-09
|
Jessica A Goodheart Allen Collins
|
Adam L Bazinet Michael P Cummings
|
Royal Society Open Science
|
Cullin4 Is Pro-Viral during West Nile Virus Infection of Culex Mosquitoes.
|
2015-09-01
|
Peter Walker Julio Rodriguez-Andres Jean-bernard Duchemin
|
Prasad N Paradkar Lee Trinidad
|
PLOS Pathogens
|
RNA-Seq analysis identifies key genes associated with haustorial development in the root hemiparasite Santalum album.
|
2015-09-01
|
Oliver Berkowitz James Whelan
|
Xinhua Zhang Jaime A Teixeira da Silva Muhan Zhang Guohua Ma Jun Duan
|
Frontiers in Plant Science
|
Integrated methylome and transcriptome analysis reveals novel regulatory elements in pediatric acute lymphoblastic leukemia.
|
2015-09-01
|
Kristen H Taylor Stephanie McKay
|
Md Almamun Benjamin T Levinson Annette C van Swaay Nathan T Johnson Gerald L Arthur J Wade Davis
|
Epigenetics
|
Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses
|
2015-09-02
|
Aviv Regev Rahul Satija Roi Avraham Alex K. Shalek
|
Nathan Haseley Douglas Brown Cristina Penaranda Humberto B Jijon John J Trombetta Ramnik J Xavier Deborah T Hung
|
Cell
|
RNAseq expression analysis of resistant and susceptible mice after influenza A virus infection identifies novel genes associated with virus replication and important for host resistance to infection
|
2015-09-02
|
Claudia Pommerenke
|
Esther Wilk Ashutosh K Pandey Sarah Rebecca Leist Bastian Hatesuer Matthias Preusse Junxi Wang Klaus Schughart
|
BMC Genomics
|
Allele-Selective Transcriptome Recruitment to Polysomes Primed for Translation: Protein-Coding and Noncoding RNAs, and RNA Isoforms.
|
2015-09-02
|
Wolfgang Sadee
|
Roshan Mascarenhas Maciej Pietrzak Ryan M Smith Amy Webb Danxin Wang Audrey C Papp Julia K Pinsonneault Michal Seweryn Grzegorz Rempala
|
PLOS ONE
|
Cell type-specific transcriptomics of hypothalamic energy-sensing neuron responses to weight-loss
|
2015-09-02
|
Scott M Sternson Henry FE Ken Sugino Tozer A Branco T
|
|
eLife
|
HiCdat: a fast and easy-to-use Hi-C data analysis tool.
|
2015-09-03
|
Ueli Grossniklaus Stefan Grob Marc W Schmid
|
|
BMC Bioinformatics
|
Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data
|
2015-09-03
|
Katharina E. Hayer Gregory R Grant
|
Angel Pizarro Nicholas F Lahens John B Hogenesch
|
Bioinformatics
|
Errors in RNA-Seq quantification affect genes of relevance to human disease.
|
2015-09-03
|
Mick Watson
|
Christelle Robert
|
Genome Biology
|
Transcriptomic Features of Bovine Blastocysts Derived by Somatic Cell Nuclear Transfer.
|
2015-09-03
|
Namshin Kim
|
Byungkuk Min Sunwha Cho Jung Sun Park Yun-Gyeong Lee Yong-Kook Kang
|
G3
|
Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline
|
2015-09-04
|
Frank Emmert-Streib
|
Yasir Rahmatallah Galina Glazko
|
Briefings in Bioinformatics
|
Transcriptome analysis of the white pine blister rust pathogen Cronartium ribicola: de novo assembly, expression profiling, and identification of candidate effectors.
|
2015-09-04
|
Jun-Jun Liu
|
Rona N Sturrock Richard A Sniezko Holly Williams Ross Benton Arezoo Zamany
|
BMC Genomics
|
Function and Regulation of Cph2 in Candida albicans.
|
2015-09-04
|
Pierre Baldi
|
Shelley Lane Pietro Di Lena Kati Tormanen Haoping Liu
|
Eukaryotic Cell
|
RNA-seq analysis of the whole transcriptome of MDA-MB-231 mammary carcinoma cells exposed to the antimetastatic drug NAMI-A.
|
2015-09-04
|
Alberto Pallavicini
|
Alberta Bergamo Marco Gerdol Marianna Lucafò Chiara Pelillo Marilena Battaglia Gianni Sava
|
Metallomics
|
Gene Ranking of RNA-Seq Data via Discriminant Non-Negative Matrix Factorization.
|
2015-09-08
|
Michael R. Barnes
|
Zhilong Jia Xiang Zhang Naiyang Guan Xiaochen Bo Zhigang Luo
|
PLOS ONE
|
Systematic identification of factors for provirus silencing in embryonic stem cells
|
2015-09-09
|
George Q. Daley Chadi A El Farran Yinghui Li Matthew C. Lorincz
|
Bin Xia Yang Hong Chao Guo Tao Yu Hai Tong Fang Hao Fei Wang Sharon Schlesinger Yu Fen Samantha Seah Germaine Yen Lin Goh Suat Peng Neo Vinay Tergaonkar Tit-Meng Lim Lingyi Chen Jayantha Gunaratne James J Collins Stephen P Goff Hu Li Frederic A Bard Yuin-Han Loh
|
Cell
|
Molecular analyses of juvenile granulosa cell tumors bearing AKT1 mutations provide insights into tumor biology and therapeutic leads.
|
2015-09-11
|
Aurélie Auguste S Caburet Sabine Sarnacki
|
Laurianne Bessière Anne-Laure Todeschini Jaime Prat Emanuela D'angelo Pierre De La Grange Olivier Ariste Fréderic Lemoine Bérangère Legois Charles Sultan Alain Zider Louise Galmiche Nicolas Kalfa Reiner A Veitia
|
Human Molecular Genetics
|
Genome-wide RNA sequencing analysis of quorum sensing-controlled regulons in the plant-associated Burkholderia glumae PG1 strain.
|
2015-09-11
|
Andreas Knapp Rolf Daniel
|
Rong Gao Dagmar Krysciak Katrin Petersen Christian Utpatel Christel Schmeisser Sonja Voget Karl-Erich Jaeger Wolfgang R Streit
|
Applied and Environmental Microbiology
|
The role of antigen presenting cells in the induction of HIV-1 latency in resting CD4(+) T-cells.
|
2015-09-11
|
Vanessa A Evans David Powell Sharon R. Lewin
|
Nitasha A Kumar Karey Cheong Candida da Fonseca Pereira Jenny Anderson Paul U Cameron
|
Retrovirology
|
The reverse transcription signature of N-1-methyladenosine in RNA-Seq is sequence dependent
|
2015-09-13
|
Andreas Hildebrandt Marie-Luise Winz Sunny Sharma Yuri Motorin Mark Helm
|
Ralf Hauenschild Lyudmil Tserovski Katharina Schmid Kathrin Thüring Karl-Dieter Entian Ludivine Wacheul Denis L J Lafontaine James Anderson Juan Alfonzo Andres Jäschke
|
Nucleic Acids Research
|
Ancient gene duplications have shaped developmental stage-specific expression in Pristionchus pacificus.
|
2015-09-15
|
Christian Rödelsperger P Baskaran Gabriel V. Markov
|
Christian Rödelsperger Neel Prabh Vahan Serobyan Antje Hirsekorn Christoph Dieterich
|
BMC Evolutionary Biology
|
Identification of candidate gonadal sex differentiation genes in the chicken embryo using RNA-seq
|
2015-09-16
|
Alicia Oshlack Nadia M Davidson Craig A. Smith Andrew H Sinclair
|
Katie L Ayers Luke S Lambeth
|
BMC Genomics
|
RNA-seq analysis of Pichia anomala reveals important mechanisms required for survival at low pH
|
2015-09-16
|
Jens Nielsen Verena Siewers SungSoo Kim
|
Eugene Fletcher Amir Feizi
|
Microbial Cell Factories
|
A novel workflow correlating RNA-seq data to Phythophthora infestans resistance levels in wild Solanum species and potato clones.
|
2015-09-17
|
Estelle Proux-Wéra Erik Andreasson
|
Itziar Frades Kibrom B Abreha Åsa Lankinen Erik Alexandersson
|
Frontiers in Plant Science
|
Tools and best practices for data processing in allelic expression analysis.
|
2015-09-17
|
Tuuli Lappalainen Pejman Mohammadi
|
Stephane E Castel Ami Levy-Moonshine Eric Banks
|
Genome Biology
|
RNA-seq analyses of changes in the Anopheles gambiae transcriptome associated with resistance to pyrethroids in Kenya: identification of candidate-resistance genes and candidate-resistance SNPs.
|
2015-09-17
|
Eric Ochomo Mariangela Bonnizoni Guiyun Yan
|
William Augustine Dunn Monica Britton Yaw Afrane Guofa Zhou Joshua Hartsel Ming-Chieh Lee Jiabao Xu Andrew Githeko Joseph Fass
|
Parasites & Vectors
|
Codon and Amino Acid Usage Are Shaped by Selection Across Divergent Model Organisms of the Pancrustacea
|
2015-09-17
|
Cassandra G. Extavour
|
Carrie A Whittle
|
G3
|
RNAseq Analysis Highlights Specific Transcriptome Signatures of Yeast and Mycelial Growth Phases in the Dutch Elm Disease Fungus Ophiostoma novo-ulmi.
|
2015-09-17
|
Louis Bernier
|
Martha Nigg Jérôme Laroche Christian R Landry
|
G3
|
In vivo Monitoring of Transcriptional Dynamics After Lower-Limb Muscle Injury Enables Quantitative Classification of Healing
|
2015-09-18
|
Alexander Meissner
|
Carlos A Aguilar Anna Shcherbina Darrell O Ricke Ramona Pop Christopher T Carrigan Casey A Gifford Maria L Urso Melissa A Kottke
|
Scientific Reports
|
Early transcriptional events linked to induction of diapause revealed by RNAseq in larvae of drosophilid fly, Chymomyza costata.
|
2015-09-21
|
Jan Provazník Konrad Schöttner Rodolphe Poupardin
|
Jaroslava Korbelová David Doležel Dinko Pavlinic Vladimír Beneš Vladimír Koštál
|
BMC Genomics
|
Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells.
|
2015-09-21
|
Sarah Teichmann Aleksandra A Kolodziejczyk Florian Buettner
|
Jason C H Tsang Yong Yu Shannon Burke Cui Wang Liming Lu Pentao Liu
|
Genome Biology
|
Semantic Assembly and Annotation of Draft RNAseq Transcripts without a Reference Genome.
|
2015-09-22
|
Andrey Ptitsyn
|
Ramzi Temanni Christelle Bouchard Peter A V Anderson
|
PLOS ONE
|
Dynamic transcriptional symmetry-breaking in pre-implantation mammalian embryo development revealed by single-cell RNA-seq.
|
2015-09-22
|
Qi Chen
|
Junchao Shi Xin Li Xiudeng Zheng Ying Zhang Jie Qiao Fuchou Tang Yi Tao Qi Zhou Enkui Duan
|
Development
|
Transcriptome Profiling of Pediatric Core Binding Factor AML.
|
2015-09-23
|
George Komatsoulis
|
Chih-Hao Hsu Cu Nguyen Chunhua Yan Rhonda E Ries Qing-Rong Chen Ying Hu Fabiana Ostronoff Derek L Stirewalt George Komatsoulis Shawn Levy Daoud Meerzaman Soheil Meshinchi
|
PLOS ONE
|
Gene expression changes in the salivary glands of Anopheles coluzzii elicited by Plasmodium berghei infection
|
2015-09-23
|
Luis Pedro Coelho Ana Domingos Alejandro Cabezas-Cruz
|
Renato Pinheiro-Silva Lara Borges James J Valdés Virgílio do Rosário José de la Fuente
|
Parasites & Vectors
|
Molecular mechanisms of D-cycloserine in facilitating fear extinction: insights from RNAseq.
|
2015-09-23
|
Soraya Seedat
|
Stefanie Malan-Müller Lorren Fairbairn Willie M U Daniels Mahjoubeh Jalali Sefid Dashti Edward J Oakeley Marc Altorfer Martin Kidd Junaid Gamieldien Sîan Megan Joanna Hemmings
|
Metabolic Brain Disease
|
RNA-Seq in Mytilus galloprovincialis: comparative transcriptomics and expression profiles among different tissues.
|
2015-09-24
|
David Posada Rebeca Moreira Carlos Canchaya
|
Patricia Pereiro Antonio Figueras Beatriz Novoa
|
BMC Genomics
|
Whose Gene Is It Anyway? The Effect of Preparation Purity on Neutrophil Transcriptome Studies
|
2015-09-24
|
Helen L Wright
|
Huw B Thomas Robert J Moots Steven W Edwards
|
PLOS ONE
|
Harnessing Next Generation Sequencing in Climate Change: RNA-Seq Analysis of Heat Stress-Responsive Genes in Wheat (Triticum aestivum L.).
|
2015-09-25
|
RANJEET RANJAN KUMAR Viswanathan Chinnusamy
|
Suneha Goswami Sushil K Sharma Yugal K Kala Gyanendra K Rai Dwijesh C Mishra Monendra Grover Gyanendra P Singh Himanshu Pathak Anil Rai Raj D Rai
|
OMICS: A Journal of Integrative Biology
|
Comprehensive Identification of Sexual Dimorphism-Associated Differentially Expressed Genes in Two-Way Factorial Designed RNA-Seq Data on Japanese Quail (Coturnix coturnix japonica).
|
2015-09-29
|
Heebal Kim
|
Kelsey Caetano-Anolles Minseok Seo Sandra Rodriguez-Zas Jae-Don Oh Jae Yong Han Kichoon Lee Tae Sub Park Sangsu Shin Zhang Jiao Jiao Mrinmoy Ghosh Dong Kee Jeong Seoae Cho Ki-Duk Song Hak-Kyo Lee
|
PLOS ONE
|
De novo transcriptome profiling of highly purified human lymphocytes primary cells
|
2015-09-29
|
Sergio Abrignani Massimiliano Pagani Grazisa Rossetti Ilaria Panzeri
|
Raoul J P Bonnal Valeria Ranzani Alberto Arrigoni Serena Curti Paola Gruarin
|
Scientific Data
|
Transcriptome Characteristics and X-Chromosome Inactivation Status in Cultured Rat Pluripotent Stem Cells.
|
2015-09-29
|
Irina S. Zakharova Sergey P Medvedev Fedor Kolpakov Suren M Zakian Alexander Karaskov
|
Evgeniya A Vaskova Anastasiya E Sorokina Artem A Nemudryy Evgeniy A Elisaphenko Alexander I Shevchenko Elena A Kizilova Antonina I Zhelezova Ivan S Evshin Ruslan N Sharipov Julia M Minina Natalia S Zhdanova Igor I Khegay Gennadiy T Sukhikh Evgeniy A Pokushalov Valentin V Vlasov Ludmila N Ivanova
|
Stem Cells and Development
|
Detecting Multivariate Gene Interactions in RNA-Seq Data Using Optimal Bayesian Classification.
|
2015-10-01
|
Edward R. Dougherty
|
Jason Knight Ivan Ivanov Karen Triff Robert Chapkin
|
IEEE/ACM Transactions on Computational Biology and Bioinformatics
|
Functional Impact and Evolution of a Novel Human Polymorphic Inversion That Disrupts a Gene and Creates a Fusion Transcript.
|
2015-10-01
|
Tõnu Esko Carla Giner-Delgado Marta Puig Magdalena Gayà-Vidal David Castellano
|
Lorena Pantano David Izquierdo José Ignacio Lucas-Lledó Chikashi Terao Fumihiko Matsuda Mario Cáceres
|
PLOS Genetics
|
SRSF1-Regulated Alternative Splicing in Breast Cancer
|
2015-10-01
|
Frédéric H-T Allain Adrian Robert Krainer Antoine Cléry
|
Olga Anczuków Martin Akerman Jie Wu Chen Shen Nitin H Shirole Amanda Raimer Shuying Sun Mads A Jensen Yimin Hua
|
Molecular Cell
|
Prdm12 specifies V1 interneurons through cross-repressive interactions with Dbx1 and Nkx6 genes in Xenopus.
|
2015-10-01
|
Carine Van Lint Benoît Van Driessche Julie Hanotel Ian Quigley Aurore Thelie Alessandra Pierani Michael Schubert
|
Simon Desiderio Benoit Van Driessche Anthony Rodari Mark D Borromeo Sadia Kricha François Lahaye Jenifer Croce Gustavo Cerda-Moya Jesús Ordoño Fernandez Barbara Bolle Katharine E Lewis Maike Sander Jane E Johnson Christopher R Kintner Tomas Pieler Kristine A Henningfeld Eric J Bellefroid Claude Van Campenhout
|
Development
|
Different exercise modalities have distinct effects on the integrin-linked kinase (ILK) and Ca2+ signaling pathways in the male rat bone.
|
2015-10-01
|
Dharani M Sontam Peter Tsai
|
Elwyn C Firth Mark H Vickers Justin M O'Sullivan
|
Physiological Reports
|
Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells.
|
2015-10-01
|
Aviv Regev Itay Tirosh
|
Monika S Kowalczyk Itay Tirosh Dirk Heckl Tata Nageswara Rao Atray Dixit Brian J Haas Rebekka K Schneider Amy J Wagers Benjamin L Ebert
|
Genome Research
|
Complete hematologic response of early T-cell progenitor acute lymphoblastic leukemia to the γ-secretase inhibitor BMS-906024: genetic and epigenetic findings in an outlier case.
|
2015-10-01
|
Matthew Meyerson Andrew L. Kung
|
Birgit Knoechel Ami Bhatt Li Pan Chandra S Pedamallu Eric Severson Alejandro Gutierrez David M Dorfman Frank C Kuo Michael Kluk Patrick Zweidler-McKay Stephen C Blacklow Daniel J DeAngelo Jon C Aster
|
Cold Spring Harbor molecular case studies
|
Dynamic expression of long noncoding RNAs and repeat elements in synaptic plasticity.
|
2015-10-01
|
Marcel E. Dinger
|
Jesper L V Maag Debabrata Panja Ida Sporild Sudarshan Patil Dominik C Kaczorowski Clive R Bramham Karin Wibrand
|
Frontiers in Neuroscience
|
BrowserGenome.org: web-based RNA-seq data analysis and visualization.
|
2015-10-01
|
Jonathan Schmid-Burgk Veit Hornung
|
|
Nature Methods
|
Defining the three cell lineages of the human blastocyst by single-cell RNA-seq.
|
2015-10-01
|
Tim Xiaoming Hu
|
Paul Blakeley Norah M E Fogarty Ignacio Del Valle Sissy E Wamaitha Kay Elder Philip Snell Leila Christie Paul Robson Kathy K Niakan
|
Development
|
Functional development of the adult ovine mammary gland--insights from gene expression profiling.
|
2015-10-05
|
Amy M Paten Sam W Peterson Elizabeth J. Duncan Peter Dearden
|
Sarah J Pain Paul R Kenyon Hugh T Blair
|
BMC Genomics
|
Discovery of progenitor cell signatures by time-series synexpression analysis during Drosophila embryonic cell immortalization.
|
2015-10-05
|
Norbert Perrimon
|
Mary-Lee Dequéant Delphine Fagegaltier Yanhui Hu Kerstin Spirohn Amanda Simcox Gregory J Hannon
|
Proceedings of the National Academy of Sciences of the United States of America
|
RNA-Seq analysis for indigo biosynthesis pathway genes in Indigofera tinctoria and Polygonum tinctorium.
|
2015-10-05
|
Sanjog T Thul
|
Bijaya K Sarangi Yoshiko Minami
|
Genomics Data
|
Giving Time Purpose: The Synechococcus elongatus Clock in a Broader Network Context.
|
2015-10-05
|
Spencer Diamond
|
Ryan K Shultzaberger Joseph S Boyd Ralph J Greenspan Susan S Golden
|
Annual Review of Genetics
|
Hierarchical Modeling and Differential Expression Analysis for RNA-seq Experiments with Inbred and Hybrid Genotypes.
|
2015-10-05
|
Dan Nettleton
|
Andrew Lithio
|
Journal of Agricultural, Biological, and Environmental Statistics
|
Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues.
|
2015-10-05
|
Susan Fanayan Ling Yen Lee
|
Julia Fangfei Yan Hoguen Kim Seul-Ki Jeong Hyoung-Joo Lee Manveen K Sethi Ronald C Beavis Hogune Im Michael P Snyder Matan Hofree Trey Ideker Shiaw-Lin Wu Young-Ki Paik William S Hancock
|
Journal of Proteome Research
|
Global analysis of physical and functional RNA targets of hnRNP L reveals distinct sequence and epigenetic features of repressed and enhanced exons.
|
2015-10-05
|
Samuel J Allon
|
Brian S Cole Iulia Tapescu Michael J Mallory Jinsong Qiu Robert J Lake Hua-Ying Fan Xiang-Dong Fu Kristen W Lynch
|
RNA
|
Alternative Splicing Signatures in RNA-seq Data: Percent Spliced in (PSI).
|
2015-10-06
|
Matthias Heinig
|
Sebastian Schafer Kui Miao Craig C Benson Stuart A Cook Norbert Hubner
|
Current protocols in human genetics / editorial board, Nicholas C, Dracapoli ... [et al.]
|
Transition from somatic embryo to friable embryogenic callus in cassava: dynamic changes in cellular structure, physiological status, and gene expression profiles.
|
2015-10-06
|
Peng Zhang
|
Qiuxiang Ma Wenzhi Zhou
|
Frontiers in Plant Science
|
Chromatin-Remodelling Complex NURF Is Essential for Differentiation of Adult Melanocyte Stem Cells.
|
2015-10-06
|
Dana Koludrovic Gabrielle Mengus Irwin Davidson
|
Patrick Laurette Thomas Strub Céline Keime Madeleine Le Coz Sebastien Coassolo Lionel Larue
|
PLOS Genetics
|
Model of fibrolamellar hepatocellular carcinomas reveals striking enrichment in cancer stem cells
|
2015-10-06
|
Vincenzo Cardinale Guido Carpino Domenico Alvaro
|
Tsunekazu Oikawa Eliane Wauthier Timothy A Dinh Sara R Selitsky Andrea Reyna-Neyra Ronald Levine David Klimstra Eugenio Gaudio Nancy Carrasco Praveen Sethupathy Lola M Reid
|
Nature Communications
|
Identification of functional networks associated with cell death in the retina of OXYS rats during the development of retinopathy.
|
2015-10-06
|
Oyuna S. Kozhevnikova
|
Darya V Telegina Elena E Korbolina Nikita I Ershov Nataliya G Kolosova
|
Cell Cycle
|
A Semi-parametric Bayesian Approach for Differential Expression Analysis of RNA-seq Data.
|
2015-10-07
|
Chong Wang
|
Fangfang Liu Peng Liu
|
Journal of Agricultural, Biological, and Environmental Statistics
|
RNA-Seq Analysis of Abdominal Fat in Genetically Fat and Lean Chickens Highlights a Divergence in Expression of Genes Controlling Adiposity, Hemostasis, and Lipid Metabolism
|
2015-10-07
|
Chuming Chen Larry A. Cogburn Michel J Duclos
|
Christopher W Resnyk Hongzhan Huang Cathy H Wu Jean Simon Elisabeth Le Bihan-Duval
|
PLOS ONE
|
The androgen receptor controls expression of the cancer-associated sTn antigen and cell adhesion through induction of ST6GalNAc1 in prostate cancer.
|
2015-10-07
|
Daniel Vodák David J Elliott Hing Y Leung Rolf Inge Skotheim
|
Jennifer Munkley Sebastian Oltean Brian T Wilson Karen E Livermore Yan Zhou Eleanor Star Vasileios I Floros Bjarne Johannessen Bridget Knight Paul McCullagh John McGrath Malcolm Crundwell Craig N Robson Lorna W Harries Prabhakar Rajan Ian G Mills
|
Oncotarget
|
The membrane proteome of male gametophyte in Solanum lycopersicum.
|
2015-10-08
|
Enrico Schleiff Arindam Ghatak Palak Chaturvedi Wolfram Weckwerth
|
Puneet Paul Mario Selymesi Anida Mesihovic Klaus-Dieter Scharf Stefan Simm
|
Journal of Proteomics
|
B-Cell and Monocyte Contribution to Systemic Lupus Erythematosus Identified by Cell-Type-Specific Differential Expression Analysis in RNA-Seq Data.
|
2015-10-08
|
Joel M Guthridge Judith A. James
|
Mikhail G Dozmorov Nicolas Dominguez Krista Bean Susan R Macwana Virginia Roberts Edmund Glass
|
Bioinformatics and Biology Insights
|
Profiling RNA editing in human tissues: towards the inosinome Atlas
|
2015-10-09
|
Graziano Pesole Anna Maria D'Erchia Ernesto Picardi
|
Caterina Manzari Francesca Mastropasqua Italia Aiello
|
Scientific Reports
|
Molecular genetic response to varied wavelengths of light in Xiphophorus maculatus skin
|
2015-10-09
|
Jordan Chang
|
Yuan Lu William T Boswell Mikki Boswell Kaela L Caballero Ronald B Walter
|
Comparative Biochemistry and Physiology C: Toxicology and Pharmacology
|
Novel RNA variants in colorectal cancers.
|
2015-10-12
|
Andreas M Hoff Torfinn Nome Ragnhild A. Lothe Rolf Inge Skotheim
|
Bjarne Johannessen Sharmini Alagaratnam Sen Zhao Marthe Løvf Anne C Bakken Merete Hektoen Anita Sveen
|
Oncotarget
|
A basal stem cell signature identifies aggressive prostate cancer phenotypes.
|
2015-10-12
|
Robert Baertsch
|
Bryan A Smith Artem Sokolov Vladislav Uzunangelov Yulia Newton Kiley Graim Colleen Mathis Donghui Cheng Joshua M Stuart Owen N Witte
|
Proceedings of the National Academy of Sciences of the United States of America
|
Hepatic Long Intergenic Noncoding RNAs: High Promoter Conservation and Dynamic, Sex-Dependent Transcriptional Regulation by Growth Hormone.
|
2015-10-12
|
David J Waxman
|
Tisha Melia Pengying Hao Feyza Yilmaz
|
Molecular and Cellular Biology
|
RNA-Seq mediated root transcriptome analysis of Chlorophytum borivilianum for identification of genes involved in saponin biosynthesis.
|
2015-10-12
|
Avneesh Kumar Jagdeep Kaur
|
Sunil Kumar Shikha Kalra Baljinder Singh Kashmir Singh
|
Functional and Integrative Genomics
|
RNAseq by Total RNA Library Identifies Additional RNAs Compared to Poly(A) RNA Library.
|
2015-10-12
|
Brian D Lehmann David C Samuels
|
Yan Guo Shilin Zhao Quanhu Sheng Mingsheng Guo Jennifer Pietenpol Yu Shyr
|
BioMed Research International
|
Assessing Transcription Regulatory Elements To Evaluate the Expression Status of Missing Protein Genes on Chromosomes 11 and 19.
|
2015-10-12
|
Zhe Ren Shaohang Xu
|
Nannan Kong Yang Zhou Yamei Deng Yang Fan Yue Zhang Liang Lin Yan Ren Quanhui Wang Jin Zi Bo Wen Siqi Liu
|
Journal of Proteome Research
|
FOXM1 cistrome predicts breast cancer metastatic outcome better than FOXM1 expression levels or tumor proliferation index.
|
2015-10-12
|
Charles J Vaske Stephen Benz
|
Christina Yau Laurence Meyer Gary Scott Brian Egan Paul Labhart Nader Pourmand Christopher C Benz
|
Breast Cancer Research and Treatment
|
Spatially distinct neutrophil responses within the inflammatory lesions of pneumonic plague
|
2015-10-13
|
Nikolas M Stasulli William E. Goldman
|
Kara R Eichelberger Paul A Price Roger D Pechous Stephanie A Montgomery Joel S Parker
|
mBio
|
Extensive tissue-specific transcriptomic plasticity in maize primary roots upon water deficit
|
2015-10-13
|
Waqas Ahmed Malik Dan Nettleton Hans-Peter Piepho
|
Nina Opitz Caroline Marcon Anja Paschold Andrew Lithio Ronny Brandt Frank Hochholdinger
|
Journal of Experimental Botany
|
Computational analysis of stochastic heterogeneity in PCR amplification efficiency revealed by single molecule barcoding.
|
2015-10-13
|
James M Heather Benny Chain
|
Katharine Best Theres Oakes John Shawe-Taylor
|
Scientific Reports
|
Dynamic association rules for gene expression data analysis
|
2015-10-14
|
Wen-Hsiung Li
|
Shu-Chuan Chen Tsung-Hsien Tsai Cheng-Han Chung
|
BMC Genomics
|
Insights into the role of immunosenescence during varicella zoster virus infection (shingles) in the aging cell model
|
2015-10-14
|
Mukesh Kumar
|
Ji-Ae Kim Seul-Ki Park Chan-Hee Lee Ok Sarah Shin
|
Oncotarget
|
Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies.
|
2015-10-14
|
Jörg Vogel Lars Barquist
|
|
Annual Review of Genetics
|
RNA-Seq workflow: gene-level exploratory analysis and differential expression.
|
2015-10-14
|
Simon Anders Wolfgang Huber Michael I Love
|
Vladislav Kim
|
F1000Research
|
Decay-Initiating Endoribonucleolytic Cleavage by RNase Y Is Kept under Tight Control via Sequence Preference and Sub-cellular Localisation.
|
2015-10-16
|
Peter Redder Julien Prados
|
Vanessa Khemici Patrick Linder
|
PLOS Genetics
|
Genome-wide analysis on Chlamydomonas reinhardtii reveals the impact of hydrogen peroxide on protein stress responses and overlap with other stress transcriptomes.
|
2015-10-16
|
Sabeeha Merchant Stefan Schmollinger María Esther Pérez-Pérez Crysten E Blaby-Haas Stéphane D Lemaire
|
Ian K Blaby Sorel Fitz-Gibbon
|
The Plant Journal
|
Effect of heparin on the biological properties and molecular signature of human mesenchymal stem cells
|
2015-10-17
|
Rebekah M Samsonraj Drew M Titmarsh Emily T Camilleri
|
Ling Ling Torben Helledie Ren Jie Chua Oliver Dreesen Christian Dombrowski David A Rider Mario Galindo Ian Lee Wanjin Hong James H Hui Victor Nurcombe Andre J van Wijnen Simon M Cool
|
Gene
|
CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in neurodevelopment.
|
2015-10-19
|
Deyou Zheng
|
Ping Wang Mingyan Lin Erika Pedrosa Anastasia Hrabovsky Zheng Zhang Wenjun Guo Herbert M Lachman
|
Molecular Autism
|
Elucidating drivers of oral epithelial dysplasia formation and malignant transformation to cancer using RNAseq.
|
2015-10-19
|
Jennifer L Graham Rebecca Chalkley Alastair Droop
|
Caroline Conway Preetha Chengot Catherine Daly Lisa Ross Pamela Rabbitts Lucy F Stead
|
Oncotarget
|
Functional analysis of NtMPK2 uncovers its positive role in response to Pseudomonas syringae pv. tomato DC3000 in tobacco.
|
2015-10-19
|
Qingyou Xia
|
Xingtan Zhang Genhong Wang Junping Gao Mengyun Nie Wenshan Liu
|
Plant Molecular Biology
|
Identification of a novel fusion transcript between human relaxin-1 (RLN1) and human relaxin-2 (RLN2) in prostate cancer.
|
2015-10-20
|
Sean D McGrath Marcel E. Dinger Elizabeth D. Williams Gregor Tevz Jyotsna Batra
|
Ryan Demeter Vincent Magrini Varinder Jeet Anja Rockstroh Stephen McPherson John Lai Nenad Bartonicek Jiyuan An Melanie L Lehman Colleen C Nelson
|
Molecular and Cellular Endocrinology
|
Comparative RNA seq analysis of the New Zealand glowworm Arachnocampa luminosa reveals bioluminescence-related genes.
|
2015-10-21
|
Peter Dearden
|
Miriam L Sharpe Gregory Gimenez Kurt L Krause
|
BMC Genomics
|
Modeling of autosomal-dominant retinitis pigmentosa in Caenorhabditis elegans uncovers a nexus between global impaired functioning of certain splicing factors and cell type-specific apoptosis.
|
2015-10-21
|
Karinna Rubio-Peña Sylvain Foissac Eric Cornes J Cerón
|
Laura Fontrodona David Aristizábal-Corrales Silvia Torres Francisco J García-Rodríguez Xènia Serrat David González-Knowles Montserrat Porta-De-La-Riva
|
RNA
|
The Human Endometrium-Specific Proteome Defined by Transcriptomics and Antibody-Based Profiling.
|
2015-10-21
|
Linn Fagerberg Mathias Uhlén
|
Agata Zieba Evelina Sjöstedt Matts Olovsson Björn M Hallström Linda Oskarsson Karolina Edlund Anna Tolf Fredrik Ponten
|
OMICS: A Journal of Integrative Biology
|
Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.
|
2015-10-22
|
Aleksandra A Kolodziejczyk John C Marioni Sarah Teichmann Jong Kyoung Kim
|
Tomislav Ilicic
|
Nature Communications
|
A Diencephalic Dopamine Source Provides Input to the Superior Colliculus, where D1 and D2 Receptors Segregate to Distinct Functional Zones.
|
2015-10-22
|
Martha Constantine-Paton Rory Kirchner Yasunobu Murata Sung-Yon Kim
|
Andrew D Bolton Andrew Young Tru Dang Yuchio Yanagawa
|
Cell Reports
|
HENMT1 and piRNA Stability Are Required for Adult Male Germ Cell Transposon Repression and to Define the Spermatogenic Program in the Mouse.
|
2015-10-23
|
Jeffrey R Mann David L. Adelson Lee H Wong Hamish S. Scott Moira O'bryan
|
Shu Ly Lim Zhi Peng Qu R Daniel Kortschak David M Lawrence Joel Geoghegan Anna-Lena Hempfling Martin Bergmann Christopher C Goodnow Christopher J Ormandy Duangporn Jamsai
|
PLOS Genetics
|
Menadione-Induced Oxidative Stress Re-Shapes the Oxylipin Profile of Aspergillus flavus and Its Lifestyle.
|
2015-10-23
|
Walter Sanseverino
|
Marco Zaccaria Matteo Ludovici Simona Marianna Sanzani Antonio Ippolito Riccardo Aiese Cigliano Marzia Scarpari Valeria Scala Corrado Fanelli Massimo Reverberi
|
Toxins
|
Circularization restores signal recognition particle RNA functionality in Thermoproteus
|
2015-10-24
|
L Randau
|
André Plagens Michael Daume Julia Wiegel
|
eLife
|
Mapping 3' transcript ends in the bank vole (Clethrionomys glareolus) mitochondrial genome with RNA-Seq.
|
2015-10-26
|
Petr Kotlík
|
Silvia Marková Karolína Filipi Jeremy B Searle
|
BMC Genomics
|
IRAK1 is a novel DEK transcriptional target and is essential for head and neck cancer cell survival.
|
2015-10-26
|
Phillip Dexheimer
|
Allie K Adams Lyndsey C Bolanos Rebekah A Karns Bruce J Aronow Kakajan Komurov Anil G Jegga Keith A Casper Yash J Patil Keith M Wilson Daniel T Starczynowski Susanne I Wells
|
Oncotarget
|
Identification of Genes Related to Growth and Lipid Deposition from Transcriptome Profiles of Pig Muscle Tissue.
|
2015-10-27
|
Hao Zhang
|
Zhixiu Wang Qinggang Li Yangzom Chamba Bo Zhang Peng Shang Changxin Wu
|
PLOS ONE
|
A Database of microRNA Expression Patterns in Xenopus laevis
|
2015-10-27
|
Sara Lopez-Gomollon Simon Moxon Tamas Dalmay
|
Ayisha Ahmed Nicole J Ward Camille Viaut Matthew L Tomlinson Ilya Patrushev Michael J Gilchrist Dario Dotlic Andrea E Münsterberg Grant N Wheeler
|
PLOS ONE
|
RNA-Seq of Tumor-Educated Platelets Enables Blood-Based Pan-Cancer, Multiclass, and Molecular Pathway Cancer Diagnostics.
|
2015-10-27
|
Bauke Ylstra Pieter Wesseling Jan Koster
|
Myron G Best Nik Sol Irsan Kooi Jihane Tannous Bart A Westerman François Rustenburg Pepijn Schellen Heleen Verschueren Edward Post Najim Ameziane Josephine Dorsman Egbert F Smit Henk M Verheul David P Noske Jaap C Reijneveld R Jonas A Nilsson Bakhos A Tannous Thomas Wurdinger
|
Cancer Cell
|
Transcriptomic Changes in Coral Holobionts Provide Insights into Physiological Challenges of Future Climate and Ocean Change.
|
2015-10-28
|
Nedeljka N. Rosic David I Kline Chon-Kit Kenneth Chan Sophie Dove David Edwards Ove Hoegh-Guldberg
|
Paulina Kaniewska Edmund Yew Siang Ling
|
PLOS ONE
|
Strand-Specific RNA-Seq Analyses of Fruiting Body Development in Coprinopsis cinerea
|
2015-10-28
|
Igor V Grigoriev Kazuo Ishii Yuichi Sakamoto Kerrie Barry
|
Hajime Muraguchi Kiwamu Umezawa Mai Niikura Makoto Yoshida Toshinori Kozaki Kiyota Sakai Motoyuki Shimizu Kiyoshi Nakahori Cindy Choi Chew Yee Ngan Eika Lindquist Anna Lipzen Andrew Tritt Sajeet Haridas Patricia J Pukkila
|
PLOS ONE
|
Sxl-Dependent, tra/tra2-Independent Alternative Splicing of the Drosophila melanogaster X-Linked Gene found in neurons.
|
2015-10-28
|
David Sturgill
|
Xia Sun Haiwang Yang Brian Oliver Leonard Rabinow Marie-Laure Samson
|
G3
|
Transcriptomic analysis of global changes in cytokine expression in mouse spleens following acute Toxoplasma gondii infection.
|
2015-10-28
|
Xing-Quan Zhu Si-Yang Huang Dong-Hui Zhou
|
Jun-Jun He Jun Ma Hui-Qun Song Jin-Lei Wang
|
Parasitology Research
|
A high-throughput RNA-seq approach to profile transcriptional responses
|
2015-10-29
|
Xiaoquan Wen Francesca Luca Roger Pique-Regi
|
G A Moyerbrailean G O Davis C T Harvey D Watza
|
Scientific Reports
|
RNA Editing in Chloroplasts of Spirodela polyrhiza, an Aquatic Monocotelydonous Species
|
2015-10-30
|
Wenqin Wang Joachim Messing
|
Wei Zhang Yongrui Wu Pal Maliga
|
PLOS ONE
|
ccmGDB: a database for cancer cell metabolism genes
|
2015-10-30
|
Feixiong Cheng
|
Pora Kim Junfei Zhao Zhongming Zhao
|
Nucleic Acids Research
|
The vitamin D-dependent transcriptome of human monocytes.
|
2015-10-30
|
Veijo Nurminen Antonio Neme Carsten Carlberg
|
Sabine Seuter
|
The Journal of Steroid Biochemistry and Molecular Biology
|
Activation of AhR-mediated toxicity pathway by emerging pollutants polychlorinated diphenyl sulfides.
|
2015-10-30
|
John P Giesy Pu Xia Rui Zhang Guanyong Su Zunyao Wang Xiaowei Zhang
|
Junjiang Zhang Yang Wu Jie Xia Jiamin Zhang Daniel L Villeneuve Hongxia Yu
|
Chemosphere
|
Cross-platform normalization of microarray and RNA-seq data for machine learning applications
|
2015-10-30
|
Casey S. Greene
|
Jeffrey A Thompson Jie Tan
|
|
Cross-platform normalization of microarray and RNA-seq data for machine learning applications
|
2015-10-30
|
Casey S. Greene
|
Jeffrey A Thompson Jie Tan
|
|
Comparative blood transcriptome analysis in idiopathic and LRRK2 G2019S-associated Parkinson's disease.
|
2015-10-31
|
Carlos Prieto
|
Jon Infante María Sierra Pascual Sánchez-Juan Isabel González-Aramburu Coro Sánchez-Quintana José Berciano Onofre Combarros Jesús Sainz
|
Neurobiology of Aging
|
Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems
|
2015-11
|
Silvana Konermann Eugene Koonin
|
Sergey Shmakov Omar O. Abudayyeh Kira S. Makarova Yuri I. Wolf Jonathan S. Gootenberg Ekaterina Semenova Leonid Minakhin Julia Joung Konstantin Severinov Feng Zhang
|
Molecular Cell
|
LEDGF/p75 interacts with mRNA splicing factors and targets HIV-1 integration to highly spliced genes.
|
2015-11-01
|
Mamuka Kvaratskhelia Stephen H. Hughes
|
Parmit Kumar Singh Matthew R Plumb Andrea L Ferris James R Iben Xiaolin Wu Hind J Fadel Brian T Luke Caroline Esnault Eric M Poeschla Henry L Levin
|
Genes & Development
|
Global Analysis of mRNA, Translation, and Protein Localization: Local Translation Is a Key Regulator of Cell Protrusions.
|
2015-11-01
|
Faraz Khosravi Mardakheh
|
Angela Paul Sandra Kümper Amine Sadok Hugh Paterson Afshan Mccarthy Yinyin Yuan Christopher J Marshall
|
Developmental Cell
|
SOX9 modulates the expression of key transcription factors required for heart valve development.
|
2015-11-02
|
Olivia Alder Pamela A. Hoodless
|
Victoria C Garside Rebecca Cullum Daphne Y Lu Ryan Vander Werff Mikhail Bilenky Yongjun Zhao Steven J M Jones Marco A Marra T Michael Underhill
|
Development
|
Global Transcriptome Analysis of Primary Cerebrocortical Cells: Identification of Genes Regulated by Triiodothyronine in Specific Cell Types.
|
2015-11-02
|
Juan Bernal
|
Pilar Gil-Ibañez Francisco García-García Joaquín Dopazo Beatriz Morte
|
Cerebral Cortex
|
Multi-Scale Molecular Deconstruction of the Serotonin Neuron System.
|
2015-11-04
|
Rachael Brust
|
Benjamin W Okaty Morgan E Freret Benjamin D Rood Morgan L Hennessy Danielle deBairos Jun Chul Kim Melloni N Cook Susan M Dymecki
|
Neuron
|
The Orthology Clause in the Next Generation Sequencing Era: Novel Reference Genes Identified by RNA-seq in Humans Improve Normalization of Neonatal Equine Ovary RT-qPCR Data.
|
2015-11-04
|
Dragos Scarlet Reinhard Ertl Christine Aurich
|
Ralf Steinborn
|
PLOS ONE
|
Spatio-Temporal Gene Expression Profiling during In Vivo Early Ovarian Folliculogenesis: Integrated Transcriptomic Study and Molecular Signature of Early Follicular Growth.
|
2015-11-05
|
Bertrand Servin
|
Agnes Bonnet Philippe Mulsant Beatrice Mandon-Pepin
|
PLOS ONE
|
Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells
|
2015-11-05
|
Zhikun Zhao Qichao Yu Liang Wu Yong Hou Karsten Kristiansen Huanming Yang Xiuqing Zhang
|
Xiaolong Zhang Ling Wang Bo Li Guibo Li Michael Dean Yanhui Wang Xinxin Lin Weijian Rao Zhanlong Mei Yang Li Runze Jiang Huan Yang Fuqiang Li Guoyun Xie Liqin Xu Kui Wu Jie Zhang Jianghao Chen Ting Wang Yingrui Li Jian Wang Xun Xu
|
GigaScience
|
A multi-omic analysis of human naïve CD4+ T cells.
|
2015-11-06
|
Danielle Thierry-Mieg Tai-Chung Huang Sneha M Pinto Jun Zhong Luigi Marchionni Jean Thierry-Mieg Min-Sik Kim
|
Christopher J Mitchell Derese Getnet Srikanth S Manda Praveen Kumar Raja Sekhar Nirujogi Mio Iwasaki Patrick G Shaw Xinyan Wu Raghothama Chaerkady Arivusudar Marimuthu Babylakshmi Muthusamy Nandini A Sahasrabuddhe Rajesh Raju Caitlyn Bowman Ludmila Danilova Jevon Cutler Dhanashree S Kelkar Charles G Drake T S Keshava Prasad Peter N Murakami Alan F Scott Leming Shi Rafael Irizarry Leslie Cope Yasushi Ishihama Charles Wang Harsha Gowda Akhilesh Pandey
|
BMC Systems Biology
|
Proper Use of Allele-Specific Expression Improves Statistical Power for cis-eQTL Mapping with RNA-Seq Data
|
2015-11-07
|
Charles M. Perou
|
Yi-Juan Hu Wei Sun Jung-Ying Tzeng
|
Journal of the American Statistical Association
|
Host Transcriptional Profiling at Early and Later Stages of the Compatible Interaction Between Phaseolus vulgaris and Meloidogyne incognita.
|
2015-11-09
|
Mário Massayuki Inomoto Maria Lucia Carneiro Vieira
|
Luciane Santini Carla de Freitas Munhoz Mauro Ferreira Bonfim Marcelo Mendes Brandão
|
Phytopathology
|
RNA sequencing of Sleeping Beauty transposon-induced tumors detects transposon-RNA fusions in forward genetic cancer screens
|
2015-11-09
|
Jesse D Riordan Adam J. Dupuy
|
Nuri A Temiz Branden S Moriarity Natalie K Wolf David A Largaespada Aaron L Sarver
|
Genome Research
|
Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers.
|
2015-11-09
|
Albin Sandelin Timo Lassmann Bogumil Kaczkowski Hideya Kawaji Masayoshi Itoh Piero Carninci Yoshihide Hayashizaki Robin Andersson
|
Yuji Tanaka Alistair R R Forrest FANTOM5 Consortium
|
Cancer Research
|
Highly proliferative primitive fetal liver hematopoietic stem cells are fueled by oxidative metabolic pathways.
|
2015-11-09
|
Ruben Boon Alex van Vliet Sarah-maria Fendt Nick van Gastel Catherine Verfaillie Peter Carmeliet
|
Javed K Manesia Zhuofei Xu Dorien Broekaert Guy Eelen Thomas Vanwelden Steve Stegen Alberto Pascual-Montano Geert Carmeliet Satish Khurana
|
Stem Cell Research
|
STEM-22LARGE-SCALE SINGLE-CELL RNA-seq REVEALS A DEVELOPMENTAL CELLULAR HIERARCHY IN HUMAN OLIGODENDROGLIOMA.
|
2015-11-09
|
Aviv Regev
|
Andrew Venteicher Itay Tirosh Christine Hebert Leah Escalante Brian Nahed Daniel Cahill William Curry Robert Martuza Bradley Bernstein David Louis Mario Suva
|
Neuro-Oncology
|
A resource of ribosomal RNA-depleted RNA-Seq data from different normal adult and fetal human tissues.
|
2015-11-10
|
Nicolas Bertin
|
Jocelyn Y H Choy Priscilla L S Boon Melissa J Fullwood
|
Scientific Data
|
An effective analytic method for detecting tissue-specific genes in RNA-seq experiments.
|
2015-11-10
|
Xiaohua Douglas Zhang
|
Guoqing Zhao Qiao Li I-Ming Wang Xiaoqiao Liu Xiangzhong Fang
|
Pharmacogenomics
|
Cancer genetics: RNA-seq for blood-based pan-cancer diagnostics.
|
2015-11-10
|
Liesbet Lieben
|
|
Nature Reviews Genetics
|
REST-Governed Gene Expression Profiling in a Neuronal Cell Model Reveals Novel Direct and Indirect Processes of Repression and Up-Regulation.
|
2015-11-10
|
Davide Cittaro
|
Jose M Garcia-Manteiga Silvia Bonfiglio Lucrezia Folladori Maria L Malosio Dejan Lazarevic Elia Stupka Jacopo Meldolesi
|
Frontiers in Cellular Neuroscience
|
Saccular Transcriptome Profiles of the Seasonal Breeding Plainfin Midshipman Fish (Porichthys notatus), a Teleost with Divergent Sexual Phenotypes.
|
2015-11-11
|
Joseph A. Sisneros
|
Joshua Faber-Hammond Manoj P Samanta Elizabeth A Whitchurch Dustin Manning Allison B Coffin
|
PLOS ONE
|
A Comprehensive RNA Sequencing Analysis of the Adeno-Associated Virus (AAV) Type 2 Transcriptome Reveals Novel AAV Transcripts, Splice Variants, and Derived Proteins
|
2015-11-11
|
Andreas Gogol-Döring
|
Catrin Stutika Laura Botschen Mario Mietzsch Stefan Weger Mirjam Feldkamp Wei Chen Regine Heilbronn
|
Journal of Virology
|
Genome-Wide Transcriptome Analysis During Anthesis Reveals New Insights into the Molecular Basis of Heat Stress Responses in Tolerant and Sensitive Rice Varieties.
|
2015-11-11
|
Ludovico Dreni Massimo Galbiati Lucia Colombo Martin M. Kater
|
Nahuel González-Schain Lovely M F Lawas Sigrid Heuer Krishna S V Jagadish
|
Plant and Cell Physiology
|
RNA-seq Brings New Insights to the Intra-Macrophage Transcriptome of Salmonella Typhimurium
|
2015-11-12
|
Shabarinath Srikumar Siân V Owen Carsten Kröger Karsten Hokamp
|
Magali Hébrard Aoife Colgan Sathesh K Sivasankaran Andrew D S Cameron Jay C D Hinton
|
PLOS Pathogens
|
Molecular response of chorioretinal endothelial cells to complement injury: implications for macular degeneration.
|
2015-11-13
|
Luke A. Wiley Budd A. Tucker Todd E. Scheetz Robert F. Mullins Elliott H Sohn Edwin M. Stone
|
Shemin Zeng S Scott Whitmore Megan J Riker
|
The Journal of Pathology
|
Diagnosis: RNA-seq for blood-based pan-cancer diagnostics.
|
2015-11-13
|
Liesbet Lieben
|
|
Nature Reviews Cancer
|
Molecular tools for studying the major malaria vector Anopheles funestus: improving the utility of the genome using a comparative poly(A) and Ribo-Zero RNAseq analysis
|
2015-11-14
|
Gareth D Weedall
|
Helen Irving Margaret A Hughes Charles S Wondji
|
BMC Genomics
|
miRge - A Multiplexed Method of Processing Small RNA-Seq Data to Determine MicroRNA Entropy
|
2015-11-16
|
Marc K. Halushka
|
Alexander S Baras Christopher J Mitchell Jason R Myers Simone Gupta Lien-Chun Weng John M Ashton Toby C Cornish Akhilesh Pandey
|
PLOS ONE
|
Tumor Repression of VCaP Xenografts by a Pyrrole-Imidazole Polyamide.
|
2015-11-16
|
Peter Dervan
|
Amanda E Hargrove Thomas F Martinez Alissa A Hare Alexis A Kurmis John W Phillips Sudha Sud Kenneth J Pienta
|
PLOS ONE
|
Interaction of Arabidopsis Trihelix-Domain Transcription Factors VFP3 and VFP5 with Agrobacterium Virulence Protein VirF.
|
2015-11-16
|
Vitaly Citovsky
|
Elena García-Cano Shimpei Magori Qi Sun Zehong Ding Sondra G Lazarowitz
|
PLOS ONE
|
High-throughput mRNA and miRNA profiling of epithelial-mesenchymal transition in MDCK cells
|
2015-11-16
|
Mathias Müller
|
Priyank Shukla Claus Vogl Barbara Wallner Doris Rigler Sabine Macho-Maschler
|
BMC Genomics
|
Dual RNA-seq of Nontypeable Haemophilus influenzae and Host Cell Transcriptomes Reveals Novel Insights into Host-Pathogen Cross Talk
|
2015-11-17
|
Buket Baddal Raffaele A. Calogero
|
Alessandro Muzzi Stefano Censini Giulia Torricelli Silvia Guidotti Anna R Taddei Antonello Covacci Mariagrazia Pizza Rino Rappuoli Marco Soriani Alfredo Pezzicoli
|
mBio
|
RNA-seq is a valuable complement of conventional diagnostic tools in newly diagnosed AML patients
|
2015-11-17
|
Vera Magistroni Carlo Gambacorti-Passerini
|
Rocco Piazza Caterina Cecchetti Alessandra Pirola Carla Donandoni Diletta Fontana Caterina Mezzatesta Benedetta Bianchi Lorenza Borin Monica Fumagalli
|
American Journal of Hematology
|
Transcriptome profiling of a spirodiclofen susceptible and resistant strain of the European red mite Panonychus ulmi using strand-specific RNA-seq.
|
2015-11-18
|
Wannes Dermauw Thomas Van Leeuwen Ralf Nauen Luc Tirry
|
Sabina Bajda Robert Greenhalgh Richard M Clark
|
BMC Genomics
|
Identification and annotation of conserved promoters and macrophage-expressed genes in the pig genome
|
2015-11-18
|
Mick Watson Ronan Kapetanovic Dario Beraldi Alan Archibald David A Hume
|
Christelle Robert
|
BMC Genomics
|
CD5L/AIM Regulates Lipid Biosynthesis and Restrains Th17 Cell Pathogenicity
|
2015-11-18
|
Aviv Regev Chuan Wu Gerd Meyer zu Hörste
|
Chao Wang Nir Yosef Jellert Gaublomme Youjin Lee Clary B Clish Jim Kaminski Sheng Xiao Mathias Pawlak Yasuhiro Kishi Nicole Joller Katarzyna Karwacz Chen Zhu Maria Ordovas-Montanes Asaf Madi Ivo Wortman Toru Miyazaki Raymond A Sobel Hongkun Park Vijay K Kuchroo
|
Cell
|
Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity.
|
2015-11-18
|
Pier Paolo Pandolfi Aviv Regev Rahul Satija Chuan Wu Alex K. Shalek Li V. Yang
|
Jellert T Gaublomme Nir Yosef Youjin Lee Rona S Gertner Tak Mak Vijay K Kuchroo Hongkun Park
|
Cell
|
A Three-Dimensional Cell Culture Model To Study Enterovirus Infection of Polarized Intestinal Epithelial Cells.
|
2015-11-18
|
Carolyn Coyne
|
Coyne G Drummond Cheryl A Nickerson
|
mSphere
|
Genome-wide RNA-Seq analysis of breast muscles of two broiler chicken groups differing in shear force.
|
2015-11-22
|
Joanna Nowak Katarzyna Połtowicz Artur Gurgul Katarzyna Ropka-Molik Katarzyna Piórkowska
|
K Żukowski
|
Animal Genetics
|
Identification of Putative Nuclear Receptors and Steroidogenic Enzymes in Murray-Darling Rainbowfish (Melanotaenia fluviatilis) Using RNA-Seq and De Novo Transcriptome Assembly.
|
2015-11-23
|
Peter A. Bain Alexie Papanicolaou
|
Anupama Kumar
|
PLOS ONE
|
Deciphering the molecular adaptation of the king scallop (Pecten maximus) to heat stress using transcriptomics and proteomics.
|
2015-11-23
|
Romain Lavaud Jonathan Flye-Sainte-Marie Fred Jean Vianney Pichereau Melody S Clark
|
Sébastien Artigaud Joëlle Richard Michael A S Thorne Lloyd S Peck
|
BMC Genomics
|
RNA-Seq and Mass-Spectrometry-Based Lipidomics Reveal Extensive Changes of Glycerolipid Pathways in Brown Adipose Tissue in Response to Cold.
|
2015-11-24
|
Susanne Mandrup
|
Ann-Britt Marcher Anne Loft Ronni Nielsen Terhi Vihervaara Jesper Grud Skat Madsen Marko Sysi-Aho Kim Ekroos
|
Cell Reports
|
Promoter-based identification of novel non-coding RNAs reveals the presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana.
|
2015-11-25
|
Zofia Szweykowska-Kulinska
|
Ge Qu Katarzyna Kruszka Patrycja Plewka Shu-Yi Yang Tzyy-Jen Chiou Artur Jarmolowski Manuel Echeverria Wojciech M Karlowski
|
BMC Genomics
|
Analysis of nucleosome positioning landscapes enables gene discovery in the human malaria parasite Plasmodium falciparum.
|
2015-11-25
|
Evelien M. Bunnik
|
Xueqing Maggie Lu Neeti Pokhriyal Sara Nasseri Stefano Lonardi Karine G Le Roch
|
BMC Genomics
|
Different mechanisms of resistance modulate sulfite tolerance in wine yeasts.
|
2015-11-28
|
Chiara Nadai Alessio Giacomini Viviana Corich Laura Treu Stefano Campanaro
|
|
Applied Microbiology and Biotechnology
|
Bromodomain Proteins Contribute to Maintenance of Bloodstream Form Stage Identity in the African Trypanosome
|
2015-12
|
Nina Papavasiliou Monica Mugnier Erik W. Debler
|
Danae Schulz Eda-Margaret Paulsen Hee-Sook Kim Chun-wa W Chung David F Tough Inmaculada Rioja Rab K Prinjha F Nina Papavasiliou
|
PLOS Biology
|
mRNA-seq reveals skeletal muscle atrophy in response to handling stress in a marine teleost, the red cusk-eel (Genypterus chilensis)
|
2015-12-01
|
Herman Silva
|
Jorge E Aedo Jonathan Maldonado Víctor Aballai Juan M Estrada Macarena Bastias-Molina Claudio Meneses Cristian Gallardo-Escarate Alfredo Molina Juan A Valdés
|
BMC Genomics
|
Ig Superfamily Ligand and Receptor Pairs Expressed in Synaptic Partners in Drosophila.
|
2015-12-01
|
Liming Tan Kelvin Xi Zhang Matthew Y Pecot Sonal Nagarkar-Jaiswal Pei-Tseng Lee Shin-ya Takemura Jason M McEwen Aljoscha Nern Shuwa Xu Wael Tadros Zhenqing Chen Kai Zinn Hugo J. Bellen Marta Morey S Lawrence Zipursky
|
|
Cell
|
Exposure to sixty minutes of hyperoxia upregulates myocardial humanins in patients with coronary artery disease - a pilot study.
|
2015-12-01
|
Joel Starkopf
|
I Karu P Tahepold A Ruusalepp E Reimann S Koks
|
Journal of Physiology and Pharmacology
|
Nitro-Fatty Acids in Plant Signaling: Nitro-Linolenic Acid Induces the Molecular Chaperone Network in Arabidopsis.
|
2015-12-01
|
Francisco J. Corpas
|
Capilla Mata-Pérez Beatriz Sánchez-Calvo María N Padilla Juan C Begara-Morales Francisco Luque Manuel Melguizo Jaime Jiménez-Ruiz Jesús Fierro-Risco Antonio Peñas-Sanjuán Raquel Valderrama Juan B Barroso
|
Plant Physiology
|
Phenotypic Heterogeneity Affects Stenotrophomonas maltophilia K279a Colony Morphotypes and β-Lactamase Expression
|
2015-12-02
|
Konrad Förstner Thomas A Kohl
|
Ebrahim M. Abda Dagmar Krysciak Ines Krohn-Molt Uwe Mamat Christel Schmeisser Ulrich E. Schaible Stefan Nieman Wolfgang R. Streit
|
Frontiers in Microbiology
|
Transcriptome profiling of two Iberian freshwater fish exposed to thermal stress.
|
2015-12-04
|
Maria Manuela Coelho Ana R. Grosso
|
Tiago Filipe Jesus Vera Maria Fonseca Almeida-Val
|
Journal of Thermal Biology
|
The Schistosome Esophagus Is a 'Hotspot' for Microexon and Lysosomal Hydrolase Gene Expression: Implications for Blood Processing
|
2015-12-07
|
Leandro Xavier Neves Leonardo P Farias Sandy J Macdonald Ricardo DeMarco
|
R Alan Wilson Xiao Hong Li Juliana Vitoriano-Souza Luciana C C Leite Sally James Peter D Ashton William Castro Borges
|
PLOS Neglected Tropical Diseases
|
Topographical mapping of α- and β-keratins on developing chicken skin integuments: Functional interaction and evolutionary perspectives
|
2015-12-08
|
Wen-Hsiung Li
|
Ping Wu Chen Siang Ng Jie Yan Yung-Chih Lai Chih-Kuan Chen Yu-Ting Lai Siao-Man Wu Jiun-Jie Chen Weiqi Luo Randall B Widelitz Cheng-Ming Chuong
|
Proceedings of the National Academy of Sciences of the United States of America
|
Reproducible features of small RNAs in C. elegans reveal NU RNAs and provide insights into 22G RNAs and 26G RNAs
|
2015-12-08
|
Antony M Jose
|
Andrew L Blumenfeld
|
RNA
|
Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation
|
2015-12-08
|
Shaun Jackman
|
René L Warren Ewan A Gibb Benjamin P Vandervalk Hamid Mohamadi Justin Chu Anthony Raymond Stephen Pleasance Robin Coope Mark R Wildung Carol E Ritland Jean Bousquet Steven J M Jones Joerg Bohlmann Inanç Birol
|
Genome Biology and Evolution
|
RNAseq analysis for the diagnosis of muscular dystrophy.
|
2015-12-08
|
Michael D. Wilson Cynthia Hawkins
|
Hernan Gonorazky Minggao Liang Beryl Cummings Monkol Lek Johann Micallef Raveen Basran Ronald Cohn Daniel MacArthur Christian R Marshall Peter N Ray James J Dowling
|
Annals of clinical and translational neurology
|
High-throughput transcriptomics reveals common and strain-specific responses of human macrophages to infection with Mycobacterium abscessus Smooth and Rough variants.
|
2015-12-09
|
Aleksandra A Miranda-CasoLuengo Kévin Rue-Albrecht Brendan Loftus David E. MacHugh A Aulicino
|
Adam M Dinan John A Browne
|
BMC Genomics
|
Cell-Specific Transcriptional Profiling of Ciliated Sensory Neurons Reveals Regulators of Behavior and Extracellular Vesicle Biogenesis
|
2015-12-09
|
David H Hall
|
Juan Wang Rachel Kaletsky Malan Silva April Williams Leonard A Haas Rebecca J Androwski Jessica N Landis Cory Patrick Alina Rashid Dianaliz Santiago-Martinez Maria Gravato-Nobre Jonathan Hodgkin Coleen T Murphy Maureen M Barr
|
Current Biology
|
RNA-seq reveals post-transcriptional regulation of Drosophila insulin-like peptide dilp8 and the neuropeptide-like precursor Nplp2 by the exoribonuclease Pacman/XRN1.
|
2015-12-09
|
Christopher Jones
|
Amy L Pashler Benjamin P Towler Sophie R Robinson Sarah F Newbury
|
Nucleic Acids Research
|
Investigating the Influence of Ribavirin on Human Respiratory Syncytial Virus RNA Synthesis by Using a High-Resolution Transcriptome Sequencing Approach.
|
2015-12-09
|
Christiane Hertz-Fowler David A. Matthews Julian Hiscox John Barr John G Kenny
|
Waleed Aljabr Olivier Touzelet Georgios Pollakis Weining Wu Diane C Munday Margaret Hughes Rachel Fearns
|
Journal of Virology
|
Transcriptome profiling of human FoxP3+ regulatory T cells
|
2015-12-10
|
Cuong K. Nguyen
|
Ravikiran Bhairavabhotla Yong C Kim Deborah D Glass Thelma M Escobar Mira C Patel Rami Zahr Gokhul K Kilaru Stefan A Muljo Ethan M Shevach
|
Human Immunology
|
Rapamycin reduces fibroblast proliferation without causing quiescence and induces STAT5A/B-mediated cytokine production.
|
2015-12-10
|
Anthony Kusalik
|
Zoe E Gillespie Kimberly MacKay Michelle Sander Brett Trost Wojciech Dawicki Aruna Wickramarathna John Gordon Mark Eramian Ian R Kill Joanna M Bridger Jennifer A Mitchell Christopher H Eskiw
|
Nucleus
|
RNA polymerase errors cause splicing defects and can be regulated by differential expression of RNA polymerase subunits.
|
2015-12-10
|
Lucas B Carey
|
|
eLife
|
Comparative transcriptome analysis reveals molecular strategies of oriental river prawn Macrobrachium nipponense in response to acute and chronic nitrite stress.
|
2015-12-11
|
Jian G. Qin
|
Zhixin Xu Tongyu Li Erchao Li Ke Chen Zhili Ding Liqiao Chen Jinyun Ye
|
Fish and Shellfish Immunology
|
Genome-wide identification of Hsp70 genes in channel catfish and their regulated expression after bacterial infection.
|
2015-12-13
|
Shikai Liu
|
Lin Song Chao Li Yangjie Xie Jiaren Zhang Jun Yao Chen Jiang Yun Li Zhanjiang Liu
|
Fish and Shellfish Immunology
|
Fine-mapping cellular QTLs with RASQUAL and ATAC-seq.
|
2015-12-14
|
Daniel J Gaffney
|
Natsuhiko Kumasaka Andrew J Knights
|
Nature Genetics
|
Comparative Transcriptome Analysis in the Hepatopancreas Tissue of Pacific White Shrimp Litopenaeus vannamei Fed Different Lipid Sources at Low Salinity.
|
2015-12-15
|
Jian G. Qin
|
Ke Chen Erchao Li Zhixin Xu Tongyu Li Chang Xu Liqiao Chen
|
PLOS ONE
|
ADAR2 affects mRNA coding sequence edits with only modest effects on gene expression or splicing in vivo
|
2015-12-15
|
Mark R Cookson
|
Allissa A Dillman Dagmar Galter
|
RNA Biology
|
Transcriptional, post-transcriptional and chromatin-associated regulation of pri-miRNAs, pre-miRNAs and moRNAs.
|
2015-12-15
|
Laure Bally-Cuif Chirag Nepal Yavor Hadzhiev Marion Coolen Jesper B. Andersen Boris Lenhard Piero Carninci
|
Delphine Cussigh Piotr Mydel Vidar M Steen Ferenc Müller
|
Nucleic Acids Research
|
A human haploid gene trap collection to study lncRNAs with unusual RNA biology
|
2015-12-15
|
Irena Vlatkovic
|
Aleksandra E Kornienko Jürgen Neesen Denise P Barlow Florian M Pauler
|
RNA Biology
|
Adeno-associated virus gene therapy vector scAAVIGF-I for transduction of equine articular chondrocytes and RNA-seq analysis.
|
2015-12-16
|
Richard Slayden
|
D D Hemphill C W McIlwraith R J Samulski L R Goodrich
|
Osteoarthritis and Cartilage
|
Hierarchical deconstruction of mouse olfactory sensory neurons: from whole mucosa to single-cell RNA-seq.
|
2015-12-16
|
Antonio Scialdone Luis R. Saraiva Darren W. Logan John C Marioni
|
Ximena Ibarra-Soria Mona Khan Masayo Omura Peter Mombaerts
|
Scientific Reports
|
Lin28A Binds Active Promoters and Recruits Tet1 to Regulate Gene Expression
|
2015-12-16
|
Guo-Li Ming Hongjun Song Jun Wan
|
Yaxue Zeng Bing Yao Jaehoon Shin Li Lin Namshik Kim Qifeng Song Shuang Liu Yijing Su Junjie U Guo Luoxiu Huang Hao Wu Jiang Qian Xiaodong Cheng Heng Zhu Peng Jin
|
Molecular Cell
|
Ectopic expression of TAPETUM DETERMINANT1 affects ovule development in Arabidopsis.
|
2015-12-17
|
Chong Tang
|
Jian Huang Asela J Wijeratne Tianyu Zhang Rebecca E Fenelon Heather A Owen Dazhong Zhao
|
Journal of Experimental Botany
|
Characterization and Comparative Analysis of the Milk Transcriptome in Two Dairy Sheep Breeds using RNA Sequencing
|
2015-12-18
|
Gwenola Tosser-Klopp Beatriz Gutierrez-Gil Gwenola Tosser-Klopp Juan J Arranz
|
Aroa Suárez-Vega Christophe Klopp Christèle Robert-Granie
|
Scientific Reports
|
Canonical pathways, networks and transcriptional factor regulation by clinical strains of Mycobacterium tuberculosis in pulmonary alveolar epithelial cells.
|
2015-12-18
|
William Bishai Manormoney Pillay
|
Nontobeko E Mvubu Balakrishna Pillay Junaid Gamieldien
|
Tuberculosis
|
Integration of electrophysiological recordings with single-cell RNA-seq data identifies neuronal subtypes
|
2015-12-21
|
Sten Linnarsson
|
János Fuzik Amit Zeisel Zoltán Máté Daniela Calvigioni Yuchio Yanagawa Gábor Szabó Tibor Harkany
|
Nature Biotechnology
|
Single-cell transcriptomes reveal characteristic features of human pancreatic islet cell types
|
2015-12-21
|
Christoph Bock Johanna Klughammer Ekaterine Berishvili Andreas Spittler
|
Jin Li Matthias Farlik Thomas Penz Charlotte Barbieux Stefan Kubicek
|
EMBO Reports
|
Human cerebral organoids recapitulate gene expression programs of fetal neocortex development
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2015-12-22
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Svante Pääbo Farhath Badsha Barbara Treutlein Madeline Lancaster Juergen A Knoblich Marta Florio
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J Gray Camp Sabina Kanton Tobias Gerber Michaela Wilsch-Bräuninger Eric Lewitus Alex Sykes Wulf Hevers Robert Lachmann Wieland B Huttner
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Proceedings of the National Academy of Sciences of the United States of America
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Meta-analysis of RNA-seq expression data across species, tissues and studies.
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2015-12-22
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Peter H Sudmant
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Maria S Alexis Christopher B Burge
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Genome Biology
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RNA Sequencing Analysis of the msl2msl3, crl, and ggps1 Mutants Indicates that Diverse Sources of Plastid Dysfunction Do Not Alter Leaf Morphology Through a Common Signaling Pathway.
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2015-12-22
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Elizabeth S. Haswell
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Darron R Luesse Margaret E Wilson
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Frontiers in Plant Science
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Multidimensional Genome-wide Analyses Show Accurate FVIII Integration by ZFN in Primary Human Cells
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2015-12-22
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Ajit Johnson Nirmal Jaichandran Sivalingam Sebastian Maurer-Stroh
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Dimitar Kenanov Hao Han Wai Har Ng Sze Sing Lee Jeyakumar Masilamani Toan Thang Phan Oi Lian Kon
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Molecular Therapy
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Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis.
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2015-12-23
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Jeremy Chien Wei Zhang Baolin Wu
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Jae-Woong Chang Lilong Lin Kay Minn Jeongsik Yong Hui Zheng Rui Kuang
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PLOS Computational Biology
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Late Embryogenesis Abundant (LEA) Constitutes a Large and Diverse Family of Proteins Involved in Development and Abiotic Stress Responses in Sweet Orange (Citrus sinensis L. Osb.).
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2015-12-23
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Marcio Gilberto Cardoso Costa
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Andresa Muniz Pedrosa Cristina de Paula Santos Martins Luana Pereira Gonçalves
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PLOS ONE
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Elimination of Chromosomal Island SpyCIM1 from Streptococcus pyogenes Strain SF370 Reverses the Mutator Phenotype and Alters Global Transcription
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2015-12-23
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Scott V Nguyen
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Christina Hendrickson Chad W Euler Maliha Rahman Kimberly A McCullor Catherine J King Vincent A Fischetti W Michael McShan
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PLOS ONE
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Transcriptomes of lineage-specific Drosophila neuroblasts profiled by genetic targeting and robotic sorting
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2015-12-23
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Tzumin Lee Ching-po Yang Chi-Cheng Fu Ken Sugino Zhiyong Liu Qingzhong Ren Ling-Yu Liu Xiaohao Yao Luke P Lee
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Development
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WheatExp: an RNA-seq expression database for polyploid wheat.
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2015-12-24
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Jorge Dubcovsky
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Stephen Pearce Hans Vazquez-Gross Sayer Y Herin David Hane Yi Wang Yong Q Gu
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BMC Plant Biology
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Chromatin and RNA Maps Reveal Regulatory Long Noncoding RNAs in Mouse.
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2015-12-28
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Miguel Beato del Rosal Marc A. Martí‐Renom
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Gireesh K Bogu Pedro Vizán Lawrence W Stanton Luciano Di Croce
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Molecular and Cellular Biology
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Anti-inflammatory therapies of amyotrophic lateral sclerosis guided by immune pathways
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2015-12-28
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Matteo Pellegrini
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Larry Lam Ramesh C Halder Dennis J Montoya Liudmilla Rubbi Arturo Rinaldi Bien Sagong Sarah Weitzman Rachel Rubattino Ram Raj Singh Milan Fiala
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American journal of neurodegenerative disease
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Simultaneous transcriptional profiling of Leishmania major and its murine macrophage host cell reveals insights into host-pathogen interactions.
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2015-12-29
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Héctor Corrada Bravo Najib El-sayed
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Laura A L Dillon Rahul Suresh Kwame Okrah David M Mosser
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BMC Genomics
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Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences.
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2015-12-30
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Mark D. Robinson Michael I Love
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Charlotte Soneson
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F1000Research
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Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq
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2015-12-31
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Ricardo DeMarco Joao Carlos Setubal Sergio Verjovski-Almeida
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Letícia Anderson Murilo S Amaral Felipe Beckedorff Lucas F Silva Bianca Dazzani Katia C Oliveira Giulliana T Almeida Monete R Gomes David S Pires
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PLOS Neglected Tropical Diseases
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Comparative Transcriptomic Analysis of Rectal Tissue from Beef Steers Revealed Reduced Host Immunity in Escherichia coli O157:H7 Super-Shedders
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2016
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Graham Plastow Tim A. McAllister
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Ou Wang Guanxiang Liang Kim Stanford Brent Selinger Le Luo Guan
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PLOS ONE
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A Novel Analytical Strategy to Identify Fusion Transcripts between Repetitive Elements and Protein Coding-Exons Using RNA-Seq
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2016
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Eric J. Nestler
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Tianyuan Wang Janine H Santos Jian Feng David C Fargo Li Shen Gonzalo Riadi Elizabeth Keeley Zachary S Rosh Richard P Woychik
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PLOS ONE
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Sphingomonas wittichii Strain RW1 Genome-Wide Gene Expression Shifts in Response to Dioxins and Clay
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2016
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Syed A. Hashsham Hui Li James Tiedje
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Benli Chai Tamara V Tsoi Shoko Iwai Cun Liu Jordan A Fish Cheng Gu Timothy A Johnson Gerben Zylstra Brian J Teppen Stephen A Boyd James R Cole
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PLOS ONE
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Multiscale Metabolic Modeling of C4 Plants: Connecting Nonlinear Genome-Scale Models to Leaf-Scale Metabolism in Developing Maize Leaves
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2016
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Christopher R. Myers
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Eli Bogart
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PLOS ONE
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Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla
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2016
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Samuel Owen Purvine
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Peter H Waltman Jian Guo Emily Nahas Reistetter Charles K Ansong Marijke J van Baren Chee-Hong Wong Chia-Lin Wei Richard D Smith Stephen J Callister Joshua M Stuart Alexandra Z Worden
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PLOS ONE
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Contrasting Potato Foliage and Tuber Defense Mechanisms against the Late Blight Pathogen Phytophthora infestans
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2016
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Liangliang Gao James M Bradeen
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PLOS ONE
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5'-Hydroxymethylcytosine Precedes Loss of CpG Methylation in Enhancers and Genes Undergoing Activation in Cardiomyocyte Maturation
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2016
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Rolf Backofen Ralf Gilsbach Björn A Grüning
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David K Kranzhöfer Thomas G Nührenberg Lutz Hein
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PLOS ONE
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Comparative Characterization of the Leaf Tissue of Physalis alkekengi and Physalis peruviana Using RNA-seq and Metabolite Profiling
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2016
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Masaki Morita Eva Knoch Go Hirai Mami Yamazaki Mikiko Sodeoka Kazuki Saito
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Atsushi Fukushima Michimi Nakamura Hideyuki Suzuki Tetsuya Mori Naoyuki Umemoto
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Frontiers in Plant Science
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Identification of Ice Plant (Mesembryanthemum crystallinum L.) MicroRNAs Using RNA-Seq and Their Putative Roles in High Salinity Responses in Seedlings
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2016
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Won Cheol Yim John Cushman
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Chih-Pin Chiang Ying-Hsuan Sun Miwa Ohnishi Tetsuro Mimura Hungchen E Yen
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Frontiers in Plant Science
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Fish-T1K (Transcriptomes of 1,000 Fishes) Project: large-scale transcriptome data for fish evolution studies
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2016
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Byrappa Venkatesh Yu Huang Jose V. Lopez Guillermo Ortí Keith A. Crandall
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Ying Sun Xiaofeng Li Carole C Baldwin Zhuocheng Zhou Zhixiang Yan Yong Zhang Xiaomeng Zhao Min Wang Alex Wong Chao Fang Xinhui Zhang Hai Huang Kirk Kilfoyle Qiong Shi
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GigaScience
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Identifying stably expressed genes from multiple RNA-Seq data sets
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2016
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Jeff H. Chang Sarah Emerson
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Bin Zhuo Yanming Di
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PeerJ
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Prediction of Gene Structures from RNA-seq Data Using Dual Decomposition
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2016
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Kengo Sato
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Tatsumu Inatsuki Yasubumi Sakakibara
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Computational Considerations in Transcriptome Assemblies and Their Evaluation, using High Quality Human RNA-Seq data
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2016
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Jordi Abante Charles D. Johnson
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Noushin Ghaffari Raminder Singh Philip D. Blood
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Computational Methods for Quality Check, Preprocessing and Normalization of RNA-Seq Data for Systems Biology and Analysis
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2016
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Haja N. Kadarmideen
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Gianluca Mazzoni
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Forkhead Box C1 Regulates Human Primary Keratinocyte Terminal Differentiation
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2016-01-01
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Lianghua Bin
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Liehua Deng Hengwen Yang Leqing Zhu Xiao Wang Michael G. Edwards Brittany Richers Donald Y. M. Leung
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PLOS ONE
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Analysis of RNA-Seq Data Using TopHat and Cufflinks.
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2016-01-01
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Sreya Ghosh Chon-Kit Kenneth Chan
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Methods in Molecular Biology
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Enhancing Structural Annotation of Yeast Genomes with RNA-Seq Data.
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2016-01-01
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Cécile Neuvéglise
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Hugo Devillers Nicolas Morin
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Methods in Molecular Biology
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Loss of neurogenesis in Hydra leads to compensatory regulation of neurogenic and neurotransmission genes in epithelial cells.
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2016-01-01
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Brigitte Galliot Y Wenger
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W Buzgariu
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Philosophical Transactions of the Royal Society B
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It's DE-licious: A Recipe for Differential Expression Analyses of RNA-seq Experiments Using Quasi-Likelihood Methods in edgeR.
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2016-01-01
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Gordon K Smyth
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Aaron T L Lun Yunshun Chen
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Methods in Molecular Biology
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Utility of next-generation RNA-sequencing in identifying chimeric transcription involving human endogenous retroviruses.
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2016-01-01
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Finn Skou Pedersen
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Martin Sokol Karen Margrethe Jessen Finn Skou Pedersen
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Acta Pathologica et Microbiologica Scandinavica
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RNA-Seq as a Tool to Study the Tumor Microenvironment.
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2016-01-01
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Guillaume Bourque
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Pudchalaluck Panichnantakul Mathieu Bourgey Alexandre Montpetit Yasser Riazalhosseini
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Methods in Molecular Biology
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In Silico Methods to Identify Exapted Transposable Element Families.
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2016-01-01
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Guillaume Bourque
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LeeAnn Ramsay
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Methods in Molecular Biology
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Using RNA-seq for Analysis of Differential Gene Expression in Fungal Species.
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2016-01-01
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Geraldine Butler
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Can Wang Markus S Schröder Stephen Hammel
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Methods in Molecular Biology
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Genome-Wide Identification of Alternative Polyadenylation Events Using 3'T-Fill.
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2016-01-01
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Vicent Pelechano
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Stefan Wilkening Lars M Steinmetz
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Methods in Molecular Biology
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Analysis RNA-seq and Noncoding RNA.
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2016-01-01
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Sergio Abrignani Massimiliano Pagani
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Alberto Arrigoni Valeria Ranzani Grazisa Rossetti Ilaria Panzeri Raoul J P Bonnal
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Methods in Molecular Biology
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Comparison of normalization and differential expression analyses using RNA-Seq data from 726 individual Drosophila melanogaster.
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2016-01-05
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Zhen-Xia Chen
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Yanzhu Lin Kseniya Golovnina Hang Noh Lee Yazmin L Serrano Negron Hina Sultana Brian Oliver Susan T Harbison
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BMC Genomics
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Assessing similarity to primary tissue and cortical layer identity in induced pluripotent stem cell-derived cortical neurons through single-cell transcriptomics.
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2016-01-05
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Satyan Chintawar Alice Giustacchini Mahito Nakanishi Sally A. Cowley
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Adam E Handel Tatjana Lalic Emma Whiteley Jane Vowles Karene Argoud Paul Sopp Rory Bowden Sarah Newey Colin Akerman Chris P Ponting M Zameel Cader
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Human Molecular Genetics
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A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages.
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2016-01-06
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Paul Blainey Gregory Szeto Alex K. Shalek
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Robert J Kimmerling Jennifer W Li Alex S Genshaft Samuel W Kazer Kristofor R Payer Jacob de Riba Borrajo Darrell J Irvine Scott R Manalis
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Nature Communications
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Tunable protein synthesis by transcript isoforms in human cells
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2016-01-06
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Jennifer Doudna Stephen N Floor
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eLife
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OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data
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2016-01-06
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Christina Kendziorski
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Ning Leng Jeea Choi Li-Fang Chu James A Thomson Ron Stewart
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Bioinformatics
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HTLV-1 bZIP Factor Impairs Anti-viral Immunity by Inducing Co-inhibitory Molecule, T Cell Immunoglobulin and ITIM Domain (TIGIT).
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2016-01-06
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Yuichi Mitobe Masao Matsuoka Keiko Yasuma
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Jun-ichirou Yasunaga Keiko Takemoto Kenji Sugata Norihiro Takenouchi Masanori Nakagawa Yutaka Suzuki
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PLOS Pathogens
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Acute Exposure to Tris(1,3-dichloro-2-propyl) Phosphate (TDCIPP) Causes Hepatic Inflammation and Leads to Hepatotoxicity in Zebrafish.
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2016-01-08
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John P Giesy Robert J Letcher
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Chunsheng Liu Guanyong Su Guangyu Li Ira Agrawal Jing Li Liqin Yu Jianghua Wang Zhiyuan Gong
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Scientific Reports
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The Female Post-Mating Response Requires Genes Expressed in the Secondary Cells of the Male Accessory Gland in Drosophila melanogaster
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2016-01-08
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Mariana Wolfner
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Jessica L Sitnik Dragan Gligorov Robert K Maeda François Karch
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Genetics
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Ribosomal protein genes are highly enriched among genes with allele-specific expression in the interspecific F1 hybrid catfish.
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2016-01-08
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Eric Peatman Luyang Sun Shikai Liu
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Ailu Chen Ruijia Wang Lisui Bao Chen Jiang Chao Li Yun Li Qifan Zeng Zhanjiang Liu
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Molecular Genetics and Genomics
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Direct and Absolute Quantification of over 1800 Yeast Proteins via Selected Reaction Monitoring.
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2016-01-10
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Robert J. Beynon Victoria M Harman Philip Brownridge Claire E. Eyers Simon J. Hubbard
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Craig Lawless Stephen W Holman Karin Lanthaler Rachel Watkins Dean E Hammond Rebecca L Miller Paul F G Sims Christopher M Grant
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Molecular & Cellular Proteomics
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NMFP: a non-negative matrix factorization based preselection method to increase accuracy of identifying mRNA isoforms from RNA-seq data.
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2016-01-11
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Jingyi Jessica Li
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Yuting Ye
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BMC Genomics
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A trans-acting Variant within the Transcription Factor RIM101 Interacts with Genetic Background to Determine its Regulatory Capacity.
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2016-01-11
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Robin Dowell
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Timothy Read Phillip A Richmond
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PLOS Genetics
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Mitochondrial iron chelation ameliorates cigarette smoke-induced bronchitis and emphysema in mice.
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2016-01-11
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John Quackenbush Kristen T Rooney Monica P Goldklang Francesca Polverino Suzanne M Cloonan Kimberly Glass
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Maria E Laucho-Contreras Abhiram R Bhashyam Morgan Cervo Maria A Pabón Csaba Konrad Ilias I Siempos Elizabeth Perez Kenji Mizumura Manik C Ghosh Harikrishnan Parameswaran Niamh C Williams Zhi-Hua Chen Guo-Cheng Yuan Stephen C Moore Dawn L Demeo Tracey A Rouault Jeanine M D'Armiento Eric A Schon Giovanni Manfredi Ashfaq Mahmood Edwin K Silverman Caroline A Owen Augustine M K Choi
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Nature Medicine
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Keratin 12 missense mutation induces the unfolded protein response and apoptosis in Meesmann epithelial corneal dystrophy.
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2016-01-11
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Sarah D Atkinson David G Courtney Ebbe Toftgaard Poulsen Deena M Leslie Pedrioli Christian Cole Johnny Moore Jan J. Enghild
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Edwin H A Allen Laura Mairs Davide Schiroli Eleonora Maurizi Robyn P Hickerson John James Helen Murgatroyd Frances J D Smith Carrie MacEwen M Andrew Nesbit W H Irwin McLean C B Tara Moore
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Human Molecular Genetics
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Adipose tissue RNASeq reveals novel gene-nutrient interactions following n-3 PUFA supplementation and evoked inflammation in humans.
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2016-01-11
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Jane Ferguson Muredach P. Reilly
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Chenyi Xue Yu Hu Mingyao Li
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Journal of Nutritional Biochemistry
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Corrigendum: Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression
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2016-01-11
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John C Marioni Aleksandra A Kolodziejczyk Jong Kyoung Kim Sarah Teichmann
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Tomislav Ilicic
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Nature Communications
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RNA-Seq identifies SPGs as a ventral skeletal patterning cue in sea urchins.
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2016-01-11
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Evan S Bardot Jonas Ibn-Salem Michael L Piacentino
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Daniel T Zuch Julie Fishman Sviatlana Rose Emily E Speranza Christy Li Jia Yu Oliver Chung Janani Ramachandran Patrick Ferrell Vijeta Patel Arlene Reyna Hajerah Hameeduddin James Chaves Finnegan B Hewitt David Lee Amanda B Core John D Hogan Jessica L Keenan Lingqi Luo Jasmin Coulombe-Huntington Todd A Blute Ekaterina Oleinik Albert J Poustka Cynthia A Bradham
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Development
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The power and promise of RNA-seq in ecology and evolution.
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2016-01-12
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Michael A. Black Neil J. Gemmell Erica V Todd
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Molecular Ecology
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Transcriptome analyses reveal genotype- and developmental stage-specific molecular responses to drought and salinity stresses in chickpea.
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2016-01-13
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Rajeev Kumar Varshney
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Rohini Garg Rama Shankar Bijal Thakkar Himabindu Kudapa Lakshmanan Krishnamurthy Nitin Mantri Sabhyata Bhatia Mukesh Jain
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Scientific Reports
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Repeated exposure to neurotoxic levels of chlorpyrifos alters hippocampal expression of neurotrophins and neuropeptides.
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2016-01-13
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Young Lee Jonathan D Stallings Pamela Lein
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John A Lewis Danielle L Ippolito Naissan Hussainzada David A Jackson
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Toxicology
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High-throughput analyses of hnRNP H1 dissects its multi-functional aspect.
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2016-01-13
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Christine Vogel
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Philip J Uren Emad Bahrami-Samani Patricia Rosa de Araujo Mei Qiao Suzanne C Burns Andrew D Smith Luiz O F Penalva
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RNA Biology
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FRAMA: from RNA-seq data to annotated mRNA assemblies.
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2016-01-14
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Matthias Platzer
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Martin Bens Arne Sahm Marco Groth Niels Jahn Michaela Morhart Susanne Holtze Thomas B Hildebrandt Karol Szafranski
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BMC Genomics
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RNA-Seq Reveals OTA-Related Gene Transcriptional Changes in Aspergillus carbonarius.
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2016-01-14
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Donato Gerin
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Rita M De Miccolis Angelini Stefania Pollastro Francesco Faretra
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PLOS ONE
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Choline Kinase Alpha (CHKα) as a Therapeutic Target in Pancreatic Ductal Adenocarcinoma: Expression, Predictive Value, and Sensitivity to Inhibitors.
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2016-01-14
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Miriam Marqués Eithne Costello Juan C. Lacal Francisco X Real
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José M Mazarico Victor J Sánchez-Arévalo Lobo Rosy Favicchio William Greenhalf Enrique Carrillo-de Santa Pau Eric Aboagye
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Molecular Cancer Therapeutics
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Genome-wide transcriptome analysis of soybean primary root under varying water-deficit conditions.
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2016-01-15
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Trupti Joshi Babu Valliyodan
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Li Song Silvas Prince Joao V Maldonado dos Santos Jiaojiao Wang Li Lin Jinrong Wan Yongqin Wang Dong Xu Henry T Nguyen
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BMC Genomics
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Dosage Compensation in the African Malaria Mosquito Anopheles gambiae.
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2016-01-18
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Graham Rose Luca Ferretti
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Elzbieta Krzywinska Jan Kim Loic Revuelta Jaroslaw Krzywinski
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Genome Biology and Evolution
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IL-36R signalling activates intestinal epithelial cells and fibroblasts and promotes mucosal healing in vivo.
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2016-01-18
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Stefan Wirtz Georg Schett
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Kristina Scheibe Ingo Backert Axel Hueber Michael Vieth Hans Christian Probst Tobias Bopp Markus F Neurath Clemens Neufert
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Gut
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Dual RNA-seq unveils noncoding RNA functions in host–pathogen interactions
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2016-01-20
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Konrad Förstner Jörg Vogel Alexander Westermann Fabian Amman Lars Barquist Peter F. Stadler Yanjie Chao Richard Reinhardt
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Leon N. Schulte Lydia Müller
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Nature
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Using high-throughput sequencing transcriptome data for INDEL detection: challenges for cancer drug discovery.
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2016-01-20
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Gabriel Wajnberg
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Fabio Passetti
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Expert Opinion on Drug Discovery
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Identification of novel noncoding transcripts in telomerase-negative yeast using RNA-seq.
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2016-01-20
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David Zappulla
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Rachel O Niederer Nickolas Papadopoulos
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Scientific Reports
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Venezuelan Equine Encephalitis Virus Induces Apoptosis through the Unfolded Protein Response Activation of EGR1.
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2016-01-20
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Kylene Kehn-Hall Jonathan D. Dinman
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Alan Baer Lindsay Lundberg Danielle Swales Nicole Waybright Chelsea Pinkham Jonathan L Jacobs
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Journal of Virology
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Cross-platform normalization of microarray and RNA-seq data for machine learning applications
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2016-01-21
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Casey S. Greene
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Jeffrey A Thompson Jie Tan
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PeerJ
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Hepatic transcriptomic and metabolic responses of hybrid striped bass (Morone saxatilis×Morone chrysops) to acute and chronic hypoxic insult.
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2016-01-21
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Eric Peatman
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Benjamin H Beck S Adam Fuller Chao Li Bartholomew W Green Honggang Zhao Steven D Rawles Carl D Webster
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Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics
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Identification of Putative Biomarkers for the Early Stage of Porcine Spermatogonial Stem Cells Using Next-Generation Sequencing
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2016-01-22
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Kyung-Woon Kim
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Won-Young Lee Jeong Tae Do Chankyu Park Jin Hoi Kim Hak-Jae Chung Chang-Hyun Gil Nam-Hyung Kim Hyuk Song
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PLOS ONE
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RNA-seq transcriptional profiling of Herbaspirillum seropedicae colonizing wheat (Triticum aestivum) roots.
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2016-01-22
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Lucélia Donatti
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V C S Pankievicz D Camilios-Neto P Bonato E Balsanelli M Z Tadra-Sfeir H Faoro L S Chubatsu G Wajnberg F Passetti R A Monteiro F O Pedrosa E M Souza
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Plant Molecular Biology
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Genome-wide dissection of AP2/ERF and HSP90 gene families in five legumes and expression profiles in chickpea and pigeonpea.
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2016-01-23
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Aamir W Khan Vanika Garg Rajeev Kumar Varshney
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Gaurav Agarwal Himabindu Kudapa Dadakhalandar Doddamani Lekha T Pazhamala Mahendar Thudi Suk-Ha Lee
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Plant Biotechnology Journal
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Social defeat leads to changes in the endocannabinoid system: An overexpression of calreticulin and motor impairment in mice.
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2016-01-24
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Vincenzo Di Marzo Stephan Lorenzen Fabiana Piscitelli
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J Tomas-Roig V Gil J A Del Río T P Moore H Agbemenyah G Salinas-Riester C Pommerenke T Beißbarth S Hoyer-Fender U Havemann-Reinecke
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Behavioural Brain Research
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Highly efficient lipid production in the green alga Parachlorella kessleri: draft genome and transcriptome endorsed by whole-cell 3D ultrastructure
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2016-01-25
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Masahira Hattori
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Shuhei Ota Kenshiro Oshima Tomokazu Yamazaki Sangwan Kim Zhe Yu Mai Yoshihara Kohei Takeda Tsuyoshi Takeshita Aiko Hirata Kateřina Bišová Vilém Zachleder Shigeyuki Kawano Masahira Hattori
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Biotechnology for Biofuels
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Cascade: an RNA-seq visualization tool for cancer genomics.
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2016-01-25
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Aaron Shifman
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Radia M Johnson Brian T Wilhelm
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BMC Genomics
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De novo transcriptome assembly of Perkinsus olseni trophozoite stimulated in vitro with Manila clam (Ruditapes philippinarum) plasma.
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2016-01-25
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Peter W Harrison Paulino Martínez
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Abul Farah Md Hasanuzzaman Diego Robledo Antonio Gómez-Tato Jose A Alvarez-Dios Asunción Cao Sergio Fernández-Boo Antonio Villalba Belén G Pardo
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Journal of Invertebrate Pathology
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A survey of best practices for RNA-seq data analysis
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2016-01-26
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Ana Conesa Michał Wojciech Szcześniak Pedro Madrigal David Gomez-Cabrero
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Sonia Tarazona Alejandra Cervera Andrew McPherson Daniel J. Gaffney Laura L. Elo Xuegong Zhang Ali Mortazavi
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Genome Biology
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The Phenazine 2-Hydroxy-Phenazine-1-Carboxylic Acid Promotes Extracellular DNA Release and Has Broad Transcriptomic Consequences in Pseudomonas chlororaphis 30-84.
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2016-01-26
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Jun Myoung Yu
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Dongping Wang Robert J Dorosky Leland S Pierson Elizabeth A Pierson
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PLOS ONE
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DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments.
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2016-01-27
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Jie Yao
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Feinan Wu Brennan G Olson
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Journal of Visualized Experiments
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Rapid Changes in the Translatome during the Conversion of Growth Cones to Synaptic Terminals.
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2016-01-27
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Matteo Pellegrini
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Kelvin Xi Zhang Liming Tan S Lawrence Zipursky Jason M McEwen
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Cell Reports
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RNASeq Based Transcriptional Profiling of Pseudomonas aeruginosa PA14 after Short- and Long-Term Anoxic Cultivation in Synthetic Cystic Fibrosis Sputum Medium.
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2016-01-28
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Fabian Amman Michael T. Wolfinger Andreas Dötsch Susanne Häussler Udo Bläsi
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Muralidhar Tata Nicole Roschanski Elisabeth Sonnleitner
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PLOS ONE
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Gene expression under thermal stress varies across a geographical range expansion front.
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2016-01-28
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Rachael Y. Dudaniec Maren Wellenreuther Erik I Svensson Bengt Hansson
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Lesley T Lancaster Pallavi Chauhan
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Molecular Ecology
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RiboGalaxy: A browser based platform for the alignment, analysis and visualization of ribosome profiling data.
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2016-01-29
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Vimalkumar Velayudhan Audrey M Michel
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James P A Mullan Patrick B F O'Connor Claire A Donohue Pavel V Baranov
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RNA Biology
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Reduced CYFIP1 in Human Neural Progenitors Results in Dysregulation of Schizophrenia and Epilepsy Gene Networks.
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2016-01-29
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Deyou Zheng
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Rebecca A Nebel Dejian Zhao Erika Pedrosa Jill Kirschen Herbert M Lachman Brett S Abrahams
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PLOS ONE
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Single-cell Transcriptome Study as Big Data
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2016-02
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Pingjian Yu
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Wei Lin
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Genomics Proteomics and Bioinformatics
|
Identification of miRNAs and Their Targets in the Liverwort Marchantia polymorpha by Integrating RNA-Seq and Degradome Analyses
|
2016-02
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Mario Arteaga-Vazquez Shih-Shun Lin Kimitsune Ishizaki Katsuyuki T. Yamato Takayuki Kohchi John L. Bowman
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Pin-Chun Lin Chia-Wei Lu Bing-Nan Shen Guan-Zong Lee Li-Yu Daisy Liu Syuan-Fei Hong Chu-Fang Lo Gong-Min Su Sabine Zachgo Felix Althoff Mizuki Takenaka
|
Plant and Cell Physiology
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Expression of mRNA Encoding Mcu and Other Mitochondrial Calcium Regulatory Genes Depends on Cell Type, Neuronal Subtype, and Ca2+ Signaling
|
2016-02-01
|
Owen Dando Peter C Kind Giles E. Hardingham
|
Nóra M Márkus Philip Hasel Jing Qiu Karen F S Bell Samuel Heron T Ian Simpson
|
PLOS ONE
|
Polyclonal breast cancer metastases arise from collective dissemination of keratin 14-expressing tumor cell clusters.
|
2016-02-01
|
Michael A Gorin
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Kevin J Cheung Veena Padmanaban Vanesa Silvestri Koen Schipper Joshua D Cohen Amanda N Fairchild James E Verdone Kenneth J Pienta Joel S Bader Andrew J Ewald
|
Proceedings of the National Academy of Sciences of the United States of America
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Proteomic and Genomic Analyses of the Rvb1 and Rvb2 Interaction Network upon Deletion of R2TP Complex Components
|
2016-02-01
|
Laurence Florens Gaye L Hattem Michael P. Washburn
|
Mahadevan Lakshminarasimhan Gina Boanca Charles A S Banks Ana E Gabriel Brad D Groppe Christine Smoyer Kate E Malanowski Allison Peak
|
Molecular & Cellular Proteomics
|
In silico prediction of the G-protein coupled receptors expressed during the metamorphic molt of Sagmariasus verreauxi (Crustacea: Decapoda) by mining transcriptomic data: RNA-seq to repertoire.
|
2016-02-02
|
Tomer Ventura Quinn P Fitzgibbon Gregory G Smith
|
Sean J Buckley
|
General and Comparative Endocrinology
|
H3K4 tri-methylation breadth at transcription start sites impacts the transcriptome of systemic lupus erythematosus
|
2016-02-02
|
Michelle A. Petri
|
Zhe Zhang Lihua Shi Noor Dawany Judith Kelsen Kathleen E Sullivan
|
Clinical epigenetics
|
WHITE PANICLE1, a Val-tRNA Synthetase Regulating Chloroplast Ribosome Biogenesis in Rice, Is Essential for Early Chloroplast Development.
|
2016-02-02
|
Yunlong Wang William Terzaghi
|
Chunming Wang Ming Zheng Jia Lyu Yang Xu Xiaohui Li Mei Niu Wuhua Long Di Wang HaiYang Wang Yihua Wang Jianmin Wan
|
Plant Physiology
|
Transcriptome Analysis of Murine Olfactory Sensory Neurons during Development Using Single Cell RNA-Seq.
|
2016-02-02
|
Hanns Hatt Günter Gisselmann
|
Paul Scholz Benjamin Kalbe Fabian Jansen Janine Altmueller Christian Becker Julia Mohrhardt Benjamin Schreiner Guenter Gisselmann Sabrina Osterloh
|
Chemical Senses
|
SPARTA: Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis
|
2016-02-04
|
Robert B Abramovitch
|
Benjamin K Johnson Matthew B Scholz Tracy K Teal
|
BMC Bioinformatics
|
Cancer-associated SF3B1 mutations affect alternative splicing by promoting alternative branchpoint usage.
|
2016-02-04
|
Sophie Piperno-Neumann Sergio Roman-Roman Franck Tirode Marc-Henri Stern Martin Dutertre
|
Samar Alsafadi Alexandre Houy Aude Battistella Tatiana Popova Michel Wassef Emilie Henry Angelos Constantinou
|
Nature Communications
|
Comparative transcriptomic profiling of hydrogen peroxide signaling networks in zebrafish and human keratinocytes: Implications toward conservation, migration and wound healing
|
2016-02-05
|
Benjamin King
|
Thomas S Lisse Sandra Rieger
|
Scientific Reports
|
Erratum to: Dynamics of gene silencing during X inactivation using allele-specific RNA-seq.
|
2016-02-05
|
Hendrik Marks Tahsin Stefan Barakat Wouter de Laat
|
Hindrik H D Kerstens Erik Splinter René A M Dirks Guido van Mierlo Onkar Joshi Shuang-Yin Wang Tomas Babak Cornelis A Albers Tüzer Kalkan Austin Smith Alice Jouneau Joost Gribnau Hendrik G Stunnenberg
|
Genome Biology
|
Implementation of an Open Source Software solution for Laboratory Information Management and automated RNAseq data analysis in a large-scale Cancer Genomics initiative using BASE with extension package Reggie
|
2016-02-06
|
Johan Vallon-Christersson
|
Jari Hakkinen Nicklas Nordborg Olle Mansson
|
|
Differences in Host Cell Invasion and Salmonella Pathogenicity Island 1 Expression between Salmonella enterica Serovar Paratyphi A and Nontyphoidal S. Typhimurium
|
2016-02-08
|
Michael McClelland
|
Dana Elhadad Prerak Desai Guntram A Grassl Galia Rahav Ohad Gal-Mor
|
Infection and Immunity
|
Comprehensive transcriptomic and proteomic characterization of human mesenchymal stem cells reveals source specific cellular markers
|
2016-02-09
|
Anja M Billing Johannes Graumann Karsten Suhre Hisham Ben Hamidane
|
Shaima S Dib Richard J Cotton Aditya M Bhagwat Pankaj Kumar Shahina Hayat Noha A Yousri Neha Goswami Arash Rafii
|
Scientific Reports
|
New insights into the Plasmodium vivax transcriptome using RNA-Seq.
|
2016-02-09
|
Bruce Russell Zbynek Bozdech François H Nosten Nicholas P J Day Nicholas John White Mallika Imwong Sachel Mok
|
Lei Zhu Anchalee Jaidee Peter R Preiser
|
Scientific Reports
|
Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines
|
2016-02-09
|
Elizabeth Theusch Wolfgang Sadee
|
A Chhibber C E French S W Yee E R Gamazon X Qin A Webb A C Papp A Wang C Q Simmons A Konkashbaev A S Chaudhry K Mitchel D Stryke T E Ferrin S T Weiss D L Kroetz D A Nickerson R M Krauss A L George E G Schuetz M W Medina N J Cox S E Scherer K M Giacomini S E Brenner
|
The Pharmacogenomics Journal
|
Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data
|
2016-02-10
|
Shailesh Kumar
|
Angie Duy Vo Fujun Qin Hui Li
|
Scientific Reports
|
Linking the T cell receptor to the single cell transcriptome in antigen-specific human T cells.
|
2016-02-10
|
Auda A. Eltahla Simone Rizzetto Rowena A Bull Katherine Kedzierska Andrew R. Lloyd Brigid D Betz-Stablein
|
Mehdi R Pirozyan Vanessa Venturi Fabio Luciani
|
Immunology & Cell Biology
|
A genome-wide search for epigenetically [corrected] regulated genes in zebra finch using MethylCap-seq and RNA-seq
|
2016-02-11
|
Annemie Van der Linden
|
Sandra Steyaert Jolien Diddens Jeroen Galle Ellen De Meester Sarah De Keulenaer Antje Bakker Nina Sohnius-Wilhelmi Carolina Frankl-Vilches Wim Van Criekinge Wim Vanden Berghe Tim De Meyer
|
Scientific Reports
|
SplAdder: identification, quantification and testing of alternative splicing events from RNA-Seq data
|
2016-02-11
|
Gunnar Rätsch
|
André Kahles Cheng Soon Ong Yi Zhong
|
Bioinformatics
|
Selective amplification and sequencing of cyclic phosphate-containing RNAs by the cP-RNA-seq method.
|
2016-02-11
|
Yohei Kirino
|
Shozo Honda Keisuke Morichika
|
Nature Protocols
|
Seqinspector: position-based navigation through the ChIP-seq data landscape to identify gene expression regulators.
|
2016-02-12
|
Ryszard Przewłocki Michał Korostyński
|
Marcin Piechota Joanna Ficek Andrzej Tomski
|
BMC Bioinformatics
|
Expression Profiling of Macrophages Reveals Multiple Populations with Distinct Biological Roles in an Immunocompetent Orthotopic Model of Lung Cancer
|
2016-02-12
|
Vinod Yadav Howard Li Teresa T Nguyen
|
Joanna M Poczobutt Subhajyoti De Trisha R Sippel Mary C M Weiser-Evans Raphael A Nemenoff
|
Journal of Immunology
|
Single-cell transcriptome analysis of endometrial tissue.
|
2016-02-13
|
Juha Kere M Vera-Rodriguez Triin Laisk-Podar Shintaro Katayama Andres Salumets
|
K Krjutškov M Saare D Lubenets K Samuel H Teder E Einarsdottir
|
Human Reproduction
|
Identification of novel long non-coding RNAs deregulated in hepatocellular carcinoma using RNA-sequencing.
|
2016-02-13
|
Nora Fernandez-Jimenez
|
Davide Degli Esposti Hector Hernandez-Vargas Catherine Voegele Nora Fernandez-Jimenez Nathalie Forey Brigitte Bancel Florence Le Calvez-Kelm James McKay Philippe Merle Zdenko Herceg
|
Oncotarget
|
Molecular signatures of age-associated chronic degeneration of shoulder muscles.
|
2016-02-14
|
Wibowo Arindrarto Yotam Raz Szymon M Kiełbasa Peter A.C. 't Hoen
|
Jan Ferdinand Henseler Arjen Kolk Zuotian Tatum Niels Kuipers Groosjohan Nisha E Verwey Jochem Nagels Rob G H H Nelissen Vered Raz
|
Oncotarget
|
An advanced bioinformatics approach for analyzing RNA-seq data reveals sigma H-dependent regulation of competence genes in Listeria monocytogenes
|
2016-02-16
|
Kathryn J Boor Martin Wiedmann
|
Yichang Liu Renato Hohl Orsi Veronica Guariglia-Oropeza
|
BMC Genomics
|
Extreme Hypoxic Conditions Induce Selective Molecular Responses and Metabolic Reset in Detached Apple Fruit.
|
2016-02-16
|
Leonardo Tenori Claudio Luchinat
|
Dubravka Cukrov Monica Zermiani Stefano Brizzolara Alessandro Cestaro Francesco Licausi Claudio Santucci Hans Van Veen Andrea Zuccolo Benedetto Ruperti Pietro Tonutti
|
Frontiers in Plant Science
|
Classification of low quality cells from single-cell RNA-seq data
|
2016-02-17
|
Aleksandra A Kolodziejczyk Davis J McCarthy Frederik Otzen Bagger John C Marioni Jong Kyoung Kim Sarah Teichmann
|
Tomislav Ilicic
|
Genome Biology
|
Fire blight disease reactome: RNA-seq transcriptional profile of apple host plant defense responses to Erwinia amylovora pathogen infection.
|
2016-02-17
|
Thomas Wicker
|
Tim Kamber Jan P Buchmann Joël F Pothier Theo H M Smits Brion Duffy
|
Scientific Reports
|
Alternative splicing modulated by genetic variants demonstrates accelerated evolution regulated by highly conserved proteins
|
2016-02-17
|
Xianzhi Lin Xinshu Xiao
|
Yun-Hua Esther Hsiao Jae Hoon Bahn Tak-Ming Chan Rena Wang
|
Genome Research
|
Molluscum Contagiosum Virus Transcriptome in Abortively Infected Cultured Cells and a Human Skin Lesion
|
2016-02-17
|
Bernard Moss
|
Jorge D Mendez-Rios Zhilong Yang Karl J Erlandson Jeffrey I Cohen Craig A Martens Daniel P Bruno Stephen F Porcella
|
Journal of Virology
|
The RNA Polymerase II C-Terminal Domain Phosphatase-Like Protein FIERY2/CPL1 Interacts with eIF4AIII and Is Essential for Nonsense-Mediated mRNA Decay in Arabidopsis.
|
2016-02-17
|
Feng Ding
|
Peng Cui Tao Chen Tao Qin Zhenyu Wang Hao Chen Liming Xiong
|
The Plant Cell
|
Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons
|
2016-02-18
|
Jennifer Erwin
|
Suguna Rani Krishnaswami Rashel V Grindberg Mark Novotny Pratap Venepally Benjamin Lacar Kunal Bhutani Sara B Linker Son Pham Jeremy A Miller Rebecca Hodge James K McCarthy Martin Kelder Jamison McCorrison Brian D Aevermann Francisco Diez Fuertes Richard H Scheuermann Jun Lee Ed S Lein Nicholas Schork Michael J McConnell Fred H Gage Roger S Lasken
|
Nature Protocols
|
GeneiASE: Detection of condition-dependent and static allele-specific expression from RNA-seq data without haplotype information.
|
2016-02-18
|
Anders Hamsten Per Tornvall Jacob Odeberg
|
Daniel Edsgärd Maria Jesus Iglesias Sarah-Jayne Reilly Olof Emanuelsson
|
Scientific Reports
|
The Nuclear Receptor, RORγ, Regulates Pathways Necessary for Breast Cancer Metastasis.
|
2016-02-18
|
Tae Gyu Oh Bipul R. Acharya Shu-Ching Mary Wang Christine Clarke Alpha S. Yap
|
Joel M Goode J Dinny Graham George E O Muscat
|
EBioMedicine
|
Hemocytome: deep sequencing analysis of mosquito blood cells in Indian malarial vector Anopheles stephensi.
|
2016-02-22
|
Rajnikant Dixit
|
Tina Thomas Tanwee Das De Punita Sharma Suman Lata Priyanka Saraswat Kailash C Pandey
|
Gene
|
RNA-seq analysis of clinical-grade osteochondral allografts reveals activation of early response genes.
|
2016-02-22
|
Annalise Noelle Larson
|
Yang Lin Eric A Lewallen Emily T Camilleri Carolina A Bonin Dakota L Jones Amel Dudakovic Catalina Galeano-Garces Wei Wang Marcel J Karperien Diane L Dahm Michael J Stuart Bruce A Levy Jay Smith Daniel B Ryssman Jennifer J Westendorf Hee-Jeong Im Andre J van Wijnen Scott M Riester Aaron J Krych
|
Journal of Orthopaedic Research
|
The MazF-regulon: a toolbox for the post-transcriptional stress response in Escherichia coli.
|
2016-02-22
|
Michael T. Wolfinger
|
Martina Sauert Oliver Vesper Christian Müller Konstantin Byrgazov Isabella Moll
|
Nucleic Acids Research
|
Enhancer methylation dynamics contribute to cancer plasticity and patient mortality.
|
2016-02-23
|
Yankel Gabet
|
Rachel E Bell Tamar Golan Danna Sheinboim Hagar Malcov David Amar Avi Salamon Tamar Liron Sahar Gelfman Ron Shamir Carmit Levy
|
Genome Research
|
Longitudinal RNA-Seq Analysis of Vertebrate Aging Identifies Mitochondrial Complex I as a Small-Molecule-Sensitive Modifier of Lifespan.
|
2016-02-24
|
Matthias Platzer
|
Mario Baumgart Steffen Priebe Marco Groth Nils Hartmann Uwe Menzel Luca Pandolfini Philipp Koch Marius Felder Michael Ristow Christoph Englert Reinhard Guthke Alessandro Cellerino
|
Cell systems
|
Nitric oxide release from nitro-fatty acids in Arabidopsis roots.
|
2016-02-24
|
Francisco J. Corpas
|
Capilla Mata-Pérez Beatriz Sánchez-Calvo Juan C Begara-Morales María N Padilla Raquel Valderrama Juan B Barroso
|
Plant Signaling and Behavior
|
Isolation of the protein and RNA content of active sites of transcription from mammalian cells.
|
2016-02-25
|
Argyris Papantonis Karsten Rippe Ian M. Carr Maïwen Caudron-Herger
|
Svitlana Melnik Lilija Brant Peter R Cook
|
Nature Protocols
|
Transcriptional signature induced by a metastasis-promoting c-Src mutant in a human breast cell line.
|
2016-02-26
|
Mathias Heikenwalder Hans Lehrach Martin Kerick Ralf Herwig Lubor Borsig
|
Felix Broecker Christopher Hardt Bernd Timmermann Andrea Wunderlich Michal R Schweiger Karin Moelling
|
FEBS Journal
|
TRX-1 Regulates SKN-1 Nuclear Localization Cell Non-autonomously in Caenorhabditis elegans.
|
2016-02-26
|
Peter Swoboda Katie C McCallum Juan Carlos Fierro-González Bin Liu Antonio Miranda-Vizuete Danielle A Garsin
|
Swathi Arur
|
Genetics
|
Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis.
|
2016-02-27
|
Nicolas Terrapon Christopher J Fields Evelyne Forano Bernard Henrissat
|
Jordane Despres Pascale Lepercq Sophie Comtet-Marre Grégory Jubelin Carl J Yeoman Margret E Berg Miller Carine Le Bourvellec Catherine M G C Renard Bryan A White Pascale Mosoni
|
BMC Genomics
|
Discrete distributional differential expression (D3E)--a tool for gene expression analysis of single-cell RNA-seq data.
|
2016-02-29
|
Mihails Delmans
|
Martin Hemberg
|
BMC Bioinformatics
|
Overlapping cell population expression profiling and regulatory inference in C. elegans.
|
2016-02-29
|
Arjun Raj
|
Joshua Burdick Travis Walton Elicia Preston Amanda Zacharias John Isaac Murray
|
BMC Genomics
|
Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations.
|
2016-02-29
|
Jason A. Hackney Florian Gnad David J. Sugarbaker
|
Raphael Bueno Eric W Stawiski Leonard D Goldstein Steffen Durinck Assunta De Rienzo Zora Modrusan Thong T Nguyen Bijay S Jaiswal Lucian R Chirieac Daniele Sciaranghella Nhien Dao Corinne E Gustafson Kiara J Munir Amitabha Chaudhuri Ravi Gupta Joseph Guillory Karen Toy Connie Ha Ying-Jiun Chen Jeremy Stinson Subhra Chaudhuri Na Zhang Thomas D Wu Frederic J de Sauvage William G Richards Somasekar Seshagiri
|
Nature Genetics
|
Expression Analysis Highlights AXL as a Candidate Zika Virus Entry Receptor in Neural Stem Cells
|
2016-03
|
Carmen Sandoval-Espinosa
|
Tomasz J. Nowakowski Alex A. Pollen Elizabeth Di Lullo Marina Bershteyn Arnold R. Kriegstein
|
Cell Stem Cell
|
Human MicroRNA miR-532-5p Exhibits Antiviral Activity against West Nile Virus via Suppression of Host Genes SESTD1 and TAB3 Required for Virus Replication
|
2016-03
|
A Slonchak Alexander A. Khromykh
|
Rory P Shannon Gabor Pali
|
Journal of Virology
|
The impact of oil spill to lung health--Insights from an RNA-seq study of human airway epithelial cells
|
2016-03-01
|
Erik K Flemington
|
Yao-Zhong Liu Astrid M Roy-Engel Melody C Baddoo Guangdi Wang He Wang
|
Gene
|
GeneAnalytics: An Integrative Gene Set Analysis Tool for Next Generation Sequencing, RNAseq and Microarray Data.
|
2016-03-01
|
Doron Lancet
|
Shani Ben-Ari Fuchs Iris Lieder Gil Stelzer Yaron Mazor Ella Buzhor Sergey Kaplan Yoel Bogoch Inbar Plaschkes Alina Shitrit Noa Rappaport Asher Kohn Ron Edgar Liraz Shenhav Marilyn Safran Yaron Guan-Golan David Warshawsky Ronit Shtrichman
|
OMICS: A Journal of Integrative Biology
|
Characterizing Milk Production Related Genes in Holstein Using RNA-seq
|
2016-03-01
|
Heebal Kim
|
Minseok Seo Hyun-Jeong Lee Kwondo Kim Kelsey Caetano-Anolles Jin Young Jeong Sungkwon Park Young Kyun Oh Seoae Cho
|
Asian-Australasian Journal of Animal Sciences
|
Genome-Wide Profiles of Extra-cranial Malignant Rhabdoid Tumors Reveal Heterogeneity and Dysregulated Developmental Pathways.
|
2016-03-01
|
Andrew Mungall
|
Hye-Jung E Chun Emilia L Lim Alireza Heravi-Moussavi Saeed Saberi Karen L Mungall Mikhail Bilenky Annaick Carles Kane Tse Inna Shlafman Kelsey Zhu Jenny Q Qian Diana L Palmquist An He William Long Rodrigo Goya Michelle Ng Veronique G LeBlanc Erin Pleasance Nina Thiessen Tina Wong Eric Chuah Yong-Jun Zhao Jacquie E Schein Daniela S Gerhard Michael D Taylor Richard A Moore Yussanne Ma Steven J M Jones Elizabeth J Perlman Martin Hirst Marco A Marra
|
Cancer Cell
|
Transcriptional profiling of subcutaneous adipose tissue in Italian Large White pigs divergent for backfat thickness.
|
2016-03-01
|
Paolo Zambonelli
|
E Gaffo M Zappaterra S Bortoluzzi R Davoli
|
Animal Genetics
|
Tolerant and Susceptible Sesame Genotypes Reveal Waterlogging Stress Response Patterns.
|
2016-03-02
|
Xin Wei Linhai Wang
|
Donghua Li Yanxin Zhang Yuan Gao Jingyin Yu Xiurong Zhang
|
PLOS ONE
|
FgSsn3 kinase, a component of the mediator complex, is important for sexual reproduction and pathogenesis in Fusarium graminearum
|
2016-03-02
|
Huiquan Liu
|
Shulin Cao Shijie Zhang Chaofeng Hao Jin-Rong Xu Qiaojun Jin
|
Scientific Reports
|
Erratum to: 'Identification of candidate gonadal sex differentiation genes in the chicken embryo using RNA-seq'.
|
2016-03-02
|
Alicia Oshlack
|
Katie L Ayers Luke S Lambeth Nadia M Davidson Andrew H Sinclair Craig A Smith
|
BMC Genomics
|
Calcium-insensitive splice variants of mammalian E1 subunit of 2-oxoglutarate dehydrogenase complex with tissue-specific patterns of expression.
|
2016-03-02
|
Timothy J Pullen
|
Richard M Denton Craig T Armstrong Kate J Heesom Guy A Rutter
|
Biochemical Journal
|
De novo assembly and comparative transcriptome analysis of Euglena gracilis in response to anaerobic conditions
|
2016-03-03
|
Takanori Maruta Kazuharu Arakawa
|
Yuta Yoshida Takuya Tomiyama Masaru Tomita Takahiro Ishikawa
|
BMC Genomics
|
Developmental Progression in the Coral Acropora digitifera Is Controlled by Differential Expression of Distinct Regulatory Gene Networks
|
2016-03-03
|
Alejandro Villar-Briones
|
Alejandro Reyes-Bermudez Catalina Ramirez-Portilla Michio Hidaka Alexander S Mikheyev
|
Genome Biology and Evolution
|
Comparative Developmental Transcriptomics Reveals Rewiring of a Highly Conserved Gene Regulatory Network during a Major Life History Switch in the Sea Urchin Genus Heliocidaris
|
2016-03-04
|
Maria Byrne
|
Jennifer W Israel Megan L Martik Elizabeth C Raff Rudolf A Raff David R McClay Gregory A Wray
|
PLOS Biology
|
Early alterations on photosynthesis-related parameters in Chlamydomonas reinhardtii cells exposed to atrazine: A multiple approach study.
|
2016-03-04
|
Marta Seoane Marta Esperanza Concepción Herrero Carmen Rioboo Ángeles Cid
|
|
Science of the Total Environment
|
Genomic and transcriptomic analysis of the streptomycin-dependent Mycobacterium tuberculosis strain 18b.
|
2016-03-05
|
Jérémie Piton Jérémie Piton Claudia Sala
|
Andrej Benjak Swapna Uplekar Ming Zhang Stewart T Cole
|
BMC Genomics
|
Spermatogenesis Drives Rapid Gene Creation and Masculinization of the X Chromosome in Stalk-Eyed Flies (Diopsidae).
|
2016-03-06
|
Josephine A Reinhardt Gerald Wilkinson
|
Richard H Baker Apurva Narechania Rob DeSalle Philip M Johns
|
Genome Biology and Evolution
|
Comparative Validation of Conventional and RNA-Seq Data-Derived Reference Genes for qPCR Expression Studies of Colletotrichum kahawae.
|
2016-03-07
|
Octávio S. Paulo Ana Cabral Ana Vieira Ana Sofia Pires Vitor Varzea Andreia Loureiro Helena Azinheira Helena Oliveira Dora Batista Maria do Céu Silva
|
Joana Fino Pedro Talhinhas Pilar Moncada
|
PLOS ONE
|
Comparative analysis of human and mouse transcriptomes of Th17 cell priming.
|
2016-03-07
|
Brigitta Stockinger Sini Rautio Ubaid Ullah Zhi Chen Helena Ahlfors Harri Lähdesmäki Tarmo Äijö
|
Soile Tuomela Viveka Öling Verna Salo Saara Hämälistö Subhash K Tripathi Omid Rasool Hayssam Soueidan Lodewyk Wessels Riitta Lahesmaa
|
Oncotarget
|
Comparative transcriptome analysis of papilla and skin in the sea cucumber, Apostichopus japonicus.
|
2016-03-07
|
Shikai Liu
|
Xiaoxu Zhou Jun Cui Derong Kong He Sun Chenlei Gu Hongdi Wang Xuemei Qiu Yaqing Chang Zhanjiang Liu Xiuli Wang
|
PeerJ
|
RNA-seq analysis of the Rhizobium tropici CIAT 899 transcriptome shows similarities in the activation patterns of symbiotic genes in the presence of apigenin and salt
|
2016-03-08
|
Mariangela Hungria
|
Francisco Pérez-Montaño Pablo Del Cerro Irene Jiménez-Guerrero Francisco Javier López-Baena Maria Teresa Cubo Mariangela Hungria Manuel Megías Francisco Javier Ollero
|
BMC Genomics
|
Bioinformatic analyses in early host response to Porcine Reproductive and Respiratory Syndrome virus (PRRSV) reveals pathway differences between pigs with alternate genotypes for a major host response QTL
|
2016-03-08
|
Paul Stothard
|
Martine Schroyen Christopher Eisley James E Koltes Eric Fritz-Waters Igseo Choi Graham S Plastow Leluo Guan Hua Bao Arun Kommadath James M Reecy Joan K Lunney Robert R R Rowland Jack C M Dekkers Christopher K Tuggle
|
BMC Genomics
|
Dissection of early transcriptional responses to water stress in Arundo donax L. by unigene-based RNA-seq.
|
2016-03-08
|
Claudio Varotto Nicola La Porta Gaurav Sablok Violeta Velikova
|
Yuan Fu Michele Poli Bo Wang Yanchun Liang Francesco Loreto Mingai Li
|
Biotechnology for Biofuels
|
Transposon Mutagenesis Reveals Fludarabine Resistance Mechanisms in Chronic Lymphocytic Leukemia.
|
2016-03-08
|
Mats Hellström
|
Tatjana Pandzic Jimmy Larsson Liqun He Snehangshu Kundu Kenneth Ban Muhammad Akhtar-Ali Anders R Hellström Anna Schuh Ruth Clifford Stuart J Blakemore Jonathan C Strefford Tycho Baumann Armando Lopez-Guillermo Elias Campo Viktor Ljungström Larry Mansouri Richard Rosenquist Tobias Sjöblom
|
Clinical Cancer Research
|
Striatal mRNA expression patterns underlying peak dose L-DOPA-induced dyskinesia in the 6-OHDA hemiparkinsonian rat.
|
2016-03-08
|
Michael A. Black
|
L M Smith L C Parr-Brownlie E J Duncan N J Gemmell P K Dearden J N J Reynolds
|
Neuroscience
|
Microglia Transcriptome Changes in a Model of Depressive Behavior after Immune Challenge.
|
2016-03-09
|
Robert Dantzer
|
Dianelys Gonzalez-Pena Scott E Nixon Jason C O'Connor Bruce R Southey Marcus A Lawson Robert H McCusker Tania Borras Debbie Machuca Alvaro G Hernandez Keith W Kelley Sandra L Rodriguez-Zas
|
PLOS ONE
|
Engineering EMT using 3D micro-scaffold to promote hepatic functions for drug hepatotoxicity evaluation.
|
2016-03-09
|
Chenyu Huang
|
Jingyu Wang Fengling Chen Longwei Liu Chunxiao Qi Bingjie Wang Xiaojun Yan Wei Hou Michael Q Zhang Yang Chen Yanan Du
|
Biomaterials
|
Changes in the miRNA-mRNA Regulatory Network Precede Motor Symptoms in a Mouse Model of Multiple System Atrophy: Clinical Implications
|
2016-03-10
|
Michaela Willi Hubert Hackl Gregor Wenning Werner Poewe
|
Simon Schafferer Rimpi Khurana Violetta Refolo Serena Venezia Edith Sturm Paolo Piatti Clara Hechenberger Roman Kessler Ronald Gstir Anne Krogsdam Alexandra Lusser Alexander Hüttenhofer Nadia Stefanova
|
PLOS ONE
|
Gene expression changes in damaged osteoarthritic cartilage identify a signature of non-chondrogenic and mechanical responses
|
2016-03-10
|
Jean-Marc Schwartz Timothy E. Hardingham
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S L Dunn J Soul S Anand R P Boot-Handford
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Osteoarthritis and Cartilage
|
High E6 Gene Expression Predicts for Distant Metastasis and Poor Survival in Patients With HPV-Positive Oropharyngeal Squamous Cell Carcinoma.
|
2016-03-10
|
Christopher R Spencer Rebecca D. Chernock
|
Shariq S Khwaja Callie Baker Wesley Haynes Hiram Gay Wade Thorstad Douglas R Adkins Brian Nussenbaum James S Lewis Xiaowei Wang
|
International Journal of Radiation Oncology Biology Physics
|
GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data
|
2016-03-11
|
David E. MacHugh Kévin Rue-Albrecht Stephen V. Gordon
|
Paul A McGettigan Belinda Hernández Nicolas C Nalpas David A Magee Andrew C Parnell
|
BMC Bioinformatics
|
Integrating RNA-seq and ChIP-seq data to characterize long non-coding RNAs in Drosophila melanogaster
|
2016-03-11
|
Fang-Hua Chu Wen-Hsiung Li
|
Mei-Ju May Chen Li-Kai Chen Yu-Shing Lai Yu-Yu Lin Dung-Chi Wu Yi-An Tung Kwei-Yan Liu Hsueh-Tzu Shih Yi-Jyun Chen Yan-Liang Lin Li-Ting Ma Jian-Long Huang Po-Chun Wu Ming-Yi Hong June-Tai Wu Chien-Yu Chen
|
BMC Genomics
|
The Ess/Type VII secretion system of Staphylococcus aureus shows unexpected genetic diversity.
|
2016-03-11
|
Catriona P Harkins Sharon Peacock
|
Ben Warne Simon R Harris Alexandra Vatsiou Nicola Stanley-Wall Julian Parkhill Tracy Palmer Matthew T G Holden
|
BMC Genomics
|
Comprehensive profiling of EBV gene expression in nasopharyngeal carcinoma through paired-end transcriptome sequencing.
|
2016-03-11
|
Elliott D. Kieff
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Lijuan Hu Zhirui Lin Yanheng Wu Juqin Dong Bo Zhao Yanbing Cheng Peiyu Huang Lihua Xu Tianliang Xia Dan Xiong Hongbo Wang Manzhi Li Ling Guo Yixin Zeng Qian Zhong Musheng Zeng
|
Frontiers of medicine
|
miR2118-triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species.
|
2016-03-12
|
Francois Sabot Yves Vigouroux
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K N Ta H Adam S De Mita A Ghesquière N V Do P Gantet S Jouannic
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Rice
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A novel method of transcriptome interpretation reveals a quantitative suppressive effect on tomato immune signaling by two domains in a single pathogen effector protein.
|
2016-03-14
|
Christopher R. Myers
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Jay N Worley Marina A Pombo Yi Zheng Diane M Dunham Zhangjun Fei Gregory B Martin
|
BMC Genomics
|
CLASS2: accurate and efficient splice variant annotation from RNA-seq reads.
|
2016-03-14
|
Sarven Sabunciyan
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Li Song Liliana Florea
|
Nucleic Acids Research
|
Transcriptional profiling of Klebsiella pneumoniae defines signatures for planktonic, sessile and biofilm-dispersed cells
|
2016-03-15
|
Damien Balestrino Nicolas Parisot
|
Cyril Guilhen Nicolas Charbonnel Nathalie Gueguen Agnès Iltis Christiane Forestier
|
BMC Genomics
|
Exploring the surfaceome of Ewing sarcoma identifies a new and unique therapeutic target
|
2016-03-15
|
Lucy F Stead Terence Rabbitts
|
Jennifer Town Helio Pais Sally Harrison Carole Bataille Wilawan Bunjobpol Jing Zhang
|
Proceedings of the National Academy of Sciences of the United States of America
|
Differential regulation of meristem size, morphology and organization by the ERECTA, CLAVATA and class III HD-ZIP pathways.
|
2016-03-17
|
Héctor Candela
|
Tali Mandel Udi Landau Lior Asis Einat Zelinger Cristel C Carles Leor Eshed Williams
|
Development
|
A mutation in the tuft mouse disrupts TET1 activity and alters the expression of genes that are crucial for neural tube closure.
|
2016-03-17
|
Scott Lozanoff
|
Keith S K Fong Robert B Hufnagel Vedbar S Khadka Michael J Corley Alika K Maunakea Ben Fogelgren Zubair M Ahmed
|
Disease Models & Mechanisms
|
Systems Biology of Metabolic Regulation by Estrogen Receptor Signaling in Breast Cancer.
|
2016-03-17
|
Zeynep Madak-Erdogan
|
Yiru Chen Zhao
|
Journal of Visualized Experiments
|
Integrative Single-Cell Transcriptomics Reveals Molecular Networks Defining Neuronal Maturation During Postnatal Neurogenesis.
|
2016-03-17
|
Yu Gao
|
Feifei Wang Brian E Eisinger Laurel E Kelnhofer Emily M Jobe Xinyu Zhao
|
Cerebral Cortex
|
Identification by FFPE RNA-Seq of a new recurrent inversion leading to RBM10-TFE3 fusion in renal cell carcinoma with subtle TFE3 break-apart FISH pattern.
|
2016-03-21
|
Eric Pasmant
|
Pierre-Alexandre Just Franck Letourneur Christelle Pouliquen Florence Dome Anne Audebourg Philippe Biquet Michel Vidaud Benoit Terris Mathilde Sibony
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Genes, Chromosomes and Cancer
|
De Novo Transcriptome Sequencing of Desert Herbaceous Achnatherum splendens (Achnatherum) Seedlings and Identification of Salt Tolerance Genes
|
2016-03-23
|
Lizhe An
|
Jiangtao Liu Yuelong Zhou Changxin Luo Yun Xiang
|
Genes
|
Genome-wide analysis of dorsal and ventral transcriptomes of the Xenopus laevis gastrula.
|
2016-03-23
|
Edward M. De Robertis
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Yi Ding Gabriele Colozza Kelvin Zhang Yuki Moriyama Diego Ploper Eric A Sosa Maria D J Benitez
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Developmental Biology
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Role of miRNAs and alternative mRNA 3'-end cleavage and polyadenylation of their mRNA targets in cardiomyocyte hypertrophy.
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2016-03-23
|
Traude H. Beilharz Thomas Preiss
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R Soetanto C J Hynes H R Patel D T Humphreys M Evers G Duan B J Parker S K Archer J L Clancy R M Graham N J Smith
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Biochimica et Biophysica Acta
|
Differential responsiveness of Holstein and Angus dermal fibroblasts to LPS challenge occurs without major differences in the methylome.
|
2016-03-24
|
Stephanie McKay
|
Aimee L Benjamin Benjamin B Green Brian A Crooker David E Kerr
|
BMC Genomics
|
Identifying Centromeric RNAs Involved in Histone Dynamics In Vivo.
|
2016-03-24
|
David Sturgill
|
D Quénet Y Dalal
|
Methods in Enzymology
|
Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis.
|
2016-03-25
|
Mark Bender Gerstein
|
Fei He Shinjae Yoo Daifeng Wang Sunita Kumari Doreen Ware Sergei Maslov
|
The Plant Journal
|
Coordinated Changes in Gene Expression Throughout Encystation of Giardia intestinalis.
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2016-03-25
|
Karin Troell Staffan G Svärd
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Elin Einarsson Marc P Hoeppner Manfred Grabherr Ulf Ribacke
|
PLOS Neglected Tropical Diseases
|
Identification of Gene Networks for Residual Feed Intake in Angus Cattle Using Genomic Prediction and RNA-seq.
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2016-03-28
|
Amy E Young Laercio R Porto-Neto
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Kristina L Weber Bryan T Welly Alison L Van Eenennaam Antonio Reverter Gonzalo Rincon
|
PLOS ONE
|
Transcriptomic and epigenomic characterization of the developing bat wing.
|
2016-03-28
|
Nicola Illing Zoe Gill Nadav Ahituv
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Walter L Eckalbar Stephen A Schlebusch Mandy K Mason Ash V Parker Betty M Booker Sierra Nishizaki Christiane Muswamba-Nday Elizabeth Terhune Kimberly A Nevonen Nadja Makki Tara Friedrich Julia E VanderMeer Katherine S Pollard Lucia Carbone Jeff D Wall Nicola Illing
|
Nature Genetics
|
How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?
|
2016-03-28
|
Geoffrey J. Barton Gordon G Simpson Nicholas Schurch Christian Cole Tom Owen-Hughes Karim Gharbi Mark Blaxter
|
Pietá Schofield Marek Gierliński Alexander Sherstnev Vijender Singh Nicola Wrobel
|
RNA
|
A mutation in SLC22A4 encoding an organic cation transporter expressed in the cochlea strial endothelium causes human recessive non-syndromic hearing loss DFNB60
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2016-03-29
|
Bouthaina Hammami Mustafa Tekin
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Mariem Ben Said M'hamed Grati Takahiro Ishimoto Bing Zou Imen Chakchouk Qi Ma Qi Yao Denise Yan Rahul Mittal Noritaka Nakamichi Abdelmonem Ghorbel Lingling Neng Xiao Rui Shi Yukio Kato Saber Masmoudi Zhongmin Lu Mounira Hmani Xuezhong Liu
|
Human Genetics
|
Prognostic and Functional Significance of MAP4K5 in Pancreatic Cancer.
|
2016-03-29
|
Nancy Azizian
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Oliver H Wang Ming Guo Michela Capello Defeng Deng Fenglin Zang Jason Fry Matthew H Katz Jason B Fleming Jeffrey E Lee Robert A Wolff Samir Hanash Huamin Wang Anirban Maitra
|
PLOS ONE
|
Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes.
|
2016-03-29
|
Roberto Galizi Omar S Akbari Sergey Koren Changde Cheng Tony Nolan Adam Phillippy Andrea Crisanti Nikolai Windbichler
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Andrew Brantley Hall Philippos-Aris Papathanos Atashi Sharma Lauren Assour Nicholas H Bergman Alessia Cagnetti Tania Dottorini Elisa Fiorentini Jonathan Hnath Xiaofang Jiang Diane Radune Maria V Sharakhova Aaron Steele Vladimir A Timoshevskiy Simo Zhang Matthew W Hahn Scott J Emrich Igor V Sharakhov Zhijian Jake Tu Nora J Besansky
|
Proceedings of the National Academy of Sciences of the United States of America
|
Quaking promotes monocyte differentiation into pro-atherogenic macrophages by controlling pre-mRNA splicing and gene expression.
|
2016-03-31
|
Hilde Van Esch Janine M van Gils Anton Jan van Zonneveld Ton J Rabelink Ilze Bot
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Ruben G de Bruin Lily Shiue Jurriën Prins Hetty C de Boer Anjana Singh W Samuel Fagg Jacques M G J Duijs Sol Katzman Adriaan O Kraaijeveld Stefan Böhringer Wai Y Leung Szymon M Kielbasa John P Donahue Patrick H J van der Zande Rick Sijbom Carla M A van Alem Cees van Kooten J Wouter Jukema Hilal Kazan Erik A L Biessen Manuel Ares Eric P van der Veer
|
Nature Communications
|
Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants.
|
2016-03-31
|
Igor V Grigoriev Jane Grimwood Hang Yu Charles Bachy Samuel Owen Purvine
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Marijke J van Baren Emily Nahas Reistetter Jane Grimwood Sebastian Sudek Camille Poirier Thomas J Deerinck Alan Kuo Chee-Hong Wong Richard D Smith Stephen J Callister Chia-Lin Wei Jeremy Schmutz Alexandra Z Worden
|
BMC Genomics
|
Transcriptome Analysis of Differentially Expressed Genes Provides Insight into Stolon Formation in Tulipa edulis
|
2016-03-31
|
Qiaosheng Guo
|
Yuanyuan Miao Zaibiao Zhu Yunhao Zhu Xiaohua Yang Yuan Sun
|
Frontiers in Plant Science
|
Wheat miRNA ancestors: evident by transcriptome analysis of A, B, and D genome donors.
|
2016-03-31
|
Hikmet Budak Burcu Alptekin
|
|
Functional and Integrative Genomics
|
Identification of reference genes for quantitative expression analysis using large-scale RNA-seq data of Arabidopsis thaliana and model crop plants.
|
2016-04-01
|
Masao Watanabe
|
Toru Kudo Yohei Sasaki Shin Terashima Noriko Matsuda-Imai Tomoyuki Takano Misa Saito Maasa Kanno Soichi Ozaki Keita Suwabe Go Suzuki Makoto Matsuoka Seiji Takayama Kentaro Yano
|
Genes and Genetic Systems
|
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq
|
2016-04-01
|
Aviv Regev Itay Tirosh Alex K. Shalek Peter K. Sorger Orit Rozenblatt-Rosen Keith Flaherty
|
Itay Tirosh Benjamin Izar Sanjay M Prakadan Marc H Wadsworth Daniel Treacy John J Trombetta Asaf Rotem Christopher Rodman Christine Lian George Murphy Mohammad Fallahi-Sichani Ken Dutton-Regester Jia-Ren Lin Ofir Cohen Parin Shah Diana Lu Alex S Genshaft Travis K Hughes Carly G K Ziegler Samuel W Kazer Aleth Gaillard Kellie E Kolb Alexandra-Chloé Villani Cory M Johannessen Aleksandr Y Andreev Eliezer M Van Allen Monica Bertagnolli Ryan J Sullivan Dennie T Frederick Judit Jané-Valbuena Charles H Yoon Levi A Garraway
|
Science
|
Metabolic Regulation of Gene Expression by Histone Lysine β-Hydroxybutyrylation.
|
2016-04-01
|
Lunzhi Dai Dongjun Chung Minjia Tan David B. Lombard
|
Zhongyu Xie Di Zhang Zhanyun Tang He Huang Shankang Qi Jingya Li Gozde Colak Yue Chen Chunmei Xia Chao Peng Haibin Ruan Matt Kirkey Danli Wang Lindy M Jensen Oh Kwang Kwon Sangkyu Lee Scott D Pletcher Kevin P White Hongyu Zhao Jia Li Robert G Roeder Xiaoyong Yang Yingming Zhao
|
Molecular Cell
|
Transcriptome sequencing reveals e-cigarette vapor and mainstream-smoke from tobacco cigarettes activate different gene expression profiles in human bronchial epithelial cells.
|
2016-04-04
|
Michael P. Timko
|
Yifei Shen Michael J Wolkowicz Tatyana Kotova Lonjiang Fan
|
Scientific Reports
|
Near-optimal probabilistic RNA-seq quantification.
|
2016-04-04
|
Lior Pachter Harold Pimentel Páll Melsted
|
Nicolas L Bray
|
Nature Biotechnology
|
De Novo Deep Transcriptome Analysis of Medicinal Plants for Gene Discovery in Biosynthesis of Plant Natural Products.
|
2016-04-04
|
Amit Rai Mami Yamazaki Kazuki Saito
|
R Han M Nakamura H Suzuki H Takahashi
|
Methods in Enzymology
|
The C-terminal motif of SiAGO1b is required for the regulation of growth, development and stress responses in foxtail millet (Setaria italica (L.) P. Beauv)
|
2016-04-04
|
James Schnable
|
Xiaotong Liu Sha Tang Guanqing Jia Haixia Su Chanjuan Tang Hui Zhi Xianmin Diao
|
Journal of Experimental Botany
|
Comparison of syncytiotrophoblast generated from human embryonic stem cells and from term placentas
|
2016-04-05
|
Yoel Sadovsky
|
Shinichiro Yabe Andrei P Alexenko Mitsuyoshi Amita Ying Yang Danny J Schust Toshihiko Ezashi R Michael Roberts
|
Proceedings of the National Academy of Sciences of the United States of America
|
Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos.
|
2016-04-05
|
Sten Linnarsson Alvaro Plaza Reyes Björn Reinius Qiaolin Deng Rickard Sandberg
|
Sophie Petropoulos Daniel Edsgärd Sarita Pauliina Panula Simone Codeluppi Fredrik Lanner
|
Cell
|
Combined Inhibition of DNMT and HDAC Blocks the Tumorigenicity of Cancer Stem-like Cells and Attenuates Mammary Tumor Growth
|
2016-04-05
|
Vadivel Ganapathy
|
Rajneesh Pathania Sabarish Ramachandran Gurusamy Mariappan Priyanka Thakur Huidong Shi Jeong-Hyeon Choi Santhakumar Manicassamy Ravindra Kolhe Puttur D Prasad Suash Sharma Bal L Lokeshwar Muthusamy Thangaraju
|
Cancer Research
|
Diagnostic and Biological Significance of KIR Expression Profile Determined by RNA-Seq in Natural Killer/T-Cell Lymphoma.
|
2016-04-06
|
Qiang Gong Philippe Gaulard
|
Can Küçük Xiaozhou Hu Bei Jiang Adam Cornish Timothy McKeithan Wing C Chan
|
The American Journal of Pathology
|
Upregulation of hydroxysteroid sulfotransferase 2B1b promotes hepatic oval cell proliferation by modulating oxysterol-induced LXR activation in a mouse model of liver injury.
|
2016-04-06
|
Joe Yeong Sifeng Chen
|
Zhengyang Wang Xiaoming Yang Liang Chen Xiuling Zhi Hanyu Lu Yanxia Ning Lianhua Yin Xinhong Wang Xiaobo Li
|
Archives of Toxicology
|
Tissue- and stage-specific Wnt target gene expression is controlled subsequent to β-catenin recruitment to cis-regulatory modules.
|
2016-04-11
|
Gert Jan C Veenstra Stefan Hoppler
|
Yukio Nakamura Eduardo de Paiva Alves
|
Development
|
RNA-seq Transcriptome Analysis of Panax japonicus, and Its Comparison with Other Panax Species to Identify Potential Genes Involved in the Saponins Biosynthesis.
|
2016-04-12
|
Amit Rai Mami Yamazaki Kazuki Saito
|
Hiroki Takahashi Michimi Nakamura Mareshige Kojoma Hideyuki Suzuki
|
Frontiers in Plant Science
|
Understanding metabolite transport and metabolism in C4 plants through RNA-seq.
|
2016-04-12
|
Andrea Bräutigam
|
Urte Schlüter Alisandra K Denton
|
Current Opinion in Plant Biology
|
Refined Pichia pastoris reference genome sequence.
|
2016-04-12
|
Ruth Birner-Gruenberger Kasey J Day Anton Glieder
|
Lukas Sturmberger Thomas Chappell Martina Geier Florian Krainer Ursa Vide Sara Trstenjak Anja Schiefer Toby Richardson Leah Soriaga Barbara Darnhofer Benjamin S Glick Ilya Tolstorukov James Cregg Knut Madden
|
Journal of Biotechnology
|
Erratum for Baddal et al., Dual RNA-seq of Nontypeable Haemophilus influenzae and Host Cell Transcriptomes Reveals Novel Insights into Host-Pathogen Cross Talk.
|
2016-04-12
|
Buket Baddal
|
Alessandro Muzzi Stefano Censini Raffaele A Calogero Giulia Torricelli Silvia Guidotti Anna R Taddei Antonello Covacci Mariagrazia Pizza Rino Rappuoli Marco Soriani Alfredo Pezzicoli
|
mBio
|
A distant trophoblast-specific enhancer controls HLA-G expression at the maternal-fetal interface.
|
2016-04-13
|
John L. Rinn
|
Leonardo M R Ferreira Torsten B Meissner Tarjei S Mikkelsen William Mallard Charles W O'Donnell Tamara Tilburgs Hannah A B Gomes Raymond Camahort Richard I Sherwood David K Gifford Chad A Cowan Jack L Strominger
|
Proceedings of the National Academy of Sciences of the United States of America
|
Single-cell analysis of long non-coding RNAs in the developing human neocortex.
|
2016-04-14
|
Jonathan Weissman
|
Siyuan John Liu Tomasz J Nowakowski Alex A Pollen Jan H Lui Max A Horlbeck Frank J Attenello Daniel He Arnold R Kriegstein Aaron A Diaz Daniel A Lim
|
Genome Biology
|
AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression.
|
2016-04-15
|
Jesse Gillis
|
Sara Ballouz
|
PLOS Computational Biology
|
Beyond comparisons of means: understanding changes in gene expression at the single-cell level.
|
2016-04-15
|
John C Marioni Catalina A Vallejos Sylvia Richardson
|
|
Genome Biology
|
A Class of Diacylglycerol Acyltransferase 1 Inhibitors Identified by a Combination of Phenotypic High-throughput Screening, Genomics, and Genetics
|
2016-04-16
|
Herbert Waldmann Mathias Beller Thomas O Eichmann
|
Kirsten Tschapalda Ya-Qin Zhang Li Liu Kseniya Golovnina Thomas Schlemper Madhu Lal-Nag Urmila Sreenivasan John McLenithan Slava Ziegler Carole Sztalryd Achim Lass Douglas Auld Brian Oliver Zhuyin Li Min Shen Matthew B Boxer
|
EBioMedicine
|
HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells.
|
2016-04-16
|
Gregory E Crawford
|
Christopher L Frank Dinesh Manandhar Raluca Gordân
|
Epigenetics & Chromatin
|
Burkholderia pseudomallei Capsule Exacerbates Respiratory Melioidosis but Does Not Afford Protection against Antimicrobial Signaling or Bacterial Killing in Human Olfactory Ensheathing Cells.
|
2016-04-18
|
Glen C Ulett
|
Samantha J Dando Deepak S Ipe Michael Batzloff Matthew J Sullivan David K Crossman Michael Crowley Emily Strong Stephanie Kyan Sophie Y Leclercq Jenny A K Ekberg James St John Ifor R Beacham
|
Infection and Immunity
|
Nuclear RNA-seq of single neurons reveals molecular signatures of activation
|
2016-04-19
|
Carolyn O'Connor Jerika Barron Baptiste N Jaeger Jennifer Erwin
|
Benjamin Lacar Sara B Linker Suguna Krishnaswami Martijn Kelder Sarah Parylak Apuã Paquola Pratap Venepally Mark Novotny Conor Fitzpatrick Jonathan Y Hsu David Husband Michael J McConnell Roger Lasken Fred H Gage
|
Nature Communications
|
Beta-Poisson model for single-cell RNA-seq data analyses.
|
2016-04-19
|
Trung N. Vu Krishna R Kalari
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Quin F Wills Nifang Niu Liewei Wang Mattias Rantalainen Yudi Pawitan
|
Bioinformatics
|
Transcriptional Profiling of Ileocecal Valve of Holstein Dairy Cows Infected with Mycobacterium avium subsp. Paratuberculosis.
|
2016-04-19
|
John P. Bannantine
|
Randy J Hempel Judith R Stabel
|
PLOS ONE
|
Insights into the Mechanisms Underlying Ultraviolet-C Induced Resveratrol Metabolism in Grapevine (V. amurensis Rupr.) cv. "Tonghua-3"
|
2016-04-19
|
Hao Wang
|
Xiangjing Yin Stacy D Singer Hengbo Qiao Yajun Liu Chen Jiao Zhi Li Zhangjun Fei Yuejin Wang Chonghui Fan Xiping Wang
|
Frontiers in Plant Science
|
TNF is a key cytokine mediating neutrophil cytotoxic activity in breast cancer patients.
|
2016-04-20
|
Larry Norton
|
Elizabeth Comen Paulina Wojnarowicz Venkatraman E Seshan Riddhi Shah Courtney Coker Robert Benezra
|
NPJ breast cancer
|
The transcriptomic response of the coral Acropora digitifera to a competent Symbiodinium strain: the symbiosome as an arrested early phagosome.
|
2016-04-20
|
Cheong Xin Chan Mark A. Ragan
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A R Mohamed V Cumbo S Harii C Shinzato D G Bourne B L Willis E E Ball N Satoh D J Miller
|
Molecular Ecology
|
Analysis of wheat microspore embryogenesis induction by transcriptome and small RNA sequencing using the highly responsive cultivar "Svilena".
|
2016-04-21
|
Jochen Kumlehn
|
Felix Seifert Sandra Bössow Heike Gnad Stefan Scholten
|
BMC Plant Biology
|
Trisomy 21 Alters DNA Methylation in Parent-of-Origin-Dependent and -Independent Manners.
|
2016-04-21
|
Bruna Lancia Zampieri Enrique Medina-Acosta
|
Antônio Francisco Alves da Silva Filipe Brum Machado Érika Cristina Pavarino Joice Matos Biselli-Périco Ronaldo da Silva Francisco Junior Pedro Thyago Mozer Rodrigues Douglas Terra Machado Cíntia Barros Santos-Rebouças Maria Gomes Fernandes Susana Marina Chuva de Sousa Lopes Álvaro Fabricio Lopes Rios
|
PLOS ONE
|
Using Synthetic Mouse Spike-In Transcripts to Evaluate RNA-Seq Analysis Tools.
|
2016-04-21
|
Yisrael Parmet
|
Dena Leshkowitz Ester Feldmesser Gilgi Friedlander Ghil Jona Elena Ainbinder Shirley Horn-Saban
|
PLOS ONE
|
Dysregulation of miRNA-9 in a Subset of Schizophrenia Patient-Derived Neural Progenitor Cells
|
2016-04-21
|
Manuel Mattheisen Jessica Johnson Gerard Cagney Kristen J. Brennand Douglas Ruderfer David R Cotter
|
Aaron Topol Shijia Zhu Brigham J Hartley Jane English Mads E Hauberg Ben Readhead Ngoc Tran Chelsea Ann Rittenhouse Anthony Simone Yoav Hadas Peter A Gochman Ying-Chih Wang Hardik Shah Judith Rapoport Fred H Gage Joel T Dudley Pamela Sklar Gang Fang
|
Cell Reports
|
RNA-seq analysis of early enteromyxosis in turbot (Scophthalmus maximus): new insights into parasite invasion and immune evasion strategies.
|
2016-04-21
|
Ariadna Sitjà-Bobadilla Paolo Ronza Ana Paula Losada Belén G Pardo Paulino Martínez
|
Diego Robledo Roberto Bermúdez María Isabel Quiroga
|
International Journal for Parasitology
|
A benchmark for RNA-seq quantification pipelines.
|
2016-04-23
|
Mingxiang Teng Michael I Love
|
Carrie A Davis Sarah Djebali Alexander Dobin Brenton R Graveley Sheng Li Christopher E Mason Sara Olson Dmitri Pervouchine Cricket A Sloan Xintao Wei Lijun Zhan Rafael A Irizarry
|
Genome Biology
|
Abnormal Osmotic Avoidance Behavior in C. elegans Is Associated with Increased Hypertonic Stress Resistance and Improved Proteostasis
|
2016-04-25
|
Benjamin King
|
Elaine C Lee Heejung Kim Jennifer Ditano Dacie Manion Kevin Strange
|
PLOS ONE
|
Survey of cryptic unstable transcripts in yeast.
|
2016-04-26
|
Robin Dowell
|
Jessica M Vera
|
BMC Genomics
|
Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons.
|
2016-04-26
|
Mark S Cembrowski Lihua Wang Ken Sugino Brenda C Shields Nelson Spruston
|
|
eLife
|
A spectrum of CodY activities drives metabolic reorganization and virulence gene expression in Staphylococcus aureus.
|
2016-04-26
|
Nicholas R Waters
|
David J Samuels Ranjan K Behera Jonathan Livny Kyu Y Rhee Marat R Sadykov Shaun R Brinsmade
|
Molecular Microbiology
|
Pooling across cells to normalize single-cell RNA sequencing data with many zero counts.
|
2016-04-27
|
John C Marioni
|
Aaron T L Lun Karsten Bach
|
Genome Biology
|
RNA-seq Identification of RACGAP1 as a Metastatic Driver in Uterine Carcinosarcoma.
|
2016-04-27
|
Deyou Zheng
|
Shijun Mi Mingyan Lin Jurriaan Brouwer-Visser Jennifer Heim David Smotkin Tiffany Hebert Marc J Gunter Gary L Goldberg Gloria S Huang
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Clinical Cancer Research
|
Transcriptional changes of mouse splenocyte organelle components following acute infection with Toxoplasma gondii.
|
2016-04-27
|
Xing-Quan Zhu
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Jun-Jun He Jun Ma Fa-Cai Li Hui-Qun Song Min-Jun Xu
|
Experimental Parasitology
|
CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq.
|
2016-04-28
|
Aviv Regev Yaron de Leeuw Leon Anavy Itai Yanai Orit Rozenblatt-Rosen
|
Tamar Hashimshony Naftalie Senderovich Gal Avital Agnes Klochendler Dave Gennert Shuqiang Li Kenneth J Livak Yuval Dor
|
Genome Biology
|
Structural and transcriptomic response to antenatal corticosteroids in an Erk3-null mouse model of respiratory distress.
|
2016-04-30
|
Kjersti M Aagaard
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Braden K Pew R Alan Harris Elena Sbrana Milenka Cuevas Guaman Cynthia Shope Rui Chen Sylvain Meloche
|
American Journal of Obstetrics and Gynecology
|
Recurrent DUX4 fusions in B cell acute lymphoblastic leukemia of adolescents and young adults.
|
2016-05
|
Toshiaki Yujiri Masahito Kawazu Eisei Kondo
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Takahiko Yasuda Shinobu Tsuzuki Fumihiko Hayakawa Shinya Kojima Toshihide Ueno Naoto Imoto Shinji Kohsaka Akiko Kunita Koichiro Doi Toru Sakura Katsumichi Fujimaki Yasunori Ueda Yasutaka Aoyama Shigeki Ohtake Junko Takita Eirin Sai Masafumi Taniwaki Mineo Kurokawa Shinichi Morishita Masashi Fukayama Hitoshi Kiyoi Yasushi Miyazaki Tomoki Naoe Hiroyuki Mano
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Nature Genetics
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The Staphylococcus aureus Global Regulator MgrA Modulates Clumping and Virulence by Controlling Surface Protein Expression
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2016-05
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Heidi A Crosby Wilmara Salgado-Pabón Patrick M. Schlievert
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Joseph A Merriman Jessica M King Alexander R Horswill
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PLOS Pathogens
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RNA-sequencing study of peripheral blood monocytes in chronic periodontitis
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2016-05-01
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Melody Baddoo Hong-Wen Deng Erik K Flemington
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Yao-Zhong Liu Pooja Maney Jyoti Puri Yu Zhou Melody Baddoo Michael Strong Yu-Ping Wang
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Gene
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Wishbone identifies bifurcating developmental trajectories from single-cell data.
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2016-05-02
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Dana Pe'er
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Manu Setty Michelle D Tadmor Shlomit Reich-Zeliger Omer Angel Tomer Meir Salame Pooja Kathail Kristy Choi Sean Bendall Nir Friedman Dana Pe'er
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Nature Biotechnology
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Transcriptomic Analysis Reveals Adaptive Responses of an Enterobacteriaceae Strain LSJC7 to Arsenic Exposure.
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2016-05-02
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Yong-Guan Zhu
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Yingjiao Zhang Songcan Chen Xiuli Hao Jian-Qiang Su Ximei Xue Yu Yan Jun Ye
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Frontiers in Microbiology
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Conserved Senescence Associated Genes and Pathways in Primary Human Fibroblasts Detected by RNA-Seq.
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2016-05-03
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Alessandro Cellerino Matthias Platzer
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S Marthandan M Baumgart S Priebe M Groth J Schaer C Kaether R Guthke S Diekmann P Hemmerich
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PLOS ONE
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Ostreococcus tauri is a new model green alga for studying iron metabolism in eukaryotic phytoplankton
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2016-05-03
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Thibaut Léger Róbert Šuťák Jean-Michel Camadro Chris Bowler
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Gaëlle Lelandais Ivo Scheiber Javier Paz-Yepes Jean-Claude Lozano Hugo Botebol Jana Pilátová Vojtěch Žárský Pierre-Louis Blaiseau François-Yves Bouget Emmanuel Lesuisse
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BMC Genomics
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Characterization of novel Bovine Leukemia Virus (BLV) antisense transcripts by deep sequencing reveals constitutive expression in tumors and transcriptional interaction with viral microRNAs.
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2016-05-03
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Anne Van den Broeke Arsène Burny Nicolas Rosewick
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Keith Durkin Maria Artesi Vincent Hahaut Philip Griebel Natasa Arsic Michel Georges Anne Van den Broeke
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Retrovirology
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Single-Cell Genomics for Virology
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2016-05-04
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Amalio Telenti
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Angela Ciuffi Sylvie Rato
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Viruses
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The Trichoderma atroviride putative transcription factor Blu7 controls light responsiveness and tolerance.
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2016-05-04
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Alfredo Herrera-Estrella
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José E Cetz-Chel Edgar Balcázar-López Edgardo U Esquivel-Naranjo
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BMC Genomics
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Xylan degradation by the human gut Bacteroides xylanisolvens XB1A(T) involves two distinct gene clusters that are linked at the transcriptional level.
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2016-05-04
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Nicolas Terrapon Christopher J Fields Evelyne Forano Bernard Henrissat
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Jordane Despres Pascale Lepercq Sophie Comtet-Marre Gregory Jubelin Christophe Chambon Carl J Yeoman Margaret E Berg Miller Eric Martens Bryan A White Pascale Mosoni
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BMC Genomics
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Modeling Doxorubicin-Induced Cardiotoxicity in Human Pluripotent Stem Cell Derived-Cardiomyocytes
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2016-05-04
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Michael R. Hayden
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Agnes Maillet Kim Tan Xiaoran Chai Singh N Sadananda Ashish Mehta Jolene Ooi Mahmoud A Pouladi Sujoy Ghosh Winston Shim Liam R Brunham
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Scientific Reports
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NUDT2 Disruption Elevates Diadenosine Tetraphosphate (Ap4A) and Down-Regulates Immune Response and Cancer Promotion Genes.
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2016-05-04
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Nikki A. Copeland
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Andrew S Marriott Olga Vasieva Yongxiang Fang Alexander G McLennan Nigel J Jones
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PLOS ONE
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Exploiting single-cell expression to characterize co-expression replicability
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2016-05-06
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Jesse Gillis
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Megan Crow Anirban Paul Sara Ballouz Z Josh Huang
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Genome Biology
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Recursive Indirect-Paths Modularity (RIP-M) for Detecting Community Structure in RNA-Seq Co-expression Networks.
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2016-05-09
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Gregory Poland
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Bahareh Rahmani Michael T Zimmermann Diane E Grill Richard B Kennedy Ann L Oberg Bill C White Brett A McKinney
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Frontiers in Genetics
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Recovery of high-quality RNA from laser capture microdissected human and rodent pancreas.
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2016-05-10
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Peter C Butler
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Alexandra E Butler Aleksey V Matveyenko David Kirakossian Johanna Park Tatyana Gurlo
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Journal of histotechnology
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Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors.
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2016-05-10
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John K. Colbourne Christoph R Haag Mikko J Frilander Dieter Ebert Anurag Chaturvedi Jouni Kvist J Asselman Ellen Decaestecker Luisa Orsini Adam Petrusek Ram Podicheti
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Donald Gilbert Mieke Jansen James B Brown Omid Shams Solari Katina I Spanier Douglas Rush Karel A C De Schamphelaere Christian Laforsch Andrew P Beckerman Tom J Little Michael E Pfrender Luc De Meester
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Scientific Data
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Candidate gene networks and blood biomarkers of methamphetamine-associated psychosis: an integrative RNA-sequencing report.
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2016-05-10
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Dan J. Stein Anne Uhlmann
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M S Breen C M Nday S J Glatt M Mitt A Metsalpu N Illing
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Translational Psychiatry
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Targeting super-enhancer-associated oncogenes in oesophageal squamous cell carcinoma.
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2016-05-10
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Ling-Wen Ding Anand Mayakonda Liang Xu
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Yan-Yi Jiang De-Chen Lin Masaharu Hazawa Wen-Wen Chien Ye Chen Jin-Fen Xiao William Senapedis Erkan Baloglu Deepika Kanojia Li Shang Xin Xu Henry Yang Jeffrey W Tyner Ming-Rong Wang H Phillip Koeffler
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Gut
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RNA-Seq of Huntington's disease patient myeloid cells reveals innate transcriptional dysregulation associated with proinflammatory pathway activation.
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2016-05-11
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Sarah J. Tabrizi
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James R C Miller Kitty K Lo Ralph Andre Davina J Hensman Moss Ulrike Träger Timothy C Stone Lesley Jones Peter Holmans Vincent Plagnol
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Human Molecular Genetics
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Persistent Alterations in Microglial Enhancers in a Model of Chronic Pain.
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2016-05-11
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Douglas M. Lopes Athanasios Didangelos Franziska Denk
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Megan Crow Stephen B McMahon
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Cell Reports
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RNA-Seq Analysis Reveals Genes Underlying Different Disease Responses to Porcine Circovirus Type 2 in Pigs.
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2016-05-12
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Shijin Jiang
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Yanping Li Hao Liu Pengfei Wang Liyuan Wang Yi Sun Gen Liu Ping Zhang Li Kang Yunliang Jiang
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PLOS ONE
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Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation
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2016-05-12
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Tapio Lönnberg Valentina Proserpio Giacomo Donati Kedar N Natarajan Oliver Billker Mario Nicodemi Sarah Teichmann
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Andrea Piccolo Liora Haim-Vilmovsky Gozde Kar Valentine Svensson Jhuma Pramanik Weichao Zhai Xiuwei Zhang Melis Kayikci Jurij Kotar Andrew N J McKenzie Ruddy Montandon Steven Woodhouse Pietro Cicuta
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Genome Biology
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An updated human snoRNAome.
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2016-05-12
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Mihaela Zavolan Jana Hertel Stephanie Kehr Peter F. Stadler
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Hadi Jorjani Dominik J Jedlinski Rafal Gumienny Andreas R Gruber
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Nucleic Acids Research
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Dual Identification and Analysis of Differentially Expressed Transcripts of Porcine PK-15 Cells and Toxoplasma gondii during in vitro Infection.
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2016-05-13
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Xing-Quan Zhu Dong-Hui Zhou
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Chun-Xue Zhou Hany M Elsheikha Qing Liu Xun Suo
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Frontiers in Microbiology
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The transcriptome of mouse central nervous system myelin.
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2016-05-13
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Sudhir Thakurela Hauke Werner
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Angela Garding Ramona B Jung Christina Müller Sandra Goebbels Robin White Vijay K Tiwari
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Scientific Reports
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Polycomb repressive complex 1 controls uterine decidualization.
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2016-05-16
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Artem Barski Anil G. Jegga
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Fenghua Bian Fei Gao Andrey V Kartashov Sanjoy K Das
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Scientific Reports
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Molecular Mechanisms of Malignant Transformation by Low Dose Cadmium in Normal Human Bronchial Epithelial Cells.
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2016-05-17
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Steven Shen
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Laura Cartularo Thomas Kluz Lisa Cohen Max Costa
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PLOS ONE
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De Novo Sequencing and Transcriptome Analysis of Pleurotus eryngii subsp. tuoliensis (Bailinggu) Mycelia in Response to Cold Stimulation.
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2016-05-17
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Songnian Hu
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Yong-Ping Fu Yuan Liang Yue-Ting Dai Chen-Tao Yang Ming-Zheng Duan Zhuo Zhang Zhi-Wu Zhang Yu Li
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Molecules
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Biased Expression of the FOXP3Δ3 Isoform in Aggressive Bladder Cancer Mediates Differentiation and Cisplatin Chemotherapy Resistance.
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2016-05-17
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Matteo Pellegrini
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Hanwei Zhang Kris Prado Kelvin X Zhang Elizabeth M Peek Jane Lee Xiaoyan Wang Jiaoti Huang Gang Li Arnold I Chin
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Clinical Cancer Research
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Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants.
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2016-05-18
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Lawrence H. Uricchio
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Noah A Zaitlen Chun Jimmie Ye John S Witte Ryan D Hernandez
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Genome Research
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Altered RNA metabolism due to a homozygous RBM7 mutation in a patient with spinal motor neuropathy.
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2016-05-18
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Yaobo Xu Aurora Gomez-Duran Rita Horvath Veronika Boczonadi
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Michele Giunta Shimon Edvardson Markus Schuelke Orly Elpeleg Juliane S Müller
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Human Molecular Genetics
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The Proteasome Stress Regulon Is Controlled by a Pair of NAC Transcription Factors in Arabidopsis.
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2016-05-18
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Richard D Vierstra
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Nicholas P Gladman Richard S Marshall Kwang-Hee Lee
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The Plant Cell
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Identification of new regulators of embryonic patterning and morphogenesis in Xenopus gastrulae by RNA sequencing.
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2016-05-18
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David K. Crossman
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Ivan K Popov Taejoon Kwon Michael R Crowley John B Wallingford Chenbei Chang
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Developmental Biology
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Hair-Cell Mechanotransduction Persists in TRP Channel Knockout Mice.
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2016-05-19
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Artur A Indzhykulian
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Xudong Wu Paul D Niksch Roxanna M Webber Miguel Garcia-Gonzalez Terry Watnick Jing Zhou Melissa A Vollrath David P Corey
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PLOS ONE
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Novel non-canonical role of STAT1 in Natural Killer cell cytotoxicity.
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2016-05-19
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Christopher Gerner Andrea Majoros Eva Maria Putz Eva M Putz Mathias Müller
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Dagmar Gotthardt Michaela Prchal-Murphy Eva Maria Zebedin-Brandl Daniela Alexandra Fux Andreas Schlattl Robert D Schreiber Sebastian Carotta Thomas Decker Veronika Sexl
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OncoImmunology
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Differential transcriptomic responses to Fusarium graminearum infection in two barley quantitative trait loci associated with Fusarium head blight resistance.
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2016-05-21
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Gary J Muehlbauer
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Yadong Huang Lin Li Kevin P Smith
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BMC Genomics
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Group II mGluRs suppress hyperexcitability in mouse and human nociceptors.
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2016-05-21
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Pradipta R Ray Theodore J. Price
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Steve Davidson Judith P Golden Bryan A Copits Sherri K Vogt Manouela V Valtcheva Robert E Schmidt Andrea Ghetti Robert W Gereau
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Pain
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Do novel genes drive morphological novelty? An investigation of the nematosomes in the sea anemone Nematostella vectensis.
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2016-05-23
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Mark Q Martindale
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Leslie S Babonis Joseph F Ryan
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BMC Evolutionary Biology
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A Laser Dissection-RNAseq Analysis Highlights the Activation of Cytokinin Pathways by Nod Factors in the Medicago truncatula Root Epidermis.
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2016-05-23
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Jérôme Gouzy Ludovic Cottret Anna Kisiala Pascal Gamas
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Marie-Françoise Jardinaud Stéphane Boivin Nathalie Rodde Olivier Catrice Agnes Lepage Sandra Moreau Brice Roux Erika Sallet Mathias Brault R J Neil Emery Florian Frugier
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Plant Physiology
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Identification of host genes leading to West Nile virus encephalitis in mice brain using RNA-seq analysis.
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2016-05-23
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Mukesh Kumar
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Mahdi Belcaid Vivek R Nerurkar
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Scientific Reports
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Rho GTPase Transcriptome Analysis Reveals Oncogenic Roles for Rho GTPase-Activating Proteins in Basal-like Breast Cancers
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2016-05-23
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Charles M. Perou
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Campbell D Lawson Cheng Fan Natalia Mitin Nicole M Baker Samuel D George David M Graham Keith Burridge Channing J Der Kent L Rossman
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Cancer Research
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Small molecule inhibition of cAMP response element binding protein in human acute myeloid leukemia cells.
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2016-05-23
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Matteo Pellegrini
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B Mitton H-D Chae K Hsu R Dutta G Aldana-Masangkay R Ferrari K Davis B C Tiu A Kaul N Lacayo G Dahl F Xie B X Li M R Breese E M Landaw G Nolan S Romanov X Xiao K M Sakamoto
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Leukemia
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Comparative transcriptomics of stickleback immune gene responses upon infection by two helminth parasites, Diplostomum pseudospathaceum and Schistocephalus solidus.
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2016-05-23
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Erich Bornberg-Bauer
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David Haase Jenny K Rieger Anika Witten Monika Stoll Martin Kalbe Alexander Schmidt-Drewello Jörn P Scharsack Thorsten B H Reusch
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Zoology
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Prediction and Quantification of Splice Events from RNA-Seq Data
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2016-05-24
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Robert Gentleman
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Leonard D Goldstein Yi Cao Gregoire Pau Michael Lawrence Thomas D Wu Somasekar Seshagiri
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PLOS ONE
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CTCF and CohesinSA-1 Mark Active Promoters and Boundaries of Repressive Chromatin Domains in Primary Human Erythroid Cells
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2016-05-24
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Vincent Schulz
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Laurie A Steiner Yelena Makismova Kimberly Lezon-Geyda Patrick G Gallagher
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PLOS ONE
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Female rat transcriptome response to infraorbital nerve transection differs from that of males: RNA-seq.
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2016-05-25
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John J Orczyk
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Richard Batka Ashleigh Gore Michelena Maio-Lexa Akhil Kulkarni Preston E Garraghty
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The Journal of Comparative Neurology
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Comprehensive RNA-Seq Analysis on the Regulation of Tomato Ripening by Exogenous Auxin.
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2016-05-26
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Jiayin Li
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Xiaoya Tao Li Li Linchun Mao Zisheng Luo Zia Ullah Khan Tiejin Ying
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PLOS ONE
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Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts
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2016-05-26
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Lior Pachter
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Vasilis Ntranos Govinda M Kamath Jesse M Zhang David N Tse
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Genome Biology
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JUMPg: An Integrative Proteogenomics Pipeline Identifying Unannotated Proteins in Human Brain and Cancer Cells.
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2016-05-26
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Thomas G Beach
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Yuxin Li Xusheng Wang Ji-Hoon Cho Timothy I Shaw Zhiping Wu Bing Bai Hong Wang Suiping Zhou Gang Wu Jinghui Zhang Junmin Peng
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Journal of Proteome Research
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Phosphorus remobilization from rice flag leaves during grain filling: an RNA-seq study.
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2016-05-26
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Tobias Kretzschmar Abdul Baten
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Kwanho Jeong Daniel L E Waters Omar Pantoja Cecile C Julia Matthias Wissuwa Sigrid Heuer Terry J Rose
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Plant Biotechnology Journal
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RNA sequencing of pancreatic adenocarcinoma tumors yields novel expression patterns associated with long-term survival and reveals a role for ANGPTL4
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2016-05-26
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Jason Gertz Donald J Buchsbaum
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Marie K Kirby Ryne C Ramaker Nicholas S Davis Bobbi E Johnston Patsy G Oliver Katherine C Sexton Edward W Greeno John D Christein Martin J Heslin James A Posey William E Grizzle Selwyn M Vickers Sara J Cooper Richard M Myers
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Molecular Oncology
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Hsf1 and Hsp90 orchestrate temperature-dependent global transcriptional remodelling and chromatin architecture in Candida albicans.
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2016-05-26
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Christina A Cuomo Robert T Wheeler Michelle D Leach Rhys A Farrer Kaeling Tan Leah E Cowen Alistair J P Brown
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Zhengqiang Miao Louise A Walker Koon Ho Wong
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Nature Communications
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An atlas of gene expression and gene co-regulation in the human retina.
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2016-05-27
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Luisa Cutillo Sandro Banfi Diego di Bernardo Annamaria Carissimo Michele Pinelli Diego Ponzin
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Ching-Hung Lai Margherita Mutarelli Maria Nicoletta Moretti Marwah Veer Singh Marianthi Karali Diego Carrella Mariateresa Pizzo Francesco Russo Stefano Ferrari Claudia Angelini
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Nucleic Acids Research
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Landscape of tumor-infiltrating T cell repertoire of human cancers
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2016-05-30
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Nir Hacohen
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Bo Li Taiwen Li Jean-Christophe Pignon Binbin Wang Jinzeng Wang Sachet A Shukla Ruoxu Dou Qianming Chen F Stephen Hodi Toni K Choueiri Catherine Wu Sabina Signoretti Jun S Liu X Shirley Liu
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Nature Genetics
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Resistance to docetaxel in prostate cancer is associated with androgen receptor activation and loss of KDM5D expression
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2016-05-31
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Philip W. Kantoff
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Kazumasa Komura Seong Ho Jeong Kunihiko Hinohara Fangfang Qu Xiaodong Wang Masayuki Hiraki Haruhito Azuma Gwo-Shu Mary Lee Christopher J. Sweeney
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Proceedings of the National Academy of Sciences of the United States of America
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The IL-4/STAT6 signaling axis establishes a conserved microRNA signature in human and mouse macrophages regulating cell survival via miR-342-3p
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2016-05-31
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Cei Abreu-Goodger Xin Yan Sudhir Gopal Tattikota Gergely Nagy Eva Varallyay Laszlo Nagy
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Zsolt Czimmerer Tamas Varga Mate Kiss Cesaré Ovando Vázquez Quang Minh Doan-Xuan Dominik Rückerl Zsuzsanna S Nagy Bence Daniel Szilard Poliska Attila Horvath Matthew N Poy Judith E Allen Zsolt Bacso
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Genome Medicine
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Combined physiological, transcriptome, and cis-regulatory element analyses indicate that key aspects of ripening, metabolism, and transcriptional program in grapes (Vitis vinifera L.) are differentially modulated accordingly to fruit size
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2016-05-31
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Darren Wong
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R Lopez Gutierrez N Dimopoulos G A Gambetta S D Castellarin
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BMC Genomics
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Diversity of ABC transporter genes across the plant kingdom and their potential utility in biotechnology.
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2016-05-31
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Gane Ka-Shu Wong Michael Melkonian Caroline Rempe Mark W. Chase
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Thomas S Lane Jack Davitt Margaret E Staton Yanhui Peng Douglas Edward Soltis Michael Melkonian Michael Deyholos James H Leebens-Mack Carl J Rothfels Dennis Stevenson Sean W Graham Jun Yu Tao Liu J Chris Pires Patrick P Edger Yong Zhang Yinlong Xie Ying Zhu Eric Carpenter C Neal Stewart
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BMC Biotechnology
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Sex differences in DNA methylation and expression in zebrafish brain: a test of an extended 'male sex drive' hypothesis.
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2016-05-31
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Julia A. Horsfield Shinichi Nakagawa Aniruddha Chatterjee Malgorzata Lagisz
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Euan J Rodger Li Zhen Peter A Stockwell Elizabeth J Duncan Justin Jeyakani Sinnakaruppan Mathavan Yuichi Ozaki
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Gene
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Bluetongue Virus NS4 Protein Is an Interferon Antagonist and a Determinant of Virus Virulence
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2016-06-01
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Anna Janowicz Marco Caporale Massimo Palmarini
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Maxime Ratinier Andrew E Shaw Gerald Barry Quan Gu Luigina Di Gialleonardo Mariana Varela Richard E Randall
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Journal of Virology
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Detection and visualization of differential splicing in RNA-Seq data with JunctionSeq
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2016-06-01
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James C Mullikin
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Stephen W Hartley
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Nucleic Acids Research
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The contribution of cell cycle to heterogeneity in single-cell RNA-seq data.
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2016-06-01
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Andrew McDavid
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Greg Finak Raphael Gottardo
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Nature Biotechnology
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ZFP57 maintains the parent-of-origin-specific expression of the imprinted genes and differentially affects non-imprinted targets in mouse embryonic stem cells
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2016-06-01
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Kristian Helin Marco Cammisa Gaetano Verde Aditya Sankar Robert Feil Andrea Riccio
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Vincenzo Riso Harpreet Kukreja Zahra Anvar Angela Sparago Basilia Acurzio Shraddha Lad Enza Lonardo Annalisa Fico Claudia Angelini Giovanna Grimaldi
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Nucleic Acids Research
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Identification of interleukin genes in Pogona vitticeps using a de novo transcriptome assembly from RNA-seq data.
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2016-06-02
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Janine E. Deakin Kristine Hardy Alexie Papanicolaou Stephen D. Sarre
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Alexandra Livernois Renae Domaschenz Arthur Georges Sudha Rao Tariq Ezaz
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Immunogenetics
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Transcriptome Profiling Identifies Multiplexin as a Target of SAGA Deubiquitinase Activity in Glia Required for Precise Axon Guidance During Drosophila Visual Development
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2016-06-03
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Vikki M. Weake
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Jingqun Ma Kaelan J Brennan Mitch R D'Aloia Pete E Pascuzzi
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G3
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Insights into the transcriptional and translational mechanisms of linear organellar chromosomes in the box jellyfish Alatina alata (Cnidaria: Medusozoa: Cubozoa)
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2016-06-06
|
Allen Collins
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Ehsan Kayal Bastian Bentlage
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RNA Biology
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RNA-seq Analysis of δ9-Tetrahydrocannabinol-treated T Cells Reveals Altered Gene Expression Profiles That Regulate Immune Response and Cell Proliferation.
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2016-06-06
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Mitzi Nagarkatti
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Xiaoming Yang Marpe Bam Prakash S Nagarkatti
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Journal of Biological Chemistry
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Erratum to: Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis.
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2016-06-06
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Christopher J Fields Evelyne Forano Bernard Henrissat
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Jordane Despres Pascale Lepercq Sophie Comtet-Marre Grégory Jubelin Carl J Yeoman Margret E Berg Miller Nicolas Terrapon Carine Le Bourvellec Catherine M G C Renard Bryan A White Pascale Mosoni
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BMC Genomics
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Genome-wide imputation study identifies novel HLA locus for pulmonary fibrosis and potential role for auto-immunity in fibrotic idiopathic interstitial pneumonia.
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2016-06-07
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Mark Lathrop Diana Zelenika Naftali Kaminski
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Tasha E Fingerlin Weiming Zhang Ivana V Yang Hannah C Ainsworth Pamela H Russell Rachel Z Blumhagen Marvin I Schwarz Kevin K Brown Mark P Steele James E Loyd Gregory P Cosgrove David A Lynch Steve Groshong Harold R Collard Paul J Wolters Williamson Z Bradford Karl Kossen Scott D Seiwert Roland M du Bois Christine Kim Garcia Megan S Devine Gunnar Gudmundsson Helgi J Isaksson Yingze Zhang Kevin F Gibson Lisa H Lancaster Toby M Maher Philip L Molyneaux Athol U Wells Miriam F Moffatt Moises Selman Annie Pardo Dong Soon Kim James D Crapo Barry J Make Elizabeth A Regan Dinesha S Walek Jerry J Daniel Yoichiro Kamatani Elissa Murphy Keith Smith David McKean Brent S Pedersen Janet Talbert Julia Powers Cheryl R Markin Kenneth B Beckman Brian Freed Carl D Langefeld David A Schwartz
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BMC Genetics
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CRAF R391W is a melanoma driver oncogene
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2016-06-08
|
Bartosz Chmielowski Antoni Ribas Anastasia Lomova Bjoern Titz Thomas Graeber
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Mohammad Atefi Jennifer Tsoi Earl Avramis Allison Le Charles Ng Amanda Lassen Michael Friedman
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Scientific Reports
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Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq
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2016-06-08
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Moritz Mall Barbara Treutlein Marius Wernig
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Qian Yi Lee J Gray Camp Winston Koh Seyed Ali Mohammad Shariati Sopheak Sim Norma F Neff Jan M Skotheim Stephen R Quake
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Nature
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Reduced Expression of Histone Methyltransferases KMT2C and KMT2D Correlates with Improved Outcome in Pancreatic Ductal Adenocarcinoma
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2016-06-08
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Frances R Balkwill Jun Wang Claude Chelala Jude Fitzgibbon
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Joshua B N Dawkins Eleni Maniati James A Heward Lola Koniali Hemant M Kocher Sarah A Martin Richard P Grose
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Cancer Research
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SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data.
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2016-06-09
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Marie-Agnès Dillies
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Hugo Varet Loraine Brillet-Guéguen Jean-Yves Coppée
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PLOS ONE
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Transcriptomic analysis illuminates genes involved in chlorophyll synthesis after nitrogen starvation in Acaryochloris sp. CCMEE 5410.
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2016-06-09
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Gautam Dantas
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Aki Yoneda Bruce J Wittmann Jeremy D King Robert E Blankenship
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Photosynthesis Research
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A unique stylopod patterning mechanism by Shox2-controlled osteogenesis.
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2016-06-10
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Marco Osterwalder Axel Visel
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Wenduo Ye Yingnan Song Zhen Huang Anja Ljubojevic Jue Xu Brent Bobick Samuel Abassah-Oppong Ningsheng Ruan Ross Shamby Diankun Yu Lu Zhang Chen-Leng Cai Yanding Zhang John Cobb YiPing Chen
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Development
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RTFBSDB: an integrated framework for transcription factor binding site analysis.
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2016-06-10
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Charles G Danko
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Zhong Wang André L Martins
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Bioinformatics
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Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research
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2016-06-11
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Anand Swaroop Rinki Ratnapriya
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Vijender Chaitankar Gökhan Karakülah Felipe O Giuste Matthew J Brooks
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Progress in Retinal and Eye Research
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Candida albicans Transcriptional Profiling Within Biliary Fluid From a Patient With Cholangitis, Before and After Antifungal Treatment and Surgical Drainage
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2016-06-11
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Nathan L Clark
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Cornelius J Clancy Camille Meslin Hassan Badrane Shaoji Cheng Liliana C Losada William C Nierman Pascalis Vergidis M Hong Nguyen
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Open forum infectious diseases
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Evolutionary origin and functional divergence of totipotent cell homeobox genes in eutherian mammals
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2016-06-13
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Juan A. Bernal Ferdinand Marlétaz Ignacio Maeso Thomas L Dunwell Manuel Irimia
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Chris D R Wyatt Borbála Vető Shan Quah Peter W H Holland
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BMC Biology
|
RNA-Seq analysis of Gtf2ird1 knockout epidermal tissue provides potential insights into molecular mechanisms underpinning Williams-Beuren syndrome
|
2016-06-13
|
Paulina Carmona-Mora
|
Susan M Corley Cesar P Canales Veronica Mendoza-Reinosa Annemiek Beverdam Edna C Hardeman Marc R Wilkins Stephen J Palmer
|
BMC Genomics
|
Boiler: lossy compression of RNA-seq alignments using coverage vectors.
|
2016-06-13
|
Ben Langmead
|
Jacob Pritt
|
Nucleic Acids Research
|
Getting Useful Information from RNA-Seq Contaminants: A Case of Study in the Oil-Collecting Bee Tetrapedia diversipes Transcriptome.
|
2016-06-13
|
Maria C. Arias
|
Natalia de Souza Araujo Alexandre Rizzo Zuntini
|
OMICS: A Journal of Integrative Biology
|
Confirmation of translatability and functionality certifies the dual endothelin1/VEGFsp receptor (DEspR) protein.
|
2016-06-14
|
Keith D Rivera
|
Victoria L M Herrera Martin Steffen Ann Marie Moran Glaiza A Tan Khristine A Pasion Darryl J Pappin Nelson Ruiz-Opazo
|
BMC Molecular Biology
|
Characterization of RON protein isoforms in pancreatic cancer: implications for biology and therapeutics.
|
2016-06-14
|
Carsten Schultz-Fademrecht
|
Jeffery Chakedis Randall French Michele Babicky Dawn Jaquish Evangeline Mose Peter Cheng Patrick Holman Haleigh Howard Jaclyn Miyamoto Paula Porras Zakk Walterscheid Christina Esdar Oliver Schadt Jan Eickhoff Andrew M Lowy
|
Oncotarget
|
Comparing the functions of equine and canine influenza H3N8 virus PA-X proteins: Suppression of reporter gene expression and modulation of global host gene expression.
|
2016-06-14
|
Edward C. Holmes
|
Kurtis H Feng Miao Sun Sho Iketani Colin R Parrish
|
Virology
|
Genome-wide analysis of pentatricopeptide-repeat proteins of an aquatic plant.
|
2016-06-15
|
Wenqin Wang Joachim Messing
|
Yongrui Wu
|
Planta
|
Transcriptome Display During Testicular Differentiation of Channel Catfish (Ictalurus punctatus) as Revealed by RNA-Seq Analysis.
|
2016-06-15
|
Shikai Liu Rex Dunham
|
Qifan Zeng Jun Yao Yu Zhang Zihao Yuan Chen Jiang Ailu Chen Qiang Fu Baofeng Su Zhanjiang Liu
|
Biology of Reproduction
|
RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR.
|
2016-06-17
|
Monther Alhamdoosh Matthew E Ritchie Gordon K Smyth
|
Charity W Law Shian Su
|
F1000Research
|
Different Endosymbiotic Interactions in Two Hydra Species Reflect the Evolutionary History of Endosymbiosis
|
2016-06-19
|
Takashi Gojobori Kazuho Ikeo
|
Masakazu Ishikawa Ikuko Yuyama Hiroshi Shimizu Masafumi Nozawa
|
Genome Biology and Evolution
|
Transcriptional Profiling of Mycobacterium tuberculosis Exposed to In Vitro Lysosomal Stress.
|
2016-06-20
|
Martin L Hibberd
|
Wenwei Lin Paola Florez de Sessions Garrett Hor Keong Teoh Ahmad Naim Nazri Mohamed Yuan O Zhu Vanessa Hui Qi Koh Michelle Lay Teng Ang Peter C Dedon Sylvie Alonso
|
Infection and Immunity
|
From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline
|
2016-06-20
|
Gordon K Smyth
|
Yunshun Chen Aaron T L Lun
|
F1000Research
|
GATA6 regulates EMT and tumour dissemination, and is a marker of response to adjuvant chemotherapy in pancreatic cancer.
|
2016-06-20
|
Marina Pajic Andrew Biankin John P Neoptolemos Paola Martinelli Nelson Dusetti Francisco X Real Eithne Costello Markus Büchler
|
Enrique Carrillo-de Santa Pau Trevor Cox Bruno Sainz William Greenhalf Lorenzo Rinaldi Paula Ghaneh Núria Malats Juan Iovanna
|
Gut
|
RNA-seq studies using wheat PHYTOCHROME B and PHYTOCHROME C mutants reveal shared and specific functions in the regulation of flowering and shade-avoidance pathways
|
2016-06-21
|
Jorge Dubcovsky Néstor Kippes Juan Manuel Debernardi
|
Stephen Pearce Andrew Chen
|
BMC Plant Biology
|
Hypoxia-related microRNA-210 is a diagnostic marker for discriminating osteoblastoma and osteosarcoma.
|
2016-06-21
|
Anne-Marie Cleton-Jansen Emily T Camilleri Annalise Noelle Larson
|
Scott M Riester Jorge Torres-Mora Amel Dudakovic Wei Wang Fuhua Xu Roman R Thaler Jared M Evans René Zwartbol Inge H Briaire-de Bruijn Avudaiappan Maran Andrew L Folpe Carrie Y Inwards Peter S Rose Thomas C Shives Michael J Yaszemski Franklin H Sim David R Deyle Mario A Galindo Arjen G H Cleven Andre M Oliveira Anne-Marie Cleton-Jansen Judith V M G Bovée Andre J van Wijnen
|
Journal of Orthopaedic Research
|
The activation of OR51E1 causes growth suppression of human prostate cancer cells.
|
2016-06-21
|
Hanns Hatt Günter Gisselmann Désirée Maßberg
|
Désirée Maßberg Nikolina Jovancevic Anne Offermann Annika Simon Aria Baniahmad Sven Perner Thanakorn Pungsrinont Katarina Luko Stathis Philippou Burkhard Ubrig Markus Heiland Lea Weber Janine Altmüller Christian Becker Günter Gisselmann Lian Gelis
|
Oncotarget
|
Prediction and Validation of Gene Regulatory Elements Activated During Retinoic Acid Induced Embryonic Stem Cell Differentiation.
|
2016-06-21
|
Zoltan Simandi Laszlo Nagy
|
Attila Horvath Peter Nagy
|
Journal of Visualized Experiments
|
Sequencing, de novo assembly and annotation of a pink bollworm larval midgut transcriptome.
|
2016-06-22
|
Yves Carrière Bruce E Tabashnik
|
Erica E Tassone Gina Zastrow-Hayes John Mathis Mark E Nelson Gusui Wu J Lindsey Flexner Jeffrey A Fabrick
|
GigaScience
|
The Ensembl gene annotation system.
|
2016-06-23
|
Bronwen Aken Laura Clarke Kevin L Howe Magali Ruffier Paul Flicek Felix Kokocinski Amonida Zadissa Daniel N Murphy Carlos García Girón Rishi Nag Julio Fernandez Banet Thibaut Hourlier Andreas K Kähäri Susan Fairley Konstantinos Billis Fergal J Martin Simon White
|
Sarah Ayling Daniel Barrell Valery Curwen Michael Schuster Y Amy Tang Jan-Hinnerk Vogel Stephen M J Searle
|
Database
|
The long intergenic non-coding RNA CCR492 functions as a let-7 competitive endogenous RNA to regulate c-Myc expression.
|
2016-06-23
|
Raffaele A. Calogero Francesco Neri
|
Mara Maldotti Danny Incarnato Anna Krepelova Stefania Rapelli Francesca Anselmi Caterina Parlato Giulia Basile Daniela Dettori Salvatore Oliviero
|
Biochimica et Biophysica Acta
|
Regulation of Gene Expression in Shewanella oneidensis MR-1 during Electron Acceptor Limitation and Bacterial Nanowire Formation.
|
2016-06-24
|
Christine M. Sambles
|
Sarah E Barchinger Sahand Pirbadian Carol S Baker Kar Man Leung Nigel J Burroughs Mohamed Y El-Naggar John H Golbeck
|
Applied and Environmental Microbiology
|
Integrating transcriptome and proteome profiling: Strategies and applications.
|
2016-06-25
|
Dhirendra Kumar
|
Gourja Bansal Ankita Narang Trayambak Basak Tahseen Abbas Debasis Dash
|
Proteomics
|
Expression of Bcl-2 genes in channel catfish after bacterial infection and hypoxia stress.
|
2016-06-25
|
Shikai Liu
|
Zihao Yuan Jun Yao Qifan Zeng Suxu Tan Zhanjiang Liu
|
Developmental and Comparative Immunology
|
Blood lipids influence DNA methylation in circulating cells.
|
2016-06-27
|
Cornelia M. van Duijn André Uitterlinden Gonneke Willemsen Cisca Wijmenga Daria V. Zhernakova Marc Jan Bonder Lude Franke Koen F Dekkers Roderick C Slieker Jenny van Dongen Rick Jansen Dorret Boomsma Peter A.C. 't Hoen Pieternella E Slagboom Albert Hofman Leonard H van den Berg Jan H Veldink Coenraad Dirk Adriaan Stehouwer Casper G. Schalkwijk Jouke-Jan Hottenga
|
Maarten van Iterson Matthijs H Moed Michiel van Galen Hailiang Mei Joris Deelen Diana van Heemst Carla J H van der Kallen Ettje F Tigchelaar Alexandra Zhernakova Joyce van Meurs Marleen M J van Greevenbroek BIOS Consortium Erik W van Zwet J Wouter Jukema Bastiaan T Heijmans
|
Genome Biology
|
Gene-Expression Profiling Suggests Impaired Signaling via the Interferon Pathway in Cstb-/- Microglia
|
2016-06-29
|
Juha Kere Elisabet Einarsdottir Kaarel Krjutškov Anna-Elina Lehesjoki Shintaro Katayama
|
Inken Körber Elisabet Einarsdottir Paula Hakala Tarja Joensuu
|
PLOS ONE
|
A Conserved MicroRNA Regulatory Circuit Is Differentially Controlled during Limb/Appendage Regeneration
|
2016-06-29
|
Benjamin King
|
Viravuth P Yin
|
PLOS ONE
|
Long-read sequencing and de novo assembly of a Chinese genome
|
2016-06-30
|
Francoise Thibaud-Nissen
|
Lingling Shi Yunfei Guo Chengliang Dong John Huddleston Hui Yang Xiaolu Han Aisi Fu Quan Li Na Li Siyi Gong Katherine E Lintner Qiong Ding Zou Wang Jiang Hu Depeng Wang Feng Wang Lin Wang Gholson J Lyon Yongtao Guan Yufeng Shen Oleg V Evgrafov James A Knowles Francoise Thibaud-Nissen Valerie Schneider Chack-Yung Yu Libing Zhou Evan E Eichler Kwok-Fai So Kai Wang
|
Nature Communications
|
CRISPR-Mediated VHL Knockout Generates an Improved Model for Metastatic Renal Cell Carcinoma.
|
2016-06-30
|
Matteo Pellegrini Diana L Moughon Junhui Hu
|
Shiruyeh Schokrpur Peijun Liu Lucia C Lin Kip Hermann Serghei Mangul Wei Guan Hua Xu Lily Wu
|
Scientific Reports
|
Comprehensive genomic analysis reveals FLT3 activation and a therapeutic strategy for a patient with relapsed adult B-lymphoblastic leukemia
|
2016-07
|
Benjamin J Ainscough Elaine Mardis Katie M Campbell Benjamin J Ainscough Kilannin Krysiak Zachary L Skidmore Sean D McGrath Christopher A. Miller Avinash Ramu Catrina Fronick
|
Malachi Griffith Obi L Griffith Matthew J Christopher Jeffery M Klco Tamara L Lamprecht Alex H Wagner Robert Lesurf Jasreet Hundal Jin Zhang Nicholas C Spies David E Larson Sharon E Heath Shelly O'Laughlin Robert S Fulton Vincent Magrini Scott M Smith Christopher A Maher Jacqueline E Payton Jason R Walker James M Eldred Matthew J Walter Daniel C Link Timothy A Graubert Peter Westervelt Shashikant Kulkarni John F DiPersio Richard K Wilson Timothy J Ley
|
Experimental Hematology
|
Novel Intronic RNA Structures Contribute to Maintenance of Phenotype in Saccharomyces cerevisiae
|
2016-07
|
Sam Griffiths-Jones Samina Naseeb
|
Katarzyna B Hooks Steven Parker Daniela Delneri
|
Genetics
|
State-feedback control of Partially-Observed Boolean Dynamical Systems using RNA-seq time series data
|
2016-07
|
Mahdi Imani
|
Ulisses Braga-Neto
|
|
GiniClust: detecting rare cell types from single-cell gene expression data with Gini index.
|
2016-07-01
|
Huidong Chen Luca Pinello
|
Lan Jiang Guo-Cheng Yuan
|
Genome Biology
|
A validated microRNA profile with predictive potential in glioblastoma patients treated with bevacizumab.
|
2016-07-01
|
Susan C. Short Josie Hayes David R. Westhead Martin J van den Bent
|
Helene Thygesen Walter Gregory Pim J French Sean E Lawler
|
Molecular Oncology
|
Epigenetic changes in T-cell and monocyte signatures and production of neurotoxic cytokines in ALS patients.
|
2016-07-01
|
Matteo Pellegrini
|
Larry Lam Lydia Chin Ramesh C Halder Bien Sagong Sam Famenini James Sayre Dennis Montoya Liudmilla Rubbi Milan Fiala
|
FASEB Journal
|
The synovial microenvironment of osteoarthritic joints alters RNA-seq expression profiles of human primary articular chondrocytes.
|
2016-07-01
|
Annalise Noelle Larson
|
Eric A Lewallen Carolina A Bonin Xin Li Jay Smith Marcel Karperien David G Lewallen Simon M Cool Jennifer J Westendorf Aaron J Krych Alexey A Leontovich Hee-Jeong Im Andre J van Wijnen
|
Gene
|
Comparison of methods to detect differentially expressed genes between single-cell populations.
|
2016-07-03
|
Laura L. Elo
|
Maria K Jaakkola Fatemeh Seyednasrollah Arfa Mehmood
|
Briefings in Bioinformatics
|
Transcriptome sequencing reveals aberrant alternative splicing in Huntington's disease.
|
2016-07-04
|
Maurice A Curtis Henry J. Waldvogel Christopher A Ross
|
Lan Lin Juw Won Park Shyam Ramachandran Yida Zhang Yu-Ting Tseng Shihao Shen Richard L M Faull Juan C Troncoso Olga Pletnikova Beverly L Davidson Yi Xing
|
Human Molecular Genetics
|
Global identification of hnRNP A1 binding sites for SSO-based splicing modulation.
|
2016-07-05
|
Brage Storstein Andresen Adrian Robert Krainer
|
Gitte H Bruun Thomas K Doktor Jonas Borch-Jensen Akio Masuda Kinji Ohno
|
BMC Biology
|
Long noncoding RNAs in B-cell development and activation.
|
2016-07-05
|
Andreas Heger Chris Ponting Jennifer Müller
|
Tiago F Brazão Jethro S Johnson Victor L J Tybulewicz
|
Blood
|
Comprehensive RNA-Seq profiling to evaluate lactating sheep mammary gland transcriptome
|
2016-07-05
|
Gwenola Tosser-Klopp Gwenola Tosser-Klopp
|
Aroa Suárez-Vega Beatriz Gutiérrez-Gil Christophe Klopp Juan-José Arranz
|
Scientific Data
|
Pho4 mediates phosphate acquisition in Candida albicans and is vital for stress resistance and metal homeostasis
|
2016-07-06
|
Janet Quinn Elizabeth A. Veal Donna M MacCallum Herrero-de-Dios CM Alistair J P Brown
|
Mélanie A C Ikeh Stavroula L Kastora Alison M Day Emma Tarrant Kevin J Waldron A Peter Banks Judith M Bain David Lydall Lars P Erwig
|
Molecular Biology of the Cell
|
Curation of the genome annotation of Pichia pastoris (Komagataella phaffii) CBS7435 from gene level to protein function.
|
2016-07-06
|
Gerhard G Thallinger Brigitte Gasser Diethard Mattanovich
|
Minoska Valli Nadine E Tatto Armin Peymann Clemens Gruber Nils Landes Heinz Ekker Alexandra B Graf
|
FEMS Yeast Research
|
Analysis of chromosomal aberrations and recombination by allelic bias in RNA-Seq.
|
2016-07-07
|
Dieter Egli
|
Uri Weissbein Maya Schachter Nissim Benvenisty
|
Nature Communications
|
Functional characterization of the 12p12.1 renal cancer-susceptibility locus implicates BHLHE41.
|
2016-07-07
|
Mitchell Machiela Stephen Chanock
|
Pierre Bigot Leandro M Colli Lea Jessop Timothy A Myers Julie Carrouget Sarah Wagner David Roberson Caroline Eymerit Daniel Henrion
|
Nature Communications
|
Expression and methylation patterns partition luminal-A breast tumors into distinct prognostic subgroups.
|
2016-07-07
|
Ayelet Avraham
|
Dvir Netanely Ayelet Avraham Adit Ben-Baruch Ella Evron Ron Shamir
|
Breast Cancer Research
|
Meta-dimensional data integration identifies critical pathways for susceptibility, tumorigenesis and progression of endometrial cancer
|
2016-07-09
|
Jason H. Moore
|
Runmin Wei Immaculata De Vivo Sijia Huang Xun Zhu Harvey Risch Herbert Yu Lana X Garmire
|
Oncotarget
|
A comprehensive next generation sequencing-based virome assessment in brain tissue suggests no major virus - tumor association.
|
2016-07-11
|
Melody Baddoo Erik K Flemington
|
Michael J Strong Eugene Blanchard Zhen Lin Cindy A Morris Melody Baddoo Christopher M Taylor Marcus L Ware
|
Acta neuropathologica communications
|
RNASeq analysis reveals biological processes governing the clinical behaviour of endometrioid and serous endometrial cancers
|
2016-07-12
|
Rajmohan Murali Jorge Reis-Filho Britta Weigelt Salvatore Piscuoglio
|
Christophe Lemetre Begoña Vieites Charlotte K Y Ng Anne M Schultheis Caterina Marchiò Maria A Lopez-García Jose C Palacios Achim A Jungbluth Luigi M Terracciano
|
European Journal of Cancer
|
A systems-oriented analysis of the grapevine R2R3-MYB transcription factor family uncovers new insights into the regulation of stilbene accumulation.
|
2016-07-12
|
José Tomás Matus
|
Darren Chern Jan Wong Rudolf Schlechter Alessandro Vannozzi Janine Höll Ibrahim Hmmam Jochen Bogs Giovanni Battista Tornielli Simone Diego Castellarin
|
DNA Research
|
Design and expression of peptides with antimicrobial activity against Salmonella typhimurium.
|
2016-07-12
|
Alessandro Weisz Ilaria Granata Francesca Rizzo
|
Amalia Porta Anna Maria Petrone Silvana Morello Domenico Memoli Bruno Maresca
|
Cellular Microbiology
|
Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies
|
2016-07-12
|
Julien Bobe
|
Cédric Cabau Frédéric Escudié Anis Djari Yann Guiguen Christophe Klopp
|
|
A Robust Analytical Pipeline for Genome-Wide Identification of the Genes Regulated by a Transcription Factor: Combinatorial Analysis Performed Using gSELEX-Seq and RNA-Seq.
|
2016-07-13
|
Tetsuo Kobayashi
|
Takaaki Kojima Emi Kunitake Kunio Ihara Hideo Nakano
|
PLOS ONE
|
Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNA-Seq.
|
2016-07-14
|
Barbara Treutlein Thomas C. Südhof Marc V Fuccillo Özgün Gökçe Robert Malenka
|
Geoff Stanley Norma F Neff Gray J Camp Patrick E Rothwell Stephen R Quake
|
Cell Reports
|
Transcriptomic Profiling Discloses Molecular and Cellular Events Related to Neuronal Differentiation in SH-SY5Y Neuroblastoma Cells.
|
2016-07-15
|
Alessandro Simonati Maciej Lalowski
|
Francesco Pezzini Laura Bettinetti Francesca Di Leva Marzia Bianchi Elisa Zoratti Rosalba Carrozzo Filippo M Santorelli Massimo Delledonne
|
Cellular and Molecular Neurobiology
|
RNA editing generates cellular subsets with diverse sequence within populations.
|
2016-07-15
|
Theodore Papamarkou Violeta Rayon-Estrada
|
Dewi Harjanto Chris J Oates Violeta Rayon-Estrada F Nina Papavasiliou Anastasia Papavasiliou
|
Nature Communications
|
Abstract 105: Bioinformatic analysis of RNA-Seq data to search for novel diagnostic/prognostic biomarkers of pancreatic ductal adenocarcinoma
|
2016-07-15
|
Joao Carlos Setubal
|
Omar J. Sosa Vinícius F. Paixão Eduardo M. Reis
|
Cancer Research
|
Increase of Alternatively Activated Antigen Presenting Cells in Active Experimental Autoimmune Encephalomyelitis.
|
2016-07-16
|
Frauke Zipp
|
Beatrice Wasser Gautam Pramanik Moritz Hess Matthias Klein Felix Luessi Klaus Dornmair Tobias Bopp Esther Witsch
|
Journal of Neuroimmune Pharmacology
|
Sympatric speciation of spiny mice, Acomys, unfolded transcriptomically at Evolution Canyon, Israel
|
2016-07-19
|
Eviatar Nevo
|
Kexin Li Huihua Wang Zhenyuan Cai Liuyang Wang Qinqin Xu Matěj Lövy Zhenlong Wang
|
Proceedings of the National Academy of Sciences of the United States of America
|
Identification and Comparative Analysis of Differential Gene Expression in Soybean Leaf Tissue under Drought and Flooding Stress Revealed by RNA-Seq.
|
2016-07-19
|
Babu Valliyodan Rupesh K. Deshmukh Rajeev Kumar Varshney Gunvant Patil
|
Wei Chen Qiuming Yao Gaurav Agarwal Li Lin Biao Wang Yongqin Wang Silvas J Prince Li Song Dong Xu Yongqiang C An Henry T Nguyen
|
Frontiers in Plant Science
|
Full Spectrum of LPS Activation in Alveolar Macrophages of Healthy Volunteers by Whole Transcriptomic Profiling.
|
2016-07-19
|
Miguel Pinilla-Vera Robert M Tighe
|
Zeyu Xiong Yutong Zhao Jing Zhao Michael P Donahoe Suchitra Barge William T Horne Jay K Kolls Bryan J McVerry Anastasiya Birukova W Michael Foster John Hollingsworth Anuradha Ray Rama Mallampalli Prabir Ray Janet S Lee
|
PLOS ONE
|
Contextual fear conditioning induces differential alternative splicing.
|
2016-07-19
|
Ted Abel John N Koberstein Shane G. Poplawski Lucia Peixoto Davide Risso
|
Giulia S Porcari Mathieu E Wimmer Anna G McNally Keiko Mizuno K Peter Giese Snehajyoti Chatterjee Terence P Speed
|
Neurobiology of Learning and Memory
|
Ago-RIP-Seq identifies Polycomb repressive complex I member CBX7 as a major target of miR-375 in prostate cancer progression.
|
2016-07-20
|
Markus Hohenfellner Holger Sültmann Boris Hadaschik
|
Julia M A Pickl Diana Tichy Vladimir Y Kuryshev Yanis Tolstov Michael Falkenstein Julia Schüler Daniel Reidenbach Agnes Hotz-Wagenblatt Glen Kristiansen Wilfried Roth Stefan Duensing Doreen Heckmann
|
Oncotarget
|
SLC9A9 Co-expression modules in autism-associated brain regions.
|
2016-07-21
|
Stephen Faraone
|
Jameson Patak Jonathan L Hess Yanli Zhang-James Stephen J Glatt
|
Autism Research
|
A Splice Defect in the EDA Gene in Dogs with an X-Linked Hypohidrotic Ectodermal Dysplasia (XLHED) Phenotype
|
2016-07-22
|
Tosso Leeb Gila Zur
|
Dominik P Waluk Ronnie Kaufmann Monika M Welle Vidhya Jagannathan Cord Drögemüller Eliane J Müller Arnaud Galichet
|
G3
|
Deep transcriptomic profiling reveals the similarity between endothelial cells cultured under static and oscillatory shear stress conditions
|
2016-07-22
|
Hanjoong Jo
|
Congzhen Qiao Fan Meng Inhwan Jang Y Eugene Chen Jifeng Zhang
|
Physiological Genomics
|
SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence
|
2016-07-25
|
Marie-France Sagot
|
Hélène Lopez-Maestre Lilia Brinza Camille Marchet Janice Kielbassa Sylvère Bastien Mathilde Boutigny David Monnin Adil El Filali Claudia Marcia Carareto Cristina Vieira Franck Picard Natacha Kremer Fabrice Vavre Vincent Lacroix
|
Nucleic Acids Research
|
PR2S2Clust: Patched RNA-seq read segments' structure-oriented clustering.
|
2016-07-25
|
Ashis Kumer Biswas
|
Jean X Gao
|
Journal of Bioinformatics and Computational Biology
|
Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq
|
2016-07-27
|
Olivier Elemento
|
David Redmond Asaf Poran
|
Genome Medicine
|
Modeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles.
|
2016-07-27
|
Chongzhi Zang Su Wang Housheng Hansen He
|
Tengfei Xiao Jingyu Fan Shenglin Mei Qian Qin Qiu Wu Xujuan Li Kexin Xu Myles Brown Clifford A Meyer X Shirley Liu
|
Genome Research
|
Novel genes on rat chromosome 10 are linked to body fat mass, preadipocyte number and adipocyte size.
|
2016-07-27
|
Matthias Blüher Michael Stumvoll
|
A Weingarten L Turchetti K Krohn I Klöting M Kern P Kovacs M Blüher N Klöting
|
International Journal of Obesity
|
End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data.
|
2016-07-28
|
Jeremy Luban
|
Alan Derr Chaoxing Yang Rapolas Zilionis Alexey Sergushichev David M Blodgett Sambra Redick Rita Bortell David M Harlan Sebastian Kadener Dale L Greiner Allon Klein Maxim N Artyomov Manuel Garber
|
Genome Research
|
FAR-RED ELONGATED HYPOCOTYL3 activates SEPALLATA2 but inhibits CLAVATA3 to regulate meristem determinacy and maintenance in Arabidopsis.
|
2016-07-28
|
Xuemei Chen
|
Dongming Li Xing Fu Lin Guo Zhigang Huang Yongpeng Li Yang Liu Zishan He Xiuwei Cao Xiaohan Ma Meicheng Zhao Guohui Zhu Langtao Xiao Haiyang Wang Renyi Liu Xigang Liu
|
Proceedings of the National Academy of Sciences of the United States of America
|
Characterization of circular RNAs in human, mouse and rat hearts.
|
2016-07-28
|
Thomas Meitinger Stephan Nothjunge Stefan Engelhardt
|
Stanislas Werfel Thomas Schwarzmayr Tim-Matthias Strom
|
Journal of Molecular and Cellular Cardiology
|
Single-Cell RNAseq Reveals That Pancreatic β-Cells From Very Old Male Mice Have a Young Gene Signature.
|
2016-07-28
|
Andrew J Murphy
|
Yurong Xin Haruka Okamoto Jinrang Kim Min Ni Christina Adler Katie Cavino Erqian Na George D Yancopoulos Calvin Lin Jesper Gromada
|
Endocrinology
|
Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons.
|
2016-07-28
|
Aviv Regev
|
Naomi Habib Yinqing Li Matthias Heidenreich Lukasz Swiech Inbal Avraham-Davidi John J Trombetta Cynthia Hession Feng Zhang
|
Science
|
Zika Virus Disrupts Phospho-TBK1 Localization and Mitosis in Human Neuroepithelial Stem Cells and Radial Glia
|
2016-08
|
Nenad Sestan Jernej Mlakar Marco Onorati
|
Zhen Li Fuchen Liu André M.M. Sousa Naoki Nakagawa Mingfeng Li Maria Teresa Dell’Anno Forrest O. Gulden Sirisha Pochareddy Andrew T.N. Tebbenkamp Wenqi Han Mihovil Pletikos Tianliuyun Gao Ying Zhu Candace Bichsel Luis Varela Klara Szigeti-Buck Steven Lisgo Yalan Zhang Anze Testen Xiao-Bing Gao Mara Popovic Marie Flamand Stephen M. Strittmatter Leonard K. Kaczmarek E.S. Anton Tamas L. Horvath Brett D. Lindenbach
|
Cell Reports
|
Atad2 is a generalist facilitator of chromatin dynamics in embryonic stem cells
|
2016-08
|
François-Loïc Cosset Saadi Khochbin Apirat Chaikuad Stefan Knapp Matthieu Gérard Fayçal Boussouar Anouk Emadali Minjia Tan Sophie Rousseaux
|
Yuichi Morozumi Mahya Jamshidikia Gozde Colak Huang He Litong Nie Carlo Petosa Maud de Dieuleveult Sandrine Curtet Anne-Laure Vitte Clothilde Rabatel Alexandra Debernardi Els Verhoeyen Norbert Schweifer Davide Gianni Marta Gut Philippe Guardiola Yingming Zhao
|
Journal of molecular cell biology
|
Tensor decomposition for multiple-tissue gene expression experiments
|
2016-08-01
|
Jonathan Marchini Ana Viñuela Kerrin S. Small Mark McCarthy
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Victoria Hore Alfonso Buil Julian Knight
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Nature Genetics
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Epigenetic remodeling regulates transcriptional changes between ovarian cancer and benign precursors
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2016-08-01
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John Quackenbush Emily MacDuffie
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Kevin M Elias Megan M Emori Thomas Westerling Henry Long Anna Budina-Kolomets Fugen Li Michelle R Davis Alexander Holman Brian Lawney Matthew L Freedman Myles Brown Ronny Drapkin
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JCI insight
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Identification and Validation of PCAT14 as Prognostic Biomarker in Prostate Cancer.
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2016-08-01
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Marcin Cieślik
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Sudhanshu Shukla Xiang Zhang Yashar S Niknafs Lanbo Xiao Rohit Mehra Ashley Ross Edward Schaeffer Bhavna Malik Shuling Guo Susan M Freier Huynh-Hoa Bui Javed Siddiqui Xiaojun Jing Xuhong Cao Saravana M Dhanasekaran Felix Y Feng Arul M Chinnaiyan Rohit Malik
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Neoplasia
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Neuraminidase A-Exposed Galactose Promotes Streptococcus pneumoniae Biofilm Formation during Colonization.
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2016-08-01
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Sean C Daugherty
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Krystle A Blanchette Anukul T Shenoy Jeffrey Milner Ryan P Gilley Erin McClure Cecilia A Hinojosa Nikhil Kumar Luke J Tallon Sandra Ott Samantha J King Daniela M Ferreira Stephen B Gordon Hervé Tettelin Carlos J Orihuela
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Infection and Immunity
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142 Genetic and Nongenetic Determinants of Cellular Architecture in IDH1-Mutant Oligodendrogliomas and Astrocytomas Using Single-Cell Transcriptome Analysis.
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2016-08-01
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Aviv Regev Itay Tirosh Brian V. Nahed
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Andrew Sean Venteicher Itay Tirosh Christine Hebert Leah Escalante Robert L Martuza William T Curry Daniel P Cahill Bradley Bernstein David N Louis Mario Suva
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Neurosurgery
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Strong down-regulation of glycophorin genes: A host defense mechanism against rotavirus infection.
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2016-08-01
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Alberto Gómez-Carballa Miriam Cebey-López Jose Gomez-Rial Antonio Salas Federico Martinón-Torres
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Guillermo Marco-Puche Juan Carlos Triviño Irene Rivero-Calle Lucía Vilanova-Trillo Carmen Rodríguez-Tenreiro
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Infection, Genetics and Evolution
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Optimized design and analysis of preclinical intervention studies in vivo
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2016-08-02
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Jukka Westermarck Mikael Jumppanen Sari Mäkelä Teemu D Laajala Tero Aittokallio
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Riikka Huhtaniemi Vidal Fey Amanpreet Kaur Matias Knuuttila Eija Aho Riikka Oksala Matti Poutanen
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Scientific Reports
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The Sinorhizobium fredii HH103 MucR1 Global Regulator Is Connected With the nod Regulon and Is Required for Efficient Symbiosis With Lotus burttii and Glycine max cv. Williams.
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2016-08-02
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Susanne Zehner Miguel A Rodríguez-Carvajal José-María Vinardell
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Sebastián Acosta-Jurado Cynthia Alias-Villegas Pilar Navarro-Gómez Piedad Del Socorro Murdoch María J Soto Francisco-Javier Ollero José E Ruiz-Sainz Michael Göttfert
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Molecular Plant-Microbe Interactions
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The (in)complete organelle genome: exploring the use and nonuse of available technologies for characterizing mitochondrial and plastid chromosomes.
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2016-08-02
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David Roy Smith
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Matheus Sanitá Lima Laura C Woods Matthew W Cartwright
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Molecular Ecology Resources
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Hierarchical RNA Processing Is Required for Mitochondrial Ribosome Assembly.
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2016-08-03
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Oliver Rackham Aleksandra Filipovska Nils-Göran Larsson
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Jakob D Busch Stanka Matic Stefan J Siira Irina Kuznetsova Ilian Atanassov Judith A Ermer Anne-Marie J Shearwood Tara R Richman James B Stewart Arnaud Mourier Dusanka Milenkovic
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Cell Reports
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Mycobacterium tuberculosis strains exhibit differential and strain-specific molecular signatures in pulmonary epithelial cells.
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2016-08-03
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William Bishai Manormoney Pillay
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Nontobeko Eunice Mvubu Balakrishna Pillay Junaid Gamieldien
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Developmental and Comparative Immunology
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microRNA-132/212 deficiency enhances Aβ production and senile plaque deposition in Alzheimer's disease triple transgenic mice.
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2016-08-03
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Maxime P Vallée Sébastien S. Hébert Frédéric Calon
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Julia Hernandez-Rapp Sara Rainone Claudia Goupil Véronique Dorval Pascal Y Smith Martine Saint-Pierre Emmanuel Planel Arnaud Droit Francesca Cicchetti
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Scientific Reports
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ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences
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2016-08-04
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Philip Rosenstiel
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Wentao Yang Hinrich Schulenburg
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BMC Genomics
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Modulatory Effects of Sex Steroids Progesterone and Estradiol on Odorant Evoked Responses in Olfactory Receptor Neurons.
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2016-08-05
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Hanns Hatt Günter Gisselmann
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Ninthujah Kanageswaran Maximilian Nagel Paul Scholz Julia Mohrhardt Günter Gisselmann
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PLOS ONE
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Identification of genes differentially regulated by vitamin D deficiency that alter lung pathophysiology and inflammation in allergic airways disease.
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2016-08-05
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Rachel E Foong Anthony Bosco Prue H Hart Graeme R. Zosky Anthony Kicic Shelley Gorman
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Niamh M Troy
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American Journal of Physiology - Lung Cellular and Molecular Physiology
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Chicken interferome: avian interferon-stimulated genes identified by microarray and RNA-seq of primary chick embryo fibroblasts treated with a chicken type I interferon (IFN-α).
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2016-08-05
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Michael A. Skinner
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Efstathios S Giotis Rebecca C Robey Natalie G Skinner Christopher D Tomlinson Stephen Goodbourn
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Veterinary Research
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scphaser: haplotype inference using single-cell RNA-seq data
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2016-08-06
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Björn Reinius Rickard Sandberg
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Daniel Edsgärd
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Bioinformatics
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Cluster analysis of Plasmodium RNA-seq time-course data identifies stage-specific co-regulated biological processes and regulatory elements.
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2016-08-08
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Itunuoluwa Isewon Jelili Oyelade
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Efejiro Ashano Ezekiel Adebiyi
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F1000Research
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Schistosome sex matters: a deep view into gonad-specific and pairing-dependent transcriptomes reveals a complex gender interplay
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2016-08-08
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Matthew Berriman
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Zhigang Lu Florian Sessler Nancy Holroyd Steffen Hahnel Thomas Quack Christoph G Grevelding
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Scientific Reports
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RNA-seq analysis identifies key long non-coding RNAs connected to the pathogenesis of alcohol-associated head and neck squamous cell carcinoma.
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2016-08-08
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Jessica Wang-Rodriguez
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Vicky Yu Pranav Singh Elham Rahimy Hao Zheng Selena Z Kuo Elizabeth Kim Weg M Ongkeko
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Oncology Letters
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Spliced synthetic genes as internal controls in RNA sequencing experiments.
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2016-08-08
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Lars K. Nielsen John Mattick Simon A Hardwick Ira Deveson
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Wendy Y Chen Ted Wong James Blackburn Stacey B Andersen Tim R Mercer
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Nature Methods
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Vacuolar Chloride Fluxes Impact Ion Content and Distribution during Early Salinity Stress.
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2016-08-08
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Enrico Martinoia
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Ulrike Baetz Cornelia Eisenach Takayuki Tohge Alexis De Angeli
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Plant Physiology
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Transcriptional Profiling of Cultured, Embryonic Epicardial Cells Identifies Novel Genes and Signaling Pathways Regulated by TGFβR3 In Vitro.
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2016-08-09
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Daniel M DeLaughter
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Daniel M DeLaughter Cynthia R Clark Danos C Christodoulou Christine E Seidman H Scott Baldwin J G Seidman Joey V Barnett
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PLOS ONE
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Co-expression analysis identifies long noncoding RNA SNHG1 as a novel predictor for event-free survival in neuroblastoma.
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2016-08-09
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Chia-Lang Hsu Wen-Ming Hsu Hsuan-Cheng Huang
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Divya Sahu Chen-Ching Lin Tz-Wen Yang Shinn-Ying Ho Hsueh-Fen Juan
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Oncotarget
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Ordered chromatin changes and human X chromosome reactivation by cell fusion-mediated pluripotent reprogramming.
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2016-08-10
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Tatyana B Nesterova Claire Rougeulle Irene Cantone Matthias Merkenschlager
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Hakan Bagci Dirk Dormann Gopuraja Dharmalingam Neil Brockdorff Celine Vallot Edith Heard Ronan Chaligne Amanda G Fisher
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Nature Communications
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Metronomic cyclophosphamide activation of anti-tumor immunity: tumor model, mouse host, and drug schedule dependence of gene responses and their upstream regulators.
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2016-08-11
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David J Waxman
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Junjie Wu Marie Jordan
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BMC Cancer
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Transcriptome analysis reveals regional and temporal differences in mucosal immune system development in the small intestine of neonatal calves.
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2016-08-11
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Paul Stothard
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Guanxiang Liang Nilusha Malmuthuge Hua Bao Philip J Griebel Le Luo Guan
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BMC Genomics
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Comparative transcriptome profiling of resistant and susceptible rice genotypes in response to the seedborne pathogen Fusarium fujikuroi.
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2016-08-11
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Davide Spadaro
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Slavica Matić Paolo Bagnaresi Chiara Biselli Luigi Orru' Greice Amaral Carneiro Ilenia Siciliano Giampiero Valé Maria Lodovica Gullino
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BMC Genomics
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Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.
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2016-08-11
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Steven Salzberg Mihaela Pertea
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Daehwan Kim Geo M Pertea Jeffrey T Leek
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Nature Protocols
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Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta.
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2016-08-11
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Robert M. Waterhouse Thorsten Burmester Ioannis Michalopoulos Julio Rozas Ramesh T Gunaratna Suyog S Kuwar Xiaolong Cao Tom K Walsh Seung-Joon Ahn Adriana Briscoe Yannick Pauchet Alexie Papanicolaou Ewald Grosse-Wilde Guillaume Tetreau René Feyereisen John G Oakeshott Gary W. Blissard Lars S Jermiin Susan J Brown Bill S. Hansson Haobo Jiang
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Michael R Kanost Estela L Arrese Yun-Ru Chen Sanjay Chellapilla Marian R Goldsmith David G Heckel Nicolae Herndon Jiaxin Qu Jose L Soulages Heiko Vogel James Walters Francisca C Almeida Chunju An Peshtewani Aqrawi Anne Bretschneider William B Bryant Sascha Bucks Hsu Chao Germain Chevignon Jayne M Christen David F Clarke Neal T Dittmer Laura C F Ferguson Spyridoula Garavelou Karl H J Gordon Yi Han Frank Hauser Yan He Hanna Heidel-Fischer Ariana Hirsh Yingxia Hu Hongbo Jiang Divya Kalra Christian Klinner Christopher König Christie Kovar Ashley R Kroll Sandy L Lee Rüdiger Lehman Kai Li Zhaofei Li Hanquan Liang Shanna Lovelace Zhiqiang Lu Jennifer H Mansfield Kyle J McCulloch Tittu Mathew Brian Morton Donna M Muzny David Neunemann Fiona Ongeri Ling-Ling Pu Ioannis Pyrousis Xiang-Jun Rao Amanda Redding Charles Roesel Alejandro Sanchez-Gracia Sarah Schaack Aditi Shukla Yang Wang Guang-Hua Xiong Walther Traut Kim C Worley Di Wu Wenbi Wu Yuan-Qing Wu Xiufeng Zhang Zhen Zou Hannah Zucker Rollie J Clem Cornelis J P Grimmelikhuijzen Stavros J Hamodrakas Elisabeth Huguet Que Lan Herman K Lehman Marce Lorenzen Hans Merzendorfer David B Morton Subbaratnam Muthukrishnan Will Palmer Yoonseong Park A Lorena Passarelli Lawrence M Schwartz Wendy Smith Agnes Southgate Andreas Vilcinskas Richard Vogt Ping Wang John Werren Xiao-Qiang Yu Jing-Jiang Zhou Steven E Scherer Stephen Richards
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Insect Biochemistry and Molecular Biology
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NVT: a fast and simple tool for the assessment of RNA-seq normalization strategies.
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2016-08-11
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Thomas Eder Florian Grebien Thomas Rattei
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Bioinformatics
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Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq)
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2016-08-12
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Konrad Förstner Cynthia Sharma Jörg Soppa Friedhelm Pfeiffer
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Julia Babski Karina A. Haas Daniela Näther-Schindler Matthias Hammelmann Rolf Hilker Anke Becker Anita Marchfelder
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BMC Genomics
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A germline mutation of CDKN2A and a novel RPLP1-C19MC fusion detected in a rare melanotic neuroectodermal tumor of infancy: a case report.
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2016-08-12
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Daniel C Swan
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David J Barnes Edward Hookway Nick Athanasou Takeshi Kashima Udo Oppermann Simon Hughes Dietrich Lueerssen John Anson A Bassim Hassan
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BMC Cancer
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Peromyscus transcriptomics: Understanding adaptation and gene expression plasticity within and between species of deer mice.
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2016-08-12
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Jason Munshi-South
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Jonathan L Richardson
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Seminars in Cell & Developmental Biology
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Single-cell RNAseq reveals cell adhesion molecule profiles in electrophysiologically defined neurons
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2016-08-16
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Thomas C. Südhof Robert Malenka
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Csaba Földy Spyros Darmanis Jason Aoto Stephen R Quake
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Proceedings of the National Academy of Sciences of the United States of America
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Proteolysis-a characteristic of tumor-initiating cells in murine metastatic breast cancer.
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2016-08-16
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Marie Follo Melanie Boerries Hauke Busch Thomas Reinheckel
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Larissa E Hillebrand Fee Bengsch Jochen Hochrein Jan Hülsdünker Julia Bender
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Oncotarget
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Whole-transcriptome brain expression and exon-usage profiling in major depression and suicide: evidence for altered glial, endothelial and ATPase activity.
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2016-08-16
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Victoria Arango
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S P Pantazatos Y-Y Huang G B Rosoklija A J Dwork J J Mann
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Molecular Psychiatry
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Critical re-evaluation of neuroglobin expression reveals conserved patterns among mammals.
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2016-08-16
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Thorsten Burmester
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Andrej Fabrizius Daniel Andre Tilmann Laufs Anne Bicker Stefan Reuss Elena Porto Thomas Hankeln
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Neuroscience
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REST is a hypoxia-responsive transcriptional repressor
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2016-08-17
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Miguel Cavadas Carsten C Scholz Zsolt Fabian Alex Cheong Murtaza M Tambuwala
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Marion Mesnieres Bianca Crifo Mario C Manresa Andrew C Selfridge Ciara E Keogh Karen A Nolan Liliane M A Rocha Stuart Brown Anita Wdowicz Danielle Corbett Keith J Murphy Catherine Godson Eoin P Cummins Cormac T Taylor
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Scientific Reports
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Decoding the Regulatory Landscape of Ageing in Musculoskeletal Engineered Tissues Using Genome-Wide DNA Methylation and RNASeq.
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2016-08-17
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Katarzyna Goljanek-Whysall
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Mandy Jayne Peffers John Collins Yongxiang Fang Michael Rushton John Loughlin Carole Proctor Peter David Clegg
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PLOS ONE
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The Spectrum and Regulatory Landscape of Intestinal Innate Lymphoid Cells Are Shaped by the Microbiome.
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2016-08-17
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Hadas Keren-Shaul
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Meital Gury-BenAri Christoph A Thaiss Nicolas Serafini Deborah R Winter Amir Giladi David Lara-Astiaso Maayan Levy Tomer Meir Salame Assaf Weiner Eyal David Hagit Shapiro Mally Dori-Bachash Meirav Pevsner-Fischer Erika Lorenzo-Vivas Hadas Keren-Shaul Franziska Paul Alon Harmelin Gérard Eberl Shalev Itzkovitz Amos Tanay James P Di Santo Eran Elinav Ido Amit
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Cell
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Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm.
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2016-08-17
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Christina Kendziorski
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Li-Fang Chu Ning Leng Jue Zhang Zhonggang Hou Daniel Mamott David T Vereide Jeea Choi Ron Stewart James A Thomson
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Genome Biology
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Integrative Genomics Outlines a Biphasic Glucose Response and a ChREBP-RORγ Axis Regulating Proliferation in β Cells.
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2016-08-17
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Jens Juul Holst Susanne Mandrup Bjørk Ditlev Larsen Louise T Dalgaard Pierre Maechler
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Søren Fisker Schmidt Jesper Grud Skat Madsen Kari Østerli Frafjord Lars la Cour Poulsen Sofia Salö Michael Boergesen Anne Loft Maria Stahl Madsen
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Cell Reports
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C. elegans Stress-Induced Sleep Emerges from the Collective Action of Multiple Neuropeptides.
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2016-08-17
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Han Wang Erich M Schwarz Paul W. Sternberg
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Ravi D Nath Elly S Chow
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Current Biology
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Paternal chronic colitis causes epigenetic inheritance of susceptibility to colitis.
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2016-08-19
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Ole Ammerpohl Johanna Klughammer
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Markus Tschurtschenthaler Priyadarshini Kachroo Femke-Anouska Heinsen Timon Erik Adolph Malte Christoph Rühlemann Felix Albert Offner Felix Krueger Sébastien Smallwood Silke Szymczak Arthur Kaser Andre Franke
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Scientific Reports
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Identification of microbial populations driving biopolymer degradation in acidic peatlands by metatranscriptomic analysis.
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2016-08-22
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Svetlana N Dedysh Anastasia A. Ivanova
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Carl-Eric Wegner Yongkyu Kim Werner Liesack
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Molecular Ecology
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Determining Physical Mechanisms of Gene Expression Regulation from Single Cell Gene Expression Data
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2016-08-23
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Daphne Ezer Berthold Göttgens
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Victoria Moignard Boris Adryan
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PLOS Computational Biology
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RNA-sequencing of a mouse-model of spinal muscular atrophy reveals tissue-wide changes in splicing of U12-dependent introns.
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2016-08-23
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Brage Storstein Andresen Adrian Robert Krainer
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Thomas Koed Doktor Yimin Hua Henriette Skovgaard Andersen Sabrina Brøner Ying Hsiu Liu Anna Wieckowska Maja Dembic Gitte Hoffmann Bruun
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Nucleic Acids Research
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Identification of novel regulators of developmental hematopoiesis using Endoglin regulatory elements as molecular probes.
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2016-08-23
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Rahul Roychoudhuri Jason Wong Elaine Dzierzak Julie Thoms
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Rabab Nasrallah Eva M Fast Parham Solaimani Kathy Knezevic Alexia Eliades Rahima Patel Roshana Thambyrajah Ashwin Unnikrishnan Dominik Beck Chris S Vink Aileen Smith Mairi Shepherd David Kent Fabian Paul Julia Klippert Annette Hammes Thomas Willnow Bertie Göttgens Leonard I Zon George Lacaud Valerie Kouskoff John E Pimanda
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Blood
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Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V'DJer.
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2016-08-24
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Jonathan S. Serody Benjamin G Vincent Charles M. Perou
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Lisle E Mose Sara R Selitsky Lisa M Bixby David L Marron Michael D Iglesia Joel S Parker
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Bioinformatics
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An integrative transcriptomic atlas of organogenesis in human embryos.
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2016-08-24
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Dave Gerrard Neil A. Hanley
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Andrew A Berry Rachel E Jennings Karen Piper Hanley Nicoletta Bobola
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eLife
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Genomewide Association Study of African Children Identifies Association of SCHIP1 and PDE8A with Facial Size and Shape.
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2016-08-25
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Washington Mio Benedikt Hallgrímsson
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Joanne B Cole Mange Manyama Emmanuel Kimwaga Joshua Mathayo Jacinda R Larson Denise K Liberton Ken Lukowiak Tracey M Ferrara Sheri L Riccardi Mao Li Washington Mio Michaela Prochazkova Trevor Williams Hong Li Kenneth L Jones Ophir D Klein Stephanie A Santorico Benedikt Hallgrimsson Richard A Spritz
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PLOS Genetics
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DNA Methylation Profiling of Uniparental Disomy Subjects Provides a Map of Parental Epigenetic Bias in the Human Genome
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2016-08-25
|
Karin Buiting Samuel G. Jacobson Corey T Watson Thomas H Wassink Noah Zaitlen
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Ricky S Joshi Paras Garg Tuuli Lappalainen Nidha Azam Daniel Ho Xin Li Stylianos E Antonarakis Han G Brunner Sau Wai Cheung Bradford Coffee Thomas Eggermann David Francis Joep P Geraedts Giorgio Gimelli Cedric Le Caignec Nicole de Leeuw Thomas Liehr Deborah J Mackay Stephen B Montgomery Alistair T Pagnamenta Peter Papenhausen David O Robinson Claudia Ruivenkamp Charles Schwartz Bernhard Steiner David A Stevenson Urvashi Surti Andrew J Sharp
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American Journal of Human Genetics
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Expression dynamics, relationships, and transcriptional regulations of diverse transcripts in mouse spermatogenic cells
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2016-08-25
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Bo Wen
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Xiwen Lin Miao Han Lu Cheng Jian Chen Zhuqiang Zhang Ting Shen Min Wang Ting Ni Chunsheng Han
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RNA Biology
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Maf1-mediated regulation of yeast RNA polymerase III is correlated with CCA addition at the 3' end of tRNA precursors.
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2016-08-26
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Dominika Wichtowska Marek Żywicki Grzegorz Kudła Wojciech M Karlowski Magdalena Rakowska-Boguta
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Przemysław Nuc
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Gene
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Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach
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2016-08-26
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Feixiong Cheng Bairong Shen
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Chuang Liu Zhongming Zhao
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BMC Systems Biology
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Erratum to: A survey of best practices for RNA-seq data analysis.
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2016-08-26
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Laura L. Elo David Gomez-Cabrero
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Ana Conesa Pedro Madrigal Sonia Tarazona Alejandra Cervera Andrew McPherson Michal Wojciech Szcześniak Daniel J Gaffney Xuegong Zhang Ali Mortazavi
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Genome Biology
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Inferring expressed genes by whole-genome sequencing of plasma DNA.
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2016-08-29
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Peter Ulz Gerhard G Thallinger Michael R. Speicher
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Martina Auer Ricarda Graf Karl Kashofer Stephan W Jahn Luca Abete Gunda Pristauz Edgar Petru Jochen B Geigl Ellen Heitzer
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Nature Genetics
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Characterization of non-olfactory GPCRs in human sperm with a focus on GPR18
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2016-08-30
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Janine Altmüller Hanns Hatt Günter Gisselmann Christa E Müller
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Caroline Flegel Felix Vogel Adrian Hofreuter Sebastian Wojcik Clara Schoeder Katarzyna Kieć-Kononowicz Norbert H Brockmeyer Christian Becker Günter Gisselmann
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Scientific Reports
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Chromatin recruitment of activated AMPK drives fasting response genes co-controlled by GR and PPARα.
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2016-08-30
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Bart Staels Réjane Paumelle Karolien De Bosscher Lode De Cauwer Michał Pawlak Nathalie Hennuyer
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Dariusz Ratman Viacheslav Mylka Nadia Bougarne Sandrine Caron Jonathan Thommis Mark H Rider Claude Libert Sam Lievens Jan Tavernier
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Nucleic Acids Research
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A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor.
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2016-08-31
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John C Marioni Davis J McCarthy
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Aaron T L Lun
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F1000Research
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RNAseq Transcriptional Profiling following Whip Development in Sugarcane Smut Disease
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2016-09-01
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Claudia B Monteiro-Vitorello
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Patricia D C Schaker Alessandra C Palhares Lucas M Taniguti Leila P Peters Silvana Creste Karen S Aitken Marie-Anne Van Sluys João P Kitajima Maria L C Vieira
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PLOS ONE
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Aiptasia sp. larvae as a model to reveal mechanisms of symbiont selection in cnidarians.
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2016-09-01
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Annika Guse Christian R. Voolstra
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Iliona Wolfowicz Sebastian Baumgarten Philipp A Voss Elizabeth A Hambleton Masayuki Hatta
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Scientific Reports
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Induction of Activating Transcription Factor 3 Is Associated with Cisplatin Responsiveness in Non-Small Cell Lung Carcinoma Cells.
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2016-09-01
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Theodore J Perkins
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Jair Bar Mohamed S Hasim Tabassom Baghai Nima Niknejad David J Stewart Harmanjatinder S Sekhon Patrick J Villeneuve Jim Dimitroulakos
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Neoplasia
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Signaling transcript profile of the asexual intraerythrocytic development cycle of Plasmodium falciparum induced by melatonin and cAMP.
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2016-09-01
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Andrei Rozanski
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Wânia Rezende Lima Giulliana Tessarin-Almeida Kleber S Parreira Miriam S Moraes David C Martins Ronaldo F Hashimoto Pedro A F Galante Célia R S Garcia
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Genes & Cancer
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ANGIOGENES: knowledge database for protein-coding and noncoding RNA genes in endothelial cells.
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2016-09-01
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Stefanie Dimmeler Tyler Weirick Shizuka Uchida
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Raphael Müller David John Giuseppe Militello Wei Chen
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Scientific Reports
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Mammary Tumor-Associated RNAs Impact Tumor Cell Proliferation, Invasion, and Migration.
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2016-09-01
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Sarah Diermeier
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Kung-Chi Chang Susan M Freier Junyan Song Osama El Demerdash Alexander Krasnitz Frank Rigo C Frank Bennett David L Spector
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Cell Reports
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Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos.
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2016-09-01
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Sten Linnarsson Björn Reinius Fredrik Lanner Rickard Sandberg
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Sophie Petropoulos Daniel Edsgärd Qiaolin Deng Sarita Pauliina Panula Simone Codeluppi Alvaro Plaza Reyes
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Cell
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A full-body transcriptome and proteome resource for the European common carp.
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2016-09-02
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Hans J Jansen Christiaan V. Henkel
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I C R M Kolder S J van der Plas-Duivesteijn G Tan G F Wiegertjes M Forlenza A T Guler D Y Travin M Nakao T Moritomo I Irnazarow J T den Dunnen S Y Anvar R P Dirks M Palmblad B Lenhard H P Spaink
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BMC Genomics
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Rail-RNA: scalable analysis of RNA-seq splicing and coverage.
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2016-09-04
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Andrew E Jaffe Jeffrey T. Leek Ben Langmead Abhinav Nellore
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Leonardo Collado-Torres José Alquicira-Hernández Christopher Wilks Jacob Pritt James Morton
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Bioinformatics
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Complementarity of SOMAscan to LC-MS/MS and RNA-seq for quantitative profiling of human embryonic and mesenchymal stem cells.
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2016-09-06
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Anja M Billing Johannes Graumann Karsten Suhre Hisham Ben Hamidane
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Aditya M Bhagwat Richard J Cotton Shaima S Dib Pankaj Kumar Shahina Hayat Neha Goswami Arash Rafii
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Journal of Proteomics
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RNAseq analysis of heart tissue from mice treated with atenolol and isoproterenol reveals a reciprocal transcriptional response.
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2016-09-07
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Corinne Berthonneche Sven Bergmann
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Andrea Prunotto Brian J Stevenson Fanny Schüpfer Jacques S Beckmann Fabienne Maurer
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BMC Genomics
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Pro-invasive Effect of Proto-oncogene PBF Is Modulated by an Interaction with Cortactin.
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2016-09-07
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Vicki E Smith Erica Gentilin Martin L. Read H Mehanna
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Rachel J Watkins Waraporn Imruetaicharoenchoke Neil Sharma Vikki L Poole Sukhchain Bansal Emy Bosseboeuf Rachel Fletcher Hannah R Nieto Ujjal Mallick Allan Hackshaw Kristien Boelaert Christopher J McCabe
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The Journal of Clinical Endocrinology and Metabolism
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Single Nucleotide Polymorphism Discovery in Bovine Pituitary Gland Using RNA-Seq Technology
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2016-09-08
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Haja N. Kadarmideen Marcin Sikora Mariusz Pierzchała Horbańczuk Jarosław Olav
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Chandra Shekhar Pareek Rafał Smoczyński Piotr Dziuba Paweł Błaszczyk Paulina Walendzik Tomasz Grzybowski Agnieszka Szostak Magdalena Ogluszka Lech Zwierzchowski Urszula Czarnik Leyland Fraser Przemysław Sobiech Krzysztof Wąsowicz Brian Gelfand Yaping Feng Dibyendu Kumar
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PLOS ONE
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TNIP2 is a Hub Protein in the NF-κB Network with Both Protein and RNA Mediated Interactions.
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2016-09-08
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Gaye L Hattem Michael P. Washburn
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Charles A S Banks Gina Boanca Zachary T Lee Cassandra G Eubanks Allison Peak Lauren E Weems Juliana J Conkright
|
Molecular & Cellular Proteomics
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Condition-dependent co-regulation of genomic clusters of virulence factors in the grapevine trunk pathogen Neofusicoccum parvum.
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2016-09-08
|
Dario Cantu
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Mélanie Massonnet Abraham Morales-Cruz Rosa Figueroa-Balderas Daniel P Lawrence Kendra Baumgartner
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Molecular Plant Pathology
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Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data
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2016-09-08
|
John C Marioni
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Aaron TL Lun
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Comprehensive Small RNA-Seq of Adeno-Associated Virus (AAV)-Infected Human Cells Detects Patterns of Novel, Non-Coding AAV RNAs in the Absence of Cellular miRNA Regulation.
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2016-09-09
|
Andreas Gogol-Döring
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Catrin Stutika Mario Mietzsch Stefan Weger Madlen Sohn Wei Chen Regine Heilbronn
|
PLOS ONE
|
Transcriptomic response of Drosophila melanogaster pupae developed in hypergravity.
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2016-09-10
|
Sharmila Bhattacharya
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Shannon Hateley Ravikumar Hosamani Shilpa R Bhardwaj Lior Pachter
|
Genomics
|
Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing
|
2016-09-12
|
Roderic Guigó i Serra Martin Oti Pedro G Ferreira Michael Sammeth Philip Rosenstiel Anna Esteve-Codina
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Matthias Barann Thomas Wieland Suzana Ezquina Marc R Friedländer Manuel A Rivas GEUVADIS Consortium Tim M Strom Tuuli Lappalainen
|
Scientific Reports
|
Localizing gene regulation reveals a staggered wood decay mechanism for the brown rot fungus Postia placenta
|
2016-09-12
|
Dehong Hu
|
Jiwei Zhang Gerald N Presley Kenneth E Hammel Jae-San Ryu Jon R Menke Melania Figueroa Galya Orr Jonathan S Schilling
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Proceedings of the National Academy of Sciences of the United States of America
|
Gene expression profiling of granule cells and Purkinje cells in the zebrafish cerebellum.
|
2016-09-12
|
Shigehiro Kuraku Masahiko Hibi
|
Miki Takeuchi Shingo Yamaguchi Yoshimasa Sakakibara Takuto Hayashi Koji Matsuda Yuichiro Hara Chiharu Tanegashima Takashi Shimizu
|
The Journal of Comparative Neurology
|
CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data.
|
2016-09-13
|
Sohiya Yotsukura
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David A duVerle Seitaro Nomura Hiroyuki Aburatani Koji Tsuda
|
BMC Bioinformatics
|
Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes
|
2016-09-13
|
Aldons Jake Lusis Matteo Pellegrini Eleazar Eskin Yehudit Hasin-Brumshtein Anneke Brümmer Paul D. Piehowski Xinshu Xiao
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Arshad H Khan Farhad Hormozdiari Calvin Pan Brian W Parks Vladislav A Petyuk Richard D Smith Desmond J Smith
|
eLife
|
Tissue enrichment analysis for C. elegans genomics.
|
2016-09-13
|
Paul W. Sternberg
|
David Angeles-Albores Raymond Y N Lee Juancarlos Chan
|
BMC Bioinformatics
|
Zinc finger protein 407 overexpression upregulates PPAR target gene expression and improves glucose homeostasis in mice.
|
2016-09-13
|
Dave Bridges David A. Buchner
|
Alyssa Charrier Li Wang Erin J Stephenson Siddharth V Ghanta Chih-Wei Ko Colleen M Croniger
|
American Journal of Physiology - Endocrinology and Metabolism
|
Temporal mixture modelling of single-cell RNA-seq data resolves a CD4+ T cell fate bifurcation
|
2016-09-13
|
Lily G Fogg Tapio Lönnberg Ismail Sebina Frederik Otzen Bagger Ashraful Haque Sarah Teichmann
|
Valentine Svensson Kylie R James Daniel Fernandez-Ruiz Ruddy Montandon Megan S F Soon Michael J T Stubbington Max Zwiessele Neil Lawrence Fernando Souza-Fonseca- Guimaraes William R Heath Oliver Billker Oliver Stegle
|
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Identification of Reference Genes for RT-qPCR Data Normalization in Cannabis sativa Stem Tissues.
|
2016-09-15
|
Sergio Esposito
|
Lauralie Mangeot-Peter Sylvain Legay Jean-Francois Hausman Gea Guerriero
|
International Journal of Molecular Sciences
|
MdMyb93 is a regulator of suberin deposition in russeted apple fruit skins.
|
2016-09-15
|
Marc Boutry
|
Sylvain Legay Gea Guerriero Christelle André Cédric Guignard Emmanuelle Cocco Sophie Charton Owen Rowland Jean-Francois Hausman
|
New Phytologist
|
Alternative Splicing May Not Be the Key to Proteome Complexity
|
2016-09-16
|
Alfonso Valencia
|
Michael L. Tress Federico Abascal
|
Trends in Biochemical Sciences
|
Regulation of X-linked gene expression during early mouse development by Rlim
|
2016-09-19
|
Aviv Regev Alex K. Shalek Oliver J Rando
|
Feng Wang JongDae Shin Jeremy M Shea Jun Yu Ana Bošković Meg Byron Xiaochun Zhu Jeanne B Lawrence Eduardo M Torres Lihua J Zhu Ingolf Bach
|
eLife
|
The dual role of LSD1 and HDAC3 in STAT5-dependent transcription is determined by protein interactions, binding affinities, motifs and genomic positions.
|
2016-09-19
|
Matthieu D Lavigne
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Aikaterini Nanou Chrisavgi Toumpeki Vassiliki Lazou Jeroen Demmers Triantafillos Paparountas Dimitris Thanos Eleni Katsantoni
|
Nucleic Acids Research
|
Transcriptomic profiles of the upper olfactory rosette in cultured and wild Senegalese sole (Solea senegalensis) males.
|
2016-09-20
|
Elvira Fatsini Manuel Manchado
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R Bautista N J Duncan
|
Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics
|
Standardizing unique molecular identifiers in SAM flags would benefit more than RNA-Seq
|
2016-09-20
|
Elisha Roberson
|
|
|
Single-Cell Transcriptomics Bioinformatics and Computational Challenges
|
2016-09-21
|
Lana Garmire
|
Olivier B. Poirion Xun Zhu Travers Ching Lana Garmire
|
Frontiers in Genetics
|
The tubulin repertoire of C. elegans sensory neurons and its context-dependent role in process outgrowth.
|
2016-09-21
|
Erich M Schwarz Michael Krieg Robert O'Hagan Paul W. Sternberg
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Dean Lockhead Sebastian Bellotti Maureen M Barr Alexander R Dunn Miriam B Goodman
|
Molecular Biology of the Cell
|
Long non-coding RNAs in human early embryonic development and their potential in ART.
|
2016-09-21
|
John De Vos
|
Julien Bouckenheimer Said Assou Sébastien Riquier Cyrielle Hou Nicolas Philippe Caroline Sansac Thierry Lavabre-Bertrand Thérèse Commes Jean-Marc Lemaître Anthony Boureux
|
Human Reproduction Update
|
Probiotic Enterococcus faecalis Symbioflor® down regulates virulence genes of EHEC in vitro and decrease pathogenicity in a Caenorhabditis elegans model.
|
2016-09-21
|
Klaus Neuhaus
|
Marina C Lamparter Benjamin Zölch Richard Landstorfer Svenja Simon Britta Spanier Matthias A Ehrmann Rudi F Vogel
|
Archives of Microbiology
|
P08.40 RNAseq of paired primary and recurrent glioblastoma samples
|
2016-09-21
|
Susan C. Short
|
L. F. Stead A. Bruns R. Morton S. Harrison A. Chakrabarty A. Ismail H. King K. Ashton K. Syed
|
Neuro-Oncology
|
SPIRE, a modular pipeline for eQTL analysis of RNA-Seq data, reveals a regulatory hotspot controlling miRNA expression in C. elegans.
|
2016-09-22
|
Ivan Kel Alessandra Mezzelani Luciano Milanesi
|
Zisong Chang Nadia Galluccio Margherita Romeo Stefano Beretta Luisa Diomede Christoph Dieterich Ivan Merelli
|
Molecular BioSystems
|
A Global Analysis of the Polygalacturonase Gene Family in Soybean (Glycine max).
|
2016-09-22
|
Fanjiang Kong
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Feifei Wang Xia Sun Xinyi Shi Hong Zhai Changen Tian Baohui Liu Xiaohui Yuan
|
PLOS ONE
|
C14orf132 gene is possibly related to extremely low birth weight
|
2016-09-22
|
Triin Viltrop Andres Salumets Sulev Kõks Ene Reimann
|
Airi Tiirats Margit Nõukas
|
BMC Genetics
|
Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms.
|
2016-09-22
|
Cornelia M. van Duijn André Uitterlinden Cisca Wijmenga Jenny van Dongen Rick Jansen Eco de Geus Morris A Swertz Dorret Boomsma Albert Hofman Leonard H van den Berg Jan H Veldink Coenraad Dirk Adriaan Stehouwer Casper G. Schalkwijk
|
Roderick C Slieker Maarten van Iterson René Luijk Marian Beekman Daria V Zhernakova Matthijs H Moed Hailiang Mei Michiel van Galen Patrick Deelen Marc Jan Bonder Alexandra Zhernakova Ettje F Tigchelaar Carla J H van der Kallen Diana van Heemst Joris Deelen Joyce van Meurs Peter A C 't Hoen Lude Franke Marleen M J van Greevenbroek BIOS consortium P Eline Slagboom Bastiaan T Heijmans
|
Genome Biology
|
A perspective on single cell behavior during infection
|
2016-09-22
|
Roi Avraham
|
Deborah T Hung
|
Gut microbes
|
A timecourse analysis of systemic and gonadal effects of temperature on sexual development of the red-eared slider turtle Trachemys scripta elegans.
|
2016-09-23
|
Czerwinski M Natarajan A Barske L Loren L Looger Capel B
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|
Developmental Biology
|
Pre-mRNA splicing repression triggers abiotic stress signaling in plants.
|
2016-09-24
|
Stefan T Arold Sahar Alshareef Yu Ling Hiroaki Fujii Jorge Lozano-Juste Paula Duque Ahmed Moustafa Magdy M. Mahfouz Pedro L Rodriguez
|
Haroon Butt Lixin Li Aya A Galal Afaque A Momin Manal Tashkandi Dale N Richardson
|
The Plant Journal
|
Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development
|
2016-09-26
|
Svante Pääbo Farhath Badsha Barbara Treutlein Zhisong He
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Felipe Mora-Bermúdez Sabina Kanton J Gray Camp Benjamin Vernot Kathrin Köhler Birger Voigt Keisuke Okita Tomislav Maricic Robert Lachmann Wieland B Huttner
|
eLife
|
Protein C receptor (PROCR) is a negative regulator of Th17 pathogenicity.
|
2016-09-26
|
Aviv Regev Chuan Wu Norio Chihara
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Yasuhiro Kishi Takaaki Kondo Sheng Xiao Nir Yosef Jellert Gaublomme Chao Wang Nicole Joller Vijay K Kuchroo
|
Journal of Experimental Medicine
|
Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq.
|
2016-09-26
|
Rickard Sandberg Daniel Ramsköld Björn Reinius Qiaolin Deng
|
Jeff E Mold Per Johnsson Jakob Michaëlsson Jonas Frisén
|
Nature Genetics
|
Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation.
|
2016-09-26
|
Michael I Love
|
John B Hogenesch Rafael A Irizarry
|
Nature Biotechnology
|
Web-based bioinformatics workflows for end-to-end RNA-seq data computation and analysis in agricultural animal species.
|
2016-09-27
|
Weizhong Li
|
R Alexander Richter Yunsup Jung Qiyun Zhu Robert W Li
|
BMC Genomics
|
Time-resolved dual RNA-seq reveals extensive rewiring of lung epithelial and pneumococcal transcriptomes during early infection.
|
2016-09-27
|
Jan-Willem Veening Jelle Slager
|
Rieza Aprianto Siger Holsappel
|
Genome Biology
|
Consensus Analysis of Whole Transcriptome Profiles from Two Breast Cancer Patient Cohorts Reveals Long Non-Coding RNAs Associated with Intrinsic Subtype and the Tumour Microenvironment.
|
2016-09-29
|
James R. Bradford Angela Cox
|
Philip Bernard Nicola J Camp
|
PLOS ONE
|
Mammalian Period represses and de-represses transcription by displacing CLOCK-BMAL1 from promoters in a Cryptochrome-dependent manner.
|
2016-09-29
|
Aziz Sancar
|
Yi-Ying Chiou Yanyan Yang Naim Rashid Rui Ye Christopher P Selby
|
Proceedings of the National Academy of Sciences of the United States of America
|
Flexible expressed region analysis for RNA-seq with derfinder.
|
2016-09-29
|
Leonardo Collado-Torres Andrew E Jaffe Jeffrey T. Leek Ben Langmead Abhinav Nellore
|
Alyssa C Frazee Christopher Wilks Michael I Love Rafael A Irizarry
|
Nucleic Acids Research
|
Single-cell RNA-seq identifies a PD-1hi ILC progenitor and defines its development pathway.
|
2016-09-29
|
Sarah Teichmann Xi Chen Gabrielle Belz
|
Yong Yu Jason C H Tsang Cui Wang Simon Clare Juexuan Wang Cordelia Brandt Leanne Kane Lia S Campos Liming Lu Andrew N J McKenzie Gordon Dougan Pentao Liu
|
Nature
|
Developing a Novel Two-Dimensional Culture System to Enrich Human Prostate Luminal Progenitors that Can Function as a Cell of Origin for Prostate Cancer.
|
2016-09-29
|
Hsueh-Ping Chao Dingxiao Zhang Yue Lu
|
Kevin Lin Kiera Rycaj Yi Zhong Tammy Calhoun-Davis Jianjun Shen Dean G Tang
|
Stem Cells Translational Medicine
|
Integrative analysis of Arabidopsis thaliana transcriptomics reveals intuitive splicing mechanism for circular RNA.
|
2016-09-29
|
Gaurav Sablok
|
Xiaoyong Sun Lin Wang Jiechao Ding Yanru Wang Jiansheng Wang Xiaoyang Zhang Yulei Che Ziwei Liu Xinran Zhang Jiazhen Ye Jie Wang Zhiping Deng Hongwei Zhao
|
FEBS Letters
|
Downregulation of sphingosine kinase-1 induces protective tumor immunity by promoting M1 macrophage response in melanoma.
|
2016-09-30
|
Nathalie Andrieu-Abadie Bruno Ségui Jean-Christophe Marine Nicole Therville Mona Diab-Assaf
|
Marguerite Mrad Caroline Imbert Virginie Garcia Florian Rambow Stéphane Carpentier Thierry Levade Rania Azar Céline Colacios
|
Oncotarget
|
Identification of Aedes aegypti Long Intergenic Non-coding RNAs and Their Association with Wolbachia and Dengue Virus Infection
|
2016-10
|
Sassan Asgari
|
Kayvan Etebari Sultan Asad Guangmei Zhang
|
PLOS Neglected Tropical Diseases
|
Integrated analysis of dysregulated lncRNA expression in breast cancer cell identified by RNA-seq study
|
2016-10
|
Pritish Kumar Varadwaj
|
Rashmi Tripathi Apoorva Soni
|
Non-coding RNA Research
|
Profiling of adhesive-related genes in the freshwater cnidarian Hydra magnipapillata by transcriptomics and proteomics.
|
2016-10-01
|
Peter Ladurner
|
Marcelo Rodrigues Thomas Ostermann Leopold Kremeser Herbert Lindner Christian Beisel Eugene Berezikov Bert Hobmayer
|
Biofouling
|
Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells.
|
2016-10-01
|
Sten Linnarsson Peter Lönnerberg Lars E Borm Daniel Gyllborg Enrique M Toledo Kaneyasu Nishimura Ernest Arenas Roger A. Barker
|
Gioele La Manno Simone Codeluppi Carmen Salto Amit Zeisel Simon R W Stott J Carlos Villaescusa Jesper Ryge
|
Cell
|
Profiling the macrofilaricidal effects of flubendazole on adult female Brugia malayi using RNAseq.
|
2016-10-01
|
Lucienne Tritten Steven A Williams Jianguo Xia
|
Maeghan O'Neill Cristina Ballesteros Erica Burkman Weam I Zaky Andrew Moorhead Timothy G Geary
|
International Journal for Parasitology: Drugs and Drug Resistance
|
Model systems of DUX4 expression recapitulate the transcriptional profile of FSHD cells.
|
2016-10-01
|
Rebecca Resnick Sujatha Jagannathan Silvère M van der Maarel
|
Sean C Shadle Lauren Snider Rabi N Tawil Robert K Bradley Stephen J Tapscott
|
Human Molecular Genetics
|
Erratum: How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?
|
2016-10-01
|
Tom Owen-Hughes
|
Nicholas J Schurch Pietà Schofield Marek Gierliński Christian Cole Alexander Sherstnev Vijender Singh Nicola Wrobel Karim Gharbi Gordon G Simpson Mark Blaxter Geoffrey J Barton
|
RNA
|
Correlation of an epigenetic mitotic clock with cancer risk
|
2016-10-03
|
Diana Kuh Andrew Wong
|
Zhen Yang Dirk S Paul Vardhman K Rakyan R David Leslie Shijie C Zheng Martin Widschwendter Stephan Beck Andrew E Teschendorff
|
Genome Biology
|
Developmental effects of fipronil on Japanese Medaka (Oryzias latipes) embryos.
|
2016-10-03
|
Bruce D. Hammock
|
Scott D Wagner Tomofumi Kurobe Bruce G Hammock Chelsea H Lam Gary Wu Natalia Vasylieva Shirley J Gee Bruce D Hammock Swee J Teh
|
Chemosphere
|
Predicting the functional states of human iPSC-derived neurons with single-cell RNA-seq and electrophysiology
|
2016-10-04
|
Cedric Bardy
|
M van den Hurk B Kakaradov J A Erwin B N Jaeger R V Hernandez T Eames A A Paucar M Gorris C Marchand R Jappelli J Barron A K Bryant M Kellogg R S Lasken B P F Rutten H W M Steinbusch G W Yeo F H Gage
|
Molecular Psychiatry
|
Ethylene responsive transcription factor ERF109 retards PCD and improves salt tolerance in plant
|
2016-10-06
|
Sherif Edris
|
Ahmed Bahieldin Ahmed Atef Nour O Gadalla Hani M Ali Sabah M Hassan Magdy A Al-Kordy Ahmed M Ramadan Rania M Makki Abdulrahman S M Al-Hajar Fotouh M El-Domyati
|
BMC Plant Biology
|
Discovering Single Nucleotide Polymorphisms Regulating Human Gene Expression Using Allele Specific Expression from RNA-seq Data.
|
2016-10-07
|
Sagiv Shifman Eyal Ben-David Aldons Jake Lusis Eleazar Eskin
|
Eun Yong Kang Lisa J Martin Serghei Mangul Warin Isvilanonda Jennifer Zou Buhm Han
|
Genetics
|
Psoriasis-Specific RNA Isoforms Identified by RNA-Seq Analysis of 173,446 Transcripts.
|
2016-10-07
|
Ene Reimann Sulev Kõks
|
Maris Keermann Ele Prans Kristi Abram Helgi Silm Gea Kõks Kulli Kingo
|
Frontiers in medicine
|
The Molecular Circuit Regulating Tooth Development in Crocodilians.
|
2016-10-07
|
A Abdelhamid
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S Tsai M K Khan A Elkarargy R B Widelitz C M Chuong P Wu
|
Journal of Dental Research
|
Optimization of techniques for multiple platform testing in small, precious samples such as human chorionic villus sampling.
|
2016-10-08
|
Charles R. Farber Jerome I Rotter
|
Margareta D Pisarska Marzieh Akhlaghpour Bora Lee Gillian M Barlow Ning Xu Erica T Wang Aaron J Mackey Stephen S Rich Yii-der I Chen Mark O Goodarzi Seth Guller John Williams
|
Prenatal Diagnosis
|
Detecting Sources of Transcriptional Heterogeneity in Large-Scale RNA-Seq Data Sets.
|
2016-10-11
|
Brian C Searle
|
Rachel M Gittelman Ohad Manor Joshua M Akey
|
Genetics
|
Transcriptomic alterations in Sitophilus zeamais in response to allyl isothiocyanate fumigation.
|
2016-10-11
|
Xing Zhang
|
Chao Zhang Zhiqing Ma Hua Wu
|
Pesticide Biochemistry and Physiology
|
Alternative genetic mechanisms of BRAF activation in Langerhans cell histiocytosis.
|
2016-10-11
|
Kenneth L McClain
|
Rikhia Chakraborty Thomas M Burke Oliver A Hampton Daniel J Zinn Karen Phaik Har Lim Harshal Abhyankar Brooks Scull Vijetha Kumar Nipun Kakkar David A Wheeler Angshumoy Roy Poulikos I Poulikakos Miriam Merad D Williams Parsons Carl E Allen
|
Blood
|
Comparative RNA-Seq profiling of berry development between table grape 'Kyoho' and its early-ripening mutant 'Fengzao'.
|
2016-10-12
|
Da-Long Guo
|
Fei-Fei Xi Yi-He Yu Xiao-Yu Zhang Guo-Hai Zhang Gan-Yuan Zhong
|
BMC Genomics
|
Tubulin C-terminal Post-translational Modifications Do Not Occur in Wood Forming Tissue of Populus
|
2016-10-13
|
Hao Hu
|
Xi Gu Liang-Jiao Xue Prashant S Swamy Scott A Harding Chung-Jui Tsai
|
Frontiers in Plant Science
|
The defence-associated transcriptome of hexaploid wheat displays homoeolog expression and induction bias.
|
2016-10-13
|
Donald M. Gardiner Jonathan J Powell Robert Henry
|
Timothy L Fitzgerald Jiri Stiller Paul J Berkman John M Manners Kemal Kazan
|
Plant Biotechnology Journal
|
Zeb2 Regulates Cell Fate at the Exit from Epiblast State in Mouse Embryonic Stem Cells
|
2016-10-14
|
Lieve Umans Steven Goossens Leo A van Grunsven Danny Huylebroeck Wilfred F J van IJcken Geert Berx Ruben Dries
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Agata Stryjewska Tim Pieters Griet Verstappen Andrea Conidi Kathleen Coddens Annick Francis Lieve Umans Frank G Grosveld Jody J Haigh
|
Stem Cells
|
Genetic divergence in the transcriptional engram of chronic alcohol abuse: A laser-capture RNA-seq study of the mouse mesocorticolimbic system.
|
2016-10-15
|
Robert W. Williams Megan K Mulligan
|
Khyobeni Mozhui Ashutosh K Pandey Maren L Smith Suzhen Gong Jesse Ingels Michael F Miles Marcelo F Lopez Lu Lu
|
Alcohol
|
Growth and maturation of heart valves leads to changes in endothelial cell distribution, impaired function, decreased metabolism and reduced cell proliferation.
|
2016-10-15
|
Samir N. Ghadiali
|
Lindsey J Anstine Chris Bobba Joy Lincoln
|
Journal of Molecular and Cellular Cardiology
|
The alternatively-included 11a sequence modifies the effects of Mena on actin cytoskeletal organization and cell behavior
|
2016-10-17
|
Douglas A Lauffenburger
|
Michele Balsamo Chandrani Mondal Guillaume Carmona Leslie M McClain Daisy N Riquelme Jenny Tadros Duan Ma Eliza Vasile John S Condeelis Frank B Gertler
|
Scientific Reports
|
Global analysis of pre-mRNA subcellular localization following splicing inhibition by spliceostatin A.
|
2016-10-17
|
Daisuke Kaida Maxwell Burroughs Yoshihide Hayashizaki
|
Rei Yoshimoto Masaaki Furuno A Maxwell Burroughs Shohei Noma Harukazu Suzuki Yumi Kawamura Akila Mayeda Minoru Yoshida
|
RNA
|
Dynamic translation regulation in Caulobacter cell cycle control.
|
2016-10-17
|
Jonathan Weissman
|
Jared M Schrader Gene-Wei Li W Seth Childers Adam M Perez Lucy Shapiro Harley H McAdams
|
Proceedings of the National Academy of Sciences of the United States of America
|
Human melanomas and ovarian cancers overexpressing mechanical barrier molecule genes lack immune signatures and have increased patient mortality risk.
|
2016-10-18
|
Ileana S Mauldin George Coukos Craig Slingluff
|
Elise P Salerno Davide Bedognetti Donna H Deacon Sofia M Shea Joel Pinczewski Joseph M Obeid Ena Wang Thomas F Gajewski Francesco M Marincola
|
OncoImmunology
|
The Ser82 RAGE Variant Affects Lung Function and Serum RAGE in Smokers and sRAGE Production In Vitro.
|
2016-10-18
|
Tracy L Rimington Amanda P Henry Andrew Wardlaw Ian P. Hall Suzanne Miller Stuart G. Parker Charlotte E Bolton Anders Malarstig Erik Melén
|
Emily Hodge Alexander K Kheirallah Charlotte K Billington Sangita K Bhaker Ma'en Obeidat Simon K Merid Caroline Swan Catherine Gowland Carl P Nelson Ceri E Stewart Iain Kilty Miriam F Moffatt Ian Sayers
|
PLOS ONE
|
High-resolution analysis of multi-copy variant surface glycoprotein gene expression sites in African trypanosomes.
|
2016-10-18
|
Horn DA
|
Sebastian Hutchinson Lucy Glover
|
BMC Genomics
|
Expression and prognostic significance of the autoimmune regulator gene in breast cancer cells.
|
2016-10-18
|
Francesca Bianchi Lucia Sfondrini Michele Sommariva Tiziana Triulzi Loris De Cecco Andrea Balsari
|
Sandra Romero-Cordoba Elda Tagliabue
|
Cell Cycle
|
Deciphering Transcriptional Programming during Pod and Seed Development Using RNA-Seq in Pigeonpea (Cajanus cajan)
|
2016-10-19
|
Rajeev Kumar Varshney
|
Lekha T Pazhamala Gaurav Agarwal Prasad Bajaj Vinay Kumar Akanksha Kulshreshtha Rachit K Saxena
|
PLOS ONE
|
The RNA-binding landscape of RBM10 and its role in alternative splicing regulation in models of mouse early development.
|
2016-10-20
|
Julie Rodor David R. FitzPatrick
|
Eduardo Eyras Javier F Cáceres
|
RNA Biology
|
A Study of TP53 RNA Splicing Illustrates Pitfalls of RNA-seq Methodology.
|
2016-10-20
|
Peter Tsai Cristin G. Print Roger R. Reddel
|
Sunali Mehta Annette Lasham Hamish Campbell Antony Braithwaite
|
Cancer Research
|
RNAseq reveals hypervirulence-specific host responses to M. tuberculosis infection
|
2016-10-20
|
Bienyameen Baker
|
Gina Leisching Ray-Dean Pietersen Carel van Heerden Paul van Helden Ian Wiid
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Virulence
|
Fine Mapping of a Dravet Syndrome Modifier Locus on Mouse Chromosome 5 and Candidate Gene Analysis by RNA-Seq
|
2016-10-21
|
Jennifer A Kearney
|
Nicole A Hawkins Nicole J Zachwieja Alison R Miller Lyndsey L Anderson
|
PLOS Genetics
|
Identification of mutations, gene expression changes and fusion transcripts by whole transcriptome RNAseq in docetaxel resistant prostate cancer cells
|
2016-10-24
|
Mikael Huss
|
Yuanjun Ma Yali Miao Zhuochun Peng Johanna Sandgren Teresita Díaz De Ståhl Lena Lennartsson Yanling Liu Monica Nistér Sten Nilsson Chunde Li
|
SpringerPlus
|
Genome-wide regulatory dynamics of G-quadruplexes in human malaria parasite Plasmodium falciparum.
|
2016-10-24
|
Niti Kumar
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Deeksha Bhartiya Vandna Chawla Sourav Ghosh Ravi Shankar
|
Genomics
|
Deep analysis of wild Vitis flower transcriptome reveals unexplored genome regions associated with sex specification.
|
2016-10-24
|
Octávio S. Paulo Patrícia Gomes de Almeida João Lucas Coito Miguel Ramos Jorge Cunha Margarida Rocheta Maria Manuela Ribeiro Costa
|
Joana Fino Helena Silva Sara Amâncio
|
Plant Molecular Biology
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Evolutionary hallmarks of the human proteome: chasing the age and coregulation of protein-coding genes.
|
2016-10-25
|
Javier De Las Rivas Ricardo Assunção Vialle
|
Katia de Paiva Lopes Francisco José Campos-Laborie José Miguel Ortega
|
BMC Genomics
|
The polymyxin B-induced transcriptomic response of a clinical, multidrug-resistant Klebsiella pneumoniae involves multiple regulatory elements and intracellular targets.
|
2016-10-25
|
Ana Tereza Ribeiro de Vasconcelos Pablo Ivan Pereira Ramos
|
Márlon Grégori Flores Custódio Guadalupe Del Rosario Quispe Saji Thiago Cardoso Gisele Lucchetti da Silva Graziela Braun Willames M B S Martins Raquel Girardello Elmer Fernández Ana Cristina Gales Marisa Fabiana Nicolás
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BMC Genomics
|
A statistical approach for identifying differential distributions in single-cell RNA-seq experiments.
|
2016-10-25
|
Christina Kendziorski
|
Keegan D Korthauer Li-Fang Chu Michael A Newton Yuan Li James Thomson Ron Stewart
|
Genome Biology
|
RNA-Seq-based analysis of differential gene expression associated with hepatitis C virus infection in a cell culture.
|
2016-10-25
|
Marek Figlerowicz
|
Anna Hojka-Osinska Lucyna Budzko Agnieszka Zmienko Agnieszka Rybarczyk Patrick Maillard Agata Budkowska Paulina Jackowiak
|
Acta Biochimica Polonica
|
RNA-Seq Count Data Modelling by Grey Relational Analysis and Nonparametric Gaussian Process
|
2016-10-26
|
Thanh Nguyen
|
Asim Bhatti Samuel Yang Saeid Nahavandi
|
PLOS ONE
|
Developmental transcriptome of resting cell formation in Mycobacterium smegmatis.
|
2016-10-26
|
Hans-Joachim Mollenkopf Martin Gengenbacher Swaine L Chen Thomas Dick
|
Mu-Lu Wu Jade C S Chung Stefan H E Kaufmann
|
BMC Genomics
|
A Multifaceted Role for Myd88-Dependent Signaling in Progression of Murine Mammary Carcinoma.
|
2016-10-27
|
Maureen A Carey
|
Mary J Higgins Antonio Serrano Kofi Y Boateng Victoria A Parsons Tiffany Phuong Alyssa Seifert Jacob M Ricca Kyle C Tucker Alec S Eidelman Robert A Kurt
|
Breast cancer : basic and clinical research
|
Cells Respond to Distinct Nanoparticle Properties with Multiple Strategies As Revealed by Single-Cell RNA-Seq.
|
2016-10-27
|
Dehong Hu Ronald Taylor
|
Hugh D Mitchell Lye Meng Markillie William B Chrisler Matthew J Gaffrey Craig J Szymanski Yumei Xie Eric S Melby Alice Dohnalkova Eva K Grate Scott K Cooley Jason E McDermott Alejandro Heredia-Langner Galya Orr
|
ACS Nano
|
Single-Cell Analysis Reveals a Close Relationship between Differentiating Dopamine and Subthalamic Nucleus Neuronal Lineages.
|
2016-10-27
|
Malin Parmar Sara Nolbrant Agnete Kirkeby Rickard Sandberg
|
Nigel Kee Nikolaos Volakakis Lina Dahl Helena Storvall Laura Lahti Åsa K Björklund Linda Gillberg Eliza Joodmardi Thomas Perlmann
|
Cell Stem Cell
|
Early molecular events during retinoic acid induced differentiation of neuromesodermal progenitors.
|
2016-10-28
|
Thomas J. Cunningham Gregg Duester
|
Alexandre Colas
|
Biology Open
|
RNA-Seq: RNA Conversion to cDNA and Amplification.
|
2016-11-01
|
Elaine Mardis
|
Elaine Mardis W Richard McCombie
|
Cold Spring Harbor Protocols
|
Responding to a Zoonotic Emergency with Multi-omics Research: Pentatrichomonas hominis Hydrogenosomal Protein Characterization with Use of RNA Sequencing and Proteomics.
|
2016-11-01
|
Po-Jung Huang Petrus Tang
|
Yi-Kai Fang Kun-Yi Chien Kuo-Yang Huang Wei-Hung Cheng Fu-Mann Ku Rose Lin Ting-Wen Chen Cheng-Hsun Chiu
|
OMICS: A Journal of Integrative Biology
|
Molecular phenotyping of infection-associated small non-coding RNAs.
|
2016-11-01
|
Alexander Westermann Jörg Vogel Lars Barquist
|
|
Philosophical Transactions of the Royal Society B
|
Identification of Differential Gene Expression Patterns after Acute Exposure to High and Low Doses of Low-LET Ionizing Radiation in a Reconstituted Human Skin Tissue.
|
2016-11-01
|
Ronald Taylor
|
Susan C Tilton Lye Meng Markillie Spencer Hays David L Stenoien
|
Radiation Research
|
Evolutionary engineering reveals divergent paths when yeast is adapted to different acidic environments.
|
2016-11-01
|
Jens Nielsen Verena Siewers
|
Eugene Fletcher Amir Feizi Markus M M Bisschops Björn M Hallström Sakda Khoomrung
|
Metabolic Engineering
|
Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma.
|
2016-11-02
|
Daniel P Cahill Rahul Satija Itay Tirosh Aviv Regev Orit Rozenblatt-Rosen Aanand A Patel Christopher W Mount Brian V. Nahed Michelle Monje Gad Getz
|
Andrew S Venteicher Christine Hebert Leah E Escalante Anoop P Patel Keren Yizhak Jonathan M Fisher Christopher Rodman Mariella G Filbin Cyril Neftel Niyati Desai Jackson Nyman Benjamin Izar Christina C Luo Joshua M Francis Maristela L Onozato Nicolo Riggi Kenneth J Livak Dave Gennert William T Curry Robert L Martuza Ravindra Mylvaganam A John Iafrate Matthew P Frosch Todd R Golub Miguel N Rivera Bradley E Bernstein David N Louis Mario L Suvà
|
Nature
|
The founder-cell transcriptome in the Arabidopsis apetala1 cauliflower inflorescence meristem.
|
2016-11-03
|
Peter Frommolt
|
Anneke Frerichs Rahere Thoma Ali Taleb Abdallah Wolfgang Werr John William Chandler
|
BMC Genomics
|
LPA receptor activity is basal specific and coincident with early pregnancy and involution during mammary gland postnatal development
|
2016-11-03
|
Bernice E. Morrow
|
Deanna Acosta Susmita Bagchi Pilib Ó Broin Daniel Hollern Silvia E Racedo Rani S Sellers John M Greally Aaron Golden Eran Andrechek Teresa Wood Cristina Montagna
|
Scientific Reports
|
The ribosome-engaged landscape of alternative splicing.
|
2016-11-07
|
Robert J Weatheritt
|
Timothy Sterne-Weiler Benjamin J Blencowe
|
Nature Structural & Molecular Biology
|
RNA-seq analyses of the midgut from blood- and serum-fed Ixodes ricinus ticks.
|
2016-11-08
|
Jan Perner Veronika Urbanová
|
Jan Provazník Jana Schrenková José M C Ribeiro Petr Kopáček
|
Scientific Reports
|
ROCK signalling induced gene expression changes in mouse pancreatic ductal adenocarcinoma cells.
|
2016-11-08
|
Michael F. Olson
|
Nicola Rath Gabriela Kalna William Clark
|
Scientific Data
|
BRM Promoter Polymorphisms and Survival of Advanced Non-Small Cell Lung Cancer Patients in the Princess Margaret Cohort and CCTG BR.24 Trial.
|
2016-11-08
|
Geoffrey Liu Ming-Sound Tsao Bingshu E Chen
|
Sinead Cuffe Shermi Liang Lu Cheng Yonathan Brhane Xin Qiu David W Cescon Jeffrey Bruce Zhuo Chen Dangxiao Cheng Devalben Patel Brandon C Tse Scott A Laurie Glenwood Goss Natasha B Leighl Rayjean Hung Penelope A Bradbury Lesley Seymour Frances A Shepherd Wei Xu David N Reisman
|
Clinical Cancer Research
|
Modeling Enzyme Processivity Reveals that RNA-Seq Libraries Are Biased in Characteristic and Correctable Ways.
|
2016-11-09
|
Daniel Hebenstreit
|
Nathan Archer Mark D Walsh Vahid Shahrezaei
|
Cell systems
|
Single-Cell Resolution of Temporal Gene Expression during Heart Development.
|
2016-11-09
|
Daniel M DeLaughter
|
Daniel M DeLaughter Alexander G Bick Hiroko Wakimoto David McKean Joshua M Gorham Irfan S Kathiriya John T Hinson Jason Homsy Jesse Gray William Pu Benoit G Bruneau J G Seidman Christine E Seidman
|
Developmental Cell
|
Transcriptome profiling of NIH3T3 cell lines expressing opsin and the P23H opsin mutant identifies candidate drugs for the treatment of retinitis pigmentosa.
|
2016-11-09
|
Krzysztof Palczewski
|
Yuanyuan Chen Matthew J Brooks Linn Gieser Anand Swaroop
|
Pharmacological Research
|
High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation.
|
2016-11-09
|
Uwe Ohler
|
Song Li Masashi Yamada Xinwei Han Philip N Benfey
|
Developmental Cell
|
Human Oocyte-Derived Methylation Differences Persist in the Placenta Revealing Widespread Transient Imprinting.
|
2016-11-11
|
Tomas Marques-Bonet Marta Sanchez-Delgado Isabel Iglesias-Platas Enrique Vidal Jose Medrano Ronald Bontrop
|
Franck Court Ana Monteagudo-Sánchez Alex Martin-Trujillo Chiharu Tayama Ivanela Kondova Maria Eugenia Poo-Llanillo Kazuhiko Nakabayashi Carlos Simón David Monk
|
PLOS Genetics
|
Dissecting Gene Expression Changes Accompanying a Ploidy-Based Phenotypic Switch.
|
2016-11-11
|
Aimée M Dudley
|
Gareth A Cromie Zhihao Tan Michelle Hays Eric W Jeffery
|
G3
|
In vitro toxicity of pirimiphos-methyl in Atlantic salmon hepatocytes.
|
2016-11-11
|
Pål A. Olsvik
|
Marc H G Berntssen Liv Søfteland
|
Toxicology in Vitro
|
Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation.
|
2016-11-12
|
Ryan Lister James Whelan
|
Reena Narsai David Secco Matthew D Schultz Joseph R Ecker
|
The Plant Journal
|
MicroRNA profiling of human intermediate monocytes.
|
2016-11-13
|
Loems Ziegler-Heitbrock
|
Adam M Zawada Lu Zhang Insa E Emrich Kyrill S Rogacev Nicolas Krezdorn Björn Rotter Danilo Fliser Yvan Devaux Loems Ziegler-Heitbrock Gunnar H Heine
|
Immunobiology
|
Genome-wide screen identifies host colonization determinants in a bacterial gut symbiont
|
2016-11-14
|
Nancy A. Moran
|
J Elijah Powell Sean P Leonard Waldan K Kwong Philipp Engel
|
Proceedings of the National Academy of Sciences of the United States of America
|
RNAseq profiling of primary microglia and astrocyte cultures in near-term ovine fetus: A glial in vivo-in vitro multi-hit paradigm in large mammalian brain.
|
2016-11-14
|
Patrick Burns
|
M Cortes M Cao H L Liu C Moore G Fecteau A Desrochers L B Barreiro J P Antel M G Frasch
|
Journal of Neuroscience Methods
|
Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella.
|
2016-11-14
|
Jörg Vogel Leon N Schulte Lei Li Silke Appenzeller
|
Antoine-Emmanuel Saliba Alexander J Westermann Daphne A C Stapels Sophie Helaine
|
Nature Microbiology
|
Organ- and Growing Stage-Specific Expression of Solanesol Biosynthesis Genes in Nicotiana tabacum Reveals Their Association with Solanesol Content.
|
2016-11-15
|
Yanhua Liu Michael P. Timko
|
Ning Yan Hongbo Zhang Zhongfeng Zhang John Shi Yongmei Du Xinmin Liu
|
Molecules
|
Integrative transcriptome network analysis of iPSC-derived neurons from schizophrenia and schizoaffective disorder patients with 22q11.2 deletion
|
2016-11-15
|
Deyou Zheng
|
Mingyan Lin Erika Pedrosa Anastasia Hrabovsky Jian Chen Benjamin R Puliafito Stephanie R Gilbert Herbert M Lachman
|
BMC Systems Biology
|
Patterns of Transposable Element Expression and Insertion in Cancer.
|
2016-11-16
|
Lavanya Rishishwar
|
Evan A Clayton Lu Wang Jianrong Wang John F McDonald I King Jordan
|
Frontiers in molecular biosciences
|
Aging is associated with impaired angiogenesis, but normal microvascular network structure, in the rat mesentery.
|
2016-11-18
|
Melody Baddoo
|
Richard S Sweat David C Sloas Scott A Stewart Malwina Czarny-Ratajczak James R Eastwood Ariana D Suarez-Martinez Mohammad S Azimi Hope E Burks Lee O Chedister Leann Myers Walter L Murfee
|
American Journal of Physiology - Heart and Circulatory Physiology
|
Isolator: accurate and stable analysis of isoform-level expression in RNA-Seq experiments
|
2016-11-20
|
Walter L. Ruzzo
|
Daniel C. Jones Kavitha T. Kuppusamy Nathan J. Palpant Xinxia Peng Charles E. Murry Hannele Ruohola-Baker
|
|
Transcriptomic and proteomic insights into innate immunity and adaptations to a symbiotic lifestyle in the gutless marine worm Olavius algarvensis
|
2016-11-21
|
Manuel Kleiner Nicole Dubilier
|
Juliane Wippler Christian Lott Alexander Gruhl Paul E Abraham Richard J Giannone Jacque C Young Robert L Hettich
|
BMC Genomics
|
Insights into the human mesenchymal stromal/stem cell identity through integrative transcriptomic profiling
|
2016-11-21
|
Javier De Las Rivas Fermin Sanchez-Guijo
|
Beatriz Roson-Burgo Consuelo Del Cañizo
|
BMC Genomics
|
Predicting causal variants affecting expression using whole genome sequence and RNA-seq from multiple human tissues
|
2016-11-21
|
Kerrin S. Small
|
Andrew Anand Brown Ana Viñuela Olivier Delaneau Timothy Spector Emmanouil Dermitzakis
|
|
Cell culture-based profiling across mammals reveals DNA repair and metabolism as determinants of species longevity
|
2016-11-22
|
Vera Gorbunova Siming Ma Charles F. Burant
|
Akhil Upneja Andrzej Galecki Yi-Miau Tsai Sasha Raskind Quanwei Zhang Zhengdong D Zhang Andrei Seluanov Clary B Clish Richard A Miller Vadim N Gladyshev
|
eLife
|
Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data
|
2016-11-22
|
Jonathan Weissman
|
Joshua G Dunn
|
BMC Genomics
|
5'-Terminal nucleotide variations in human cytoplasmic tRNAHisGUG and its 5'-halves.
|
2016-11-22
|
Yohei Kirino
|
Megumi Shigematsu
|
RNA
|
Cancer somatic mutations cluster in a subset of regulatory sites predicted from the ENCODE data
|
2016-11-25
|
David R. Westhead
|
Nisar A Shar M S Vijayabaskar
|
Molecular Cancer
|
Tsetse fly tolerance to T. brucei infection: transcriptome analysis of trypanosome-associated changes in the tsetse fly salivary gland
|
2016-11-25
|
Jan Van Den Abbeele Guy Caljon
|
Irina Matetovici
|
BMC Genomics
|
RNA-Sequencing for profiling goat milk transcriptome in colostrum and mature milk.
|
2016-11-25
|
Alessandra Crisà Bianca Moioli Giovanni Chillemi
|
Fabrizio Ferrè
|
BMC Veterinary Research
|
Mapping heterogeneity in patient-derived melanoma cultures by single-cell RNA-seq.
|
2016-11-26
|
Manfred Schartl Barbara Treutlein Dirk Schadendorf
|
Tobias Gerber Edith Willscher Henry Loeffler-Wirth Lydia Hopp Manfred Schartl Ulf Anderegg Gray Camp Hans Binder Manfred Kunz
|
Oncotarget
|
Spliceosomal protein eftud2 mutation leads to p53-dependent apoptosis in zebrafish neural progenitors.
|
2016-11-28
|
Yumei Li Jia-Yu Chen
|
Lei Lei Shou-Yu Yan Ran Yang Ye Bu Nannan Chang Qinchao Zhou Xiaojun Zhu Chuan-Yun Li Jing-Wei Xiong
|
Nucleic Acids Research
|
A comprehensive approach to expression of L1 loci.
|
2016-11-28
|
Melody Baddoo Erik K Flemington
|
Prescott Deininger Maria E Morales Travis B White Melody Baddoo Dale J Hedges Geraldine Servant Sudesh Srivastav Madison E Smither Monica Concha Dawn L DeHaro Victoria P Belancio
|
Nucleic Acids Research
|
RNA-seq mixology: designing realistic control experiments to compare protocols and analysis methods
|
2016-11-29
|
Matthew E Ritchie Gordon K Smyth
|
Aliaksei Z Holik Charity W Law Ruijie Liu Zeya Wang Wenyi Wang Jaeil Ahn Marie-Liesse Asselin-Labat
|
Nucleic Acids Research
|
Transcriptomic Analysis Implicates the p53 Signaling Pathway in the Establishment of HIV-1 Latency in Central Memory CD4 T Cells in an In Vitro Model.
|
2016-11-29
|
Alberto Bosque David M. Margolis
|
Cory H White Bastiaan Moesker Nadejda Beliakova-Bethell Laura J Martins Celsa A Spina Douglas D Richman Vicente Planelles Christopher H Woelk
|
PLOS Pathogens
|
Complete genome sequence and transcriptomic analysis of a novel marine strain Bacillus weihaiensis reveals the mechanism of brown algae degradation.
|
2016-11-30
|
Jibin Sun
|
Yueming Zhu Peng Chen Yunjuan Bao Yan Men Yan Zeng Jiangang Yang Yuanxia Sun
|
Scientific Reports
|
A SLM2 Feedback Pathway Controls Cortical Network Activity and Mouse Behavior.
|
2016-12-01
|
Gavin Clowry David J Elliott Yoseph Barash Mauro Santibanez-Korev
|
Ingrid Ehrmann Matthew R Gazzara Vittoria Pagliarini Caroline Dalgliesh Mahsa Kheirollahi-Chadegani Yaobo Xu Eleonora Cesari Marina Danilenko Marie Maclennan Kate Lowdon Tanja Vogel Piia Keskivali-Bond Sara Wells Heather Cater Philippe Fort Silvia Middei Claudio Sette Mark O Cunningham
|
Cell Reports
|
The Lair: a resource for exploratory analysis of published RNA-Seq data.
|
2016-12-01
|
Lior Pachter Harold Pimentel Páll Melsted
|
Pascal Sturmfels Nicolas Bray
|
BMC Bioinformatics
|
Transcriptome and Multivariable Data Analysis of Corynebacterium glutamicum under Different Dissolved Oxygen Conditions in Bioreactors.
|
2016-12-01
|
Yankun Yang
|
Yang Sun Wenwen Guo Fen Wang Feng Peng Xiaofeng Dai Xiuxia Liu Zhonghu Bai
|
PLOS ONE
|
InFusion: Advancing Discovery of Fusion Genes and Chimeric Transcripts from Deep RNA-Sequencing Data.
|
2016-12-01
|
Thomas F. Meyer Lukas Rajkowitsch
|
Konstantin Okonechnikov Aki Imai-Matsushima Alexander Seitz Fernando Garcia-Alcalde
|
PLOS ONE
|
QSEA-modelling of genome-wide DNA methylation from sequencing enrichment experiments.
|
2016-12-01
|
Ralf Herwig Holger Sültmann
|
Matthias Lienhard Sabrina Grasse Jana Rolff Steffen Frese Uwe Schirmer Michael Becker Stefan Börno Bernd Timmermann Lukas Chavez Gunda Leschber Iduna Fichtner Michal R Schweiger
|
Nucleic Acids Research
|
Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.
|
2016-12-01
|
Nir Friedman Jenny Chen Jonathan Weissman
|
Atray Dixit Oren Parnas Biyu Li Charles P Fulco Livnat Jerby-Arnon Nemanja D Marjanovic Danielle Dionne Tyler Burks Britt Adamson Thomas M Norman
|
Cell
|
A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response.
|
2016-12-01
|
Aviv Regev Marco Y. Hein Jonathan Weissman
|
Britt Adamson Thomas M Norman Marco Jost Min Y Cho James K Nuñez Yuwen Chen Jacqueline E Villalta Luke A Gilbert Max A Horlbeck Ryan A Pak Andrew N Gray Carol A Gross Atray Dixit Oren Parnas
|
Cell
|
Global Deletion of TSPO Does Not Affect the Viability and Gene Expression Profile.
|
2016-12-01
|
Weiqing Wang
|
Huaishan Wang Kangle Zhai Yingchao Xue Jia Yang Qi Yang Yi Fu Yu Hu Fang Liu Lianxian Cui Hui Chen Jianmin Zhang Wei He
|
PLOS ONE
|
Epigenomics-Based Identification of Major Cell Identity Regulators within Heterogeneous Cell Populations.
|
2016-12-01
|
Peter Frommolt Alvaro Rada-Iglesias
|
Rizwan Rehimi Milos Nikolic Sara Cruz-Molina Christina Tebartz Esther Mahabir Mathieu Clément-Ziza
|
Cell Reports
|
Notch Pathway Is Activated via Genetic and Epigenetic Alterations and Is a Therapeutic Target in Clear Cell Renal Cancer.
|
2016-12-01
|
John Greally Katalin Susztak Shizheng Huang Niraj Shenoy
|
Tushar D Bhagat Yiyu Zou Jihwan Park Matthew B Palmer Caroline Hu Weijuan Li Orsolya Giricz Gaurav Choudhary Yiting Yu Yi-An Ko María C Izquierdo Ae Seo Deok Park Nishanth Vallumsetla Remi Laurence Robert Lopez Masako Suzuki James Pullman Justin Kaner Benjamin Gartrell A Ari Hakimi Bharvin Patel Karim Benhadji Kith Pradhan Amit Verma
|
Journal of Biological Chemistry
|
LncPRESS1 Is a p53-Regulated LncRNA that Safeguards Pluripotency by Disrupting SIRT6-Mediated De-acetylation of Histone H3K56.
|
2016-12-01
|
Michelle Craig Barton Abhinav K Jain Lalit Patel Kendra Allton
|
Yuanxin Xi Ryan McCarthy Kadir C Akdemir Bruce Aronow Chunru Lin Wei Li Liuqing Yang
|
Molecular Cell
|
Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq.
|
2016-12-01
|
Alexander van Oudenaarden Hadas Keren-Shaul
|
Diego Adhemar Jaitin Assaf Weiner Ido Yofe David Lara-Astiaso Hadas Keren-Shaul Eyal David Tomer Meir Salame Amos Tanay Ido Amit
|
Cell
|
MS23, a master basic helix-loop-helix factor, regulates the specification and development of the tapetum in maize.
|
2016-12-02
|
Blake Meyers
|
Guo-Ling Nan Jixian Zhai Siwaret Arikit Darren Morrow John Fernandes Lan Mai Nhi Nguyen Virginia Walbot
|
Development
|
How well do RNA-Seq differential gene expression tools perform in a eukaryote with a complex transcriptome?
|
2016-12-02
|
Kimon Froussios Nicholas Schurch Marek Gierlinski Geoffrey J. Barton
|
Katarzyna Mackinnon Céline Duc Gordon G Simpson
|
|
Transcriptomic Analysis of Mouse Cochlear Supporting Cell Maturation Reveals Large-Scale Changes in Notch Responsiveness Prior to the Onset of Hearing.
|
2016-12-05
|
Andrew K. Groves Zhandong Liu
|
Juan C Maass Rende Gu Tiantian Cai Ying-Wooi Wan Silvia C Cantellano Joanna S T Asprer Hongyuan Zhang Hsin-I Jen Renée K Edlund
|
PLOS ONE
|
Transcriptome and long noncoding RNA sequencing of three extracellular vesicle subtypes released from the human colon cancer LIM1863 cell line.
|
2016-12-05
|
Richard Simpson
|
Maoshan Chen Rong Xu Hong Ji David W Greening Alin Rai Keiichi Izumikawa Hideaki Ishikawa Nobuhiro Takahashi
|
Scientific Reports
|
Identification of context-dependent expression quantitative trait loci in whole blood.
|
2016-12-05
|
Lude Franke Harm-Jan Westra André Uitterlinden Cornelia M. van Duijn Cisca Wijmenga Wibowo Arindrarto Patrick Deelen Marc Jan Bonder Jenny van Dongen Yang Li Rick Jansen Marian Beekman Morris A Swertz Dorret Boomsma Peter A.C. 't Hoen Albert Hofman Leonard H van den Berg Jan H Veldink Coenraad Dirk Adriaan Stehouwer Casper G. Schalkwijk Jouke-Jan Hottenga
|
Daria V Zhernakova Martijn Vermaat Maarten van Iterson Michiel van Galen Peter van 't Hof Hailiang Mei Freerk van Dijk Jeroen van Rooij Marijn Verkerk P Mila Jhamai Matthijs Moed Szymon M Kielbasa Jan Bot Irene Nooren René Pool Carla J H van der Kallen Alexandra Zhernakova Ettje F Tigchelaar Niek de Klein Joris Deelen Diana van Heemst André G Uitterlinden Marleen M J van Greevenbroek P Eline Slagboom Aaron Isaacs Joyce B J van Meurs Bastiaan T Heijmans
|
Nature Genetics
|
Dynamic Changes in Chromatin Accessibility Occur in CD8+ T Cells Responding to Viral Infection.
|
2016-12-05
|
James P Scott-Browne
|
Isaac F López-Moyado Sara Trifari Victor Wong Lukas Chavez Anjana Rao Renata M Pereira
|
Immunity
|
Loss of Rearranged L-Myc Fusion (RLF) results in defects in heart development in the mouse.
|
2016-12-05
|
Pamela M. Pollock
|
L M Bourke G Del Monte-Nieto J E Outhwaite V Bharti D G Simmons A Adam S S J Hur G J Maghzal E Whitelaw R Stocker C M Suter R P Harvey S K Harten
|
Differentiation
|
Macrophage Colony Stimulating Factor Derived from CD4+ T Cells Contributes to Control of a Blood-Borne Infection
|
2016-12-06
|
Mary F Fontana Chioma Anidi Charles C. Kim
|
Gabrielly L de Melo Rebecca Hamburger Chris Y Kim So Youn Lee Jennifer Pham
|
PLOS Pathogens
|
Identification of senescence-associated circular RNAs (SAC-RNAs) reveals senescence suppressor CircPVT1
|
2016-12-07
|
Amaresh C Panda Myriam Gorospe Kotb Abdelmohsen
|
Ioannis Grammatikakis Kyoung Mi Kim Supriyo De Jennifer L Martindale Rachel Munk Xiaoling Yang
|
Nucleic Acids Research
|
Identification and quantification of novel RNA isoforms in horn cancer of Bos indicus by comprehensive RNA-Seq.
|
2016-12-07
|
Subhash J Jakhesara Chaitanya G. Joshi
|
Prakash G Koringa Neelam M Nathani
|
3 Biotech
|
Acfs: accurate circRNA identification and quantification from RNA-Seq data.
|
2016-12-08
|
Tim Conrad
|
Xintian You
|
Scientific Reports
|
Catalase deletion promotes prediabetic phenotype in mice.
|
2016-12-08
|
Kristofer S Fritz
|
Claire Heit Stephanie Marshall Surrendra Singh Xiaoqing Yu Georgia Charkoftaki Hongyu Zhao David J Orlicky David C Thompson Vasilis Vasiliou
|
Free Radical Biology and Medicine
|
Single-cell barcoding and sequencing using droplet microfluidics.
|
2016-12-08
|
David Zemmour
|
Rapolas Zilionis Juozas Nainys Adrian Veres Virginia Savova Allon M Klein Linas Mazutis
|
Nature Protocols
|
Whole-Organism Developmental Expression Profiling Identifies RAB-28 as a Novel Ciliary GTPase Associated with the BBSome and Intraflagellar Transport.
|
2016-12-08
|
Breandan N Kennedy
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PLOS Genetics
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Sugarcane transcriptome analysis in response to infection caused by Acidovorax avenae subsp. avenae.
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2016-12-09
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Clícia Grativol
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PLOS ONE
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Developmental Stage, Muscle and Genetic Type Modify Muscle Transcriptome in Pigs: Effects on Gene Expression and Regulatory Factors Involved in Growth and Metabolism.
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2016-12-09
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PLOS ONE
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Identification and Analysis of NaHCO3 Stress Responsive Genes in Wild Soybean (Glycine soja) Roots by RNA-seq.
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2016-12-09
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Yan Li
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Jinlong Zhang Jiaxue Wang Wei Jiang Juge Liu Songnan Yang Junyi Gai
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Frontiers in Plant Science
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Cardiac inflammation in genetic dilated cardiomyopathy caused by MYBPC3 mutation.
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2016-12-09
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Sakthivel Sadayappan Anil G. Jegga
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Thomas L Lynch Mohamed Ameen Ismahil Michael J Zilliox Christian Troidl Sumanth D Prabhu
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Journal of Molecular and Cellular Cardiology
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Simulation-based comprehensive benchmarking of RNA-seq aligners.
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2016-12-12
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Katharina E. Hayer Gregory R Grant
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Giacomo Baruzzo Eun Ji Kim Barbara Di Camillo Garret A FitzGerald
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Nature Methods
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Prediction and prioritization of neoantigens: integration of RNA sequencing data with whole-exome sequencing.
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2016-12-13
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Osamu Ohara
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Takahiro Karasaki Kazuhiro Nagayama Hideki Kuwano Jun-Ichi Nitadori Masaaki Sato Masaki Anraku Akihiro Hosoi Hirokazu Matsushita Masaki Takazawa Jun Nakajima Kazuhiro Kakimi
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Cancer Science
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Large-scale mapping of mammalian transcriptomes identifies conserved genes associated with different cell states.
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2016-12-14
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Jiapei Yuan
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Yang Yang Yu-Cheng T Yang Zhi John Lu Jingyi Jessica Li
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Nucleic Acids Research
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Microbial Community Composition Impacts Pathogen Iron Availability during Polymicrobial Infection.
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2016-12-14
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Marvin Whiteley
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Apollo Stacy Nader Abraham Peter Jorth
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PLOS Pathogens
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Identification of the RNA Pyrophosphohydrolase RppH of Helicobacter pylori and Global Analysis of Its RNA Targets.
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2016-12-14
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Thorsten Bischler
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Ping-Kun Hsieh Marcus Resch Quansheng Liu Hock Siew Tan Patricia L Foley Anika Hartleib Cynthia M Sharma Joel G Belasco
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Journal of Biological Chemistry
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Characterization of a TUTase/RNase complex required for Drosophila gametogenesis.
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2016-12-14
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Jiayu Wen Eric C Lai
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Ching-Jung Lin Fernando Bejarano Fuqu Hu Diane Bortolamiol-Becet Lijuan Kan Piero Sanfilippo
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RNA
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FAM13A is associated with non-small cell lung cancer (NSCLC) progression and controls tumor cell proliferation and survival.
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2016-12-14
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Arif B. Ekici
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Felix Eisenhut Lisanne Heim Sonja Trump Susanne Mittler Nina Sopel Katerina Andreev Fulvia Ferrazzi Ralf Rieker Rebekka Springel Vera L Assmann Matthias Lechmann Sonja Koch Marina Engelhardt Christina Warnecke Denis I Trufa Horia Sirbu Arndt Hartmann Susetta Finotto
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OncoImmunology
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SLICE: determining cell differentiation and lineage based on single cell entropy.
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2016-12-19
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Erik L Bao
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Minzhe Guo Michael Wagner Jeffrey A Whitsett Yan Xu
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Nucleic Acids Research
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An atlas of transcriptional, chromatin accessibility, and surface marker changes in human mesoderm development.
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2016-12-20
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Lay Teng Ang Anshul Kundaje
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Pang Wei Koh Rahul Sinha Amira A Barkal Rachel M Morganti Angela Chen Irving L Weissman Kyle M Loh
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Scientific Data
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Limb patterning genes and heterochronic development of the emu wing bud.
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2016-12-20
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Alicia Oshlack Nadia M Davidson Craig A. Smith Claire E. Hirst David M Lambert
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Peter G Farlie Kelly N Roeszler
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EvoDevo
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Transcriptome Profiling of Trypanosoma brucei Development in the Tsetse Fly Vector Glossina morsitans
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2016-12-21
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Aurélien Vigneron
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Amy F Savage Nikolay G Kolev Joseph B Franklin Serap Aksoy Christian Tschudi
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PLOS ONE
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A Rapid Spin Column-Based Method to Enrich Pathogen Transcripts from Eukaryotic Host Cells Prior to Sequencing.
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2016-12-21
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Robert J. Meagher
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Zachary W Bent Kunal Poorey Annette E LaBauve Rachelle Hamblin Kelly P Williams
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PLOS ONE
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Molecular mechanisms underlying active desalination and low water permeability in the esophagus of eels acclimated to seawater.
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2016-12-21
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Wataru Iwasaki
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Yoshio Takei Marty K-S Wong Supriya Pipil Haruka Ozaki Yutaka Suzuki Makoto Kusakabe
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American Journal of Physiology - Regulatory, Integrative and Comparative Physiology
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Logic programming to infer complex RNA expression patterns from RNA-seq data.
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2016-12-22
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Stefanie Dimmeler Yuliya Ponomareva Tyler Weirick Shizuka Uchida
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Giuseppe Militello David John Claudia Döring
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Briefings in Bioinformatics
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Stable Binding of the Conserved Transcription Factor Grainy Head to its Target Genes Throughout Drosophila melanogaster Development.
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2016-12-22
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Tommy Kaplan
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Markus Nevil Eliana R Bondra Katharine N Schulz Melissa M Harrison
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Genetics
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CYP716A179 functions as a triterpene C-28 oxidase in tissue-cultured stolons of Glycyrrhiza uralensis.
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2016-12-22
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Toshiya Muranaka Kazuki Saito
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Keita Tamura Hikaru Seki Hideyuki Suzuki Mareshige Kojoma
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Plant Cell Reports
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ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery.
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2016-12-23
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Vivek Krishnakumar Erik S Ferlanti Jason R Miller Matthew Vaughn
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Sergio Contrino Chia-Yi Cheng Irina Belyaeva Gos Micklem Christopher D Town Agnes P Chan
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Plant and Cell Physiology
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Derivation of marker gene signatures from human skin and their use in the interpretation of the transcriptional changes associated with dermatological disorders
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2016-12-23
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Thomas Freeman Barbara Shih Arne N Akbar
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Ajit J Nirmal Denis J Headon Neil A Mabbott
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The Journal of Pathology
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RNA sequencing of archived neonatal dried blood spots.
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2016-12-24
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Marie Bækvad-Hansen Jonas Bybjerg-Grauholm Mads Vilhelm Hollegaard
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Christian Munch Hagen Sok Kean Khoo Maria Louise Johannesen Christine Søholm Hansen Michael Christiansen David Michael Hougaard
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Molecular Genetics and Metabolism Reports
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Alternative splicing in tomato pollen in response to heat stress.
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2016-12-26
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Enrico Schleiff
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Mario Keller Yangjie Hu Anida Mesihovic Sotirios Fragkostefanakis Stefan Simm
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DNA Research
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Whole-genome expression analysis of mammalian-wide interspersed repeat elements in human cell lines.
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2016-12-27
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Matteo Pellegrini Davide Carnevali Anastasia Conti
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Giorgio Dieci
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DNA Research
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Transcriptomic gene profiling of porcine muscle tissue depending on histological properties.
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2016-12-27
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Artur Gurgul Katarzyna Ropka-Molik Katarzyna Piórkowska
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Anna Bereta Kacper Żukowski Grzegorz Żak
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Animal Science Journal
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Differential expression of alternatively spliced transcripts related to energy metabolism in colorectal cancer.
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2016-12-28
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Alex Zhavoronkov
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Anastasiya Vladimirovna Snezhkina George Sergeevich Krasnov Andrew Rostislavovich Zaretsky Kirill Mikhailovich Nyushko Alexey Alexandrovich Moskalev Irina Yurievna Karpova Anastasiya Isaevna Afremova Anastasiya Valerievna Lipatova Dmitriy Vladimitovich Kochetkov Maria Sergeena Fedorova Nadezhda Nikolaevna Volchenko Asiya Fayazovna Sadritdinova Nataliya Vladimirovna Melnikova Dmitry Vladimirovich Sidorov Anatoly Yurievich Popov Dmitry Valerievich Kalinin Andrey Dmitrievich Kaprin Boris Yakovlevich Alekseev Alexey Alexandrovich Dmitriev Anna Viktorovna Kudryavtseva
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BMC Genomics
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Succession of splicing regulatory elements determines cryptic 5΄ss functionality.
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2016-12-29
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Emanuele Buratti
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Anna-Lena Brillen Katrin Schöneweis Lara Walotka Linda Hartmann Lisa Müller Johannes Ptok Wolfgang Kaisers Gereon Poschmann Kai Stühler Stephan Theiss Heiner Schaal
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Nucleic Acids Research
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Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive.
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2016-12-30
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Kasper D. Hansen Leonardo Collado-Torres Andrew E Jaffe Jeffrey T. Leek Ben Langmead Abhinav Nellore
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Jean-Philippe Fortin José Alquicira-Hernández Siruo Wang Robert A Phillips Iii Nishika Karbhari
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Genome Biology
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Correlated 5-Hydroxymethylcytosine (5hmC) and Gene Expression Profiles Underpin Gene and Organ-Specific Epigenetic Regulation in Adult Mouse Brain and Liver
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2017
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I-Hsuan Lin
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Yi-Fan Chen Ming-Ta Hsu
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PLOS ONE
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QmihR: Pipeline for Quantification of Microbiome in Human RNA-seq
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2017
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Luisa Pereira Nuno A. Fonseca
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Bruno Cavadas Joana Ferreira Rui Camacho
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Advances in Intelligent Systems and Computing
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Pathway Analysis and Omics Data Visualization Using Pathway Genome Databases: FragariaCyc, a Case Study.
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2017-01-01
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Rohit jain
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Sushma Naithani Pankaj Jaiswal
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Methods in Molecular Biology
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Coupled Proliferation and Apoptosis Maintain the Rapid Turnover of Microglia in the Adult Brain
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2017-01-01
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Olga Garaschuk Amanda Sierra Yajie Liang Diego Gómez-Nicola Zoltán Molnár Mark S Cragg
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Katharine Askew Kaizhen Li Adrian Olmos-Alonso Fernando Garcia-Moreno Philippa Richardson Tom Tipton Mark A Chapman Kristoffer Riecken Sol Beccari V Hugh Perry
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Cell Reports
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Simple Analysis of Deposited Gene Expression Datasets for the Non-Bioinformatician: How to Use GEO for Fibrosis Research.
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2017-01-01
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Lam C. Tsoi
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Yang Guo Richard Townsend
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Methods in Molecular Biology
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Some Thoughts on Experimental Design.
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2017-01-01
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Claudio Daniel Stern
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Methods in Molecular Biology
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RNA-Seq investigations of human post-mortem trigeminal ganglia.
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2017-01-01
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Danielle Thierry-Mieg Stephen J Raithel Jean Thierry-Mieg
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Danielle M LaPaglia Matthew R Sapio Peter D Burbelo Danielle Thierry-Mieg Christopher E Ramsden Michael J Iadarola Andrew J Mannes
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Cephalalgia
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Bioinformatics Pipeline for Transcriptome Sequencing Analysis.
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2017-01-01
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Thomas Derrien
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Sarah Djebali Valentin Wucher Sylvain Foissac Christophe Hitte Evan Corre
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Methods in Molecular Biology
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Understanding development and stem cells using single cell-based analyses of gene expression.
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2017-01-01
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Patrick Cahan
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Pavithra Kumar Yuqi Tan
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Development
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RNA-Seq in the Collaborative Cross.
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2017-01-01
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Michael Gale Courtney Wilkins
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Richard Green Martin T Ferris
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Methods in Molecular Biology
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Analysis of EBV Transcription Using High-Throughput RNA Sequencing.
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2017-01-01
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Melody Baddoo Tina O'Grady Erik K Flemington
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Melody Baddoo
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Methods in Molecular Biology
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Next-Generation Sequencing Analysis of Long Noncoding RNAs in CD4+ T Cell Differentiation.
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2017-01-01
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Sergio Abrignani
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Valeria Ranzani Alberto Arrigoni Grazisa Rossetti Ilaria Panzeri Raoul J P Bonnal Massimiliano Pagani
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Methods in Molecular Biology
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Major Shifts in Glial Regional Identity Are a Transcriptional Hallmark of Human Brain Aging.
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2017-01-01
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Rickie Patani Jernej Ule John Anthony Hardy Mina Ryten North American Brain Expression Consortium Mark R Cookson
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Lilach Soreq UK Brain Expression Consortium Jamie Rose Eyal Soreq Daniah Trabzuni Colin Smith
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Cell Reports
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Simultaneous Transcriptional and Epigenomic Profiling from Specific Cell Types within Heterogeneous Tissues In Vivo
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2017-01-01
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Linus T-Y Tsai
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Hyun Cheol Roh Anna Lyubetskaya Danielle Tenen Manju Kumari Evan D Rosen
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Cell Reports
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RNA-Seq Data Analysis Protocol: Combining In-House and Publicly Available Data.
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2017-01-01
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Marc W Schmid
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Methods in Molecular Biology
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Optimized Whole Transcriptome Profiling of Motor Axons.
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2017-01-01
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Michael Sendtner
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Lena Saal-Bauernschubert Michael Briese
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Methods in Molecular Biology
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Analysis of Mitochondrial RNA-Processing Defects in Patient-Derived Tissues by qRT-PCR and RNAseq.
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2017-01-01
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Johannes A Mayr Holger Prokisch
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Robert Kopajtich
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Methods in Molecular Biology
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Genetic screens: Combining CRISPR perturbations and RNA-seq.
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2017-01-01
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Darren J. Burgess
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Nature Reviews Genetics
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Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data.
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2017-01-02
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Andrea Bräutigam
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Alisandra K Denton Janina Maß Canan Külahoglu Martin J Lercher Andreas P M Weber
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Journal of Experimental Botany
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ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data.
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2017-01-03
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Roderic Guigó i Serra Emilio Palumbo A Rastrojo
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Bernardo Rodríguez-Martín Santiago Marco-Sola Thasso Griebel Paolo Ribeca Graciela Alonso Begoña Aguado Sarah Djebali
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BMC Genomics
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An Oxygen-Sensing Two-Component System in the Burkholderia cepacia Complex Regulates Biofilm, Intracellular Invasion, and Pathogenicity.
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2017-01-03
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Matthew M Schaefers Deborah R Yoder-Himes Damien Roux
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Tiffany L Liao Nicole M Boisvert Gregory P Priebe
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PLOS Pathogens
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JACUSA: site-specific identification of RNA editing events from replicate sequencing data.
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2017-01-03
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Markus Landthaler Christoph Dieterich Emanuel Wyler Uwe Ohler
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Michael Piechotta
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BMC Bioinformatics
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A three-lncRNA signature derived from the Atlas of ncRNA in cancer (TANRIC) database predicts the survival of patients with head and neck squamous cell carcinoma.
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2017-01-03
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Ze-Guang Han
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Wei Cao Jian-Nan Liu Zeqi Liu Xu Wang Tong Ji Wan-Tao Chen Xin Zou
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Oral Oncology
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Targeted RNA-Seq profiling of splicing pattern in the DMD gene: exons are mostly constitutively spliced in human skeletal muscle
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2017-01-03
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Eva M Murauer Magali Taulan Mireille Claustres Sylvie Tuffery-Giraud
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Anne-Laure Bougé Emmanuelle Beyne Julie Miro Jessica Varilh Michel Koenig
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Scientific Reports
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Blocking Tumor-Educated MSC Paracrine Activity Halts Osteosarcoma Progression.
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2017-01-04
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Sonia A. Melo Roberta Bonafede Anne-Marie Cleton-Jansen Agostino Steffan Massimo Dominici
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S Rubina Baglio Tonny Lagerweij Maria Pérez-Lanzón Xuan Dung Ho Nicolas Léveillé Anne-Marie Cleton-Jansen Ekaterina S Jordanova Laura Roncuzzi Michelina Greco Monique A J van Eijndhoven Giulia Grisendi Sinead M Lougheed Tanja D de Gruijl Nicoletta Zini Silvia Cervo Vincenzo Canzonieri Aare Martson Katre Maasalu Sulev Köks Tom Wurdinger Nicola Baldini D Michiel Pegtel
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Clinical Cancer Research
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In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways
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2017-01-05
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Konrad Förstner Jörg Vogel Lei Li Kai Papenfort Hans-Joachim Wieden Richard Reinhardt
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Yanjie Chao Dylan Girodat Nelly Said Colin Corcoran Michał Śmiga Ben F Luisi
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Molecular Cell
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Mutations in EBF3 Disturb Transcriptional Profiles and Cause Intellectual Disability, Ataxia, and Facial Dysmorphism
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2017-01-05
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Kerstin Kutsche Stéphane Bézieau Sébastien Küry
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Frederike Leonie Harms Katta M. Girisha Andrew A. Hardigan Fanny Kortüm Anju Shukla Malik Alawi Ashwin Dalal Lauren Brady Mark Tarnopolsky Lynne M. Bird Sophia Ceulemans Martina Bebin Kevin M. Bowling Susan M. Hiatt Edward J. Lose Michelle Primiano Wendy K. Chung Jane Juusola Zeynep C. Akdemir Matthew Bainbridge Wu-Lin Charng Margaret Drummond-Borg Mohammad K. Eldomery Ayman W. El-Hattab Mohammed A. M. Saleh Stéphane Bézieau Benjamin Cogné Bertrand Isidor Sébastien Küry James R. Lupski Richard M. Myers Gregory M. Cooper
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American Journal of Human Genetics
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iSmaRT: a toolkit for a comprehensive analysis of small RNA-Seq data.
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2017-01-05
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Giorgio Giurato Francesca Rizzo Roberta Tarallo Alessandro Weisz Luciano Milanesi
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Riccardo Panero Antonio Rinaldi Domenico Memoli Giovanni Nassa Maria Ravo
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Bioinformatics
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Mapping eQTLs with RNA-seq reveals novel susceptibility genes, non-coding RNAs and alternative-splicing events in systemic lupus erythematosus
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2017-01-05
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Amy L Roberts Ana Viñuela Kerrin S. Small Christopher A Odhams Timothy J Vyse
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Andrea Cortini Lingyan Chen Alfonso Buil Emmanouil T Dermitzakis David L Morris Deborah S Cunninghame Graham
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Human Molecular Genetics
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SBDS-Deficient Cells Have an Altered Homeostatic Equilibrium due to Translational Inefficiency Which Explains their Reduced Fitness and Provides a Logical Framework for Intervention.
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2017-01-05
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Elisa Pesce Sara Ricciardi Stefano Biffo Diego Luis Medina Massimiliano Pagani
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Piera Calamita Annarita Miluzio Arianna Russo Farhat Khanim Cristina Cheroni Roberta Alfieri Marilena Mancino Chiara Gorrini Grazisa Rossetti Ivana Peluso Johanna Rommens
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PLOS Genetics
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LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells.
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2017-01-05
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Alicja Pacholewska
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Eliane Marti Tosso Leeb Vidhya Jagannathan Vincent Gerber
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BMC Genomics
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Transcriptome profiles reveal gene regulation of peanut (Arachis hypogaea L.) nodulation.
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2017-01-06
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Dev Paudel
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Ze Peng Fengxia Liu Liping Wang Hai Zhou Lubin Tan James Maku Maria Gallo Jianping Wang
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Scientific Reports
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Single-cell transcriptomics of small microbial eukaryotes: limitations and potential.
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2017-01-06
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Karla B Heidelberg
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Zhenfeng Liu Sarah K Hu Victoria Campbell Avery O Tatters David A Caron
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The ISME Journal
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The nature and nurture of cell heterogeneity: accounting for macrophage gene-environment interactions with single-cell RNA-Seq
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2017-01-07
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Sergi Padilla-Parra William James
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Quin F Wills Esther Mellado-Gomez Rory Nolan Damien Warner Eshita Sharma John Broxholme Benjamin Wright Helen Lockstone Mark Lynch Michael Gonzales Jay West Anne Leyrat Sarah Filippi Chris Holmes Michael D Moore Rory Bowden
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BMC Genomics
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KANK1 inhibits cell growth by inducing apoptosis though regulating CXXC5 in human malignant peripheral nerve sheath tumors
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2017-01-09
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GuangJun Zhang
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Zhibin Cui Yingjia Shen Kenny H Chen Suresh K Mittal Jer-Yen Yang
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Scientific Reports
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Quorum Sensing Regulators Are Required for Metabolic Fitness in Vibrio parahaemolyticus.
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2017-01-09
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Sharon Rozovsky
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Sai Siddarth Kalburge Megan R Carpenter E Fidelma Boyd
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Infection and Immunity
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Allele-specific wild-type TP53 expression in the unaffected carrier parent of children with Li-Fraumeni syndrome.
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2017-01-09
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Jeffrey S. Buzby
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Shirley A Williams Lana Schaffer Steven R Head Diane J Nugent
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Cancer Genetics
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Whole-Genome Sequencing of Invasion-Resistant Cells Identifies Laminin α2 as a Host Factor for Bacterial Invasion
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2017-01-10
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Victor Nizet Bjørn Voldborg Nathan E. Lewis
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Xander M van Wijk Simon Döhrmann Björn M Hallström Shangzhong Li Brandon X Meng Karen K McKee Toin H van Kuppevelt Peter D Yurchenco Bernhard O Palsson Jeffrey D Esko
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mBio
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A Hypothesis Testing Based Method for Normalization and Differential Expression Analysis of RNA-Seq Data.
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2017-01-10
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Jun Zhang
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Yan Zhou Guochang Wang Han Li
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PLOS ONE
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Long noncoding RNA repertoire in chicken liver and adipose tissue
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2017-01-10
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Hervé Acloque Fabrice Legeai Kévin Muret Thomas Derrien Sandrine Lagarrigue
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Christophe Klopp Valentin Wucher Diane Esquerré Frédéric Lecerf Colette Désert Morgane Boutin Frédéric Jehl Elisabetta Giuffra Sarah Djebali Sylvain Foissac
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Genetics Selection Evolution
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Nitro-fatty acids in plant signaling: New key mediators of nitric oxide metabolism.
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2017-01-10 2017-04-01
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Francisco J. Corpas Juan C Begara-Morales
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Capilla Mata-Pérez Beatriz Sánchez-Calvo María N Padilla Raquel Valderrama Juan B Barroso
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Redox Biology
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Hydrogel scaffolds promote neural gene expression and structural reorganization in human astrocyte cultures.
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2017-01-11
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Elba Serrano
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PeerJ
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High variability of expression profiles of homeologous genes for Wnt, Hh, Notch, and Hippo signaling pathways in Xenopus laevis.
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2017-01-12
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Takayoshi Yamamoto Yuuri Yasuoka Takuya Nakayama
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Tatsuo Michiue Toshiyasu Goto Takafumi Ikeda Kei Nagura Masanori Taira Tsutomu Kinoshita
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Developmental Biology
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Global Gene Expression Analysis of Cross-Protected Phenotype of Pectobacterium atrosepticum.
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2017-01-12
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Stanford Kwenda Elena Osipova Lucy Moleleki
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Vladimir Gorshkov Olga Petrova Yuri Gogolev
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PLOS ONE
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Transcriptome and network analyses in Saccharomyces cerevisiae reveal that amphotericin B and lactoferrin synergy disrupt metal homeostasis and stress response.
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2017-01-12
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Chi Nam Ignatius Pang Dee A Carter
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Yu-Wen Lai Leona T Campbell Sharon C-A Chen Marc R Wilkins
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Scientific Reports
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Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R
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2017-01-14
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Davis J McCarthy
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Kieran R Campbell Aaron T L Lun Quin F Wills
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Bioinformatics
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Effective detection of variation in single-cell transcriptomes using MATQ-seq.
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2017-01-16
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Chenghang Zong
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Kuanwei Sheng Wenjian Cao Yichi Niu Qing Deng
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Nature Methods
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PEDF Is Associated with the Termination of Chondrocyte Phenotype and Catabolism of Cartilage Tissue.
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2017-01-16
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Arif B. Ekici
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BioMed Research International
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Transcriptional analysis of mating and pre-infection stages of the anther smut, Microbotryum lychnidis-dioicae.
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2017-01-17
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Christina A Cuomo
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Su San Toh Zehua Chen David J Schultz Michael H Perlin
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Microbiology
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Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis
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2017-01-18
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Pär G Engström Janne Lehtiö Kaustuv Sanyal Joseph Heitman Teun Boekhout
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Yafeng Zhu Christian Tellgren-Roth Charles D Baudo John C Kennell Sheng Sun R Blake Billmyre Markus S Schröder Anna Andersson Tina Holm Benjamin Sigurgeirsson Guangxi Wu Sundar Ram Sankaranarayanan Rahul Siddharthan Joakim Lundeberg Björn Nystedt Thomas L Dawson Annika Scheynius
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Nucleic Acids Research
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Nematophagous fungus Arthrobotrys oligospora mimics olfactory cues of sex and food to lure its nematode prey.
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2017-01-18
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Erich M Schwarz Yen-Ping Hsueh Frank C Schroeder Paul W. Sternberg
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Matthew R Gronquist Ravi David Nath Ching-Han Lee Shalha Gharib
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eLife
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UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy
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2017-01-18
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Andreas Heger Tom Smith Ian Sudbery
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Genome Research
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Feasibility of sample size calculation for RNA-seq studies.
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2017-01-18
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Alicia Poplawski
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Harald Binder
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Briefings in Bioinformatics
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Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization
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2017-01-19
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Lana Garmire
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Xun Zhu Travers Ching Xinghua Pan Sherman M Weissman Lana Garmire
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PeerJ
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Lemna minor plants chronically exposed to ionising radiation: RNA-seq analysis indicates a dose rate dependent shift from acclimation to survival strategies.
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2017-01-22
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Arne Van Hoeck Ronny Blust
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Nele Horemans Robin Nauts May Van Hees Hildegarde Vandenhove
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Plant Science
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Genome-wide identification and analysis of biotic and abiotic stress regulation of small heat shock protein (HSP20) family genes in bread wheat.
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2017-01-22
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Senthilkumar K Muthusamy Viswanathan Chinnusamy
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Monika Dalal Kailash C Bansal
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The Journal of Plant Physiology
|
The choreography of the chemical defensome response to insecticide stress: insights into the Anopheles stephensi transcriptome using RNA-Seq
|
2017-01-23
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Claudio Bandi
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Leone De Marco Davide Sassera Sara Epis Valentina Mastrantonio Marco Ferrari Irene Ricci Francesco Comandatore Daniele Porretta Sandra Urbanelli
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Scientific Reports
|
A novel role for transcription-coupled nucleotide excision repair for the in vivo repair of 3,N4-ethenocytosine.
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2017-01-23
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Alycia Gardner
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Isaac A Chaim Jie Wu Teruaki Iyama David M Wilson Leona D Samson
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Nucleic Acids Research
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RNA-Sequencing Reveals Biological Networks during Table Grapevine ('Fujiminori') Fruit Development.
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2017-01-24
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Jinggui Fang
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Lingfei Shangguan Qian Mu Xiang Fang Kekun Zhang Haifeng Jia Xiaoying Li Yiqun Bao
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PLOS ONE
|
Single-cell epigenomic variability reveals functional cancer heterogeneity.
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2017-01-24
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Nathan C. Sheffield William Greenleaf
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Ulrike M Litzenburger Jason D Buenrostro Beijing Wu Ying Shen Arwa Kathiria Howard Y Chang
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Genome Biology
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Large-scale analysis of branchpoint usage across species and cell lines.
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2017-01-24
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Allison J Taggart William G Fairbrother
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Chien-Ling Lin Barsha Shrestha Claire Heintzelman Seongwon Kim
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Genome Research
|
Short bowel syndrome results in increased gene expression associated with proliferation, inflammation, bile acid synthesis and immune system activation: RNA sequencing a zebrafish SBS model
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2017-01-25
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Matthew E Thornton
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Kathy A Schall Mubina Isani Kathleen A Holoyda Xiaogang Hou Ching-Ling Lien Brendan H Grubbs Tracy C Grikscheit
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BMC Genomics
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A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples.
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2017-01-25
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Marc Dabad Nuria de la Iglesia Avelina Tortosa Carmen Balaña Anna Esteve-Codina
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Oriol Arpi Maria Martinez-García Estela Pineda Mar Mallo Marta Gut Cristina Carrato Anna Rovira Raquel Lopez Sonia Del Barco Simon Heath Silvia Bagué Teresa Ribalta Francesc Alameda GLIOCAT Group
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PLOS ONE
|
Two-Way Chemical Communication between Artificial and Natural Cells.
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2017-01-25
|
Luca Belmonte Sheref S. Mansy
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Roberta Lentini Noël Yeh Martín Michele Forlin Jason Fontana Michele Cornella Laura Martini Sabrina Tamburini William E Bentley Olivier Jousson
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ACS Central Science
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Guanylate-binding protein 1 (GBP1) contributes to the immunity of human mesenchymal stromal cells against Toxoplasma gondii.
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2017-01-25
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Geoff Hide De-Hua Lai Francisco J. Ayala
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Aiping Qin Qifa Liu Weijun Huang Ya-Ping Wu Xiaoyong Chen Sunxing Yan Huimin Xia Zhao-Rong Lun Andy Peng Xiang
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Proceedings of the National Academy of Sciences of the United States of America
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Stably Expressed Genes Involved in Basic Cellular Functions.
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2017-01-26
|
Vikrant Vijay
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Kejian Wang James C Fuscoe
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PLOS ONE
|
Epigenetic Alterations Affecting Transcription Factors and Signaling Pathways in Stromal Cells of Endometriosis
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2017-01-26
|
Lukas Kenner Iveta Yotova
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Emily Hsu Catherine Do Aulona Gaba Matthias Sczabolcs Sabine Dekan Rene Wenzl Benjamin Tycko
|
PLOS ONE
|
Molecular phenotyping of multiple mouse strains under metabolic challenge uncovers a role for Elovl2 in glucose-induced insulin secretion.
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2017-01-26
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Céline Cruciani-Guglielmacci Christophe Magnan Lara Bellini Robin Liechti Ioannis Xenarios
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Jessica Denom Masaya Oshima Neïké Fernandez Priscilla Normandie-Levi Xavier P Berney Nadim Kassis Claude Rouch Julien Dairou Tracy Gorman David M Smith Anna Marley Dmitry Kuznetsov Leonore Wigger Frédéric Burdet Anne-Laure Lefèvre Isabelle Wehrle Ingo Uphues Tobias Hildebrandt Werner Rust Catherine Bernard Alain Ktorza Guy A Rutter Raphael Scharfmann Hervé Le Stunff Bernard Thorens Mark Ibberson
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Molecular Metabolism
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Profiling of human epigenetic regulators using a semi-automated real-time qPCR platform validated by next generation sequencing.
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2017-01-27
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Allan B. Dietz
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Amel Dudakovic Martina Gluscevic Christopher R Paradise Halil Dudakovic Farzaneh Khani Roman Thaler Farah S Ahmed Xiaodong Li Gary S Stein Martin A Montecino David R Deyle Jennifer J Westendorf Andre J van Wijnen
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Gene
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Regulation of miR-29b-1/a transcription and identification of target mRNAs in CHO-K1 cells.
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2017-01-28
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Justin L. Mott
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Penn Muluhngwi Kirsten Richardson Joshua Napier Eric C Rouchka Carolyn M Klinge
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Molecular and Cellular Endocrinology
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MicroRNA and mRNA Transcriptome Profiling in Primary Human Astrocytes Infected with Borrelia burgdorferi
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2017-01-30
|
Timothy Casselli Ata Abbas
|
Humaira Qureshi Elizabeth Peterson Danielle Perley Emily Blake Bradley Jokinen Sergei Nechaev John A Watt Archana Dhasarathy Catherine A Brissette
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PLOS ONE
|
Comparative genomics of two jute species and insight into fibre biogenesis.
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2017-01-30
|
Xuehua Wan
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Md Shahidul Islam Jennifer A Saito Emdadul Mannan Emdad Borhan Ahmed Mohammad Moinul Islam Abdul Halim Quazi Md Mosaddeque Hossen Md Zakir Hossain Rasel Ahmed Md Sabbir Hossain Shah Md Tamim Kabir Md Sarwar Alam Khan Md Mursalin Khan Rajnee Hasan Nasima Aktar Ummay Honi Rahin Islam Md Mamunur Rashid Shaobin Hou Taslima Haque Muhammad Shafiul Azam Mahdi Muhammad Moosa Sabrina M Elias A M Mahedi Hasan Niaz Mahmood Md Shafiuddin Saima Shahid Nusrat Sharmeen Shommu Sharmin Jahan Saroj Roy Amlan Chowdhury Ashikul Islam Akhand Golam Morshad Nisho Khaled Salah Uddin Taposhi Rabeya S M Ekramul Hoque Afsana Rahman Snigdha Sarowar Mortoza Syed Abdul Matin Md Kamrul Islam M Z H Lashkar Mahboob Zaman Anton Yuryev Md Kamal Uddin Md Sharifur Rahman Md Samiul Haque Md Monjurul Alam Haseena Khan Maqsudul Alam
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Nature Plants
|
Identification and evolutionary analysis of long non-coding RNAs in zebra finch.
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2017-01-31
|
Chun-Ping Yu
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Chih-Kuan Chen Sung-Chou Li Siao-Man Wu Mei-Yeh Jade Lu Yi-Hua Chen Di-Rong Chen Chen Siang Ng Chau-Ti Ting Wen-Hsiung Li
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BMC Genomics
|
Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors.
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2017-01-31
|
Ellen Decaestecker Luisa Orsini John K. Colbourne
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Donald Gilbert Ram Podicheti Mieke Jansen James B Brown Omid Shams Solari Katina I Spanier Douglas B Rusch Jana Asselman Karel A C De Schamphelaere Dieter Ebert Christoph R Haag Jouni Kvist Christian Laforsch Adam Petrusek Andrew P Beckerman Tom J Little Anurag Chaturvedi Michael E Pfrender Luc De Meester Mikko J Frilander
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Scientific Data
|
Promiscuous DNA-binding of a mutant zinc finger protein corrupts the transcriptome and diminishes cell viability
|
2017-02-01
|
Timothy L. Bailey Melissa D Ilsley Michael W Parker Kevin R Gillinder Michael J Landsberg Joel P Mackay Luanne L Peters Andrew C Perkins
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Danitza Nébor Ravi Sachidanandam Mathieu Lajoie Graham W Magor Michael R Tallack Luke A Miles Joel H Graber James J Bieker
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Nucleic Acids Research
|
Competitive regulation of alternative splicing and alternative polyadenylation by hnRNP H and CstF64 determines acetylcholinesterase isoforms.
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2017-02-01
|
Mohammad Nazim Kinji Ohno
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Akio Masuda Mohammad Alinoor Rahman Farhana Nasrin Jun-Ichi Takeda Kenji Ohe Bisei Ohkawara Mikako Ito
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Nucleic Acids Research
|
Impact of exudative diathesis induced by selenium deficiency on LncRNAs and their roles in the oxidative reduction process in broiler chick veins.
|
2017-02-01
|
Changyu Cao
|
Ruifeng Fan Jinxin Zhao Xia Zhao Jie Yang Ziwei Zhang Shiwen Xu
|
Oncotarget
|
An Intrinsic Transcriptional Program Underlying Synaptic Scaling during Activity Suppression
|
2017-02-01
|
Ege T Kavalali
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Katie Schaukowitch Austin L Reese Seung-Kyoon Kim Gokhul Kilaru Jae-Yeol Joo Tae-Kyung Kim
|
Cell Reports
|
USP39 Deubiquitinase Is Essential for KRAS Oncogene-driven Cancer.
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2017-02-01
|
Víctor Quesada Amaia Lujambio
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Julia M Fraile Eusebio Manchado Diana Campos-Iglesias Thomas R Webb Scott W Lowe Carlos López-Otín José M P Freije
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Journal of Biological Chemistry
|
Comparative Analysis of Single-Cell RNA Sequencing Methods.
|
2017-02-01
|
Swati Parekh Beate Vieth Björn Reinius
|
Christoph Ziegenhain Amy Guillaumet-Adkins Martha Smets Heinrich Leonhardt Holger Heyn Ines Hellmann Wolfgang Enard
|
Molecular Cell
|
CAN1 Arginine Permease Deficiency Extends Yeast Replicative Lifespan via Translational Activation of Stress Response Genes.
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2017-02-01
|
Matt Kaeberlein
|
Carine Beaupere Brian M Wasko Jared Lorusso Brian K Kennedy Vyacheslav M Labunskyy
|
Cell Reports
|
RNA-Seq Analysis of Gene Expression, Viral Pathogen, and B-Cell/T-Cell Receptor Signatures in Complex Chronic Disease.
|
2017-02-01
|
Jerome Bouquet Theodore S Steiner Charles Y. Chiu
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Jennifer L Gardy Scott Brown Jacob Pfeil Ruth R Miller Muhammad Morshed Antonio Avina-Zubieta Kam Shojania Mark McCabe Shoshana Parker Miguel Uyaguari Scot Federman Patrick Tang Michael Otterstater Rob Holt Richard Moore David M Patrick Complex Chronic Disease Study Group
|
Clinical Infectious Diseases
|
The START App: a web-based RNAseq analysis and visualization resource.
|
2017-02-01
|
Jessica Minnier
|
Jonathan W Nelson Jiri Sklenar Anthony P Barnes
|
Bioinformatics
|
Histone H3.3 regulates mitotic progression in mouse embryonic fibroblasts.
|
2017-02-01
|
Kiran Padmanabhan Christophe Papin
|
Aysegul Ors Bertrand Favier Yohan Roulland Defne Dalkara Mehmet Ozturk Ali Hamiche Stefan Dimitrov
|
Biochemistry and Cell Biology
|
Gene expression: Host-pathogen duels revealed by dual RNA-seq in vivo.
|
2017-02-01
|
Darren J. Burgess
|
|
Nature Reviews Genetics
|
Discovery of new candidate genes for rheumatoid arthritis through integration of genetic association data with expression pathway analysis.
|
2017-02-02
|
Leonid Padyukov Lars Klareskog
|
Klementy Shchetynsky Lina-Marcella Diaz-Gallo Lasse Folkersen Aase Haj Hensvold Anca Irinel Catrina Louise Berg
|
Arthritis Research and Therapy
|
Transcriptional characterization of Vibrio fischeri during colonization of juvenile Euprymna scolopes.
|
2017-02-02
|
Shu Pan Luke R Thompson Rob Knight Jennifer L Reed
|
Kiel Nikolakakis Edward G Ruby
|
Environmental Microbiology
|
Integrated Proteomic and Transcriptomic-Based Approaches to Identifying Signature Biomarkers and Pathways for Elucidation of Daoy and UW228 Subtypes.
|
2017-02-03
|
Eugene Kolker
|
Roger Higdon Jessie Kala Devan Wilkins Julia Fangfei Yan Manveen K Sethi Liang Lin Siqi Liu Elizabeth Montague Imre Janko John Choiniere Natali Kolker William S Hancock Susan Fanayan
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Proteomes
|
miR-135a-5p-mediated downregulation of protein tyrosine phosphatase receptor delta is a candidate driver of HCV-associated hepatocarcinogenesis.
|
2017-02-03
|
Markus H Heim Simonetta Bandiera Diego Calabrese Joachim Lupberger Nathalie Pochet
|
Nicolaas Van Renne Armando Andres Roca Suarez Francois H T Duong Claire Gondeau Nelly Fontaine Amina Ababsa Tom Croonenborghs Vito De Blasi Patrick Pessaux Tullio Piardi Daniele Sommacale Atsushi Ono Kazuaki Chayama Masashi Fujita Hidewaki Nakagawa Yujin Hoshida Mirjam B Zeisel Thomas F Baumert
|
Gut
|
RNA-seq in kinetoplastids: A powerful tool for the understanding of the biology and host-pathogen interactions.
|
2017-02-04
|
Juan D Ramírez
|
Luz Helena Patino
|
Infection, Genetics and Evolution
|
A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma
|
2017-02-06
|
Gregory P Way Robert J Allaway Casey S. Greene
|
Stephanie J Bouley Camilo E Fadul Yolanda Sanchez
|
BMC Genomics
|
Evaluation of logistic regression models and effect of covariates for case-control study in RNA-Seq analysis.
|
2017-02-06
|
Kathryn L. Lunetta Josée Dupuis Adam Labadorf
|
Seung Hoan Choi Richard H Myers Anita L DeStefano
|
BMC Bioinformatics
|
Expression map of a complete set of gustatory receptor genes in chemosensory organs of Bombyx mori.
|
2017-02-06
|
Qingyou Xia Tingcai Cheng Emmanuelle Jacquin-Joly
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Huizhen Guo Zhiwei Chen Liang Jiang Youbing Guo Jianqiu Liu Shenglong Li Kiyoko Taniai Kiyoshi Asaoka Keiko Kadono-Okuda Kallare P Arunkumar Jiaqi Wu Hirohisa Kishino Huijie Zhang Rakesh K Seth Karumathil P Gopinathan Nicolas Montagné Marian R Goldsmith Kazuei Mita
|
Insect Biochemistry and Molecular Biology
|
Analysis of The Cancer Genome Atlas sequencing data reveals novel properties of the human papillomavirus 16 genome in head and neck squamous cell carcinoma.
|
2017-02-07
|
Mikhail G Dozmorov
|
Tara J Nulton Amy L Olex Iain M Morgan Brad Windle
|
Oncotarget
|
PIGN gene expression aberration is associated with genomic instability and leukemic progression in acute myeloid leukemia with myelodysplastic features.
|
2017-02-07
|
Emmanuel K Teye Jeffrey Pu Thomas Abraham
|
Abigail Sido Ping Xin Niklas K Finnberg Prashanth Gokare Yuka I Kawasawa Anna C Salzberg Sara Shimko Michael Bayerl W Christopher Ehmann David F Claxton Witold B Rybka Joseph J Drabick Hong-Gang Wang Wafik S El-Deiry Robert A Brodsky Raymond J Hohl
|
Oncotarget
|
RNA-seq Analysis of Cold and Drought Responsive Transcriptomes of Zea mays ssp. mexicana L.
|
2017-02-07
|
Meixue Zhou
|
Xiang Lu Xuan Zhou Yu Cao David McNeil Shan Liang Chengwei Yang
|
Frontiers in Plant Science
|
Expression and splicing of ABC and SLC transporters in the human blood-brain barrier measured with RNAseq.
|
2017-02-07
|
Wolfgang Sadee
|
Adam M Suhy Amy Webb Audrey C Papp Ethan G Geier
|
European Journal of Pharmaceutical Sciences
|
Transcriptional regulation of male-sterility in 7B-1 male-sterile tomato mutant.
|
2017-02-08
|
Irina Mohorianu Tamas Dalmay
|
Vahid Omidvar Yi Zheng Zhangjun Fei Anna Pucci Andrea Mazzucato Vendula Večeřová Michaela Sedlářova Martin Fellner
|
PLOS ONE
|
RNA-seq analysis of Drosophila clock and non-clock neurons reveals neuron-specific cycling and novel candidate neuropeptides
|
2017-02-09
|
Michael Rosbash Katharine C Abruzzi
|
Abigail Zadina Weifei Luo Evelyn Wiyanto Reazur Rahman Fang Guo Orie Shafer
|
PLOS Genetics
|
If it transcribes, we can sequence it: mining the complexities of host-pathogen-environment interactions using RNA-seq.
|
2017-02-09
|
Carsten Kröger Andrew Ds Cameron
|
Aoife M Colgan
|
Current Opinion in Microbiology
|
Reduced mitochondrial activity in colonocytes facilitates AMPKα2-dependent inflammation.
|
2017-02-09
|
Melody Baddoo Harrison M Penrose Erik K Flemington
|
Sandra Heller Chloe Cable Debjani Biswas Hani Nakhoul Susan E Crawford Suzana D Savkovic
|
FASEB Journal
|
Immortalized human myotonic dystrophy muscle cell lines to assess therapeutic compounds.
|
2017-02-10
|
Arnaud F Klein Denis Furling Vincent Mouly
|
Ludovic Arandel Micaela Polay Espinoza Magdalena Matloka Audrey Bazinet Damily De Dea Diniz Naïra Naouar Frédérique Rau Arnaud Jollet Frédérique Edom-Vovard Kamel Mamchaoui Mark Tarnopolsky Jack Puymirat Christophe Battail Anne Boland Jean-Francois Deleuze
|
Disease Models & Mechanisms
|
CirComPara: A Multi-Method Comparative Bioinformatics Pipeline to Detect and Study circRNAs from RNA-seq Data.
|
2017-02-10
|
Stefania Bortoluzzi Geertruy Te Kronnie Enrico Gaffo
|
Annagiulia Bonizzato
|
Non-coding RNA
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Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput.
|
2017-02-13
|
Alex K. Shalek Rahul Satija
|
Todd M Gierahn Marc H Wadsworth Travis K Hughes Bryan D Bryson Andrew Butler Sarah Fortune J Christopher Love
|
Nature Methods
|
Subinhibitory Concentrations of Ciprofloxacin Enhance Antimicrobial Resistance and Pathogenicity of Enterococcus faecium.
|
2017-02-13
|
Maurizio Sanguinetti
|
Clara Sinel Margherita Cacaci Pierrick Meignen François Guérin Bryan W Davies Jean-Christophe Giard Vincent Cattoir
|
Antimicrobial Agents and Chemotherapy
|
Transcriptomic, cellular and life-history responses of Daphnia magna chronically exposed to benzotriazoles: Endocrine-disrupting potential and molting effects.
|
2017-02-14
|
Magali Houde
|
Maeva Giraudo Mélanie Douville Guillaume Cottin
|
PLOS ONE
|
A reference gene set construction using RNA-seq of multiple tissues of Chinese giant salamander, Andrias davidianus
|
2017-02-15
|
Xiaodong Fang
|
Xiaofang Geng Wanshun Li Haitao Shang Qiang Gou Fuchun Zhang Xiayan Zang Benhua Zeng Jiang Li Ying Wang Ji Ma Jianlin Guo Jianbo Jian Bing Chen Zhigang Qiao Minghui Zhou Hong Wei Cunshuan Xu
|
GigaScience
|
Endometrial factors similarly induced by IFNT2 and IFNTc1 through transcription factor FOXS1
|
2017-02-15
|
Kazuya Kusama
|
Rulan Bai Keigo Nakamura Sayaka Okada Jiro Yasuda Kazuhiko Imakawa
|
PLOS ONE
|
Variant discovery in the sheep milk transcriptome using RNA sequencing
|
2017-02-15
|
Gwenola Tosser-Klopp Gwenola Tosser-Klopp Juan J Arranz
|
Aroa Suárez-Vega Beatriz Gutiérrez-Gil Christophe Klopp
|
BMC Genomics
|
Modeling the Genetic Regulation of Cancer Metabolism: Interplay between Glycolysis and Oxidative Phosphorylation.
|
2017-02-15
|
José Onuchic
|
Linglin Yu Mingyang Lu Dongya Jia Jianpeng Ma Eshel Ben-Jacob Herbert Levine Benny Abraham Kaipparettu
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Cancer Research
|
Identification of a novel series of anti-inflammatory and anti-oxidative phospholipid oxidation products containing the cyclopentenone moiety in vitro and in vivo: Implication in atherosclerosis.
|
2017-02-15
|
Sotirios Tsimikas
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Jianhong Lu Shuyuan Guo Xinli Xue Qun Chen Jing Ge Yujuan Zhuo Huiqin Zhong Buxing Chen Mingming Zhao Wei Han Takashi Suzuki Mingjiang Zhu Lin Xia Claus Schneider Timothy S Blackwell Ned A Porter Lemin Zheng Huiyong Yin
|
Journal of Biological Chemistry
|
RNA-Seq analysis of chikungunya virus infection and identification of granzyme A as a major promoter of arthritic inflammation
|
2017-02-16
|
Francesca Di Giallonardo Pierre Roques Andreas Suhrbier Suresh Mahalingam
|
Natalie A. Prow Wayne A. Schroder Jonathan J. Ellis Helen E. Cumming Linden J. Gearing Yee Suan Poo Adam Taylor Paul J. Hertzog Linda Hueston Roger Le Grand Bing Tang Thuy T. Le Joy Gardner Phillip I. Bird
|
PLOS Pathogens
|
Resolving host-pathogen interactions by dual RNA-seq.
|
2017-02-16 2017-02-01
|
Jörg Vogel Lars Barquist
|
Alexander J Westermann
|
PLOS Pathogens
|
RNA-seq and metabolomic analyses of Akt1-mediated muscle growth reveals regulation of regenerative pathways and changes in the muscle secretome.
|
2017-02-16
|
Kenneth Walsh
|
Chia-Ling Wu Yoshinori Satomi
|
BMC Genomics
|
Transcriptional analysis of defense mechanisms in upland tetraploid switchgrass to greenbugs
|
2017-02-16
|
Scott E. Sattler
|
Teresa Donze-Reiner Nathan A Palmer Erin D Scully Travis J Prochaska Kyle G Koch Tiffany Heng-Moss Jeffrey D Bradshaw Paul Twigg Keenan Amundsen Gautam Sarath
|
BMC Plant Biology
|
Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies.
|
2017-02-16
|
Yann Guiguen Julien Bobe
|
Cédric Cabau Frédéric Escudié Anis Djari Christophe Klopp
|
PeerJ
|
Epigenetic and genetic dissections of UV-induced global gene dysregulation in skin cells through multi-omics analyses
|
2017-02-17
|
Deyou Zheng
|
Yao Shen Milda Stanislauskas Gen Li Liang Liu
|
Scientific Reports
|
Epigenomics of human CD8 T cell differentiation and aging.
|
2017-02-17
|
Sabine Le Saux Bin Hu David Moskowitz William Greenleaf
|
David W Zhang Rolando E Yanes Zhongde Ye Jason D Buenrostro Cornelia M Weyand Jörg J Goronzy
|
Science immunology
|
Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research.
|
2017-02-20
|
Eric Peatman Geoff Waldbieser Terrence Tiersch Acacia Alcivar-Warren Wilawan Thongda Brian P Bosworth Shikai Liu Rex Dunham
|
Aquaculture Genomics, Genetics and Breeding Workshop Hisham Abdelrahman Mohamed ElHady Acacia Alcivar-Warren Standish Allen Rafet Al-Tobasei Lisui Bao Ben Beck Harvey Blackburn John Buchanan Jesse Chappell William Daniels Sheng Dong Evan Durland Ahmed Elaswad Marta Gomez-Chiarri Kamal Gosh Ximing Guo Perry Hackett Terry Hanson Dennis Hedgecock Tiffany Howard Leigh Holland Molly Jackson Yulin Jin Karim Kahlil Thomas Kocher Tim Leeds Ning Li Lauren Lindsey Zhanjiang Liu Kyle Martin Romi Novriadi Ramjie Odin Yniv Palti Dina Proestou Guyu Qin Benjamin Reading Caird Rexroad Steven Roberts Mohamed Salem Andrew Severin Huitong Shi Craig Shoemaker Sheila Stiles Suxu Tan Kathy F J Tang Wilawan Thongda Terrence Tiersch Joseph Tomasso Wendy Tri Prabowo Roger Vallejo Hein van der Steen Khoi Vo Geoff Waldbieser Hanping Wang Xiaozhu Wang Jianhai Xiang Yujia Yang Roger Yant Zihao Yuan Qifan Zeng Tao Zhou
|
BMC Genomics
|
MINTmap: fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data.
|
2017-02-21
|
Isidore Rigoutsos
|
Phillipe Loher Aristeidis G Telonis
|
Scientific Reports
|
Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads.
|
2017-02-22
|
Marie-France Sagot
|
Leandro Lima Blerina Sinaimeri Gustavo Sacomoto Helene Lopez-Maestre Camille Marchet Vincent Miele Vincent Lacroix
|
Algorithms for Molecular Biology
|
Pentose sugars inhibit metabolism and increase expression of an AgrD-type cyclic pentapeptide in Clostridium thermocellum.
|
2017-02-23
|
Thomas Rydzak James G. Elkins Adam Guss Nancy Engle Timothy Tschaplinski
|
Tobin J Verbeke Richard J Giannone Dawn M Klingeman Steven D Brown Robert L Hettich
|
Scientific Reports
|
CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor.
|
2017-02-23
|
D Yap
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Tyler Funnell Shinya Tasaki Arusha Oloumi Shinsuke Araki Esther Kong Yusuke Nakayama Christopher S Hughes S-W Grace Cheng Hirokazu Tozaki Misa Iwatani Satoshi Sasaki Tomohiro Ohashi Tohru Miyazaki Nao Morishita Daisuke Morishita Mari Ogasawara-Shimizu Momoko Ohori Shoichi Nakao Masatoshi Karashima Masaya Sano Aiko Murai Toshiyuki Nomura Noriko Uchiyama Tomohiro Kawamoto Ryujiro Hara Osamu Nakanishi Karey Shumansky Jamie Rosner Adrian Wan Steven McKinney Gregg B Morin Atsushi Nakanishi Sohrab Shah Hiroyoshi Toyoshiba Samuel Aparicio
|
Nature Communications
|
Single nucleotide polymorphism discovery in bovine liver using RNA-seq technology
|
2017-02-24
|
Haja N. Kadarmideen Mariusz Pierzchała
|
Chandra Shekhar Pareek Paweł Błaszczyk Piotr Dziuba Urszula Czarnik Leyland Fraser Przemysław Sobiech Yaping Feng Dibyendu Kumar
|
PLOS ONE
|
Can milk cell or skim milk miRNAs be used as biomarkers for early pregnancy detection in cattle?
|
2017-02-24
|
Benedikt Kirchner Michael W Pfaffl
|
Corina I Schanzenbach Susanne E Ulbrich
|
PLOS ONE
|
MINT: a multivariate integrative method to identify reproducible molecular signatures across independent experiments and platforms
|
2017-02-27
|
Kim-Anh Lê Cao
|
Florian Rohart Aida Eslami Nicholas Matigian Stéphanie Bougeard Kim-Anh Lê Cao
|
BMC Bioinformatics
|
Essentiality of mmpL3 and impact of its silencing on Mycobacterium tuberculosis gene expression.
|
2017-02-27
|
Riccardo Manganelli Giorgio Palù
|
Giulia Degiacomi Andrej Benjak Jan Madacki Francesca Boldrin Roberta Provvedi Jana Kordulakova Stewart T Cole
|
Scientific Reports
|
Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions.
|
2017-02-27
|
Daniel M Stoebel
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Ciaran Evans Johanna Hardin
|
Briefings in Bioinformatics
|
Comprehensive mapping of the effects of azacitidine on DNA methylation, repressive/permissive histone marks and gene expression in primary cells from patients with MDS and MDS-related disease.
|
2017-02-28
|
Eva Hellström-Lindberg Elisabet Einarsdottir Kaarel Krjutškov Francesco Marabita Shintaro Katayama Juha Kere Karl Ekwall Andreas Lennartsson
|
Magnus Tobiasson Hani Abdulkadir Ayla De Paepe Mohsen Karimi Michael Grövdal Monika Jansson Asmaa Ben Azenkoud Lina Corddedu Sören Lehmann Eva Hellström-Lindberg Johanna Ungerstedt
|
Oncotarget
|
Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq - ryhB encodes the regulatory RNA RyhB and a peptide, RyhP
|
2017-02-28
|
Klaus Neuhaus Siegfried Scherer
|
Richard Landstorfer Svenja Simon Steffen Schober Patrick R Wright Cameron Smith Rolf Backofen Romy Wecko Daniel A Keim
|
BMC Genomics
|
Conserved expression of transposon-derived non-coding transcripts in primate stem cells.
|
2017-02-28
|
Guillaume Bourque
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LeeAnn Ramsay Maria C Marchetto Maxime Caron Shu-Huang Chen Stephan Busche Tony Kwan Tomi Pastinen Fred H Gage
|
BMC Genomics
|
Insights into Dynamic Polymicrobial Synergy Revealed by Time-Coursed RNA-Seq.
|
2017-02-28
|
Marvin Whiteley
|
Erik L Hendrickson David A C Beck Daniel P Miller Qian Wang Richard J Lamont Murray Hackett
|
Frontiers in Microbiology
|
Human Mesenchymal Stem Cell-Educated Macrophages Are a Distinct High IL-6-Producing Subset that Confer Protection in Graft-versus-Host-Disease and Radiation Injury Models.
|
2017-02-28
|
Andrea B Moffitt Jaehyup Kim Christian M. Capitini
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Myriam N Bouchlaka John A Kink Debra D Bloom Cassandra Love Sandeep Dave Peiman Hematti
|
Biology of Blood and Marrow Transplantation
|
Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria.
|
2017-03-01
|
Tapio Lönnberg Ismail Sebina Frederik Otzen Bagger Oliver Stegle Kylie R James Valentine Svensson Ashraful Haque William R Heath Sarah Teichmann
|
Daniel Fernandez-Ruiz Ruddy Montandon Megan S F Soon Lily G Fogg Arya Sheela Nair Urijah Liligeto Michael J T Stubbington Lam-Ha Ly Max Zwiessele Neil D Lawrence Fernando Souza-Fonseca-Guimaraes Patrick T Bunn Christian R Engwerda Oliver Billker
|
Science immunology
|
Novel lincRNA SLINKY is a prognostic biomarker in kidney cancer.
|
2017-03-01
|
Jonathan R. Pollack
|
Xue Gong Zurab Siprashvili Okyaz Eminaga Zhewei Shen Yusuke Sato Haruki Kume Yukio Homma Seishi Ogawa Paul A Khavari James D Brooks
|
Oncotarget
|
Enhancer-Mediated Oncogenic Function of the Menin Tumor Suppressor in Breast Cancer.
|
2017-03-01
|
Elgene Lim Wouter de Laat
|
Koen M A Dreijerink Anna C Groner Erica S M Vos Alba Font-Tello Lei Gu David Chi Jaime Reyes Jennifer Cook Charles Y Lin Prakash K Rao Henry W Long Myles Brown
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Cell Reports
|
Transcriptomic and histological responses of African rice (Oryza glaberrima) to Meloidogyne graminicola provide new insights into root-knot nematode resistance in monocots.
|
2017-03-01
|
Janice de Almeida Engler Tina Kyndt Diana Fernandez
|
Anne-Sophie Petitot Rana Haidar Alexis Dereeper Myriam Collin Godelieve Gheysen
|
Annals of Botany
|
Hypomorphic Pathogenic Variants in TAF13 Are Associated with Autosomal-Recessive Intellectual Disability and Microcephaly.
|
2017-03-01
|
Heinrich Sticht Igor Martianov Fulvia Ferrazzi Irwin Davidson André Reis
|
Hasan Tawamie Natalie Wohlfahrt Rebecca Buchert Gabrielle Mengus Steffen Uebe Luigi Janiri Franz Wolfgang Hirsch Johannes Schumacher Roberto Colombo Rami Abou Jamra
|
American Journal of Human Genetics
|
Dissecting common and divergent molecular pathways elicited by CdSe/ZnS quantum dots in freshwater and marine sentinel invertebrates.
|
2017-03-01
|
Beatriz Pelaz Abuelmagd M. Abdelmonem Angela Tino Claudia Tortiglione
|
Alfredo Ambrosone Modi Roopin Lisa-Maria Ackermann Lucia Mattera Mariateresa Allocca Markus Klapper Wolfgang J Parak Oren Levy
|
Nanotoxicology
|
DExD/H-box RNA helicase genes are differentially expressed between males and females during the critical period of male sex differentiation in channel catfish.
|
2017-03-01
|
Shikai Liu
|
Changxu Tian Suxu Tan Lisui Bao Qifan Zeng Yujia Yang Xiaoxiao Zhong Zhanjiang Liu
|
Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics
|
Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq.
|
2017-03-01
|
Daniel P Cahill Itay Tirosh Orit Rozenblatt-Rosen Aviv Regev Shawn M. Gillespie Christopher W Mount Brian V. Nahed Michelle Monje Gad Getz
|
Andrew S Venteicher Christine Hebert Keren Yizhak Cyril Neftel Mariella G Filbin Volker Hovestadt Leah E Escalante McKenzie L Shaw Christopher Rodman Danielle Dionne Christina C Luo Hiranmayi Ravichandran Ravindra Mylvaganam Maristela L Onozato Hiroaki Wakimoto William T Curry A John Iafrate Miguel N Rivera Matthew P Frosch Todd R Golub Priscilla K Brastianos Anoop P Patel David N Louis Bradley E Bernstein Mario L Suvà
|
Science
|
RED-ML: a novel, effective RNA editing detection method based on machine learning.
|
2017-03-02
|
Huanming Yang
|
Heng Xiong Dongbing Liu Qiye Li Mengyue Lei Liqin Xu Liang Wu Zongji Wang Shancheng Ren Wangsheng Li Min Xia Lihua Lu Haorong Lu Yong Hou Shida Zhu Xin Liu Yinghao Sun Jian Wang Kui Wu Xun Xu Leo J Lee
|
GigaScience
|
Single-cell transcriptomics reveals specific RNA editing signatures in the human brain
|
2017-03-03
|
Graziano Pesole Ernesto Picardi
|
David S Horner
|
RNA
|
Laser capture microdissection enables transcriptomic analysis of dividing and quiescent liver stages of Plasmodium relapsing species.
|
2017-03-03
|
Nathalie Dereuddre-Bosquet Jean-François Franetich
|
Roger Cubi Shruthi S Vembar Anne Biton Jean-Francois Franetich Mallaury Bordessoulles Daniel Sossau Gigliola Zanghi Henriette Bosson-Vanga Magalie Benard Alicia Moreno Roger Le Grand Artur Scherf Dominique Mazier
|
Cellular Microbiology
|
A GLABRA1 ortholog on LG A9 controls trichome number in the Japanese leafy vegetables Mizuna and Mibuna (Brassica rapa L. subsp. nipposinica L. H. Bailey): evidence from QTL analysis.
|
2017-03-03
|
Seisuke Kimura
|
Yaichi Kawakatsu Hokuto Nakayama Kaori Kaminoyama Kaori Igarashi Masaki Yasugi Hiroshi Kudoh Atsushi J Nagano Kentaro Yano Nakao Kubo
|
Journal of Plant Research
|
Molecular mechanism and structural basis of gain-of-function of STAT1 caused by pathogenic R274Q mutation.
|
2017-03-03
|
Atsushi Hijikata Satoshi Okada
|
Ryoji Fujiki Tsuyoshi Shirai Masao Kobayashi
|
Journal of Biological Chemistry
|
Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning.
|
2017-03-06
|
Daniele Ramazzotti
|
Bo Wang Junjie Zhu Emma Pierson Serafim Batzoglou
|
Nature Methods
|
Total RNA-seq to identify pharmacological effects on specific stages of mRNA synthesis.
|
2017-03-06
|
Sarah A Boswell Andrew Snavely
|
Heather M Landry L Stirling Churchman Jesse M Gray Michael Springer
|
Nature Chemical Biology
|
Abnormalities in A-to-I RNA editing patterns in CNS injuries correlate with dynamic changes in cell type composition.
|
2017-03-07
|
Erez Y. Levanon Eli Eisenberg
|
Nurit Gal-Mark Lea Shallev Sahar Sweetat Michal Barak Jin Billy Li Oded Behar
|
Scientific Reports
|
Transcriptome Remodeling of Acinetobacter baumannii during Infection and Treatment.
|
2017-03-07
|
Robert A Bonomo
|
Meredith S Wright Michael R Jacobs Mark D Adams
|
mBio
|
The transcriptome of the avian malaria parasite Plasmodium ashfordi displays host-specific gene expression.
|
2017-03-07
|
Gediminas Valkiūnas Elin Videvall Olof Hellgren
|
Charlie K Cornwallis Dag Ahrén Vaidas Palinauskas
|
Molecular Ecology
|
The novel long non-coding RNA TALNEC2, regulates tumor cell growth and the stemness and radiation response of glioma stem cells.
|
2017-03-07
|
Simona Cazacu Chaya Brodie
|
Shlomit Brodie Hae Kyung Lee Wei Jiang Simona Cazacu Cunli Xiang Laila M Poisson Indrani Datta Steve Kalkanis Doron Ginsberg
|
Oncotarget
|
TT-seq captures enhancer landscapes immediately after T-cell stimulation.
|
2017-03-07
|
Julien Gagneur Björn Schwalb
|
Margaux Michel Carina Demel Benedikt Zacher Stefan Krebs Helmut Blum Patrick Cramer
|
Molecular Systems Biology
|
Activation of odorant receptor in colorectal cancer cells leads to inhibition of cell proliferation and apoptosis.
|
2017-03-08
|
Hanns Hatt Günter Gisselmann S Hahn
|
Lea Weber Klaudia Al-Refae Juliane Ebbert Peter Jägers Janine Altmüller Christian Becker Günter Gisselmann
|
PLOS ONE
|
VCNet: Vector based gene Co-expression Network construction and its application to RNA-seq data.
|
2017-03-08
|
Nelson Leung-Sang Tang
|
Zengmiao Wang Huaying Fang Minghua Deng
|
Bioinformatics
|
Quantifying circular RNA expression from RNA-seq data using model-based framework.
|
2017-03-08
|
Tong Zhou Eun-A Ko
|
Musheng Li Xueying Xie Jing Zhou Mengying Sheng Xiaofeng Yin Wanjun Gu
|
Bioinformatics
|
Variation-preserving normalization unveils blind spots in gene expression profiling.
|
2017-03-09
|
Janeck J Scott-Fordsmand
|
Carlos P Roca Susana I L Gomes Mónica J B Amorim
|
Scientific Reports
|
Responses of the picoprasinophyte Micromonas commoda to light and ultraviolet stress.
|
2017-03-09
|
Frédéric Partensky
|
Marie L Cuvelier Jian Guo Alejandra C Ortiz Marijke J van Baren Muhammad Akram Tariq Alexandra Z Worden
|
PLOS ONE
|
Imiquimod has strain-dependent effects in mice and does not uniquely model human psoriasis.
|
2017-03-09
|
Mrinal K. Sarkar Nicole L. Ward
|
William R Swindell Kellie A Michaels Andrew J Sutter Doina Diaconu Yi Fritz Xianying Xing Yun Liang Alex Tsoi Johann E Gudjonsson
|
Genome Medicine
|
Transcriptome and Functional Genomics Reveal the Participation of Adenine Phosphoribosyltransferase in Trypanosoma cruzi Resistance to Benznidazole.
|
2017-03-09
|
Omar Triana-Chávez
|
Paola García-Huertas Ana María Mejía-Jaramillo Laura González
|
Journal of Cellular Biochemistry
|
High-throughput sequencing reveals circular substrates for an archaeal RNA ligase.
|
2017-03-09
|
Roxane Lestini Kamel Djaout Hubert F Becker Hannu Myllykallio
|
Alice Héliou Mireille Regnier
|
RNA Biology
|
Smooth muscle cell-specific deletion of Col15a1 unexpectedly leads to impaired development of advanced atherosclerotic lesions.
|
2017-03-10
|
Joshua T Butcher Delphine Gomez Brant E Isakson
|
Brittany G Durgin Olga A Cherepanova Themistoclis Karaoli Gabriel F Alencar Yu-Qing Zhou Michelle P Bendeck Gary K Owens Jessica J Connelly
|
American Journal of Physiology - Heart and Circulatory Physiology
|
Heterarchy of transcription factors driving basal and luminal cell phenotypes in human urothelium.
|
2017-03-10
|
Simon Moxon Jennifer Southgate Sarah Bastkowski
|
Carl Fishwick Janet Higgins Lawrence Percival-Alwyn Arianna Hustler Joanna Pearson David Swarbreck Chris D Greenman
|
Cell Death & Differentiation
|
Model-based unsupervised learning informs metformin-induced cell-migration inhibition through an AMPK-independent mechanism in breast cancer
|
2017-03-10
|
Richard Weinshilboum
|
Arjun P Athreya Krishna R Kalari Junmei Cairns Alan J Gaglio Quin F Wills Nifang Niu Ravishankar K Iyer Liewei Wang
|
Oncotarget
|
Lipid degradation promotes prostate cancer cell survival.
|
2017-03-11
|
Etienne Waelkens Elai Davicioni Nicholas Erho
|
Harri M Itkonen Michael Brown Alfonso Urbanucci Gregory Tredwell Chung Ho Lau Stefan Barfeld Claire Hart Ingrid J Guldvik Mandeep Takhar Hannelore V Heemers Katarzyna Bloch Rita Derua James L Mohler Noel Clarke Johan V Swinnen Hector C Keun Ole P Rekvig Ian G Mills
|
Oncotarget
|
Transcriptomic responses to environmental temperature by turtles with temperature-dependent and genotypic sex determination assessed by RNAseq inform the genetic architecture of embryonic gonadal development.
|
2017-03-15
|
Robert Literman Nicole Valenzuela
|
Srihari Radhakrishnan Jennifer Neuwald Andrew Severin Nicole Valenzuela
|
PLOS ONE
|
Network reconstruction of the mouse secretory pathway applied on CHO cell transcriptome data.
|
2017-03-15
|
Julian Brandl Claus Kristensen Lasse Ebdrup Pedersen Helene Faustrup Kildegaard Mikael Rørdam Andersen
|
Anne Mathilde Lund Christian Schrøder Kaas
|
BMC Systems Biology
|
Large-scale gene network analysis reveals the significance of extracellular matrix pathway and homeobox genes in acute myeloid leukemia: an introduction to the Pigengene package and its applications.
|
2017-03-16
|
Habil Zare Linda Chang
|
Amir Foroushani Rupesh Agrahari Roderick Docking Gerben Duns Monika Hudoba Aly Karsan
|
BMC Medical Genomics
|
The duplication mutation of Quebec platelet disorder dysregulates PLAU, but not C10orf55, selectively increasing production of normal PLAU transcripts by megakaryocytes but not granulocytes.
|
2017-03-16
|
Andrew D. Paterson
|
Catherine P M Hayward Minggao Liang Subia Tasneem Asim Soomro John S Waye Georges E Rivard Michael D Wilson
|
PLOS ONE
|
Correspondence of D. melanogaster and C. elegans developmental stages revealed by alternative splicing characteristics of conserved exons.
|
2017-03-16
|
Jingyi Jessica Li
|
Ruiqi Gao
|
BMC Genomics
|
Assessing the miRNA sponge potential of RUNX1T1 in t(8;21) acute myeloid leukemia.
|
2017-03-16
|
Jan Gorodkin Alexander Junge
|
Roza Zandi Jakob Hull Havgaard Jack Bernard Cowland
|
Gene
|
Lentinula edodes Genome Survey and Postharvest Transcriptome Analysis.
|
2017-03-17
|
Yuichi Sakamoto
|
Keiko Nakade Shiho Sato Kentaro Yoshida Kazuhiro Miyazaki Satoshi Natsume Naotake Konno
|
Applied and Environmental Microbiology
|
Transcriptomics Indicates Active and Passive Metronidazole Resistance Mechanisms in Three Seminal Giardia Lines.
|
2017-03-17
|
Staffan G Svärd Robin B. Gasser Aaron R Jex
|
Brendan R E Ansell Louise Baker Samantha J Emery Malcolm J McConville
|
Frontiers in Microbiology
|
Marginal likelihood estimation of negative binomial parameters with applications to RNA-seq data.
|
2017-03-19
|
Sarah Emerson
|
Luis León-Novelo Claudio Fuentes
|
Biostatistics
|
Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato-Pseudomonas pathosystem.
|
2017-03-20
|
Hernan G. Rosli
|
Marina A Pombo Yi Zheng Zhangjun Fei Gregory B Martin
|
Scientific Reports
|
CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in cerebral organoids derived from iPS cells.
|
2017-03-20
|
Michael Kirschenbaum Deyou Zheng
|
Ping Wang Ryan Mokhtari Erika Pedrosa Can Bayrak Herbert M Lachman
|
Molecular Autism
|
Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors.
|
2017-03-20
|
Elise T Courtois Paul Robson
|
Huipeng Li Debarka Sengupta Yuliana Tan Kok Hao Chen Jolene Jie Lin Goh Say Li Kong Clarinda Chua Lim Kiat Hon Wah Siew Tan Mark Wong Paul Jongjoon Choi Lawrence J K Wee Axel M Hillmer Iain Beehuat Tan Shyam Prabhakar
|
Nature Genetics
|
Cross-Platform Normalization Enables Machine Learning Model Training On Microarray And RNA-Seq Data Simultaneously
|
2017-03-20
|
Jaclyn N Taroni Casey S. Greene
|
|
|
Huntington’s disease blood and brain show a common gene expression pattern and share an immune signature with Alzheimer’s disease
|
2017-03-21
|
Davina J Hensman Moss James R C Miller Peter A.C. 't Hoen Sarah J. Tabrizi
|
Flower MD Lo KK van Ommen GJ Stone TC Guinee A Langbehn DR Jones L Plagnol V van Roon-Mom WM Holmans P
|
Scientific Reports
|
Discovery of novel determinants of endothelial lineage using chimeric heterokaryons.
|
2017-03-21
|
Wing Tak Wong James K Chen John P. Cooke
|
Gianfranco Matrone XiaoYu Tian Simion Alin Tomoiaga Kin Fai Au Shu Meng Sayumi Yamazoe Daniel Sieveking Kaifu Chen David M Burns Helen M Blau
|
eLife
|
Identification and functional analysis of differentially expressed genes in poorly differentiated hepatocellular carcinoma using RNA-seq.
|
2017-03-21
|
Jianbo Pan
|
Yi Huang Dunyan Chen Jiaying Zheng Funan Qiu Feng Li Yanan Wu Wenbing Wu Xiaoli Huang Jiang Qian
|
Oncotarget
|
Activation of Epithelial Signal Transducer and Activator of Transcription 1 by Interleukin 28 Controls Mucosal Healing in Mice With Colitis and Is Increased in Mucosa of Patients With Inflammatory Bowel Disease.
|
2017-03-22
|
Arif B. Ekici
|
Mircea T Chiriac Barbara Buchen Alexandra Wandersee Gheorghe Hundorfean Claudia Günther Yvonne Bourjau Sean E Doyle Benjamin Frey Christian Büttner Benno Weigmann Raja Atreya Stefan Wirtz Christoph Becker Jürgen Siebler Markus F Neurath
|
Gastroenterology
|
Widespread promoter methylation of synaptic plasticity genes in long-term potentiation in the adult brain in vivo.
|
2017-03-23
|
Marcel E. Dinger
|
Jesper L V Maag Dominik C Kaczorowski Debabrata Panja Timothy J Peters Clive R Bramham Karin Wibrand
|
BMC Genomics
|
Seten: a tool for systematic identification and comparison of processes, phenotypes, and diseases associated with RNA-binding proteins from condition-specific CLIP-seq profiles.
|
2017-03-23
|
Gungor Budak Sarath Chandra Janga
|
Rajneesh Srivastava
|
RNA
|
Cytochrome P450 Monooxygenase CYP716A141 is a Unique β-Amyrin C-16β Oxidase Involved in Triterpenoid Saponin Biosynthesis in Platycodon grandiflorus.
|
2017-03-23
|
Toshiya Muranaka Kazuki Saito
|
Keita Tamura Yuga Teranishi Shinya Ueda Hideyuki Suzuki Noriaki Kawano Kayo Yoshimatsu Nobuo Kawahara Hikaru Seki
|
Plant and Cell Physiology
|
RNA-Seq transcriptomics and pathway analyses reveal potential regulatory genes and molecular mechanisms in high- and low-residual feed intake in Nordic dairy cattle
|
2017-03-24
|
Peter Lund
|
M S Salleh G Mazzoni J K Höglund D W Olijhoek P Løvendahl H N Kadarmideen
|
BMC Genomics
|
Insights into electrosensory organ development, physiology and evolution from a lateral line-enriched transcriptome
|
2017-03-27
|
Gos Micklem Marcus C Davis
|
Melinda S Modrell Mike Lyne Adrian R Carr Harold H Zakon David Buckley Alexander S Campbell Clare Vh Baker
|
eLife
|
SC3: consensus clustering of single-cell RNA-seq data
|
2017-03-27
|
Mauricio Barahona Tallulah Andrews Kedar N Natarajan Kristina Kirschner Anthony R Green Wolf Reik
|
Vladimir Yu Kiselev Michael T Schaub Andrew Yiu Tamir Chandra Martin Hemberg
|
Nature Methods
|
Epipodial Tentacle Gene Expression and Predetermined Resilience to Summer Mortality in the Commercially Important Greenlip Abalone, Haliotis laevigata.
|
2017-03-27
|
Nicholas A. Robinson Ira R Cooke Jan Strugnell
|
Brett P Shiel Nathan E Hall
|
Marine Biotechnology
|
Molecular, phenotypic, and sample-associated data to describe pluripotent stem cell lines and derivatives.
|
2017-03-28
|
Kenneth Daily Phillip Dexheimer Winston Hide Lynn Schriml Alexander R. Pico
|
Shannan J Ho Sui Lynn M Schriml Nathan Salomonis Robin Schroll Stacy Bush Mehdi Keddache Christopher Mayhew Samad Lotia Thanneer M Perumal Kristen Dang Lorena Pantano Elke Grassman Diana Nordling Antonis K Hatzopoulos Punam Malik Jose A Cancelas Carolyn Lutzko Bruce J Aronow Larsson Omberg
|
Scientific Data
|
RNA-sequence analysis of gene expression from honeybees (Apis mellifera) infected with Nosema ceranae.
|
2017-03-28
|
John L. Williams
|
Bouabid Badaoui André Fougeroux Fabien Petit Anna Anselmo Chiara Gorni Marco Cucurachi Antonella Cersini Anna Granato Giusy Cardeti Giovanni Formato Franco Mutinelli Elisabetta Giuffra Sara Botti
|
PLOS ONE
|
Erratum: Targeted RNA-Seq profiling of splicing pattern in the DMD gene: exons are mostly constitutively spliced in human skeletal muscle.
|
2017-03-28
|
Mireille Claustres Sylvie Tuffery-Giraud
|
Anne-Laure Bougé Eva Murauer Emmanuelle Beyne Julie Miro Jessica Varilh Magali Taulan Michel Koenig
|
Scientific Reports
|
Transcriptome analysis of microglia in a mouse model of Rett syndrome: differential expression of genes associated with microglia/macrophage activation and cellular stress
|
2017-03-29
|
Dejian Zhao Deyou Zheng
|
Ryan Mokhtari Erika Pedrosa Rayna Birnbaum Herbert M Lachman
|
Molecular Autism
|
Defining Brugia malayi and Wolbachia symbiosis by stage-specific dual RNA-seq.
|
2017-03-30
|
Sara Lustigman Thomas R Unnasch
|
Alexandra Grote Denis Voronin Tao Ding Alan Twaddle Elodie Ghedin
|
PLOS Neglected Tropical Diseases
|
Integrating Sequence-based GWAS and RNA-Seq Provides Novel Insights into the Genetic Basis of Mastitis and Milk Production in Dairy Cattle.
|
2017-03-30
|
Mogens Sandø Lund
|
Lingzhao Fang Goutam Sahana Guosheng Su Ying Yu Shengli Zhang Peter Sørensen
|
Scientific Reports
|
Top2b is involved in the formation of outer segment and synapse during late-stage photoreceptor differentiation by controlling key genes of photoreceptor transcriptional regulatory network.
|
2017-03-30
|
Ronald P Hart
|
Ying Li Hailing Hao Mavis R Swerdel Hyeon-Yeol Cho Ki-Bum Lee Yi Lisa Lyu Li Cai
|
Journal of Neuroscience Research
|
Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors.
|
2017-04-01
|
Aviv Regev Rahul Satija Nir Hacohen Gary Reynolds Andrew Butler Shiwei Zheng Orit Rozenblatt-Rosen
|
Alexandra-Chloé Villani Siranush Sarkizova Karthik Shekhar James Fletcher Morgane Griesbeck Suzan Lazo Laura Jardine David Dixon Emily Stephenson Emil Nilsson Ida Grundberg David McDonald Andrew Filby Weibo Li Philip L De Jager Andrew A Lane Muzlifah Haniffa
|
Science
|
Differentially expressed genes during spontaneous lytic switch of Marek's disease virus in lymphoblastoid cell lines determined by global gene expression profiling.
|
2017-04-01
|
Mick Watson Venugopal Nair
|
William N Mwangi Deepali Vasoya Lydia B Kgosana
|
Journal of General Virology
|
An Activating STAT3 Mutation Causes Neonatal Diabetes through Premature Induction of Pancreatic Differentiation.
|
2017-04-01
|
Diego Balboa Salla Keskitalo Markku Varjosalo Noel G Morgan
|
Jonna Saarimäki-Vire Mark A Russell Juha Saarikettu Matias Kinnunen Amrinder Malhi Cristina Valensisi Colin Andrus Solja Eurola Heli Grym Jarkko Ustinov Kirmo Wartiovaara R David Hawkins Olli Silvennoinen Timo Otonkoski
|
Cell Reports
|
Characterization of RBP9 and RBP10, two developmentally regulated RNA-binding proteins in Trypanosoma brucei.
|
2017-04-01
|
Luis M De Pablos Janaina de Freitas Nascimento Jack D Sunter
|
Steve Kelly Mark Carrington
|
Open Biology
|
Rapid Genome-wide Recruitment of RNA Polymerase II Drives Transcription, Splicing, and Translation Events during T Cell Responses.
|
2017-04-01
|
Matthias Heinig Caroline C Friedel
|
Kathrin Davari Johannes Lichti Christian Gallus Franziska Greulich N Henriette Uhlenhaut Elke Glasmacher
|
Cell Reports
|
Functional Enhancer Screening in Single Cells.
|
2017-04-01
|
Bas van Steensel
|
Joris van Arensbergen
|
Molecular Cell
|
Reproducible RNA-seq analysis using recount2.
|
2017-04-01
|
Kasper D. Hansen Leonardo Collado-Torres Andrew E Jaffe Jeffrey T. Leek Ben Langmead Abhinav Nellore
|
Kai Kammers Shannon E Ellis Margaret A Taub
|
Nature Biotechnology
|
Osteoblast-specific deletion of Hrpt2/Cdc73 results in high bone mass and increased bone turnover.
|
2017-04-03
|
Bin Tean Teh
|
Casey J Droscha Cassandra R Diegel Nicole J Ethen Travis A Burgers Mitchell J McDonald Kevin A Maupin Agni S Naidu PengFei Wang Bart O Williams
|
Bone
|
Intranuclear Actin Structure Modulates Mesenchymal Stem Cell Differentiation.
|
2017-04-03
|
Rebekah M Samsonraj
|
Buer Sen Gunes Uzer Zhihui Xie Cody McGrath Maya Styner Amel Dudakovic Andre J van Wijnen Janet Rubin
|
Stem Cells
|
An immunoaffinity-based method for isolating ultrapure adult astrocytes based on ATP1B2 targeting by the ACSA-2 antibody.
|
2017-04-03
|
Takashi Saito
|
Mykhailo Y Batiuk Filip de Vin Sandra I Duqué Chen Li Takaomi Saido Mark Fiers T Grant Belgard Matthew G Holt
|
Journal of Biological Chemistry
|
The Transcriptome of Leishmania major Developmental Stages in Their Natural Sand Fly Vector
|
2017-04-04
|
Najib El-sayed
|
Ehud Inbar V Keith Hughitt Laura A L Dillon Kashinath Ghosh David L Sacks
|
mBio
|
Measuring Signaling and RNA-Seq in the Same Cell Links Gene Expression to Dynamic Patterns of NF-κB Activation.
|
2017-04-04
|
Dana Pe'er
|
Keara Lane David Van Valen Mialy M DeFelice Derek N Macklin Takamasa Kudo Ariel Jaimovich Ambrose Carr Tobias Meyer Dana Pe'er Stéphane C Boutet Markus W Covert
|
Cell systems
|
Transcriptome profiling of Arabian horse blood during training regimens.
|
2017-04-05
|
Artur Gurgul Katarzyna Ropka-Molik Katarzyna Piórkowska
|
Monika Stefaniuk-Szmukier Kacper Żukowski Monika Bugno-Poniewierska
|
BMC Genetics
|
Severe acute dehydration in a desert rodent elicits a transcriptional response that effectively prevents kidney injury.
|
2017-04-05
|
Matthew D. MacManes
|
|
American Journal of Physiology - Renal Physiology
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Spontaneous lung metastasis formation of human Merkel cell carcinoma cell lines transplanted into scid mice.
|
2017-04-05
|
Max Heiland
|
Jill Knips Manja Czech-Sioli Michael Spohn Ingrid Moll Adam Grundhoff Udo Schumacher Nicole Fischer
|
International Journal of Cancer
|
Bidirectional terminators in Saccharomyces cerevisiae prevent cryptic transcription from invading neighboring genes.
|
2017-04-05
|
Célia Jeronimo
|
Nicole Uwimana Pierre Collin Benjamin Haibe-Kains François Robert
|
Nucleic Acids Research
|
Genome-wide RNA-seq of iPSC-derived motor neurons indicates selective cytoskeletal perturbation in Brown-Vialetto disease that is partially rescued by riboflavin.
|
2017-04-06
|
Enrico Bertini Nereo Bresolin Andreina Bordoni
|
Federica Rizzo Agnese Ramirez Claudia Compagnucci Sabrina Salani Valentina Melzi Francesco Fortunato Alessia Niceforo Giacomo P Comi Monica Nizzardo Stefania Corti
|
Scientific Reports
|
LncATLAS database for subcellular localization of long noncoding RNAs.
|
2017-04-06
|
Roderic Guigó i Serra Antoni Hermoso Rory Johnson David Mas-Ponte Joana Carlevaro-Fita Emilio Palumbo
|
|
RNA
|
The functional genomic studies of curcumin.
|
2017-04-06
|
Lukasz B Huminiecki Horbańczuk Jarosław Olav Atanas G. Atanasov
|
|
Seminars in Cancer Biology
|
ZINB-WaVE: A general and flexible method for signal extraction from single-cell RNA-seq data
|
2017-04-06
|
Jean-Philippe Vert
|
Davide Risso Fanny Perraudeau Svetlana Gribkova Sandrine Dudoit
|
|
De novo RNA sequence assembly during in vivo inflammatory stress reveals hundreds of unannotated lincRNAs in human blood CD14+ monocytes and in adipose tissue.
|
2017-04-07
|
Muredach P. Reilly Xuan Zhang
|
Chenyi Xue Hanrui Zhang Jane F Ferguson Ying Wang Christine C Hinkle Mingyao Li
|
Physiological Genomics
|
Novel insights into systemic autoimmune rheumatic diseases using shared molecular signatures and an integrative analysis.
|
2017-04-07
|
Celia Greenwood
|
Marie Hudson Sasha Bernatsky Ines Colmegna Maximilien Lora Tomi Pastinen Kathleen Klein Oros
|
Epigenetics
|
Expression and functional assessment of candidate type 2 diabetes susceptibility genes identify four new genes contributing to human insulin secretion.
|
2017-04-08
|
Philippe Froguel Mickaël Canouil Odile Poulain-Godefroy Lorella Marselli Amar Abderrahmani Amélie Bonnefond
|
Fatou K Ndiaye Ana Ortalli Marlène Huyvaert Clara Salazar-Cardozo Cécile Lecoeur Marie Verbanck Valérie Pawlowski Raphaël Boutry Emmanuelle Durand Iandry Rabearivelo Olivier Sand Julie Kerr-Conte Vikash Chandra Raphaël Scharfmann Piero Marchetti François Pattou
|
Molecular Metabolism
|
Analysis of Purified Pancreatic Islet Beta and Alpha Cell Transcriptomes Reveals 11β-Hydroxysteroid Dehydrogenase (Hsd11b1) as a Novel Disallowed Gene.
|
2017-04-10
|
Timothy J Pullen Guy A. Rutter
|
Mark O Huising
|
Frontiers in Genetics
|
Stem Cell-Intrinsic, Seven-up-Triggered Temporal Factor Gradients Diversify Intermediate Neural Progenitors.
|
2017-04-10
|
Tzumin Lee Qingzhong Ren Ching-po Yang Zhiyong Liu Ken Sugino Kent Mok Yisheng He Masayoshi Ito Aljoscha Nern Hideo Otsuna
|
|
Current Biology
|
CRISPR/Cas9-mediated targeted gene correction in amyotrophic lateral sclerosis patient iPSCs.
|
2017-04-11
|
Juan Carlos Izpisúa Belmonte
|
Lixia Wang Fei Yi Lina Fu Jiping Yang Si Wang Zhaoxia Wang Keiichiro Suzuki Liang Sun Xiuling Xu Yang Yu Jie Qiao Ze Yang Yun Yuan Jing Qu Guang-Hui Liu
|
Protein & cell
|
A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing.
|
2017-04-11
|
Heribert Hirt
|
Runxuan Zhang Cristiane P G Calixto Yamile Marquez Peter Venhuizen Nikoleta A Tzioutziou Wenbin Guo Mark Spensley Juan Carlos Entizne Dominika Lewandowska Sara Ten Have Nicolas Frei Dit Frey Allan B James Hugh G Nimmo Andrea Barta Maria Kalyna John W S Brown
|
Nucleic Acids Research
|
Temporal, spatial, and phenotypical changes of PDGFRα expressing fibroblasts during late lung development.
|
2017-04-11
|
Mehari Endale Erik L Bao
|
Shawn Ahlfeld Xiaoting Chen Jenna Green Zach Bess Matthew T Weirauch Yan Xu Anne Karina Perl
|
Developmental Biology
|
Spicule formation in calcareous sponges: Coordinated expression of biomineralization genes and spicule-type specific genes.
|
2017-04-13
|
Oliver Voigt Maja Adamska Gert Wörheide
|
Marcin Adamski André Kittelmann Lukardis Wencker
|
Scientific Reports
|
Transcriptome analysis reveals potential mechanisms underlying differential heart development in fast- and slow-growing broilers under heat stress.
|
2017-04-13
|
Jibin Zhang Carl J Schmidt
|
Susan J Lamont
|
BMC Genomics
|
Transcriptome profiling reveals expression signatures of cranial neural crest cells arising from different axial levels.
|
2017-04-13
|
Sam Buckberry Quenten P. Schwarz
|
Rachael Lumb Genevieve Secker David Lawrence
|
BMC Developmental Biology
|
Epithelial-Mesenchymal Micro-niches Govern Stem Cell Lineage Choices.
|
2017-04-13
|
Elaine Fuchs
|
Hanseul Yang Rene C Adam Yejing Ge Zhong L Hua
|
Cell
|
Single-Cell RNA-Seq Analysis Maps Development of Human Germline Cells and Gonadal Niche Interactions.
|
2017-04-13
|
Fan Guo Jie Qiao
|
Li Li Ji Dong Liying Yan Jun Yong Xixi Liu Yuqiong Hu Xiaoying Fan Xinglong Wu Hongshan Guo Xiaoye Wang Xiaohui Zhu Rong Li Jie Yan Yuan Wei Yangyu Zhao Wei Wang Yixin Ren Peng Yuan Zhiqiang Yan Boqiang Hu Lu Wen Fuchou Tang
|
Cell Stem Cell
|
Omics and cytokine discovery in fish: Presenting the Yellowtail kingfish (Seriola lalandi) as a case study.
|
2017-04-14
|
Steve Bird Maria Forlenza
|
Gregory Jacobson Simon Muncaster Koen Mensink Nick Elliot Grant Broomfield Beth Signal
|
Developmental and Comparative Immunology
|
Reprogramming towards totipotency is greatly facilitated by synergistic effects of small molecules
|
2017-04-15
|
Kei Miyamoto John Gurdon
|
Yosuke Tajima Koki Yoshida Mami Oikawa Rika Azuma George E Allen Tomomi Tsujikawa Tomomasa Tsukaguchi Charles R Bradshaw Jerome Jullien Kazuo Yamagata Kazuya Matsumoto Masayuki Anzai Hiroshi Imai Masayasu Yamada
|
Biology Open
|
Enhanced offspring predisposition to steatohepatitis with maternal high-fat diet is associated with epigenetic and microbiome alterations
|
2017-04-17
|
Umesh Wankhade Kartik Shankar
|
Ying Zhong Ping Kang Maria Alfaro Sree V Chintapalli Keshari M Thakali
|
PLOS ONE
|
A Kinase-Independent Role for Cyclin-Dependent Kinase 19 in p53 Response.
|
2017-04-17
|
Robin Dowell
|
K Audrey Audetat Matthew D Galbraith Aaron T Odell Thomas Lee Ahwan Pandey Joaquin M Espinosa Dylan J Taatjes
|
Molecular and Cellular Biology
|
SCnorm: robust normalization of single-cell RNA-seq data.
|
2017-04-17
|
Christina Kendziorski Michael Newton Rhonda Bacher
|
Li-Fang Chu Ning Leng Audrey P Gasch James A Thomson Ron M Stewart
|
Nature Methods
|
Genome improvement of the acarbose producer Actinoplanes sp. SE50/110 and annotation refinement based on RNA-seq analysis.
|
2017-04-17
|
Susanne Schneiker-Bekel Alfred Pühler Jörn Kalinowski
|
Timo Wolf Susanne Schneiker-Bekel Armin Neshat Vera Ortseifen Daniel Wibberg Till Zemke
|
Journal of Biotechnology
|
Comprehensive Transcriptome Analyses Reveal Differential Gene Expression Profiles of Camellia sinensis Axillary Buds at Para-, Endo-, Ecodormancy, and Bud Flush Stages.
|
2017-04-18
|
Xinchao Wang
|
Xinyuan Hao Yajun Yang Chuan Yue Lu Wang David P Horvath
|
Frontiers in Plant Science
|
Reduced changes in protein compared to mRNA levels across non-proliferating tissues
|
2017-04-18
|
Karen B Avraham
|
Kobi Perl Kathy Ushakov Yair Pozniak Ofer Yizhar-Barnea Yoni Bhonker Shaked Shivatzki Tamar Geiger Ron Shamir
|
BMC Genomics
|
Prospective Isolation and Comparison of Human Germinal Matrix and Glioblastoma EGFR+ Populations with Stem Cell Properties.
|
2017-04-19
|
Roland H. Friedel Rut Tejero Robert Sebra
|
Jessica Tome-Garcia German Nudelman Raymund L Yong Huaien Wang Mary Fowkes Margret Magid Martin Walsh Violeta Silva-Vargas Elena Zaslavsky Fiona Doetsch Nadejda M Tsankova
|
Stem Cell Reports
|
LncRNA-Six1 Encodes a Micropeptide to Activate Six1 in Cis and Is Involved in Cell Proliferation and Muscle Growth.
|
2017-04-20
|
Bahareldin A Abdalla
|
Bolin Cai Zhenhui Li Manting Ma Zhijun Wang Peigong Han Qinghua Nie Xiquan Zhang
|
Frontiers in Physiology
|
Transcriptomic analysis of maternally provisioned cues for phenotypic plasticity in the annual killifish, Austrofundulus limnaeus
|
2017-04-21
|
Jason E Podrabsky
|
Amie L Romney
|
EvoDevo
|
Direct comparison of distinct naive pluripotent states in human embryonic stem cells.
|
2017-04-21
|
Dieter Deforce
|
S Warrier M Van der Jeught G Duggal L Tilleman E Sutherland J Taelman M Popovic S Lierman S Chuva De Sousa Lopes A Van Soom L Peelman F Van Nieuwerburgh D I M De Coninck B Menten P Mestdagh J Van de Sompele P De Sutter B Heindryckx
|
Nature Communications
|
Genome-Wide Investigation of Biofilm Formation in Bacillus cereus.
|
2017-04-21
|
Yun Chen
|
Fang Yan Yiyang Yu Kevin Gozzi Jian-Hua Guo Yunrong Chai
|
Applied and Environmental Microbiology
|
Whole transcriptome profiling of the human hippocampus suggests an involvement of the KIBRA rs17070145 polymorphism in differential activation of the MAPK signaling pathway.
|
2017-04-22
|
Isabelle Schrauwen Ignazio Stefano Piras Thomas G Beach
|
Jonida Krate Jason J Corneveaux Geidy E Serrano Lucia Sue Matthew J Huentelman
|
Hippocampus
|
Draft genome of the lined seahorse, Hippocampus erectus.
|
2017-04-22
|
Geng Qin Byrappa Venkatesh
|
Qiang Lin Ying Qiu Ruobo Gu Meng Xu Jia Li Chao Bian Huixian Zhang Yanhong Zhang Wei Luo Jieming Chen Xinxin You Mingjun Fan Min Sun Pao Xu Junming Xu Hongtuo Fu Qiong Shi
|
GigaScience
|
Multi-class computational evolution: development, benchmark evaluation and application to RNA-Seq biomarker discovery.
|
2017-04-24
|
Jason H. Moore
|
Nathaniel M Crabtree John F Bowyer Nysia I George
|
BioData Mining
|
IL-10 improves cardiac remodeling after myocardial infarction by stimulating M2 macrophage polarization and fibroblast activation.
|
2017-04-24
|
Merry L. Lindsey Andriy Yabluchanskiy
|
Mira Jung Yonggang Ma Rugmani Padmanabhan Iyer Kristine Y DeLeon-Pennell Michael R Garrett
|
Basic Research in Cardiology
|
Next-Generation Sequencing Analysis and Algorithms for PDX and CDX Models.
|
2017-04-25
|
Crispin J. Miller Caroline Dive
|
Garima Khandelwal María Romina Girotti Christopher Smowton Sam Taylor Christopher Wirth Marek Dynowski Kristopher K Frese Ged Brady Richard Marais
|
Molecular Cancer Research
|
Effects of RNA integrity on transcript quantification by total RNA sequencing of clinically collected human placental samples.
|
2017-04-26
|
Maris Laan Kristiina Rull Siim Sõber
|
Mario Reiman
|
FASEB Journal
|
Poly(A)-ClickSeq: click-chemistry for next-generation 3΄-end sequencing without RNA enrichment or fragmentation.
|
2017-04-26
|
Andrew Routh
|
Ping Ji Elizabeth Jaworski Zheng Xia Wei Li Eric J Wagner
|
Nucleic Acids Research
|
Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways
|
2017-04-27
|
Lior Pachter Harold Pimentel Lynn Yi
|
|
PLOS ONE
|
miRNA-mRNA network involved in folliculogenesis interactome: systems biology approach.
|
2017-04-27
|
Ali Najafi
|
Abolfazl Bahrami Seyed Reza Miraie-Ashtiani Mostafa Sadeghi
|
Reproduction
|
Assessment of engineered cells using CellNet and RNA-seq.
|
2017-04-27
|
Patrick Cahan
|
Arthur H Radley Remy M Schwab Yuqi Tan Jeesoo Kim Emily K W Lo
|
Nature Protocols
|
Signal Transductions of BEAS-2B Cells in Response to Carcinogenic PM2.5 Exposure Based on a Microfluidic System.
|
2017-04-27
|
Jian Xu
|
Lulu Zheng Sixiu Liu Guoshun Zhuang Qi Liu Xinlian Zhang Congrui Deng Zhigang Guo Wang Zhao Tingna Liu Yiqi Wang Yuxiao Zhang Jing Lin Qiongzhen Wang Guodong Sui
|
Analytical Chemistry
|
Altered nucleocytoplasmic proteome and transcriptome distributions in an in vitro model of amyotrophic lateral sclerosis
|
2017-04-28
|
Jong-Il Kim
|
Jee-Eun Kim Yoon Ho Hong Jin Young Kim Gye Sun Jeon Jung Hee Jung Byung-Nam Yoon Sung-Yeon Son Kwang-Woo Lee Jung-Joon Sung
|
PLOS ONE
|
The Distinct Transcriptional Response of the Midgut of Amblyomma sculptum and Amblyomma aureolatum Ticks to Rickettsia rickettsii Correlates to Their Differences in Susceptibility to Infection
|
2017-04-28
|
Andréa C Fogaça Sirlei Daffre Marcelo B. Labruna
|
Larissa A Martins Maria F B de Melo Galletti José M Ribeiro André Fujita Francisco B Costa
|
Frontiers in cellular and infection microbiology
|
The landscape of BRAF transcript and protein variants in human cancer.
|
2017-04-28
|
Letizia Pitto Alberto Mercatanti Simone Lubrano Giovanni Signore Monica Evangelista Giorgio Cozza Laura Poliseno
|
Andrea Marranci Zhijie Jiang Marianna Vitiello Elena Guzzolino Laura Comelli Samanta Sarti Cinzia Franchin Ileabett Echevarría-Vargas Andrea Tuccoli Paolo Sportoletti Ettore Luzi Enrico Capobianco Jessie Villanueva Giorgio Arrigoni Silvia Rocchiccioli Nicholas Tsinoremas
|
Molecular Cancer
|
Gene length and detection bias in single cell RNA sequencing protocols.
|
2017-04-28
|
Alicia Oshlack Luke Zappia Belinda Phipson
|
|
F1000Research
|
Exercise-induced modification of the skeletal muscle transcriptome in Arabian horses.
|
2017-04-28
|
Katarzyna Ropka-Molik Katarzyna Piórkowska
|
Monika Stefaniuk-Szmukier Kacper Z Ukowski Monika Bugno-Poniewierska
|
Physiological Genomics
|
550. Delineating Transcriptomic Profiles in PTSD: An RNAseq Investigation
|
2017-05
|
Sian Hemmings Soraya Seedat
|
Laetitia Dicks Mahjoubeh Jalali Junaid Gamieldien Leigh vd Heuvel
|
Biological Psychiatry
|
High-Resolution RNA Maps Suggest Common Principles of Splicing and Polyadenylation Regulation by TDP-43.
|
2017-05-01
|
Tomaž Curk Ina Huppertz Miha Modic Christian von Mering Jernej Ule
|
Gregor Rot Zhen Wang Tina Lenče Martina Hallegger Nejc Haberman
|
Cell Reports
|
Optimized approach for Ion Proton RNA sequencing reveals details of RNA splicing and editing features of the transcriptome
|
2017-05-01
|
Scott Ness
|
Roger B Brown Nathaniel J Madrid Hideaki Suzuki
|
PLOS ONE
|
A comparison of per sample global scaling and per gene normalization methods for differential expression analysis of RNA-seq data.
|
2017-05-01
|
Xiaohong Li Guy Brock
|
Eric C Rouchka Nigel G F Cooper Dongfeng Wu Timothy E O'Toole Ryan S Gill Abdallah M Eteleeb Liz O'Brien Shesh N Rai
|
PLOS ONE
|
Large-Scale Analysis of Loss of Imprinting in Human Pluripotent Stem Cells.
|
2017-05-01
|
Nissim Benvenisty
|
Shiran Bar Maya Schachter Talia Eldar-Geva
|
Cell Reports
|
Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development.
|
2017-05-01
|
Tom Maniatis Raul Rabadan
|
Abbas H Rizvi Pablo G Camara Elena K Kandror Thomas J Roberts Ira Schieren
|
Nature Biotechnology
|
Conditional knockin of Dnmt3a R878H initiates acute myeloid leukemia with mTOR pathway involvement.
|
2017-05-01
|
Yue-Ying Wang
|
Yu-Jun Dai Jin-Yan Huang Li Xia Xiao-Dong Shi Jie Xu Jing Lu Xian-Bin Su Ying Yang Wei-Na Zhang Pan-Pan Wang Song-Fang Wu Ting Huang Jian-Qing Mi Ze-Guang Han Zhu Chen Sai-Juan Chen
|
Proceedings of the National Academy of Sciences of the United States of America
|
Genomic Characterization of Murine Monocytes Reveals C/EBPβ Transcription Factor Dependence of Ly6C- Cells.
|
2017-05-01
|
Achim Leutz Franziska Paul Alexander Mildner Steffen Jung Josef Priller
|
Jörg Schönheit Amir Giladi Eyal David David Lara-Astiaso Erika Lorenzo-Vivas Louise Chappell-Maor Ido Amit
|
Immunity
|
Integrating Results across Methodologies Is Essential for Producing Robust Neuronal Taxonomies.
|
2017-05-01
|
Mark S Cembrowski Nelson Spruston
|
|
Neuron
|
HAND2 Target Gene Regulatory Networks Control Atrioventricular Canal and Cardiac Valve Development.
|
2017-05-01
|
Javier Lopez-Rios Marco Osterwalder Aimée Zuniga Rolf Zeller
|
Frédéric Laurent Ausra Girdziusaite Julie Gamart Iros Barozzi Jennifer A Akiyama Joy Lincoln
|
Cell Reports
|
Neurons and neuronal activity control gene expression in astrocytes to regulate their development and metabolism.
|
2017-05-02
|
Alison C Todd Owen Dando Roser Masgrau Elena Galea David J Wyllie Giles E. Hardingham Siddharthan Chandran Abel Eraso-Pichot
|
Philip Hasel Zoeb Jiwaji Paul Baxter Samuel Heron Nóra M Márkus Jamie McQueen David W Hampton Megan Torvell Sachin S Tiwari Sean McKay Antonio Zorzano T Ian Simpson
|
Nature Communications
|
Power analysis for RNA-Seq differential expression studies.
|
2017-05-03
|
Guy Brock
|
Lianbo Yu Soledad Fernandez
|
BMC Bioinformatics
|
Vitamin A-Retinoic Acid Signaling Regulates Hematopoietic Stem Cell Dormancy.
|
2017-05-03
|
Michael A Rieger Oliver Stegle Timm Schroeder Andreas Trumpp
|
Nina Cabezas-Wallscheid Florian Buettner Pia Sommerkamp Daniel Klimmeck Luisa Ladel Frederic B Thalheimer Daniel Pastor-Flores Leticia P Roma Simon Renders Petra Zeisberger Adriana Przybylla Katharina Schönberger Roberta Scognamiglio Sandro Altamura Carolina M Florian Malak Fawaz Dominik Vonficht Melania Tesio Paul Collier Dinko Pavlinic Hartmut Geiger Vladimir Benes Tobias P Dick
|
Cell
|
Transcriptome-wide analysis of jasmonate-treated BY-2 cells reveals new transcriptional regulators associated with alkaloid formation in tobacco.
|
2017-05-04
|
Michael P. Timko
|
Yuping Yang Pengcheng Yan Che Yi Wenzheng Li Yuhui Chai Lingling Fei Ping Gao Heping Zhao Yingdian Wang Bingwu Wang Shengcheng Han
|
The Journal of Plant Physiology
|
Gene expression profiling in Pekin duck embryonic breast muscle.
|
2017-05-04
|
Kyle Schachtschneider
|
Tie-Shan Xu Li-Hong Gu Wei Huang Wan-Liang Xia Yun-Sheng Zhang Ya-Ge Zhang Guang Rong Shui-Sheng Hou
|
PLOS ONE
|
Rice Expression Database (RED): An integrated RNA-Seq-derived gene expression database for rice.
|
2017-05-04
|
Zhang Zhang
|
Lin Xia Dong Zou Jian Sang Xingjian Xu Hongyan Yin Mengwei Li Shuangyang Wu Songnian Hu Lili Hao
|
Journal of Genetics and Genomics
|
Age, gender and UV-exposition related effects on gene expression in in vivo aged short term cultivated human dermal fibroblasts
|
2017-05-05
|
Wolfgang Kaisers
|
Petra Boukamp Hans-Jürgen Stark Holger Schwender Julia Tigges Jean Krutmann Heiner Schaal
|
PLOS ONE
|
Connective Tissue Growth Factor Promotes Efficient Generation of Human Induced Pluripotent Stem Cell-Derived Choroidal Endothelium.
|
2017-05-05
|
Budd A. Tucker Kristan S Worthington Robert F. Mullins Edwin M. Stone
|
Allison E Songstad Kathleen R Chirco Joseph C Giacalone S Scott Whitmore Kristin R Anfinson Dalyz Ochoa Cathryn M Cranston Megan J Riker Maurine Neiman
|
Stem Cells Translational Medicine
|
Effects of cold-acclimation on gene expression in Fall field cricket (Gryllus pennsylvanicus) ionoregulatory tissues
|
2017-05-08
|
Brent J Sinclair
|
Lauren E Des Marteaux Alexander H McKinnon Hiroko Udaka Jantina Toxopeus
|
BMC Genomics
|
Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production
|
2017-05-08
|
Sabeeha Merchant Matteo Pellegrini Sean D Gallaher Melissa S Roth
|
Shawn J Cokus Andreas Walter David Lopez Erika Erickson Benjamin Endelman Daniel Westcott Carolyn A Larabell Krishna K Niyogi
|
Proceedings of the National Academy of Sciences of the United States of America
|
Characterization of joining sites of a viral histone H4 on host insect chromosomes
|
2017-05-09
|
Yonggyun Kim
|
Sunil Kumar Jin-Kyo Jung
|
PLOS ONE
|
iTRAQ and RNA-Seq Analyses Provide New Insights into Regulation Mechanism of Symbiotic Germination of Dendrobium officinale Seeds (Orchidaceae).
|
2017-05-10
|
Annegret Kohler
|
Juan Chen Si Si Liu Bo Yan Hong Mei Luo Xiao Mei Chen Shun Xing Guo
|
Journal of Proteome Research
|
Protein-only RNase P function in Escherichia coli: viability, processing defects and differences between PRORP isoenzymes.
|
2017-05-11
|
Roland Hartmann
|
Markus Gößringer Marcus Lechner Nadia Brillante Christoph Weber Walter Rossmanith
|
Nucleic Acids Research
|
Alternative TSSs are co-regulated in single cells in the mouse brain.
|
2017-05-11
|
Sten Linnarsson Peter Lönnerberg
|
Kasper Karlsson
|
Molecular Systems Biology
|
The core transcriptome of mammalian placentas and the divergence of expression with placental shape.
|
2017-05-12
|
Eviatar Nevo Don L Armstrong Roberto Romero
|
Michael R McGowen Amy Weckle Priyadarshini Pantham Jason Caravas Dalen Agnew Kurt Benirschke Sue Savage-Rumbaugh Chong J Kim Günter P Wagner Derek E Wildman
|
Placenta
|
RNA-seq analyses reveal that cervical spinal cords and anterior motor neurons from amyotrophic lateral sclerosis subjects show reduced expression of mitochondrial DNA-encoded respiratory genes, and rhTFAM may correct this respiratory deficiency.
|
2017-05-13
|
Nicholas J Tustison
|
Amy C Ladd David G Brohawn Ravindar R Thomas Paula M Keeney Stuart S Berr Shaharyar M Khan Francisco R Portell Meiram Zh Shakenov Patrick F Antkowiak Bijoy Kundu James P Bennett
|
Brain Research
|
Sexual Dimorphism and Retinal Mosaic Diversification Following the Evolution of a Violet Receptor in Butterflies.
|
2017-05-15
|
Adriana Briscoe Peter Andolfatto
|
Kyle J McCulloch Furong Yuan Ying Zhen Matthew L Aardema Gilbert Smith Jorge Llorente-Bousquets
|
Molecular Biology and Evolution
|
A computational approach for the functional classification of the epigenome.
|
2017-05-15
|
Anna Tramontano
|
Francesco Gandolfi
|
Epigenetics & Chromatin
|
Elevated PTTG and PBF predicts poor patient outcome and modulates DNA damage response genes in thyroid cancer.
|
2017-05-15
|
Martin L. Read
|
J C Fong B Modasia A Fletcher W Imruetaicharoenchoke R J Thompson H Nieto J J Reynolds A Bacon U Mallick A Hackshaw J C Watkinson K Boelaert A S Turnell C J McCabe
|
Oncogene
|
Isolation of tissues and preservation of RNA from intact, germinated barley grain.
|
2017-05-16
|
Oliver Berkowitz Natalie Betts Ruijie Liu Rachel A Burton James Whelan
|
Helen M Collins Birgitte Skadhauge Christoph Dockter Geoffrey B Fincher
|
The Plant Journal
|
Identification of human short introns.
|
2017-05-17
|
Syed H Ali
|
Emmanuel L Abebrese Zachary R Arnold Victoria M Andrews Katharine Armstrong Lindsay Burns Hannah R Crowder R Thomas Day Daniel G Hsu Katherine Jarrell Grace Lee Yi Luo Daphine Mugayo Zain Raza Kyle Friend
|
PLOS ONE
|
A Generalized Linear Model for Decomposing Cis-regulatory, Parent-of-Origin, and Maternal Effects on Allele-Specific Gene Expression
|
2017-05-17
|
Naoki Osada Aya Takahashi
|
Yasuaki Takada Ryutaro Miyagi Toshinori Endo
|
G3
|
Transcriptomics technologies.
|
2017-05-18
|
Thomas Shafee Rohan Lowe Mark Bleackley Neil Shirley
|
Stephen Dolan
|
PLOS Computational Biology
|
Cell fixation and preservation for droplet-based single-cell transcriptomics.
|
2017-05-19
|
Nikolaus Rajewsky Philipp Wahle Salah Ayoub Robert P Zinzen
|
Jonathan Alles Nikos Karaiskos Samantha D Praktiknjo Stefanie Grosswendt Pierre-Louis Ruffault Luisa Schreyer Anastasiya Boltengagen Carmen Birchmeier Christine Kocks
|
BMC Biology
|
An analysis of MyoD-dependent transcription using CRISPR/Cas9 gene targeting in Xenopus tropicalis embryos.
|
2017-05-20
|
Caitlin McQueen Mary E. Pownall
|
|
Mechanisms of Development
|
The Atypical Response Regulator AtvR Is a New Player in Pseudomonas aeruginosa Response to Hypoxia and Virulence.
|
2017-05-22
|
Regina L Baldini
|
Gilberto Hideo Kaihami Leandro Carvalho Dantas Breda José Roberto Fogaça de Almeida Thays de Oliveira Pereira Gianlucca Gonçalves Nicastro Ana Laura Boechat Sandro Rogério de Almeida
|
Infection and Immunity
|
N-of-1-pathways MixEnrich: advancing precision medicine via single-subject analysis in discovering dynamic changes of transcriptomes.
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2017-05-24
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Haiquan Li Vincent Gardeux Joanne Berghout Yves A. Lussier A. Grant Schissler
|
Qike Li Ikbel Achour Colleen Kenost Hao Helen Zhang
|
BMC Medical Genomics
|
Krüppel-like factors compete for promoters and enhancers to fine-tune transcription.
|
2017-05-24
|
Timothy L. Bailey Melissa D Ilsley Stephen Huang Kevin R Gillinder Merlin Crossley Andrew C Perkins
|
Graham W Magor
|
Nucleic Acids Research
|
scImpute: Accurate And Robust Imputation For Single Cell RNA-Seq Data
|
2017-05-24
|
Jingyi Jessica Li
|
Wei Vivian Li
|
|
Type 2 diabetes and obesity induce similar transcriptional reprogramming in human myocytes
|
2017-05-25
|
Jens Nielsen Bente Klarlund Pedersen Mathias Uhlén Leif Väremo Camilla Scheele Tora Henriksen
|
Christa Broholm Maria Pedersen
|
Genome Medicine
|
ROTS: An R package for reproducibility-optimized statistical testing
|
2017-05-25
|
Laura L. Elo Tomi Suomi
|
Fatemeh Seyednasrollah Maria K Jaakkola Thomas Faux
|
PLOS Computational Biology
|
The identification of switch-like alternative splicing exons among multiple samples with RNA-Seq data.
|
2017-05-25
|
Xuegong Zhang
|
Zhiyi Qin
|
PLOS ONE
|
No counts, no variance: allowing for loss of degrees of freedom when assessing biological variability from RNA-seq data.
|
2017-05-25
|
Gordon K Smyth
|
Aaron T L Lun Gordon K Smyth
|
Statistical Applications in Genetics and Molecular Biology
|
Cholinergic neuron gene expression differences captured by translational profiling in a mouse model of Alzheimer's disease.
|
2017-05-25
|
Andrew R. Hesketh Peter Henry St George-Hyslop
|
Paul M McKeever TaeHyung Kim Laura MacNair Denise Miletic Giorgio Favrin Stephen G Oliver Zhaolei Zhang Janice Robertson
|
Neurobiology of Aging
|
Contribution of systemic and somatic factors to clinical response and resistance to PD-L1 blockade in urothelial cancer: An exploratory multi-omic analysis.
|
2017-05-26
|
Tavi Nathanson Eliza J Chang Samuel Funt Jacqueline L. Buros Bülent Arman Aksoy
|
Alexandra Snyder Arun Ahuja Matthew D Hellmann Hikmat Al-Ahmadie Erik Yusko Marissa Vignali Sharon Benzeno Mariel Boyd Meredith Moran Gopa Iyer Harlan S Robins Elaine R Mardis Taha Merghoub Jeff Hammerbacher Jonathan E Rosenberg Dean F Bajorin
|
PLOS Medicine
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RNAseq Reveals Complex Response of Campylobacter jejuni to Ovine Bile and In vivo Gallbladder Environment.
|
2017-05-29
|
Qijing Zhang
|
Amanda J Kreuder Jennifer A Schleining Michael Yaeger Paul J Plummer
|
Frontiers in Microbiology
|
Accurate characterization of the IFITM locus using MiSeq and PacBio sequencing shows genetic variation in Galliformes
|
2017-05-30
|
Paul Kellam Nathan Lawless Swee Hoe Ong
|
Irene Bassano Thomas Whitehead Mark Fife
|
BMC Genomics
|
The common transcriptional subnetworks of the grape berry skin in the late stages of ripening
|
2017-05-30
|
Karen Schlauch Richard L. Tillett David Toubiana Grant Cramer
|
Ryan Ghan Juli Petereit Aaron Fait
|
BMC Plant Biology
|
Biphasic Metabolism and Host Interaction of a Chlamydial Symbiont
|
2017-05-30
|
Cecilia Wentrup
|
Lena König Alexander Siegl Thomas Penz Susanne Haider Julia Polzin Evelyne Mann Stephan Schmitz-Esser Daryl Domman Matthias Horn
|
mSystems
|
RNA-seq reveals conservation of function among the yolk sacs of human, mouse, and chicken.
|
2017-05-30
|
Sungsam Gong Michael G Elliot
|
Tereza Cindrova-Davies Eric Jauniaux Graham J Burton D Stephen Charnock-Jones
|
Proceedings of the National Academy of Sciences of the United States of America
|
Pervasive yet nonuniform contributions of Dcp2 and Cnot7 to maternal mRNA clearance in zebrafish.
|
2017-05-30
|
Yuichiro Mishima
|
Yukihide Tomari
|
Genes to Cells
|
Reprint of: MicroRNA profiling of human intermediate monocytes.
|
2017-05-31
|
Loems Ziegler-Heitbrock
|
Adam M Zawada Lu Zhang Insa E Emrich Kyrill S Rogacev Nicolas Krezdorn Björn Rotter Danilo Fliser Yvan Devaux Loems Ziegler-Heitbrock Gunnar H Heine
|
Immunobiology
|
Revealing allele-specific gene expression by single-cell transcriptomics.
|
2017-05-31
|
Qiaolin Deng
|
Julio Aguila Benitez Shangli Cheng
|
International Journal of Biochemistry & Cell Biology
|
Genome-Wide Target Analyses of Otx2 Homeoprotein in Postnatal Cortex
|
2017-05-31
|
Ryuichiro Nakato Katsuhiko Shirahige
|
Akiko Sakai Yiwei Ling Xubin Hou Norikazu Hara Tomoya Iijima Yuchio Yanagawa Ryozo Kuwano Shujiro Okuda Sayaka Sugiyama
|
Frontiers in Neuroscience
|
Large-scale genomic analyses of in vitro yeast-mycelium dimorphism in human, insect and plant pathogenic fungi: From ESTs to RNAseq experiments
|
2017-06
|
Louis Bernier
|
M. Nigg
|
Fungal Biology Reviews
|
Ly6Chi Monocytes and Their Macrophage Descendants Regulate Neutrophil Function and Clearance in Acetaminophen-Induced Liver Injury.
|
2017-06-01
|
Metsada Pasmanik-Chor Steffen Jung
|
Nadine Graubardt Milena Vugman Odelia Mouhadeb Gabriele Caliari Metsada Pasmanik-Chor Debby Reuveni Ehud Zigmond Eli Brazowski Eyal David Lousie Chappell-Maor Chen Varol
|
Frontiers in Immunology
|
Reconstructing the suberin pathway in poplar by chemical and transcriptomic analysis of bark tissues.
|
2017-06-01
|
Isabel Molina
|
Meghan K Rains Nayana Dilini Gardiyehewa de Silva
|
Tree Physiology
|
Single-cell entropy for accurate estimation of differentiation potency from a cell's transcriptome
|
2017-06-01
|
Tariq Enver
|
Andrew E Teschendorff
|
Nature Communications
|
IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment.
|
2017-06-01
|
Aviv Regev Itay Tirosh Olga Troyanskaya Alex K. Shalek Niroshana Anandasabapathy Michelle A Lowes Tae-Gyun Kim
|
Christopher J Nirschl Mayte Suárez-Fariñas Benjamin Izar Sanjay Prakadan Ruth Dannenfelser Itay Tirosh Yong Liu Qian Zhu K Sanjana P Devi Shaina L Carroll David Chau Melika Rezaee Ruiqi Huang Judilyn Fuentes-Duculan George X Song-Zhao Nicholas Gulati Sandra L King Francisco J Quintana Young-Suk Lee James G Krueger Kavita Y Sarin Charles H Yoon Levi Garraway
|
Cell
|
Single-Cell RNA-Seq Analysis Maps Development of Human Germline Cells and Gonadal Niche Interactions.
|
2017-06-01
|
Jie Qiao
|
Li Li Ji Dong Liying Yan Jun Yong Xixi Liu Yuqiong Hu Xiaoying Fan Xinglong Wu Hongshan Guo Xiaoye Wang Xiaohui Zhu Rong Li Jie Yan Yuan Wei Yangyu Zhao Wei Wang Yixin Ren Peng Yuan Zhiqiang Yan Boqiang Hu Fan Guo Lu Wen Fuchou Tang
|
Cell Stem Cell
|
Gene and metabolite time-course response to cigarette smoking in mouse lung and plasma.
|
2017-06-02
|
Charmion I Cruickshank-Quinn Thomas Danhorn
|
Mikaela A Miller Sonia M Leach Sean Jacobson Matthew J Strand Nichole A Reisdorph Russell P Bowler Irina Petrache Katerina Kechris
|
PLOS ONE
|
Bcl11b and combinatorial resolution of cell fate in the T-cell gene regulatory network.
|
2017-06-05
|
Ellen V. Rothenberg Maile Romero-Wolf Hiroyuki Hosokawa
|
William J R Longabaugh Weihua Zeng Jingli A Zhang Camden S Jansen Long Li Pentao Liu Hao Yuan Kueh Ali Mortazavi
|
Proceedings of the National Academy of Sciences of the United States of America
|
lncRNA-screen: an interactive platform for computationally screening long non-coding RNAs in large genomics datasets.
|
2017-06-05
|
Aristotelis Tsirigos
|
Yixiao Gong Hsuan-Ting Huang Yu Liang Thomas Trimarchi Iannis Aifantis
|
BMC Genomics
|
Analysis of aquaporins in Brassicaceae species reveals high-level of conservation and dynamic role against biotic and abiotic stress in canola.
|
2017-06-05
|
Humira Sonah Rupesh K. Deshmukh
|
Caroline Labbé Richard R Bélanger
|
Scientific Reports
|
The Landscape of Isoform Switches in Human Cancers.
|
2017-06-05
|
Kristoffer Vitting-Seerup Albin Sandelin
|
|
Molecular Cancer Research
|
DNA methylation variations are required for epithelial-to-mesenchymal transition induced by cancer-associated fibroblasts in prostate cancer cells.
|
2017-06-05
|
Mattia Pelizzola Monica Mancini Kamal Kishore Nora Sahnane Giorgio Giurato Alessandro Weisz
|
C Pistore E Giannoni T Colangelo F Rizzo E Magnani L Muccillo S Rizzo M Riccardi V Del Vescovo M Mandruzzato F Macchi M A Denti D Furlan V Colantuoni P Chiarugi I M Bonapace
|
Oncogene
|
Differential analysis of RNA-seq incorporating quantification uncertainty.
|
2017-06-05
|
Páll Melsted
|
Harold Pimentel Nicolas L Bray Suzette Puente Lior Pachter
|
Nature Methods
|
RNA sequencing and transcriptome arrays analyses show opposing results for alternative splicing in patient derived samples
|
2017-06-06
|
Gunnar Dittmar
|
Petr V Nazarov Arnaud Muller Tony Kaoma Nathalie Nicot Cristina Maximo Philippe Birembaut Nhan L Tran Laurent Vallar
|
BMC Genomics
|
RNA-Seq and metabolic flux analysis of Tetraselmis sp. M8 during nitrogen starvation reveals a two-stage lipid accumulation mechanism.
|
2017-06-06
|
Jacqueline Batley Felipe Aguilera David Edwards
|
David K Y Lim Holger Schuhmann Skye R Thomas-Hall Kenneth C K Chan Taylor J Wass T Catalina Adarme-Vega Cristiana G O Dal'Molin Glen J Thorpe Peer M Schenk
|
Bioresource Technology
|
A Unique Microglia Type Associated with Restricting Development of Alzheimer's Disease.
|
2017-06-07
|
Hadas Keren-Shaul Orit Matcovitch-Natan
|
Hadas Keren-Shaul Amit Spinrad Assaf Weiner Orit Matcovitch-Natan Raz Dvir-Szternfeld Tyler K Ulland Eyal David Kuti Baruch David Lara-Astaiso Beata Toth Shalev Itzkovitz Marco Colonna Michal Schwartz Ido Amit
|
Cell
|
Dataset on transcriptional profiles and the developmental characteristics of PDGFRα expressing lung fibroblasts.
|
2017-06-07
|
Mehari Endale
|
Shawn Ahlfeld Erik Bao Xiaoting Chen Jenna Green Zach Bess Matthew Weirauch Yan Xu Anne Karina Perl
|
Data in Brief
|
Immunoglobulin characteristics and RNAseq data of FcRL4+ B cells sorted from synovial fluid and tissue of patients with rheumatoid arthritis.
|
2017-06-07
|
Daniel Ramsköld Caroline Grönwall Vivianne Malmström
|
Khaled Amara Elizabeth Clay Lorraine Yeo Julia Spengler Natalie Sippl James Cameron Lena Israelsson Philip J Titcombe Ilfita Sahbudin Andrew Filer Karim Raza Dagmar Scheel-Toellner
|
Data in Brief
|
Divergent roles of the Drosophila melanogaster globins.
|
2017-06-09
|
Thorsten Burmester
|
Agnes Wawrowski Ines Diepenbruck Katharina Schrick Nina Seiwert Fabian Ripp Andreas Prothmann Thomas Hankeln
|
Journal of Insect Physiology
|
A Novel In Vitro Human Granuloma Model of Sarcoidosis and Latent TB Infection.
|
2017-06-09
|
Peter White Wolfgang Sadee
|
Elliott D Crouser Evelyn Guirado Caceres Mark W Julian Audrey C Papp Landon W Locke Larry S Schlesinger
|
American Journal of Respiratory Cell and Molecular Biology
|
Use of Angiotensin System Inhibitors Is Associated with Immune Activation and Longer Survival in Nonmetastatic Pancreatic Ductal Adenocarcinoma.
|
2017-06-09
|
Kohei Shigeta Kamila Naxerova Ronald M. Evans
|
Hao Liu Matthias Pinter Joao Incio Hang Lee William W Ho Jonathan A Crain Alex Jacobson Theodoros Michelakos Daniella Dias-Santos Andrea Zanconato Theodore S Hong Jeffrey W Clark Janet E Murphy David P Ryan Vikram Deshpande Keith D Lillemoe Carlos Fernandez-Del Castillo Michael Downes James Michaelson Cristina R Ferrone Yves Boucher Rakesh K Jain
|
Clinical Cancer Research
|
Gaining insights from RNA-Seq data using iDEP
|
2017-06-09
|
Steven Ge
|
Eun Wo Son
|
|
The Model-Based Study of the Effectiveness of Reporting Lists of Small Feature Sets Using RNA-Seq Data
|
2017-06-12
|
Edward R. Dougherty
|
Eunji Kim Ivan Ivanov Jianping Hua Johanna W Lampe Meredith Aj Hullar Robert S Chapkin
|
Cancer Informatics
|
Genome-wide analysis of gene expression and protein secretion of Babesia canis during virulent infection identifies potential pathogenicity factors.
|
2017-06-13
|
Peter Deplazes Adrian B. Hehl Ramon M. Eichenberger
|
Chandra Ramakrishnan Giancarlo Russo
|
Scientific Reports
|
Optimized Method for Robust Transcriptome Profiling of Minute Tissues Using Laser Capture Microdissection and Low-Input RNA-Seq.
|
2017-06-13
|
James M Ward Shannon Farris Serena M. Dudek
|
Yu Wang
|
Frontiers in molecular neuroscience
|
Integration of quantitated expression estimates from polyA-selected and rRNA-depleted RNA-seq libraries
|
2017-06-13
|
Stephen J Bush David A Hume Kim M Summers
|
Mary E B McCulloch Emily L Clark
|
BMC Bioinformatics
|
The Transcription Factor T-bet Limits Amplification of Type I IFN Transcriptome and Circuitry in T Helper 1 Cells.
|
2017-06-13
|
Yohei Mikami Han-Yu Shih Toshinori Nakayama
|
Shigeru Iwata Hong-Wei Sun Stephen R Brooks Dragana Jankovic Kiyoshi Hirahara Atsushi Onodera Takeshi Kawabe Kan Jiang Alan Sher John J O'Shea Fred P Davis Yuka Kanno
|
Immunity
|
Correspondence on Lovell et al.: identification of chicken genes previously assumed to be evolutionarily lost.
|
2017-06-14
|
Susanne Bornelöv Miriam Friedman-Einat
|
Susanne Bornelöv Eyal Seroussi Sara Yosefi Ken Pendavis Shane C Burgess Manfred Grabherr Leif Andersson
|
Genome Biology
|
Pseudogymnoascus destructans transcriptome changes during white-nose syndrome infections.
|
2017-06-14
|
Jonathan M. Palmer Kenneth A Field
|
Sophia M Reeder Jenni M Prokkola Thomas M Lilley DeeAnn M Reeder
|
Virulence
|
MicroRNAs control mRNA fate by compartmentalization based on 3' UTR length in male germ cells.
|
2017-06-15
|
Wei Yan Chong Tang Huili Zheng
|
Ying Zhang Chong Tang Tian Yu Ruirui Zhang
|
Genome Biology
|
Insufficient antibody validation challenges oestrogen receptor beta research.
|
2017-06-15
|
Ola Söderberg
|
Sandra Andersson Mårten Sundberg Nusa Pristovsek Ahmed Ibrahim Philip Jonsson Borbala Katona Carl-Magnus Clausson Agata Zieba Margareta Ramström Cecilia Williams Anna Asplund
|
Nature Communications
|
Supplementation with small-extracellular vesicles from ovarian follicular fluid during in vitro production modulates bovine embryo development
|
2017-06-15
|
Rafael Vilar Sampaio Felipe Perecin Rinaldo Wellerson Pereira Luiz L Coutinho
|
Juliano C da Silveira Gabriella M Andrade Maite Del Collado Juliano R Sangalli Luciano A Silva Fábio V L Pinaffi Izabelle B Jardim Marcelo C Cesar Marcelo F G Nogueira Aline S M Cesar Flávio V Meirelles
|
PLOS ONE
|
RNA-seq implicates deregulation of the immune system in the pathogenesis of diverticulitis.
|
2017-06-15
|
Kathleen M. Schieffer
|
Christine S Choi Scott Emrich Leonard Harris Sue Deiling Dipti M Karamchandani Anna Salzberg Yuka I Kawasawa Gregory S Yochum Walter A Koltun
|
American Journal of Physiology - Gastrointestinal and Liver Physiology
|
Transcriptomic Profiling in Human Decidua of Severe Preeclampsia Detected by RNA Sequencing.
|
2017-06-15
|
Zi-Jiang Chen
|
Jing Tong Weixiu Zhao Hong Lv Wei-Ping Li Cong Zhang
|
Journal of Cellular Biochemistry
|
Multiplexed Spliced-Leader Sequencing: A high-throughput, selective method for RNA-seq in Trypanosomatids.
|
2017-06-16
|
Peter J. Myler Franck Dumetz Bart Cuypers Manu Vanaerschot Hideo Imamura Pieter Meysman Kris Laukens
|
Malgorzata A Domagalska Géraldine de Muylder Thomas Wolf Verdonckt Gowthaman Ramasamy Jean-Claude Dujardin
|
Scientific Reports
|
Characterization of slow cycling corneal limbal epithelial cells identifies putative stem cell markers.
|
2017-06-19
|
Chao Zhang
|
R Sartaj P Wan Z Pasha V Guaiquil A Liu J Liu Y Luo E Fuchs M I Rosenblatt
|
Scientific Reports
|
Evaluation and improvement of the regulatory inference for large co-expression networks with limited sample size.
|
2017-06-19
|
Robbie Waugh
|
Wenbin Guo Cristiane P G Calixto Nikoleta Tzioutziou Ping Lin John W S Brown Runxuan Zhang
|
BMC Systems Biology
|
Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome.
|
2017-06-19
|
Timothy W Yu Stefan Wiemann Ganeshwaran H Mochida
|
Gilad D Evrony Dwight R Cordero Jun Shen Jennifer N Partlow Rachel E Rodin R Sean Hill Michael E Coulter Anh-Thu N Lam Divya Jayaraman Dianne Gerrelli Diana G Diaz Chloe Santos Victoria Morrison Antonella Galli Ulrich Tschulena M Jocelyne Martel Betty Spooner Steven C Ryu Princess C Elhosary Jillian M Richardson Danielle Tierney Christopher A Robinson Rajni Chibbar Dana Diudea Rebecca Folkerth Sheldon Wiebe A James Barkovich James Irvine Edmond G Lemire Patricia Blakley Christopher A Walsh
|
Genome Research
|
qSVA framework for RNA quality correction in differential expression analysis
|
2017-06-20
|
Daniel R. Weinberger Andrew E Jaffe Jeffrey T. Leek Abhinav Nellore
|
Ran Tao Alexis L Norris Marc Kealhofer Joo Heon Shin Dewey Kim Yankai Jia Thomas M Hyde Joel E Kleinman Richard E Straub
|
Proceedings of the National Academy of Sciences of the United States of America
|
The RNA-seq analysis suggests a potential multi-component complement system in oyster Crassostrea gigas.
|
2017-06-20
|
Linsheng Song Hao Wang
|
Lingling Wang Huan Zhang Leilei Wang Daoxiang Zhang Zhao Lv Zhaoqun Liu Weilin Wang Zhi Zhou Limei Qiu Jun Li
|
Developmental and Comparative Immunology
|
Identification of Putative Transmembrane Proteins Involved in Salinity Tolerance in Chenopodium quinoa by Integrating Physiological Data, RNAseq, and SNP Analyses.
|
2017-06-21
|
Rozaimi Razali Mark Tester
|
Sandra M Schmöckel Damien J Lightfoot David E Jarvis
|
Frontiers in Plant Science
|
A TRPV1-to-secretagogin regulatory axis controls pancreatic β-cell survival by modulating protein turnover.
|
2017-06-21
|
Roman A Romanov Stefan Kubicek Tomas Hökfelt Fabiana Piscitelli Rickard Sandberg
|
Katarzyna Malenczyk Fatima Girach Edit Szodorai Petter Storm Åsa Segerstolpe Giuseppe Tortoriello Robert Schnell Jan Mulder Erzsébet Borók Vincenzo Di Marzo Gábor Szabó Gert Lubec Ludwig Wagner Leif Groop Tibor Harkany
|
The EMBO Journal
|
A novel bZIP protein, Gsb1, is required for oxidative stress response, mating, and virulence in the human pathogen Cryptococcus neoformans.
|
2017-06-22
|
Yong-Sun Bahn
|
Seon Ah Cheon Eun Jung Thak Hyun Ah Kang
|
Scientific Reports
|
Comparative transcriptomic analysis of the evolution and development of flower size in Saltugilia (Polemoniaceae).
|
2017-06-23
|
Pamela S. Soltis
|
Jacob B Landis Douglas E Soltis
|
BMC Genomics
|
Identification of a novel fungus, Trichoderma asperellum GDFS1009, and comprehensive evaluation of its biocontrol efficacy.
|
2017-06-23
|
Mi Ni
|
Qiong Wu Ruiyan Sun Jia Yu Yaqian Li Chuanjin Yu Kai Dou Jianhong Ren Jie Chen
|
PLOS ONE
|
The emerging role of circular RNAs in transcriptome regulation.
|
2017-06-24
|
Michael Janitz
|
S Huang B Yang B J Chen N Bliim U Ueberham T Arendt
|
Genomics
|
Senescence-associated microRNAs target cell cycle regulatory genes in normal human lung fibroblasts.
|
2017-06-25
|
Georgios Markopoulos Evangelos Kolettas Maria Hatziapostolou
|
Eugenia Roupakia Maria Tokamani George Vartholomatos Theodore Tzavaras Frank O Fackelmayer Raphael Sandaltzopoulos Christos Polytarchou
|
Experimental Gerontology
|
Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expression.
|
2017-06-26
|
Jérôme Gouzy
|
Olivier Arnaiz Erwin Van Dijk Mireille Bétermier Maoussi Lhuillier-Akakpo Augustin de Vanssay Sandra Duharcourt Erika Sallet Linda Sperling
|
BMC Genomics
|
WetA bridges cellular and chemical development in Aspergillus flavus.
|
2017-06-28
|
Jae-Hyuk Yu Antonis Rokas
|
Ming-Yueh Wu Matthew E Mead Sun-Chang Kim
|
PLOS ONE
|
Hepatitis C Virus Strain-Dependent Usage of Apolipoprotein E Modulates Assembly Efficiency and Specific Infectivity of Secreted Virions.
|
2017-06-28
|
Daniel Todt
|
Romy Weller Kathrin Hueging Richard J P Brown Sebastian Joecks Florian W R Vondran Thomas Pietschmann
|
Journal of Virology
|
RNA-Seq and CyTOF immuno-profiling of regenerating lacrimal glands identifies a novel subset of cells expressing muscle-related proteins
|
2017-06-29
|
Dillon R Hawley Hema S Aluri
|
Jian Ding Suharika Thotakura Scott Haskett Claire Kublin Audrey Michel Lisa Clapisson Michael Mingueneau Driss Zoukhri
|
PLOS ONE
|
Transcriptional consequences of XPA disruption in human cell lines.
|
2017-06-29
|
Yue Lu
|
Mandira Manandhar Megan G Lowery Karen S Boulware Kevin H Lin
|
DNA Repair
|
Regulating cellular trace metal economy in algae.
|
2017-06-30
|
Sabeeha Merchant
|
Crysten E Blaby-Haas
|
Current Opinion in Plant Biology
|
zingeR: unlocking RNA-seq tools for zero-inflation and single cell applications
|
2017-06-30
|
Koen Van den Berge Charlotte Soneson Mark D. Robinson
|
Michael I. Love Lieven Clement
|
|
Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data.
|
2017-07-01
|
John C Marioni
|
Aaron T L Lun
|
Biostatistics
|
The RNASeq-er API - a gateway to systematically updated analysis of public RNA-Seq data.
|
2017-07-01
|
Robert Petryszak Alvis Brazma Anja Füllgrabe Maria C Keays
|
Laura Huerta Y Amy Tang
|
Bioinformatics
|
Deep Sequencing of RNA from Blood and Oral Swab Samples Reveals the Presence of Nucleic Acid from a Number of Pathogens in Patients with Acute Ebola Virus Disease and Is Consistent with Bacterial Translocation across the Gut.
|
2017-07-01
|
Stephan Günther David A. Matthews Lisa Fong Poh Ng Laurent Rénia Bernadett Pályi Antonino Di Caro Armand Sprecher Roman Wölfel Fara Raymond Koundouno Kilian Stoecker Joseph Akoi Bore
|
Miles W Carroll Sam Haldenby Natasha Y Rickett Isabel Garcia-Dorival Xuan Liu Gary Barker E Diane Williamson Thomas R Laws Romy Kerber Daouda Sissoko Nóra Magyar Mirella Biava Tom E Fletcher N'faly Magassouba Julian A Hiscox
|
mSphere
|
Integration of Metabolomics and Transcriptomics Reveals a Complex Diet of Mycobacterium tuberculosis during Early Macrophage Infection.
|
2017-07-01
|
Hans-Joachim Mollenkopf Martin Gengenbacher
|
Michael Zimmermann Maria Kogadeeva Gayle McEwen Nicola Zamboni Stefan Hugo Ernst Kaufmann Uwe Sauer
|
mSystems
|
Intestinal Enteroendocrine Lineage Cells Possess Homeostatic and Injury-Inducible Stem Cell Activity.
|
2017-07-01
|
Linheng Li
|
Kelley S Yan Olivier Gevaert Grace X Y Zheng Benedict Anchang Christopher S Probert Kathryn A Larkin Paige S Davies Zhuan-Fen Cheng John S Kaddis Arnold Han Kelly Roelf Ruben I Calderon Esther Cynn Xiaoyi Hu Komal Mandleywala Julie Wilhelmy Sue M Grimes David C Corney Stéphane C Boutet Jessica M Terry Phillip Belgrader Solongo B Ziraldo Tarjei S Mikkelsen Fengchao Wang Richard J von Furstenberg Nicholas R Smith Parthasarathy Chandrakesan Randal May Mary Ann S Chrissy Rajan Jain Christine A Cartwright Joyce C Niland Young-Kwon Hong Jill Carrington David T Breault Jonathan Epstein Courtney W Houchen John P Lynch Martin G Martin Sylvia K Plevritis Christina Curtis Hanlee P Ji Susan J Henning Melissa H Wong Calvin J Kuo
|
Cell Stem Cell
|
Integrated gut/liver microphysiological systems elucidates inflammatory inter-tissue crosstalk.
|
2017-07-01
|
Douglas A Lauffenburger
|
Wen L K Chen Collin Edington Emily Suter Jiajie Yu Jeremy J Velazquez Jason G Velazquez Michael Shockley Emma M Large Raman Venkataramanan David J Hughes Cynthia L Stokes David L Trumper Rebecca L Carrier Murat Cirit Linda G Griffith
|
Biotechnology and Bioengineering
|
Progesterone Receptor Isoform Ratio: A Breast Cancer Prognostic and Predictive Factor for Antiprogestin Responsiveness.
|
2017-07-01
|
Charles M. Perou
|
Paola A Rojas María May Gonzalo R Sequeira Andrés Elia Michelle Alvarez Paula Martínez Pedro Gonzalez Stephen Hewitt Xiaping He Alfredo Molinolo Luz Gibbons Martin C Abba Hugo Gass Claudia Lanari
|
Journal of the National Cancer Institute
|
Threshold-seq: a tool for determining the threshold in short RNA-seq datasets.
|
2017-07-01
|
Isidore Rigoutsos
|
Rogan Magee Phillipe Loher Eric Londin
|
Bioinformatics
|
Identification of miRNAs involved in DRG neurite outgrowth and their putative targets.
|
2017-07-02
|
Vance P. Lemmon Dario Motti
|
Jessica K Lerch Matt C Danzi Jared H Gans Frank Kuo Tatiana I Slepak John L Bixby
|
FEBS Letters
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Transcriptional Profiling of Biofilm Regulators Identified by an Overexpression Screen in Saccharomyces cerevisiae.
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2017-07-03
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Aimée M Dudley Amy Sirr
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Gareth A Cromie Zhihao Tan Michelle Hays Eric W Jeffery
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G3
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MassBlast: A workflow to accelerate RNA-seq and DNA database analysis
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2017-07-03
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Marie-France Sagot Jean-Etienne Bassard Susana Vinga
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André Veríssimo Alice Julien-Laferrière
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Recessive mutation in EXOSC3 associates with mitochondrial dysfunction and pontocerebellar hypoplasia.
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2017-07-04
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Richard J Rodenburg Angela Kaindl
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Gudrun Schottmann Sylvie Picker-Minh Jana Marie Schwarz Esther Gill Werner Stenzel Markus Schuelke
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Mitochondrion
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PLATINUM SENSITIVE 2 LIKE impacts growth, root morphology, seed set, and stress responses.
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2017-07-05
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Cathrine Lillo
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Amr R A Kataya Maria T Creighton Toga P Napitupulu Christine Sætre Behzad Heidari Peter Ruoff
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PLOS ONE
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Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis.
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2017-07-05
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Robert Sebra Mark Bender Gerstein
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Sayed Mohammad Ebrahim Sahraeian Marghoob Mohiyuddin Hagen Tilgner Pegah T Afshar Kin Fai Au Narges Bani Asadi Wing Hung Wong Michael P Snyder Eric Schadt Hugo Y K Lam
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Nature Communications
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Defects in dosage compensation impact global gene regulation in the mouse trophoblast.
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2017-07-06
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Takashi Sado Koji Nagao
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Yuka Sakata Yuko Hoki Hiroyuki Sasaki Chikashi Obuse
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Development
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RNAseq-based transcriptome comparison of Saccharomyces cerevisiae strains isolated from diverse fermentative environments.
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2017-07-06
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Eladio Barrio
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Clara Ibáñez Roberto Pérez-Torrado Miguel Morard Christina Toft Amparo Querol
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International Journal of Food Microbiology
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Genome-Scale Model and Omics Analysis of Metabolic Capacities of Akkermansia muciniphila Reveal a Preferential Mucin-Degrading Lifestyle.
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2017-07-07
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Peter J. Schaap Mark Davids Noora Ottman Hauke Smidt Maria Suarez-Diez
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Sjef Boeren Vitor A P Martins Dos Santos Clara Belzer Willem M de Vos
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Applied and Environmental Microbiology
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Single-cell transcriptomics of East-Asian pancreatic islets cells.
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2017-07-10
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Jianjun Liu
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Rajkumar Dorajoo Yusuf Ali Vanessa S Y Tay Jonathan Kang Sudhagar Samydurai Bernhard O Boehm
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Scientific Reports
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6S RNA in Rhodobacter sphaeroides: 6S RNA and pRNA transcript levels peak in late exponential phase and gene deletion causes a high salt stress phenotype.
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2017-07-10
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Roland Hartmann
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Daria Elkina Lennart Weber Marcus Lechner Olga Burenina Andrea Weisert Elena Kubareva Gabriele Klug
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RNA Biology
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Neat1 is a p53-inducible lincRNA essential for transformation suppression.
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2017-07-11
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Stephano S. Mello Tetsuro Hirose John L. Rinn
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Carolyn Sinow Nitin Raj Pawel K Mazur Kathryn Bieging-Rolett Daniela Kenzelmann Broz Jamie F Conklin Imam Hannes Vogel Laura D Wood Julien Sage Shinichi Nakagawa Laura D Attardi
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Genes & Development
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A Case of AML Characterized by a Novel t(4;15)(q31;q22) Translocation That Confers a Growth-Stimulatory Response to Retinoid-Based Therapy.
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2017-07-11
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Francisco Vega Kevin Petrie
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Justin M Watts Aymee Perez Lutecia Pereira Yao-Shan Fan Geoffrey Brown Ronan T Swords Arthur Zelent
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International Journal of Molecular Sciences
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Multi-omics Analyses of Starvation Responses Reveal a Central Role for Lipoprotein Metabolism in Acute Starvation Survival in C. elegans.
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2017-07-12
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Nils Joakim Færgeman Richard R Sprenger Susanne Mandrup
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Eva Bang Harvald Kathrine Brændgaard Dall Christer S Ejsing Ronni Nielsen Alejandro Brenes Murillo Mark Larance Anton Gartner Angus I Lamond
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Cell systems
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PLAG1 deficiency impairs spermatogenesis and sperm motility in mice.
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2017-07-13
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Stephen R. Doyle Anne E O'Connor Moira O'bryan Daniel Barriga
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Almas R Juma Sylvia V H Grommen D Jo Merriner Nathan E Hall Pauliina E Damdimopoulou Adam H Hart Wim J M Van de Ven Bert De Groef
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Scientific Reports
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Rapid recovery gene downregulation during excess-light stress and recovery in Arabidopsis.
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2017-07-13
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Aaron B Smith Peter A Crisp Diep R. Ganguly Kevin D Murray Ryan Lister Justin O Borevitz Barry J Pogson
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Gonzalo M Estavillo Iain R Searle Ethan Ford Ozren Bogdanović Steven R Eichten
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The Plant Cell
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Spatiotemporal expression patterns of wheat amino acid transporters reveal their putative roles in nitrogen transport and responses to abiotic stress
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2017-07-14
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Keywan Hassani-Pak Robert C. King
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Yongfang Wan Rowan A C Mitchell Malcolm J Hawkesford
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Scientific Reports
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Mapping stripe rust resistance gene YrZH22 in Chinese wheat cultivar Zhoumai 22 by bulked segregant RNA-Seq (BSR-Seq) and comparative genomics analyses.
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2017-07-15
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Dengcai Liu
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Yong Wang Jingzhong Xie Huaizhi Zhang Bingmin Guo Shunzong Ning Yongxing Chen Ping Lu Qiuhong Wu Miaomiao Li Deyun Zhang Guanghao Guo Yan Zhang Shaokui Zou Jianwei Tang Hong Zhao Xicheng Wang Jun Li Wuyun Yang Tingjie Cao Guihong Yin Zhiyong Liu
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Theoretical and Applied Genetics
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Widespread alternative exon usage in clinically distinct subtypes of Invasive Ductal Carcinoma
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2017-07-17
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Anne-Lise Børresen-Dale Anshuman Panda Surendra Kumar Vessela Kristensen Bjørn Naume
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Sunniva Stordal Bjørklund Michael Seiler Doug Robinson Jinesh Gheeya Ming Yao Grethe I Grenaker Alnæs Deborah Toppmeyer Margit Riis Shridar Ganesan Gyan Bhanot
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Scientific Reports
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Genome-wide RNA-Sequencing analysis identifies a distinct fibrosis gene signature in the conjunctiva after glaucoma surgery
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2017-07-17
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Christine Orengo Jonathan Lees
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Cynthia Yu-Wai-Man Nicholas Owen Aristides D Tagalakis Stephen L Hart Andrew R Webster Peng T Khaw
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Scientific Reports
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Lack of AcrB Efflux Function Confers Loss of Virulence on Salmonella enterica Serovar Typhimurium.
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2017-07-18
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Xuan Wang-Kan Jonathan Betts Barbara Chirullo Vito Ricci Roberto M La Ragione
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Jessica M A Blair Alasdair Ivens Timothy J Opperman Laura J V Piddock
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mBio
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Human iPSC Glial Mouse Chimeras Reveal Glial Contributions to Schizophrenia.
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2017-07-18
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Maiken Nedergaard Steven A. Goldman Paul J. Tesar
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Martha S Windrem Mikhail Osipovitch Zhengshan Liu Janna Bates Devin Chandler-Militello Lisa Zou Jared Munir Steven Schanz Katherine McCoy Robert H Miller Su Wang Robert L Findling Steven A Goldman
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Cell Stem Cell
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RNA-Seq Identifies Circulating miR-125a-5p, miR-125b-5p, and miR-143-3p as Potential Biomarkers for Acute Ischemic Stroke.
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2017-07-19
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Martin Dichgans Rainer Malik Marco Duering
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Steffen Tiedt Matthias Prestel Nicola Schieferdecker Veronika Kautzky Ivelina Stoycheva Julia Böck Bernd H Northoff Matthias Klein Franziska Dorn Knut Krohn Daniel Teupser Arthur Liesz Nikolaus Plesnila Lesca Miriam Holdt
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Circulation Research
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Deletion of the celA gene in Aspergillus nidulans triggers overexpression of secondary metabolite biosynthetic genes.
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2017-07-20
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Frank Maixner Joseph Strauss Michael Sulyok
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Gea Guerriero Lucia Silvestrini Sylvain Legay Jean-Francois Hausman
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Scientific Reports
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Comparative analysis of signature genes in PRRSV-infected porcine monocyte-derived cells to different stimuli.
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2017-07-20
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Laura C Miller
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Damarius S Fleming Xiangdong Li Darrell O Bayles Frank Blecha Yongming Sang
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PLOS ONE
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Gigaspora margarita with and without its endobacterium shows adaptive responses to oxidative stress.
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2017-07-20
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Paola Bonfante Stefano Ghignone Maria C de Pinto
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Francesco Venice Mara Novero Alessandra Salvioli
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Mycorrhiza
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Cell wall modifications of two Arabidopsis thaliana ecotypes, Col and Sha, in response to sub-optimal growth conditions: An integrative study.
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2017-07-20
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Thierry Balliau Christophe Dunand Elisabeth Jamet
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Harold Duruflé Vincent Hervé Philippe Ranocha Michel Zivy Josiane Chourré Hélène San Clemente Vincent Burlat Cécile Albenne Sébastien Déjean
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Plant Science
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Direct targets of pSTAT5 signalling in erythropoiesis.
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2017-07-21
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Andrew C Perkins
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Kevin R Gillinder Hugh Tuckey Charles C Bell Graham W Magor Stephen Huang Melissa D Ilsley
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PLOS ONE
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Methylation of protein phosphatase 2A-Influence of regulators and environmental stress factors.
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2017-07-25
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Cathrine Lillo Jodi Maple-Grødem
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Maria T Creighton Anna Kolton Amr R A Kataya Irina O Averkina Behzad Heidari
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Plant, Cell and Environment
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Active nuclear transcriptome analysis reveals inflammasome-dependent mechanism for early neutrophil response to Mycobacterium marinum.
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2017-07-26
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Daria Gavriouchkina Tatjana Sauka-Spengler Vincenzo Cerundolo
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Amy Kenyon Jernej Zorman Giorgio Napolitani
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Scientific Reports
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Dual RNA-Seq of Lysobacter capsici AZ78 - Phytophthora infestans interaction shows the implementation of attack strategies by the bacterium and unsuccessful oomycete defense responses.
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2017-07-26
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Paolo Sonego
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Selena Tomada Marco Moretto Kristof Engelen Ilaria Pertot Michele Perazzolli Gerardo Puopolo
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Environmental Microbiology
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Advantages of RNA-seq compared to RNA microarrays for transcriptome profiling of anterior cruciate ligament tears.
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2017-07-27
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Eric Tycksen Muhammad Farooq Rai
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Linda J Sandell Robert H Brophy
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Journal of Orthopaedic Research
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Comprehensive discovery of noncoding RNAs in acute myeloid leukemia cell transcriptomes.
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2017-07-28
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Sean D McGrath
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Jin Zhang Malachi Griffith Christopher A Miller Obi L Griffith David H Spencer Jason R Walker Vincent Magrini Amy Ly Nichole M Helton Maria Trissal Daniel C Link Ha X Dang David E Larson Shashikant Kulkarni Matthew G Cordes Catrina C Fronick Robert S Fulton Jeffery M Klco Elaine R Mardis Timothy J Ley Richard K Wilson Christopher A Maher
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Experimental Hematology
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FOXA1 hypermethylation: link between parity and ER-negative breast cancer in African American women?
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2017-07-29
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Elisa V. Bandera Christine Ambrosone
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Allyson C Espinal Matthew F Buas Dan Wang David Ting-Yuan Cheng Lara Sucheston-Campbell Qiang Hu Li Yan Rochelle Payne-Ondracek Eduardo Cortes Li Tang Zhihong Gong Gary Zirpoli Thaer Khoury Song Yao Angela Omilian Kitaw Demissie Song Liu Michael J Higgins
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Breast Cancer Research and Treatment
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Rps26 directs mRNA-specific translation by recognition of Kozak sequence elements.
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2017-07-31
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Katrin Karbstein
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Max B Ferretti Homa Ghalei Ethan A Ward Elizabeth L Potts
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Nature Structural & Molecular Biology
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Simultaneous epitope and transcriptome measurement in single cells.
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2017-07-31
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Harold Swerdlow Christoph Hafemeister Marlon Stoeckius Brian Houck-Loomis Rahul Satija Peter Smibert William Stephenson Pratip K. Chattopadhyay
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Nature Methods
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Copper homeostasis networks in the bacterium Pseudomonas aeruginosa.
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2017-07-31
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Lorena Novoa-Aponte Julia Quintana
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José M Argüello
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Journal of Biological Chemistry
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Comprehensive single-cell transcriptional profiling of a multicellular organism.
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2017-08-01
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Jay Shendure Junyue Cao Darren A Cusanovich Scott Furlan
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Jonathan S Packer Vijay Ramani Chau Huynh Riza Daza Xiaojie Qiu Choli Lee Frank J Steemers Andrew Adey Robert H Waterston Cole Trapnell
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Science
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Impact of Alternative Splicing on the Human Proteome.
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2017-08-01
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John C Marioni Vihandha O Wickramasinghe Yansheng Liu Alvis Brazma Ruedi Aebersold
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Mar Gonzàlez-Porta Sergio Santos Ashok R Venkitaraman
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Cell Reports
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SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation.
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2017-08-01
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Itoshi Nikaido
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Hirotaka Matsumoto Hisanori Kiryu Chikara Furusawa Minoru S H Ko Shigeru B H Ko Norio Gouda Tetsutaro Hayashi
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Bioinformatics
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Cell-Type-Specific Translation Profiling Reveals a Novel Strategy for Treating Fragile X Syndrome.
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2017-08-01
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Caoimhe Kirby Owen Dando Peter C Kind David J Wyllie Giles E. Hardingham Emily Osterweil
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Sophie R Thomson Sang S Seo Stephanie A Barnes Susana R Louros Melania Muscas
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Neuron
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Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation.
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2017-08-01
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Antonio Scialdone John C Marioni Carla Mulas Iain C Macaulay Jennifer Nichols Wolf Reik
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Hisham Mohammed Irene Hernando-Herraez Aurora Savino Tamir Chandra Thierry Voet Wendy Dean
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Cell Reports
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Single-cell RNA-sequencing reveals a distinct population of proglucagon-expressing cells specific to the mouse upper small intestine.
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2017-08-01
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Berthold Göttgens Leslie L Glass Pierre Larraufie Fernando J Calero-Nieto Wajid Jawaid Fiona M Gribble Frank Reimann
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Richard G Kay
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Molecular Metabolism
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TREM2 Maintains Microglial Metabolic Fitness in Alzheimer's Disease.
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2017-08-01
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Tyler K Ulland Susan Gilfillan Yingyue Zhou Herbert W. "Skip" Virgin David M. Holtzman
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Wilbur M Song Stanley Ching-Cheng Huang Jason D Ulrich Alexey Sergushichev Wandy L Beatty Alexander A Loboda Nigel J Cairns Amal Kambal Ekaterina Loginicheva Marina Cella Emil R Unanue Yaming Wang Maxim N Artyomov Marco Colonna
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Cell
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Human Astrocyte Maturation Captured in 3D Cerebral Cortical Spheroids Derived from Pluripotent Stem Cells.
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2017-08-01
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Steven A. Sloan
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Spyros Darmanis Nina Huber Themasap A Khan Fikri Birey Christine Caneda Richard Reimer Stephen R Quake Ben A Barres Sergiu P Paşca
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Neuron
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Transcription Factors Sp8 and Sp9 Coordinately Regulate Olfactory Bulb Interneuron Development.
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2017-08-01
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Jiwen Li Arturo Alvarez-Buylla
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Chunyang Wang Zhuangzhi Zhang Yan Wen Lei An Qifei Liang Zhejun Xu Song Wei Weiwei Li Teng Guo Guoping Liu Guangxu Tao Yan You Heng Du Zhuoning Fu Miao He Bin Chen Kenneth Campbell John L Rubenstein Zhengang Yang
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Cerebral Cortex
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Therapeutic radiation for childhood cancer drives structural aberrations of NF2 in meningiomas.
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2017-08-04
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Felix Sahm Andreas von Deimling Trevor J Pugh
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Sameer Agnihotri Suganth Suppiah Peter D Tonge Shahrzad Jalali Arnavaz Danesh Jeffery P Bruce Yasin Mamatjan George Klironomos Lior Gonen Karolyn Au Sheila Mansouri Sharin Karimi Michael D Taylor Normand J Laperriere Kenneth D Aldape Gelareh Zadeh
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Nature Communications
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A novel mutation of adenomatous polyposis coli (APC) gene results in the formation of supernumerary teeth.
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2017-08-07
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Wenping Cai
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Fang Yu Beizhan Jiang Laijun Xu Shangfeng Liu Shouliang Zhao
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Journal of Cellular and Molecular Medicine
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Comparison of alternative approaches for analysing multi-level RNA-seq data.
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2017-08-08
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Tamas Dalmay
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Irina Mohorianu Amanda Bretman Damian T Smith Emily K Fowler Tracey Chapman
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PLOS ONE
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Whole transcriptome profiling of taste bud cells.
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2017-08-08
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Alexander Bachmanov Sunil K Sukumaran Robert F. Margolskee
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Brian C Lewandowski Yumei Qin Ramana Kotha
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Scientific Reports
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Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation.
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2017-08-08
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Nadav Ahituv
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Ann H Ryu Walter L Eckalbar Anat Kreimer Nir Yosef
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Scientific Reports
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Amiloride, An Old Diuretic Drug, Is a Potential Therapeutic Agent for Multiple Myeloma.
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2017-08-08
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Ramón García-Sanz Irena Misiewicz-Krzeminska Enrique M Ocio Norma C. Gutiérrez
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Elizabeta A Rojas Luis Antonio Corchete Laura San-Segundo Juan F Martínez-Blanch Francisco M Codoñer Teresa Paíno Noemí Puig María Victoria Mateos
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Clinical Cancer Research
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Modeling Glaucoma: Retinal Ganglion Cells Generated from Induced Pluripotent Stem Cells of Patients with SIX6 Risk Allele Show Developmental Abnormalities.
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2017-08-09
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Pooja Teotia
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Matthew J Van Hook Christopher S Wichman R Rand Allingham Michael A Hauser Iqbal Ahmad
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Stem Cells
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Identification of competing endogenous RNAs of the tumor suppressor gene PTEN: A probabilistic approach.
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2017-08-10
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Pier Paolo Pandolfi
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Kourosh Zarringhalam Yvonne Tay Prajna Kulkarni Assaf C Bester Rahul V Kulkarni
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Scientific Reports
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High Resolution Mapping of Chromatin Conformation in Cardiac Myocytes Reveals Structural Remodeling of the Epigenome in Heart Failure
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2017-08-11
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Matteo Pellegrini Manuel Rosa-Garrido Yibin Wang
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Douglas J Chapski Anthony D Schmitt Todd H Kimball Elaheh Karbassi Emma Monte Enrique Balderas Tsai-Ting Shih Elizabeth Soehalim Peipei Ping Niels J Galjart Shuxun Ren Bing Ren Thomas M Vondriska David Liem
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Circulation
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Characterization of the human thyroid epigenome.
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2017-08-14
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Andrew Mungall Steven Jones
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Celia Siu Sam Michael Wiseman Sitanshu Gakkhar Alireza Heravi-Moussavi Misha Bilenky Annaick Carles Thomas Sierocinski Angela Tam Eric Yang Zhao Katayoon Kasaian Richard A Moore Blair Walker Thomas Thomson Marco A Marra Martin Hirst
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Journal of Endocrinology
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Mapping the mouse Allelome reveals tissue-specific regulation of allelic expression.
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2017-08-14
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Josef M Penninger Christoph Bock Quanah J Hudson Tomasz Kuliński
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Daniel Andergassen Christoph P Dotter Daniel Wenzel Verena Sigl Philipp C Bammer Markus Muckenhuber Daniela Mayer Hans-Christian Theussl Denise P Barlow Florian M Pauler
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eLife
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Heart morphogenesis gene regulatory networks revealed by temporal expression analysis.
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2017-08-14
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Jonathon T Hill
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Bradley Demarest Megan Smith Bushra Gorsi H Joseph Yost
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Development
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Zygotic Genome Activation Occurs Shortly after Fertilization in Maize.
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2017-08-16
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Nicholas Putz
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Junyi Chen Nadia G Krohn Philipp Cyprys Stefanie Sprunck Julia C Engelmann Thomas Dresselhaus
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The Plant Cell
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Detection and removal of barcode swapping in single-cell RNA-seq data
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2017-08-16
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Aaron Lun
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Jonathan A. Griffiths Arianne C. Richard Karsten Bach John C. Marioni
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A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications.
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2017-08-18
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Tapio Lönnberg Sarah Teichmann Ashraful Haque
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Jessica Engel
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Genome Medicine
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Itm2a silencing rescues lamin A mediated inhibition of 3T3-L1 adipocyte differentiation.
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2017-08-18
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Pavel V Baranov
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Stephanie J Davies James Ryan Patrick B F O'Connor Elaine Kenny Derek Morris Rosemary O'Connor Tommie V McCarthy
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Adipocyte
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RNA-seq reveals more consistent reference genes for gene expression studies in human non-melanoma skin cancers.
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2017-08-21
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Lisa Putral Duncan Lambie Lynlee L Lin Tarl W. Prow Ian Frazer
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Van L T Hoang Xiu-Cheng Quek Jean-Marie Tan Elizabeth J Payne Sudipta Sinnya Anthony P Raphael Marcel E Dinger H Peter Soyer
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PeerJ
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p53 pulses lead to distinct patterns of gene expression albeit similar DNA-binding dynamics.
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2017-08-21
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Jacob Stewart-Ornstein
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Antonina Hafner Jeremy E Purvis William C Forrester Martha L Bulyk Galit Lahav
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Nature Structural & Molecular Biology
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Architecture and Dynamics of the Jasmonic Acid Gene Regulatory Network.
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2017-08-21
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Johanna Rhodes Katherine J Denby Richard Hickman Lotte Caarls
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Marcel C Van Verk Anja J H Van Dijken Marciel Pereira Mendes Irene A Vroegop-Vos Merel Steenbergen Ivo Van der Nagel Gert Jan Wesselink Aleksey Jironkin Adam Talbot Michel De Vries Robert C Schuurink Corné M J Pieterse Saskia C M Van Wees
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The Plant Cell
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Unmasking Transcriptional Heterogeneity in Senescent Cells.
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2017-08-21
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Victor Guryev
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Alejandra Hernandez-Segura Tristan V de Jong Simon Melov Judith Campisi Marco Demaria
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Current Biology
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Multi-tissue RNA-seq and transcriptome characterisation of the spiny dogfish shark (Squalus acanthias) provides a molecular tool for biological research and reveals new genes involved in osmoregulation
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2017-08-23
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Christian Bendixen Frank Panitz
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Andres Chana-Munoz Agnieszka Jendroszek Malene Sønnichsen Rune Kristiansen Jan K Jensen Peter A Andreasen
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PLOS ONE
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Transcriptional Analysis Allows Genome Reannotation and Reveals that Cryptococcus gattii VGII Undergoes Nutrient Restriction during Infection.
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2017-08-23
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Livia Kmetzsch Patrícia Aline Gröhs Ferrareze Augusto Schrank Marilene H Vainstein
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Rodrigo Silva Araujo Streit Patricia Ribeiro Dos Santos Francine Melise Dos Santos Rita Maria Cunha de Almeida
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Microorganisms
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Regulation of a minimal transcriptome by repeat domain proteins.
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2017-08-23
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Aleksandra Filipovska
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Nicola Ferreira Oliver Rackham
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Seminars in Cell & Developmental Biology
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New skin for the old RNA-Seq ceremony: the age of single-cell multi-omics.
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2017-08-24
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Itai Yanai
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Maayan Baron
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Genome Biology
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recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor.
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2017-08-24
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Leonardo Collado-Torres Andrew E Jaffe Abhinav Nellore
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F1000Research
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RNA-seq reveals distinctive RNA profiles of small extracellular vesicles from different human liver cancer cell lines.
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2017-08-24
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Anna C. Berardi Annalisa Radeghieri M Gallorini Igea D'Agnano Paolo Bergese
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Martina Berardocco Sara Busatto Chiara Raggi Clarissa Gissi Armando Felsani
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Oncotarget
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Streptococcus pneumoniae in the heart subvert the host response through biofilm-mediated resident macrophage killing.
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2017-08-25
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Sean C Daugherty
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Anukul T Shenoy Terry Brissac Ryan P Gilley Nikhil Kumar Yong Wang Norberto Gonzalez-Juarbe Whitney S Hinkle Amol C Shetty Sandra Ott Luke J Tallon Jessy Deshane Hervé Tettelin Carlos J Orihuela
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PLOS Pathogens
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Massively parallel single-nucleus RNA-seq with DroNc-seq.
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2017-08-28
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Aviv Regev Kristin Ardlie Orit Rozenblatt-Rosen
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Naomi Habib Inbal Avraham-Davidi Anindita Basu Tyler Burks Karthik Shekhar Matan Hofree Sourav R Choudhury François Aguet Ellen Gelfand David A Weitz Feng Zhang
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Nature Methods
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Hypoxia-inducible factor 2α (HIF-2α) promotes colon cancer growth by potentiating Yes-associated protein 1 (YAP1) activity.
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2017-08-28
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Xiaoya Ma
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Huabing Zhang Xiang Xue Yatrik M Shah
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Journal of Biological Chemistry
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Single cell analysis of normal and leukemic hematopoiesis.
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2017-08-29
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Adam J Mead
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Benjamin J Povinelli Alba Rodriguez-Meira
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Molecular Aspects of Medicine
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An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms.
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2017-08-30
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Julia Ponomarenko Javier Tapial Ulrich Braunschweig Antoni Hermoso Miguel Manzanares
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Kevin C H Ha Timothy Sterne-Weiler Andre Gohr Mathieu Quesnel-Vallières Jon Permanyer Reza Sodaei Yamile Marquez Luca Cozzuto Xinchen Wang Melisa Gómez-Velázquez Teresa Rayon Benjamin Blencowe Manuel Irimia
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Genome Research
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Functional analysis of a novel, thyroglobulin-embedded microRNA gene deregulated in papillary thyroid carcinoma.
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2017-08-30
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Krystian Jażdżewski Barbara Górnicka
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Monika Kolanowska Anna Wójcicka Anna Kubiak Michał Świerniak Marta Kotlarek Monika Maciąg Paweł Gaj Łukasz Koperski
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Scientific Reports
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Cell-type- and tissue-specific transcriptomes of the white spruce (Picea glauca) bark unmask fine-scale spatial patterns of constitutive and induced conifer defense.
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2017-08-30
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Jörg Bohlmann
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Jose M Celedon Macaire M S Yuen Angela Chiang Hannah Henderson Karen E Reid
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The Plant Journal
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Characterization and Genomic Localization of a SMAD4 Processed Pseudogene.
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2017-08-31
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Julian Weldon Adlard David T. Bonthron Ian M. Carr Alexander Markham
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Christopher M Watson Nick Camm Laura A Crinnion Agne Antanaviciute Ruth Charlton
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The Journal of Molecular Diagnostics
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Antitumor activity and expression profiles of genes induced by sulforaphane in human melanoma cells.
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2017-09-01
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Andrea Crisanti
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Paola Arcidiacono Francesco Ragonese Anna Stabile Alessandra Pistilli Ekaterina Kuligina Mario Rende Ugo Bottoni Stefano Calvieri Roberta Spaccapelo
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European Journal of Nutrition
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Targeted reconstruction of T cell receptor sequence from single cell RNA-seq links CDR3 length to T cell differentiation state.
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2017-09-01
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Paul Klenerman
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Shaked Afik Kathleen B Yates Kevin Bi Samuel Darko Jernej Godec Ulrike Gerdemann Leo Swadling Daniel C Douek Eleanor J Barnes Arlene H Sharpe W Nicholas Haining Nir Yosef
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Nucleic Acids Research
|
Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures.
|
2017-09-01
|
Thalia E Chan
|
Thalia E Chan Michael P H Stumpf Ann C Babtie
|
Cell systems
|
Thyroid hormone receptor beta and NCOA4 regulate terminal erythrocyte differentiation.
|
2017-09-01
|
Harvey Lodish
|
Xiaofei Gao Hsiang-Ying Lee Wenbo Li Randall Jeffrey Platt M Inmaculada Barrasa Qi Ma Russell R Elmes Michael G Rosenfeld
|
Proceedings of the National Academy of Sciences of the United States of America
|
Single-cell analyses to tailor treatments.
|
2017-09-01
|
Alex K. Shalek
|
Mikael Benson
|
Science Translational Medicine
|
Dual RNA-seq reveals no plastic transcriptional response of the coccidian parasite Eimeria falciformis to host immune defenses.
|
2017-09-05
|
Richard Lucius
|
Totta Ehret Simone Spork Christoph Dieterich Richard Lucius Emanuel Heitlinger
|
BMC Genomics
|
Effects of toxic Microcystis aeruginosa on the silver carp Hypophthalmichtys molitrix revealed by hepatic RNA-seq and miRNA-seq.
|
2017-09-05
|
Youji Wang
|
Menghong Hu Xiancheng Qu Lisha Pan Chunxue Fu Peixuan Jia Qigen Liu Youji Wang
|
Scientific Reports
|
Integrative analysis of DNA methylation and mRNA expression during differentiation of umbilical cord blood derived mononuclear cells to endothelial cells.
|
2017-09-05
|
Ja-Young Kwon
|
Yoonjeong Jeong Yukyung Jun Jihye Kim Hyojin Park Kyu-Sung Choi Haiying Zhang Jeong Ae Park Young-Myeong Kim Sanghyuk Lee Young-Guen Kwon
|
Gene
|
A protein with an unusually short PPR domain, MEF8, affects editing at over 60 Arabidopsis mitochondrial C targets of RNA editing.
|
2017-09-05
|
Maureen R. Hanson
|
Michael F Diaz Stephane Bentolila Michael L Hayes R Michael Mulligan
|
The Plant Journal
|
Assessing the activity of nonsense-mediated mRNA decay in lung cancer.
|
2017-09-06
|
Zhenguo Zhang
|
Meng Wang Peiwei Zhang Yufei Zhu Xiangyin Kong Landian Hu
|
BMC Medical Genomics
|
Toward the human cellular microRNAome.
|
2017-09-06
|
Valina L. Dawson Avi Rosenberg Marc K. Halushka Arun H Patil Min-Sik Kim Ted M. Dawson
|
Matthew N McCall Mohammed Adil Yin Lu Christopher J Mitchell Pamela Leal-Rojas Jinchong Xu Manoj Kumar Alexander S Baras Dan E Arking Kathleen H Burns Akhilesh Pandey
|
Genome Research
|
Genomic characterization of chromosome translocations in patients with T/myeloid mixed-phenotype acute leukemia.
|
2017-09-07
|
Steven Salzberg
|
Aparna Pallavajjala Daehwan Kim Tongbin Li Gabriel Ghiaur Richard J Jones Kathleen H Burns Yi Ning
|
Leukemia & Lymphoma
|
Discovery of Human-Similar Gene Fusions in Canine Cancers.
|
2017-09-07
|
Thomas Derrien
|
Ronan Ulvé Mélanie Rault Mathieu Bahin Laetitia Lagoutte Jérôme Abadie Clotilde De Brito Jean-Michel Coindre Nadine Botherel Audrey Rousseau Valentin Wucher Edouard Cadieu Catherine Thieblemont Christophe Hitte Laurence Cornevin Florian Cabillic Laura Bachelot David Gilot Benoit Hennuy Thierry Guillaudeux Arnaud Le Goff Benoît Hédan Catherine André
|
Cancer Research
|
Identification of immunity-related genes in Plutella xylostella in response to fungal peptide destruxin A: RNA-Seq and DGE analysis.
|
2017-09-08
|
Muhammad Shakeel
|
Xiaoxia Xu Jin Xu Xun Zhu Shuzhong Li Xianqiang Zhou Jialin Yu Xiaojing Xu Qiongbo Hu Xiaoqiang Yu Fengliang Jin
|
Scientific Reports
|
Genome-wide miRNA response to anacardic acid in breast cancer cells.
|
2017-09-08
|
Carolyn M. Klinge
|
David J Schultz Penn Muluhngwi Negin Alizadeh-Rad Madelyn A Green Eric C Rouchka Sabine J Waigel
|
PLOS ONE
|
RALE051: a novel established cell line of sporadic Burkitt lymphoma.
|
2017-09-11
|
Anna Ferrari Angelo Lonoce Alberto L'Abbate Clelia Tiziana Storlazzi Elisa Ficarra Giovanni Martinelli Ilaria Iacobucci
|
Antonella Turchiano Giulia Paciello Federica Cattina Enrica Imbrogno Claudio Agostinelli Pierluigi Zinzani Enrico Derenzini
|
Leukemia & Lymphoma
|
MAJIQ-SPEL: Web-tool to interrogate classical and complex splicing variations from RNA-Seq data.
|
2017-09-11
|
Yoseph Barash
|
Christopher J Green Matthew R Gazzara
|
Bioinformatics
|
Regulatory network changes between cell lines and their tissues of origin.
|
2017-09-12
|
John Quackenbush Cho-Yi Chen Abhijeet R Sonawane Kimberly Glass John Platig
|
Camila M Lopes-Ramos Joseph N Paulson Marieke L Kuijjer Maud Fagny Dawn L DeMeo
|
BMC Genomics
|
Novel endogenous retrovirus-derived transcript expressed in the bovine placenta is regulated by WNT signaling.
|
2017-09-12
|
So Nakagawa
|
Toshihiro Sakurai Hanako Bai Rulan Bai Kazuya Kusama Atsushi Ideta Yoshito Aoyagi Kazuyuki Kaneko Kosuke Iga Jiro Yasuda Takayuki Miyazawa Kazuhiko Imakawa
|
Biochemical Journal
|
Splatter: simulation of single-cell RNA sequencing data.
|
2017-09-12
|
Alicia Oshlack Luke Zappia Belinda Phipson
|
|
Genome Biology
|
Assessment of T-cell receptor repertoire and clonal expansion in peripheral T-cell lymphoma using RNA-seq data.
|
2017-09-12
|
Qiang Gong Raul Rabadan
|
Chao Wang Weiwei Zhang Javeed Iqbal Yang Hu Timothy C Greiner Adam Cornish Jo-Heon Kim Francesco Abate Xin Wang Giorgio G Inghirami Timothy W McKeithan Wing C Chan
|
Scientific Reports
|
Simultaneously Monitoring Immune Response and Microbial Infections During Pregnancy through Plasma cfRNA Sequencing.
|
2017-09-13
|
Gary M Shaw
|
Wenying Pan Thuy T M Ngo Joan Camunas-Soler Chun-Xiao Song Mark Kowarsky Yair J Blumenfeld Ronald J Wong David K Stevenson Stephen R Quake
|
Clinical Chemistry
|
Analysis of the relationship between coexpression domains and chromatin 3D organization.
|
2017-09-13
|
José C Reyes
|
María E Soler-Oliva José A Guerrero-Martínez Valentina Bachetti
|
PLOS Computational Biology
|
Wounding Triggers Callus Formation via Dynamic Hormonal and Transcriptional Changes.
|
2017-09-13
|
Momoko Ikeuchi Akira Iwase Hitoshi Sakakibara Bart Rymen Shunsuke Watanabe
|
Alice Lambolez Mikiko Kojima Yumiko Takebayashi Jefri Heyman Mitsunori Seo Lieven de Veylder Keiko Sugimoto
|
Plant Physiology
|
Insights into interplay between rexinoid signaling and myogenic regulatory factor-associated chromatin state in myogenic differentiation.
|
2017-09-13
|
Jihong Chen
|
Munerah Hamed Saadia Khilji Katherine Dixon Alexandre Blais Ilya Ioshikhes
|
Nucleic Acids Research
|
RNA-Seq reveals a central role for lectin, C1q and von Willebrand factor A domains in the defensive glue of a terrestrial slug.
|
2017-09-13
|
Christopher W Reid
|
Andrew M Smith Cassandra Papaleo Joseph M Bliss
|
Biofouling
|
Massive Mining of Publicly Available RNA-seq Data from Human and Mouse
|
2017-09-14
|
Alexander Lachmann Avi Ma'ayan
|
Denis Torre Alexandra B. Keenan Kathleen M. Jagodnik Hyojin J. Lee Moshe C. Silverstein Lily Wang
|
|
A high resolution atlas of gene expression in the domestic sheep (Ovis aries).
|
2017-09-15
|
Mick Watson Emily L Clark Chunlei Wu Stephen J Bush David A Hume Alan Archibald Kim M Summers
|
Mary E B McCulloch Iseabail L Farquhar Rachel Young Lucas Lefevre Clare Pridans Hiu G Tsang Cyrus Afrasiabi C Bruce Whitelaw Tom C Freeman
|
PLOS Genetics
|
Phosphoproteomics reveals that glycogen synthase kinase-3 phosphorylates multiple splicing factors and is associated with alternative splicing.
|
2017-09-15
|
Yoseph Barash
|
Mansi Y Shinde Simone Sidoli Katarzyna Kulej Michael J Mallory Caleb M Radens Amanda L Reicherter Rebecca L Myers Kristen W Lynch Benjamin A Garcia Peter S Klein
|
Journal of Biological Chemistry
|
Small RNA-seq during acute maximal exercise reveal RNAs involved in vascular inflammation and cardiometabolic health: brief report.
|
2017-09-15
|
Olivia Ziegler
|
Ravi Shah Ashish Yeri Avash Das Amanda Courtright-Lim Ernest Gervino Jeffrey Ocel Pablo Quintero-Pinzon Luke Wooster Cole Shields Bailey Kahraman Tanriverdi Lea M Beaulieu Jane E Freedman Ionita Ghiran Gregory D Lewis Kendall Van Keuren-Jensen Saumya Das
|
American Journal of Physiology - Heart and Circulatory Physiology
|
Comparative transcriptomics of female and male gametocytes in Plasmodium berghei and the evolution of sex in alveolates.
|
2017-09-18
|
Stuart A Ralph
|
Lee M Yeoh Christopher D Goodman Vanessa Mollard Geoffrey I McFadden
|
BMC Genomics
|
Comparative analysis reveals genomic features of stress-induced transcriptional readthrough.
|
2017-09-19
|
Joan A. Steitz
|
Anna Vilborg Niv Sabath Yuval Wiesel Jenny Nathans Flonia Levy-Adam Therese A Yario Reut Shalgi
|
Proceedings of the National Academy of Sciences of the United States of America
|
RNA-seq analysis of the head-kidney transcriptome response to handling-stress in the red cusk-eel (Genypterus chilensis).
|
2017-09-20
|
Herman Silva
|
Víctor Aballai Jorge E Aedo Jonathan Maldonado Macarena Bastias-Molina Claudio Meneses Sebastian Boltaña Ariel Reyes Alfredo Molina Juan Antonio Valdés
|
Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics
|
Pervasive, Genome-Wide Transcription in the Organelle Genomes of Diverse Plastid-Bearing Protists.
|
2017-09-21
|
David Roy Smith
|
Matheus Sanitá Lima
|
G3
|
In-depth genetic analysis of sclerosing epithelioid fibrosarcoma reveals recurrent genomic alterations and potential treatment targets.
|
2017-09-22
|
Maria Debiec-Rychter Raf Sciot Fredrik Mertens
|
Elsa Arbajian Florian Puls Cristina R Antonescu M Fernanda Amary Vaiyapuri Sumathi Marcus Järås Linda Magnusson Jenny Nilsson Jakob Hofvander
|
Clinical Cancer Research
|
Two's company: studying interspecies relationships with dual RNA-seq.
|
2017-09-25
|
Sascha Brunke
|
Thomas Wolf Philipp Kämmer Jörg Linde
|
Current Opinion in Microbiology
|
Global and targeted approaches to single-cell transcriptome characterization.
|
2017-09-25
|
Tapio Lönnberg
|
Aleksandra A Kolodziejczyk
|
Briefings in functional genomics
|
Mirnovo: genome-free prediction of microRNAs from small RNA sequencing data and single-cells using decision forests.
|
2017-09-25
|
Anton J. Enright Elissavet Kentepozidou Matthew P Davis Dimitrios M Vitsios
|
Leonor Quintais Elia Benito-Gutiérrez Stijn van Dongen
|
Nucleic Acids Research
|
Super-enhancers promote transcriptional dysregulation in nasopharyngeal carcinoma.
|
2017-09-26
|
Ling-Wen Ding
|
Jiang Yuan Yan-Yi Jiang Anand Mayakonda Moli Huang Han Lin Fenggang Yu Yanan Lu Thomas Kwok Seng Loh Marilynn Chow Samantha L Savage Jeffrey W Tyner De-Chen Lin H Phillip Koeffler
|
Cancer Research
|
The Biofilm Inhibitor Carolacton Enters Gram-Negative Cells: Studies Using a TolC-Deficient Strain of Escherichia coli.
|
2017-09-27
|
Irene Wagner-Döbler Jan P Meier-Kolthoff Boyke Bunk Jörg Overmann
|
Jannik Donner Michael Reck Michael Jarek Constantin Benjamin App Rolf Müller Andreas Kirschning Irene Wagner-Döbler
|
mSphere
|
HLAProfiler utilizes k-mer profiles to improve HLA calling accuracy for rare and common alleles in RNA-seq data.
|
2017-09-27
|
Benjamin G Vincent
|
Martin L Buchkovich Chad C Brown Kimberly Robasky Shengjie Chai Sharon Westfall Eric T Weimer Jason G Powers
|
Genome Medicine
|
ENPP1 Mutation Causes Recessive Cole Disease by Altering Melanogenesis.
|
2017-09-27
|
Jianjun Liu
|
Marwa Chourabi Mei Shan Liew Shawn Lim Dorra H'mida-Ben Brahim Lobna Boussofara Liang Dai Pui Mun Wong Jia Nee Foo Badreddine Sriha Kim Samirah Robinson Simon Denil John Ea Common Ons Mamaï Youcef Ben Khalifa Mathieu Bollen Mohamed Denguezli Carine Bonnard Ali Saad Bruno Reversade
|
Journal of Investigative Dermatology
|
Transcriptional regulation of endothelial cell behavior during sprouting angiogenesis.
|
2017-09-28
|
Hans Schöler Juan M. Vaquerizas Rocio Enriquez-Gasca Ralf H Adams Benjamín Hernández-Rodríguez
|
Hyun-Woo Jeong JungMo Kim Kee-Pyo Kim Juyong Yoon Susanne Adams
|
Nature Communications
|
Mutant p53 shapes the enhancer landscape of cancer cells in response to chronic immune signaling.
|
2017-09-29
|
Homa Rahnamoun Shannon M Lauberth Sascha H Duttke Christopher K Glass
|
Hanbin Lu Christopher Benner
|
Nature Communications
|
Hexokinases link DJ-1 to the PINK1/parkin pathway.
|
2017-09-29
|
David N Hauser Wolfdieter Springer Fabienne C. Fiesel Mark R Cookson
|
Adamantios Mamais Melissa M Conti Christopher T Primiani Ravindran Kumaran Allissa A Dillman Rebekah G Langston Alexandra Beilina Joseph H Garcia Alberto Diaz-Ruiz Michel Bernier Xu Hou Yan Li Rafael de Cabo
|
Molecular Neurodegeneration
|
Transcriptome analysis of hypoxic cancer cells uncovers intron retention in EIF2B5 as a mechanism to inhibit translation.
|
2017-09-29
|
Cristina Ivan Yoseph Barash
|
Lauren K Brady Hejia Wang Caleb M Radens Yue Bi Milan Radovich Amit Maity Mircea Ivan Constantinos Koumenis
|
PLOS Biology
|
ASAP: a Web-based platform for the analysis and interactive visualization of single-cell RNA-seq data.
|
2017-10-01
|
Vincent Gardeux
|
Fabrice P A David Adrian Shajkofci Petra C Schwalie Bart Deplancke
|
Bioinformatics
|
Epithelial-Cell-Derived Phospholipase A2 Group 1B Is an Endogenous Anthelmintic.
|
2017-10-01
|
Lewis J Entwistle Mariana Silva Dos Santos Helena Helmby Lucy Collinson
|
Victoria S Pelly Stephanie M Coomes Yashaswini Kannan Jimena Perez-Lloret Stephanie Czieso James I MacRae Abdul Sesay Nikolay Nikolov Amina Metidji David Y Hui Mark S Wilson
|
Cell Host & Microbe
|
Adenohypophysis placodal precursors exhibit distinctive features within the rostral preplacodal ectoderm.
|
2017-10-01
|
Paola Bovolenta
|
Luisa Sanchez-Arrones África Sandonís Marcos Julián Cardozo
|
Development
|
Chromatin and Single-Cell RNA-Seq Profiling Reveal Dynamic Signaling and Metabolic Transitions during Human Spermatogonial Stem Cell Development.
|
2017-10-01
|
Anne Goriely Jingtao Guo
|
Edward J Grow Chongil Yi Hana Mlcochova Geoffrey J Maher Cecilia Lindskog Patrick J Murphy Candice L Wike Douglas T Carrell James M Hotaling Bradley R Cairns
|
Cell Stem Cell
|
Role of the Astroglial Glutamate Exchanger xCT in Ventral Hippocampus in Resilience to Stress.
|
2017-10-01
|
Paul Greengard
|
Carla Nasca Benedetta Bigio Danielle Zelli Paolo de Angelis Timothy Lau Masahiro Okamoto Hideyo Soya Jason Ni Lars Brichta Rachael L Neve Francis S Lee Bruce S McEwen
|
Neuron
|
Comparative Transcriptomics of Steinernema and Caenorhabditis Single Embryos Reveals Orthologous Gene Expression Convergence during Late Embryogenesis.
|
2017-10-01
|
Ali Mortazavi
|
Marissa Macchietto Dristi Angdembey Negar Heidarpour Lorrayne Serra Bryan Rodriguez Nicole El-Ali
|
Genome Biology and Evolution
|
Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma.
|
2017-10-01
|
Derek Croote Steven A. Sloan
|
Spyros Darmanis Marco Mignardi Sophia Chernikova Peyman Samghababi Ye Zhang Norma Neff Mark Kowarsky Christine Caneda Gordon Li Steven D Chang Ian David Connolly Yingmei Li Ben A Barres Melanie Hayden Gephart Stephen R Quake
|
Cell Reports
|
Antigen receptor repertoire profiling from RNA-seq data.
|
2017-10-01
|
Mikhail Shugay Dmitriy M. Chudakov Olga I Zolotareva
|
Dmitriy A Bolotin Stanislav Poslavsky Alexey N Davydov Felix E Frenkel Lorenzo Fanchi Saskia Hemmers Ekaterina V Putintseva Anna S Obraztsova Ravshan I Ataullakhanov Alexander Y Rudensky Ton N Schumacher
|
Nature Biotechnology
|
Fasciclin-like arabinogalactan protein gene expression is associated with yield of flour in the milling of wheat.
|
2017-10-02
|
Agnelo Furtado Robert Henry
|
Ravi C Nirmal Parimalan Rangan
|
Scientific Reports
|
Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data.
|
2017-10-03
|
Cho-Yi Chen John Quackenbush Abhijeet R Sonawane Kimberly Glass John Platig
|
Joseph N Paulson Camila M Lopes-Ramos Marieke L Kuijjer Maud Fagny
|
BMC Bioinformatics
|
XBSeq2: a fast and accurate quantification of differential expression and differential polyadenylation.
|
2017-10-03
|
Wasim H. Chowdhury
|
Yuanhang Liu Ping Wu Jingqi Zhou Teresa L Johnson-Pais Zhao Lai Ronald Rodriguez Yidong Chen
|
BMC Bioinformatics
|
The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: summary and innovation in genomics.
|
2017-10-03
|
Zhandong Liu
|
Zhongming Zhao Ken Chen Yan Guo Genevera I Allen Jiajie Zhang W Jim Zheng Jianhua Ruan
|
BMC Genomics
|
Functional genomics of stromal cells in chronic inflammatory diseases.
|
2017-10-04
|
Kamil Slowikowski
|
Kevin Wei Michael B Brenner Soumya Raychaudhuri
|
Current Opinion in Rheumatology
|
CRISPR-mediated HDAC2 disruption identifies two distinct classes of target genes in human cells
|
2017-10-05
|
Paul S Knoepfler
|
Priyanka Somanath Rachel Herndon Klein
|
PLOS ONE
|
Johne's disease in cattle: an in vitro model to study early response to infection of Mycobacterium avium subsp. paratuberculosis using RNA-seq.
|
2017-10-05
|
Francesco Strozzi John L. Williams
|
Rosanna Marino Rossana Capoferri Simona Panelli Giulietta Minozzi Erminio Trevisi Gustavo G M Snel Paolo Ajmone-Marsan
|
Molecular Immunology
|
voomDDA: discovery of diagnostic biomarkers and classification of RNA-seq data.
|
2017-10-06
|
Dincer Goksuluk
|
Gokmen Zararsiz Bernd Klaus Selcuk Korkmaz Vahap Eldem Erdem Karabulut Ahmet Ozturk
|
PeerJ
|
The nuclear receptor ERβ engages AGO2 in regulation of gene transcription, RNA splicing and RISC loading.
|
2017-10-06
|
Alessandro Weisz Luca Ricciardi Giorgio Giurato Roberta Tarallo
|
Giuseppina Bruno Maria Ravo Francesca Rizzo Annamaria Salvati Giovanna Marchese Angela Cordella Teresa Rocco Valerio Gigantino Biancamaria Pierri Giovanni Cimmino Luciano Milanesi Concetta Ambrosino Tuula A Nyman Giovanni Nassa
|
Genome Biology
|
RNA sequencing identifies novel non-coding RNA and exon-specific effects associated with cigarette smoking.
|
2017-10-06
|
Alejandro Reyes
|
Margaret M Parker Robert P Chase Andrew Lamb Aabida Saferali Jeong H Yun Blanca E Himes Edwin K Silverman Craig P Hersh Peter J Castaldi
|
BMC Medical Genomics
|
Mouse embryonic stem cells can differentiate via multiple paths to the same state.
|
2017-10-09
|
James Alexander Briggs
|
Victor C Li Seungkyu Lee Clifford J Woolf Allon Klein Marc W Kirschner
|
eLife
|
Cardiovascular homeostasis dependence on MICU2, a regulatory subunit of the mitochondrial calcium uniporter.
|
2017-10-09
|
Kimberli J Kamer Christine E. Seidman Daniel M DeLaughter
|
Alexander G Bick Hiroko Wakimoto Yasemin Sancak Olga Goldberger Anna Axelsson Daniel M DeLaughter Joshua M Gorham Vamsi K Mootha J G Seidman
|
Proceedings of the National Academy of Sciences of the United States of America
|
SCENIC: single-cell regulatory network inference and clustering.
|
2017-10-09
|
Jean-Christophe Marine J Wouters Thomas Moerman Carmen Bravo González-Blas Gert Hulselmans Sara Aibar Jan Aerts
|
Vân Anh Huynh-Thu Florian Rambow Pierre Geurts Joost van den Oord
|
Nature Methods
|
Alcohol feeding in mice promotes colonic hyperpermeability and changes in colonic organoid stem cell fate.
|
2017-10-09
|
Hemraj Dodiya Faraz Bishehsari
|
Christopher B Forsyth Maliha Shaikh Garth Swanson Robin M Voigt Peter Wilkinson Beata Samelco Shiwen Song Ali Keshavarzian
|
Alcoholism: Clinical and Experimental Research
|
Dynamic transcriptomic analysis in hircine longissimus dorsi muscle from fetal to neonatal development stages.
|
2017-10-09
|
Siyuan Zhan
|
Wei Zhao Tianzeng Song Yao Dong Jiazhong Guo Jiaxue Cao Tao Zhong Linjie Wang Li Li Hongping Zhang
|
Functional and Integrative Genomics
|
Identification of circular RNAs in human aortic valves.
|
2017-10-09
|
Jun Wang
|
Jianle Chen Yun Jiang Weidong Gu Buqing Ni Haoliang Sun Wanjun Gu Liang Chen Yongfeng Shao
|
Gene
|
Toxicogenomics of the flame retardant tris (2-butoxyethyl) phosphate in HepG2 cells using RNA-seq.
|
2017-10-09
|
Gerrit Beemster Bart Cuypers Kris Laukens Ronny Blust
|
Boris V Krivoshiev Katrien Sprangers Steven J Husson
|
Toxicology in Vitro
|
Molecular architecture underlying fluid absorption by the developing inner ear
|
2017-10-10
|
Michael Hoa
|
Keiji Honda Sung Huhn Kim Michael C Kelly Joseph C Burns Laura Constance Xiangming Li Fei Zhou Matthew W Kelley Philine Wangemann Robert J Morell Andrew J Griffith
|
eLife
|
Building a locally diploid genome and transcriptome of the diatom Fragilariopsis cylindrus.
|
2017-10-10
|
Jan Strauss Mark McMullan
|
Pirita Paajanen Cock van Oosterhout Matthew D Clark Thomas Mock
|
Scientific Data
|
Modified RNA-seq method for microbial community and diversity analysis using rRNA in different types of environmental samples.
|
2017-10-10
|
Zhe-Xue Quan
|
Yong-Wei Yan Bin Zou Ting Zhu Wael N Hozzein
|
PLOS ONE
|
Differential gene regulatory networks in development and disease.
|
2017-10-10
|
Arun J Singh Chrissa Kioussi
|
Stephen A Ramsey Theresa M Filtz
|
Cellular and Molecular Life Sciences
|
Broad role for YBX1 in defining the small noncoding RNA composition of exosomes.
|
2017-10-10
|
Randy Schekman Matthew J Shurtleff
|
Jun Yao Yidan Qin Ryan M Nottingham Morayma M Temoche-Diaz Alan M Lambowitz
|
Proceedings of the National Academy of Sciences of the United States of America
|
RNASeq analysis of differentiated keratinocytes reveals a massive response to late events during human papillomavirus type 16 infection, including loss of epithelial barrier function.
|
2017-10-11
|
Derek Gatherer
|
T Klymenko Q Gu I Herbert A Stevenson V Iliev G Watkins C Pollock R Bhatia K Cuschieri P Herzyk S V Graham
|
Journal of Virology
|
Transcriptome analyses reveal SR45 to be a neutral splicing regulator and a suppressor of innate immunity in Arabidopsis thaliana.
|
2017-10-11
|
Xiao-Ning Zhang
|
Yifei Shi Jordan J Powers Nikhil B Gowda Chong Zhang Heba M M Ibrahim Hannah B Ball Samuel L Chen Hua Lu Stephen M Mount
|
BMC Genomics
|
Mitochondrial Cardiomyopathy Caused by Elevated Reactive Oxygen Species and Impaired Cardiomyocyte Proliferation.
|
2017-10-11
|
Zhiqiang Lin
|
Donghui Zhang Yifei Li Danielle A Heims-Waldron Vassilios J Bezzerides Silvia Guatimosim Yuxuan Guo Fei Gu Pingzhu Zhou Qing Ma Jianming Liu Da-Zhi Wang William T Pu
|
Circulation Research
|
Network modeling of kinase inhibitor polypharmacology reveals pathways targeted in chemical screens.
|
2017-10-12
|
Oana Ursu Ernest Fraenkel
|
Sara J C Gosline Neil Beeharry Lauren Fink Vikram Bhattacharjee Shao-Shan Carol Huang Yan Zhou Tim Yen
|
PLOS ONE
|
Antifungal defense of probiotic Lactobacillus rhamnosus GG is mediated by blocking adhesion and nutrient depletion.
|
2017-10-12
|
Christina Braunsdorf Jeanette Wagener
|
Daniela Mailänder-Sánchez Christian Grumaz Christoph Müller Stefan Lorenz Philip Stevens Betty Hebecker Bernhard Hube Franz Bracher Kai Sohn Martin Schaller
|
PLOS ONE
|
Differential regulation of two FLNA transcripts explains some of the phenotypic heterogeneity in the loss-of-function filaminopathies.
|
2017-10-12
|
Zandra A Jenkins Wenhua Wei David Markie Stephen Robertson
|
Alison Macharg Cheng-Yee Chang Margriet van Kogelenberg Tim Morgan Sophia Frentz Jacek Pilch Mark Hannibal Nicola Foulds George McGillivray Richard J Leventer Sixto García-Miñaúr Stuart Sugito Scott Nightingale Tracy Dudding Raj P Kapur
|
Human Mutation
|
Insights into grapevine defense response against drought as revealed by biochemical, physiological and RNA-Seq analysis.
|
2017-10-13
|
Jinggui Fang
|
Muhammad Salman Haider Cheng Zhang Mahantesh M Kurjogi Tariq Pervaiz Ting Zheng Chaobo Zhang Chen Lide Lingfie Shangguan
|
Scientific Reports
|
Merkel cell polyomavirus recruits MYCL to the EP400 complex to promote oncogenesis.
|
2017-10-13
|
Laurence Florens Myles Brown Rosa Yoon Reety Arora Alexander J Federation Peter M Howley
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Jingwei Cheng Donglim Esther Park Christian Berrios Elizabeth A White Timothy Branigan Tengfei Xiao Thomas Westerling Rhamy Zeid Benjamin Strober Selene K Swanson James E Bradner Megha Padi Michael P Washburn James A DeCaprio
|
PLOS Pathogens
|
Comparing two approaches of miR-34a target identification, biotinylated-miRNA pulldown vs miRNA overexpression.
|
2017-10-13
|
Ge Shan
|
Hassaan Mehboob Awan Abdullah Shah Farooq Rashid Shuai Wei Liang Chen
|
RNA Biology
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Cell Type-Specific Chromatin Signatures Underline Regulatory DNA Elements in Human Induced Pluripotent Stem Cells and Somatic Cells.
|
2017-10-13
|
Ning-Yi Shao
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Mingtao Zhao Shijun Hu Ning Ma Rajini Srinivasan Fereshteh Jahanbani Jaecheol Lee Sophia L Zhang Michael P Snyder Joseph C Wu
|
Circulation Research
|
MCM2-regulated functional networks in lung cancer by multi-dimensional proteomic approach.
|
2017-10-16
|
Chia-Lang Hsu Hsuan-Cheng Huang Hsueh-Fen Juan
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Chantal Hoi Yin Cheung Kai-Pu Chen Siao-Ting Chong Chang-Hsun Wu
|
Scientific Reports
|
A root-knot nematode small glycine and cysteine-rich secreted effector, MiSGCR1, is involved in plant parasitism.
|
2017-10-16
|
Bruno Favery
|
Chinh-Nghia Nguyen Laetitia Perfus-Barbeoch Michaël Quentin Jianlong Zhao Marc Magliano Nathalie Marteu Martine Da Rocha Nicolas Nottet Pierre Abad
|
New Phytologist
|
Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS.
|
2017-10-17
|
Dan Nettleton
|
Hung-Ying Lin Qiang Liu Xiao Li Jinliang Yang Sanzhen Liu Yinlian Huang Michael J Scanlon Patrick S Schnable
|
Genome Biology
|
An analysis of 67 RNA-seq datasets from various tissues at different stages of a model insect, Manduca sexta
|
2017-10-17
|
Xiaolong Cao Haobo Jiang
|
|
BMC Genomics
|
Characterization of amylolytic enzyme overproducing mutant of Aspergillus luchuensis obtained by ion beam mutagenesis.
|
2017-10-17
|
Taiki Futagami
|
Toshihiro Kojo Chihiro Kadooka Marisa Komohara Shiori Onitsuka Miya Tanimura Yukiko Muroi Shugo Kurazono Yohei Shiraishi Ken Oda Kazuhiro Iwashita Masahira Onoue Kayu Okutsu Yumiko Yoshizaki Kazunori Takamine Kazuki Mori Hisanori Tamaki
|
The Journal of General and Applied Microbiology
|
Genome-Wide Analysis of the Transcription Start Sites and Promoter Motifs of Phytoplasmas.
|
2017-10-17
|
Yutaro Neriya
|
Takamichi Nijo Hiroaki Koinuma Nozomu Iwabuchi Yugo Kitazawa Kazuyuki Tanno Yukari Okano Kensaku Maejima Yasuyuki Yamaji Kenro Oshima Shigetou Namba
|
DNA and Cell Biology
|
Simultaneous RNA-seq based transcriptional profiling of intracellular Brucella abortus and B. abortus-infected murine macrophages.
|
2017-10-17
|
Wongi Min
|
Huynh Tan Hop Lauren Togonon Arayan Alisha Wehdnesday Bernardo Reyes Tran Xuan Ngoc Huy Hu Jang Lee Jee Soo Son Suk Kim
|
Microbial Pathogenesis
|
The antibody repertoire of colorectal cancer.
|
2017-10-18
|
Seong Won Cha Vineet Bafna
|
Stefano Bonissone Seungjin Na Pavel A Pevzner
|
Molecular & Cellular Proteomics
|
MicroRNA profiling of human primary macrophages exposed to dengue virus identifies miRNA-3614-5p as antiviral and regulator of ADAR1 expression.
|
2017-10-18
|
Mayra Diosa-Toro Silvio Urcuqui-Inchima
|
Liliana Echavarría-Consuegra Jacky Flipse Geysson Javier Fernández Joost Kluiver Anke van den Berg Jolanda M Smit
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PLOS Neglected Tropical Diseases
|
Tomato CRY1a plays a critical role in the regulation of phytohormone homeostasis, plant development and carotenoid metabolism in fruits.
|
2017-10-18
|
Golam Jalal Ahammed
|
Chao-Chao Liu Guo-Ting Wang Chang-Jie Xu Kun-Song Chen Yan-Hong Zhou Jing-Quan Yu
|
Plant, Cell and Environment
|
The Impacts of Genome-wide Analyses on our Understanding of Human Herpesvirus Diversity and Evolution.
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2017-10-18 2018-01-01
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Moriah L. Szpara
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Daniel W Renner
|
Journal of Virology
|
Comparative transcriptome analysis reveals multiple functions for Mhy1p in lipid biosynthesis in the oleaginous yeast Yarrowia lipolytica.
|
2017-10-18
|
Guangyuan Wang
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Delong Li Zhengang Miao Shanshan Zhang Wenxing Liang Lin Liu
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Biochimica et Biophysica Acta
|
Lipoprotein lipase reaches the capillary lumen in chickens despite an apparent absence of GPIHBP1.
|
2017-10-19
|
Haibo Jiang André Bensadoun
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Cuiwen He Xuchen Hu Rachel S Jung Mikael Larsson Yiping Tu Sandra Duarte-Vogel Paul Kim Norma P Sandoval Tara R Price Christopher M Allan Brian Raney Rosemary L Walzem Richard I Kuo Anne P Beigneux Loren G Fong Stephen G Young
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JCI insight
|
Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium.
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2017-10-19
|
Gina Chaput
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Roberto Orellana Lye Meng Markillie Hugh Mitchell Matt Gaffrey Galya Orr Kristen M DeAngelis
|
PLOS ONE
|
The type II transmembrane serine protease matriptase cleaves the amyloid precursor protein and reduces its processing to β amyloid.
|
2017-10-20
|
François Béliveau
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Erwan Lanchec Antoine Désilets Anthony Flamier Shaimaa Mahmoud Gilbert Bernier Denis Gris Richard Leduc Christine Lavoie
|
Journal of Biological Chemistry
|
Profiling RNA-Seq at multiple resolutions markedly increases the number of causal eQTLs in autoimmune disease.
|
2017-10-23
|
Timothy J Vyse
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Christopher A Odhams Deborah S Cunninghame Graham
|
PLOS Genetics
|
Gene expression atlas of fruit ripening and transcriptome assembly from RNA-seq data in octoploid strawberry (Fragaria × ananassa).
|
2017-10-23
|
Aureliano Bombarely
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José F Sánchez-Sevilla José G Vallarino Sonia Osorio David Posé Catharina Merchante Miguel A Botella Iraida Amaya Victoriano Valpuesta
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Scientific Reports
|
Predicting causal variants affecting expression by using whole-genome sequencing and RNA-seq from multiple human tissues.
|
2017-10-23
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Andrew A Brown Kerrin S. Small Ana Viñuela
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Olivier Delaneau Tim D Spector Emmanouil T Dermitzakis
|
Nature Genetics
|
Whole Transcriptome Profiling: An RNA-Seq Primer and Implications for Pharmacogenomics Research.
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2017-10-23 2018-03-01
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Wolfgang Sadee
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Ana Caroline C Sá Julie A Johnson
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Clinical and Translational Science
|
Development of functional ectopic compound eyes in scarabaeid beetles by knockdown of orthodenticle.
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2017-10-24
|
Eduardo E. Zattara
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Anna L M Macagno Hannah A Busey Armin P Moczek
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Proceedings of the National Academy of Sciences of the United States of America
|
Neuromedin B expression defines the mouse retrotrapezoid nucleus.
|
2017-10-24
|
Suna Onengut-Gumuscu Douglas A Bayliss Patrice G Guyenet Ruth L Stornetta
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Yingtang Shi Daniel S Stornetta Emily A Farber Stephen D Turner
|
Journal of Neuroscience
|
FlyAtlas 2: a new version of the Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data.
|
2017-10-24
|
David P Leader
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Sue A Krause Aniruddha Pandit Shireen A Davies Julian A T Dow
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Nucleic Acids Research
|
An ApiAP2 member regulates expression of clonally variant genes of the human malaria parasite Plasmodium falciparum.
|
2017-10-25
|
Xue Yan Yam Mats Wahlgren
|
Rafael M Martins Cameron R Macpherson Aurélie Claes Christine Scheidig-Benatar Hiroshi Sakamoto Peter Preiser Suchi Goel Odile Sismeiro Jean-Yves Coppée Artur Scherf
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Scientific Reports
|
Efficient protein production by yeast requires global tuning of metabolism.
|
2017-10-25
|
Jens Nielsen Jichen Bao
|
Mingtao Huang Björn M Hallström Dina Petranovic
|
Nature Communications
|
A review of genome-wide transcriptomics studies in Parkinson's disease.
|
2017-10-25
|
Soraya Seedat Helena Kuivaniemi
|
Genevie Borrageiro William Haylett Soraya Bardien
|
European Journal of Neuroscience
|
Single-cell analysis identifies cellular markers of the HIV permissive cell.
|
2017-10-26
|
Sylvie Rato Antonio Rausell Angela Ciuffi
|
Miguel Muñoz Amalio Telenti
|
PLOS Pathogens
|
Dynamic changes in eIF4F-mRNA interactions revealed by global analyses of environmental stress responses.
|
2017-10-27
|
Joseph L Costello Graham D. Pavitt
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Christopher J Kershaw Lydia M Castelli David Talavera William Rowe Paul F G Sims Mark P Ashe Christopher M Grant Simon J Hubbard
|
Genome Biology
|
UClncR: Ultrafast and comprehensive long non-coding RNA detection from RNA-seq.
|
2017-10-27
|
Zhifu Sun
|
Asha Nair Xianfeng Chen Naresh Prodduturi Junwen Wang Jean-Pierre Kocher
|
Scientific Reports
|
Variant calling from RNA-seq data of the brain transcriptome of pigs and its application for allele-specific expression and imprinting analysis.
|
2017-10-27
|
Katarzyna Piórkowska Maria Oczkowicz Katarzyna Ropka-Molik
|
Tomasz Szmatoła
|
Gene
|
Bilin-dependent photoacclimation in Chlamydomonas reinhardtii.
|
2017-10-30
|
Sabeeha Merchant
|
Tyler M Wittkopp Stefan Schmollinger Shai I Saroussi Wei Hu Weiqing Zhang Qiuling Fan Sean D Gallaher Michael T Leonard Eric Soubeyrand Gilles Basset Arthur R Grossman Deqiang Duanmu J Clark Lagarias
|
The Plant Cell
|
Alterations in the host transcriptome in vitro following Rift Valley fever virus infection.
|
2017-10-30
|
Gustavo Palacios Brett Beitzel Aura Garrison
|
Chelsea Pinkham Bibha Dahal Cynthia L de la Fuente Nicole Bracci Michael Lindquist Connie Schmaljohn Aarthi Narayanan Catherine E Campbell Kylene Kehn-Hall
|
Scientific Reports
|
Cross platform analysis of transcriptomic data identifies ageing has distinct and opposite effects on tendon in males and females.
|
2017-10-31
|
Simon J. Cockell
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Louise I Pease Peter D Clegg Carole J Proctor Daryl J Shanley Mandy J Peffers
|
Scientific Reports
|
The non-invasive exfoliated transcriptome (exfoliome) reflects the tissue-level transcriptome in a mouse model of NSAID enteropathy.
|
2017-10-31
|
Brad R. Weeks
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Canaan M Whitfield-Cargile Kejun He Ivan Ivanov Jennifer S Goldsby Ana Chamoun-Emanuelli Laurie A Davidson Robert S Chapkin
|
Scientific Reports
|
An Accessible Proteogenomics Informatics Resource for Cancer Researchers.
|
2017-11-01
|
Lennart Martens
|
Matthew C Chambers Pratik D Jagtap James E Johnson Thomas McGowan Praveen Kumar Getiria Onsongo Candace R Guerrero Harald Barsnes Marc Vaudel Björn Grüning Ira R Cooke Mohammad Heydarian Karen L Reddy Timothy J Griffin
|
Cancer Research
|
MicroRNAs promote skeletal muscle differentiation of mesodermal iPSC-derived progenitors.
|
2017-11-01
|
Maurilio Sampaolesi Hanne Grosemans
|
Giorgia Giacomazzi Bryan Holvoet Sander Trenson Ellen Caluwé Bojana Kravic Álvaro Cortés-Calabuig Christophe M Deroose Stefan Janssens Elizabeth McNally Mattia Quattrocelli
|
Nature Communications
|
The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas.
|
2017-11-01
|
Aviv Regev Nenad Sestan
|
Joseph R Ecker Daniel H Geschwind Arnold R Kriegstein John Ngai Pavel Osten Damon Polioudakis Nenad Sestan Ian R Wickersham Hongkui Zeng
|
Neuron
|
Guidelines for Genome-Scale Analysis of Biological Rhythms.
|
2017-11-01
|
Frédéric Gachon Han Wang Maria Olmedo Pål O. Westermark Dmitri A. Nusinow Herman Wijnen E Nagoshi Charissa de Bekker Debra J. Skene Aziz Sancar Eric E. Zhang Paolo Sassone-Corsi Francis J. Doyle III Pierre Baldi Kristin Eckel-Mahan Martha Merrow
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Michael E Hughes Katherine C Abruzzi Ravi Allada Ron Anafi Alaaddin Bulak Arpat Gad Asher Deborah Bell-Pedersen Justin Blau Steve Brown M Fernanda Ceriani Zheng Chen Joanna C Chiu Juergen Cox Alexander M Crowell Jason P DeBruyne Luciano DiTacchio Giles E Duffield Jay C Dunlap Karyn A Esser Garret A FitzGerald Daniel B Forger Lauren J Francey Ying-Hui Fu Paul de Goede Susan S Golden Carla Green John Harer Stacey Harmer Jeff Haspel Michael H Hastings Hanspeter Herzel Erik D Herzog Christy Hoffmann Christian Hong Jacob J Hughey Jennifer M Hurley Horacio O de la Iglesia Carl Johnson Steve A Kay Nobuya Koike Karl Kornacker Achim Kramer Katja Lamia Tanya Leise Scott A Lewis Jiajia Li Xiaodong Li Andrew C Liu Jennifer J Loros Tami A Martino Jerome S Menet Andrew J Millar Todd Mockler Felix Naef Michael N Nitabach Louis J Ptáček David Rand Akhilesh B Reddy Maria S Robles Till Roenneberg Michael Rosbash Marc D Ruben Samuel S C Rund Amita Sehgal Scott Sherrill-Mix Kai-Florian Storch Joseph S Takahashi Hiroki R Ueda Charles Weitz Ying Xu Gang Wu Seung-Hee Yoo Michael Young Tomasz Zielinski John B Hogenesch
|
Journal of Biological Rhythms
|
RNA-sequencing-based comparative analysis of human hepatic progenitor cells and their niche from alcoholic steatohepatitis livers.
|
2017-11-02
|
Matthias Van Haele Olivier Govaere Juan-Jose Ventura Leo A van Grunsven
|
An Ceulemans Stefaan Verhulst Tania Roskams
|
Cell Death and Disease
|
RNA-Seq de novo assembly and differential transcriptome analysis of the nematode Ascaridia galli in relation to in vivo exposure to flubendazole.
|
2017-11-03
|
Johan Höglund
|
Mihaela M Martis Behdad Tarbiat Eva Tydén Désirée S Jansson
|
PLOS ONE
|
Detailed transcriptome analysis of the plant growth promoting Paenibacillus riograndensis SBR5 by using RNA-seq technology.
|
2017-11-03
|
Jörn Kalinowski
|
Luciana Fernandes Brito Marta Irla Volker F Wendisch
|
BMC Genomics
|
A survey of software tools for microRNA discovery and characterization using RNA-seq.
|
2017-11-06
|
Stefania Bortoluzzi Enrico Gaffo
|
Michele Bortolomeazzi
|
Briefings in Bioinformatics
|
RNA-Seq analysis reveals insight into enhanced rice Xa7-mediated bacterial blight resistance at high temperature.
|
2017-11-06
|
Stephen P Cohen Jan E Leach Andy Pereira
|
Hongxia Liu Cristiana T Argueso Casiana Vera Cruz Valerie Verdier
|
PLOS ONE
|
A comparison of honeybee (Apis mellifera) queen, worker and drone larvae by RNA-Seq.
|
2017-11-06
|
Andrew B. Barron
|
Xu-Jiang He Wu-Jun Jiang Mi Zhou Zhi-Jiang Zeng
|
Insect Science
|
f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq.
|
2017-11-07
|
Oliver Stegle Davis J McCarthy John C Marioni
|
Florian Buettner Naruemon Pratanwanich
|
Genome Biology
|
Unsupervised Trajectory Analysis of Single-Cell RNA-Seq and Imaging Data Reveals Alternative Tuft Cell Origins in the Gut.
|
2017-11-07
|
Ken S. Lau
|
Charles A Herring Amrita Banerjee Eliot T McKinley Alan J Simmons Jie Ping Joseph T Roland Jeffrey L Franklin Qi Liu Michael J Gerdes Robert J Coffey
|
Cell systems
|
bcbioRNASeq: R package for bcbio RNA-seq analysis
|
2017-11-08
|
Michael J Steinbaugh
|
Lorena Pantano Rory D. Kirchner Victor Barrera Brad A. Chapman Mary E. Piper Meeta Mistry Radhika S. Khetani Kayleigh D. Rutherford Oliver Hofmann John N. Hutchinson Shannan Ho Sui
|
F1000Research
|
Characteristics of allelic gene expression in human brain cells from single-cell RNA-seq data analysis.
|
2017-11-10
|
Deyou Zheng Dejian Zhao
|
Mingyan Lin Erika Pedrosa Herbert M Lachman
|
BMC Genomics
|
A transcriptomic study of myogenic differentiation under the overexpression of PPARγ by RNA-Seq.
|
2017-11-10
|
Wen-Xing Li
|
Kan He Guoying Wu Daogang Guan Wenwen Lv Mengting Gong Shoudong Ye Aiping Lu
|
Scientific Reports
|
Innate Cell-Mediated Cytotoxic Activity of European Sea Bass Leucocytes Against Nodavirus-Infected Cells: A Functional and RNA-seq Study.
|
2017-11-13
|
Tyler Alioto Alberto Cuesta Anna Esteve-Codina
|
Elena Chaves-Pozo Yulema Valero Jèssica Gómez-Garrido Marc Dabad José Meseguer M Ángeles Esteban
|
Scientific Reports
|
Coupling shRNA screens with single-cell RNA-seq identifies a dual role for mTOR in reprogramming-induced senescence.
|
2017-11-14
|
Nadine Martin Wolf Reik
|
Marieke Aarts Athena Georgilis Meryam Beniazza Patrizia Beolchi Ana Banito Thomas Carroll Marizela Kulisic Daniel F Kaemena Gopuraja Dharmalingam Johannes Zuber Keisuke Kaji Tamir Chandra Jesús Gil
|
Genes & Development
|
Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi
|
2017-11-14
|
Michael Han Jens Keilwagen
|
Frank Hartung Sven O. Twardziok Jan Grau
|
|
Beyond pseudotime: Following T-cell maturation in single-cell RNAseq time series
|
2017-11-14
|
Fabian J. Theis
|
David S. Fischer Anna K. Fiedler Eric Kernfeld Ryan M. J. Genga Jan Hasenauer Rene Maehr
|
|
The fractured landscape of RNA-seq alignment: The default in our STARs
|
2017-11-16
|
Sara Ballouz Jesse Gillis
|
Alexander Dobin Thomas R Gingeras
|
|
Deep RNAseq indicates protective mechanisms of cold-tolerant indica rice plants during early vegetative stage.
|
2017-11-18
|
Felipe Klein Ricachenevsky Janette Palma Fett Rinaldo Pires Dos Santos
|
Raul Antonio Sperotto Artur Teixeira de Araújo Junior Janete Mariza Adamski Denise Cargnelutti Ben-Hur Neves de Oliveira Renata Pereira da Cruz Leila Picolli da Silva
|
Plant Cell Reports
|
RNA-seq and Tn-seq reveal fitness determinants of vancomycin-resistant Enterococcus faecium during growth in human serum.
|
2017-11-21
|
Willem van Schaik Tomasz K Prajsnar
|
Xinglin Zhang Vincent de Maat Ana M Guzmán Prieto Jumamurat R Bayjanov Mark de Been Malbert R C Rogers Marc J M Bonten Stéphane Mesnage Rob J L Willems
|
BMC Genomics
|
Oregano dietary supplementation modifies the liver transcriptome profile in broilers: RNASeq analysis.
|
2017-11-21
|
Camillo Pieramati Stefano Capomaccio
|
Marcella Sabino Katia Cappelli Andrea Verini-Supplizi Lorenzo Bomba Paolo Ajmone-Marsan Gabriella Cobellis Oliviero Olivieri Massimo Trabalza-Marinucci
|
Research in Veterinary Science
|
A multiple near isogenic line (multi-NIL) RNA-seq approach to identify candidate genes underpinning QTL.
|
2017-11-23
|
Meixue Zhou Sergey Shabala
|
Ahsan Habib Jonathan J Powell Jiri Stiller Miao Liu Donald M Gardiner Chunji Liu
|
Theoretical and Applied Genetics
|
Transcriptome profiling of sorted endoreduplicated nuclei from tomato fruits: how the global shift in expression ascribed to DNA ploidy influences RNA-Seq data normalization and interpretation.
|
2017-11-24
|
Elie Maza Nathalie Gonzalez Chris Bowler
|
Julien Pirrello Cynthia Deluche Nathalie Frangne Frédéric Gévaudant Anis Djari Mickaël Bourge Jean-Pierre Renaudin Spencer Brown Mohamed Zouine Christian Chevalier
|
The Plant Journal
|
Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data.
|
2017-11-25
|
Antonio Scialdone John C Marioni Jonathan A Griffiths
|
|
BMC Genomics
|
Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq.
|
2017-11-27
|
Ruolin Liu Julie Dickerson
|
|
PLOS Computational Biology
|
STRT-seq-2i: dual-index 5' single cell and nucleus RNA-seq on an addressable microwell array.
|
2017-11-27
|
Jaromír Mikes Peter Lönnerberg Sten Linnarsson
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Hannah Hochgerner Rebecca Hodge Abeer Heskol Hermann Hubschle Philip Lin Simone Picelli Gioele La Manno Michael Ratz Jude Dunne Syed Husain Ed Lein Maithreyan Srinivasan Amit Zeisel
|
Scientific Reports
|
Whole transcriptome RNA-Seq analysis reveals extensive cell type-specific compartmentalization in Volvox carteri.
|
2017-11-28
|
Armin Hallmann
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Benjamin Klein Daniel Wibberg
|
BMC Biology
|
A dual transcript-discovery approach to improve the delimitation of gene features from RNA-seq data in the chicken model.
|
2017-11-28
|
Delphine Duprez Sigmar Stricker Marvin Martens
|
Mickael Orgeur Stefan T Börno Bernd Timmermann
|
Biology Open
|
Formation of Staphylococcus aureus Biofilm in the Presence of Sublethal Concentrations of Disinfectants Studied via a Transcriptomic Analysis Using Transcriptome Sequencing (RNA-seq).
|
2017-12-01
|
Jan Oppelt
|
M Slany L Cincarova
|
Applied and Environmental Microbiology
|
Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population.
|
2017-12-05
|
Harm Nijveen Wilco Ligterink
|
Elise A R Serin L B Snoek Leo A J Willems Jose M Jiménez-Gómez Henk W M Hilhorst
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Frontiers in Genetics
|
A RNA-Seq Analysis of the Response of Photosynthetic System to Low Nitrogen Supply in Maize Leaf.
|
2017-12-05
|
Lixing Yuan
|
Xiaohuan Mu Qinwu Chen Fanjun Chen Guohua Mi
|
International Journal of Molecular Sciences
|
Telomere heterogeneity linked to metabolism and pluripotency state revealed by simultaneous analysis of telomere length and RNA-seq in the same human embryonic stem cell.
|
2017-12-08
|
Yu Sun
|
Hua Wang Kunshan Zhang Yifei Liu Yudong Fu Shan Gao Peng Gong Haiying Wang Zhongcheng Zhou Ming Zeng Zhenfeng Wu Tong Chen Siguang Li Lin Liu
|
BMC Biology
|
Optimizing RNA-seq studies to investigate herbicide resistance.
|
2017-12-09
|
Patrick J. Tranel
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Darci A Giacomini Todd Gaines Roland Beffa
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Pest Management Science
|
Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates.
|
2017-12-11
|
Yoseph Barash
|
Scott Norton Jorge Vaquero-Garcia Nicholas F Lahens Gregory R Grant
|
Bioinformatics
|
DaMiRseq-an R/Bioconductor package for data mining of RNA-Seq data: normalization, feature selection and classification.
|
2017-12-11
|
Luca Piacentini Gualtiero I Colombo
|
Mattia Chiesa
|
Bioinformatics
|
netSmooth: Network-smoothing based imputation for single cell RNA-seq
|
2017-12-13
|
Altuna Akalin
|
Jonathan Ronen
|
|
The transcriptome of Mycobacterium tuberculosis in a lipid-rich dormancy model through RNAseq analysis.
|
2017-12-15
|
Filip Van Nieuwerburgh Dieter Deforce Laurentijn Tilleman Peter Vandamme
|
Diana A Aguilar-Ayala Juan Carlos Palomino Jorge A Gonzalez-Y-Merchand Anandi Martin
|
Scientific Reports
|
Elucidating the 16S rRNA 3' boundaries and defining optimal SD/aSD pairing in Escherichia coli and Bacillus subtilis using RNA-Seq data.
|
2017-12-15
|
Xuhua Xia Yulong Wei
|
Jordan R Silke
|
Scientific Reports
|
High-Throughput RNA-Seq Data Analysis of the Single Nucleotide Polymorphisms (SNPs) and Zygomorphic Flower Development in Pea (Pisum sativum L.).
|
2017-12-20
|
Shihao Su
|
Keyuan Jiao Xin Li Wuxiu Guo Da Luo
|
International Journal of Molecular Sciences
|
RNA-Seq differential expression analysis: An extended review and a software tool.
|
2017-12-21
|
Fabrício M Lopes Douglas Domingues
|
Juliana Costa-Silva
|
PLOS ONE
|
RNA-seq identifies a diminished differentiation gene signature in primary monolayer keratinocytes grown from lesional and uninvolved psoriatic skin.
|
2017-12-22
|
William R Swindell Mrinal K. Sarkar
|
Yun Liang Xianying Xing Jaymie Baliwag James T Elder Andrew Johnston Nicole L Ward Johann E Gudjonsson
|
Scientific Reports
|
SAKE (Single-cell RNA-Seq Analysis and Klustering Evaluation) Identifies Markers of Resistance to Targeted BRAF Inhibitors in Melanoma Cell Populations
|
2017-12-24
|
Molly Hammell
|
Yu-Jui Ho Naishitha Anaparthy David Molik Toby Aicher Ami Patel James Hicks
|
|
Combination of iTRAQ proteomics and RNA-seq transcriptomics reveals multiple levels of regulation in phytoplasma-infected Ziziphus jujuba Mill.
|
2017-12-27
|
Jiancan Feng
|
Xia Ye Huiyu Wang Peng Chen Bing Fu Mengyang Zhang Jidong Li Xianbo Zheng Bin Tan
|
Horticulture research
|
DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition.
|
2017-12-28
|
Daniel Gautheret Mélina Gallopin
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Jérôme Audoux Nicolas Philippe Rayan Chikhi Mikaël Salson Mélina Gallopin Marc Gabriel Jérémy Le Coz Emilie Drouineau Thérèse Commes
|
Genome Biology
|
A systematic performance evaluation of clustering methods for single-cell RNA-seq data
|
2018
|
Charlotte Soneson Mark D. Robinson
|
Angelo Duò
|
F1000Research
|
Phylogeny of the spider mite sub-family Tetranychinae (Acari: Tetranychidae) inferred from RNA-Seq data
|
2018
|
Kazuo Ishii Tomoko Matsuda
|
Toshinori Kozaki Tetsuo Gotoh
|
PLOS ONE
|
Transcriptomics and RNA-Seq Data Analysis
|
2018
|
Xuhua Xia
|
|
|
RNA Sequencing (RNA-Seq) Reveals Extremely Low Levels of Reticulocyte-Derived Globin Gene Transcripts in Peripheral Blood From Horses () and Cattle ()
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2018
|
Carolina N Correia Stephen V. Gordon
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Kirsten E McLoughlin Nicolas C Nalpas David A Magee John A Browne Kevin Rue-Albrecht David E MacHugh
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Frontiers in Genetics
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Using Supervised Learning Methods for Gene Selection in RNA-Seq Case-Control Studies
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2018
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Stephane Wenric
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Ruhollah Shemirani
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Frontiers in Genetics
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Clinical significance and effect of MTDH/AEG-1 in bladder urothelial cancer: a study based on immunohistochemistry, RNA-seq, and in vitro verification
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2018
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Gang Chen
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Yu Zhang Li-Jie Zhang Yi-Wu Dang Sheng-Hua Li Hai-Biao Yan
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Cancer Management and Research
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Correction of gene model annotations improves isoform abundance estimates: the example of ketohexokinase ( )
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2018
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Christophe D Chabbert Tanja Eberhart Werner J Kovacs
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Ilaria Guccini Wilhelm Krek
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F1000Research
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Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples.
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2018-01-01
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Ben Langmead Abhinav Nellore
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Christopher Wilks Phani Gaddipati
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Bioinformatics
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Accurate Profiling and Quantification of tRNA Fragments from RNA-Seq Data: A Vade Mecum for MINTmap.
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2018-01-01
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Aristeidis G Telonis Isidore Rigoutsos
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Phillipe Loher
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Methods in Molecular Biology
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Brachypodium distachyon Long Noncoding RNAs: Genome-Wide Identification and Expression Analysis.
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2018-01-01
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Edoardo Bertolini
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Concetta De Quattro Erica Mica Mario Enrico Pè
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Methods in Molecular Biology
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Preparing cDNA Libraries from Lytic Phage-Infected Cells for Whole Transcriptome Analysis by RNA-Seq.
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2018-01-01
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Bob G Blasdel
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Pieter-Jan Ceyssens Rob Lavigne
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Methods in Molecular Biology
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A Workflow Guide to RNA-seq Analysis of Chaperone Function and Beyond.
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2018-01-01
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Benjamin J Lang
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Kristina M Holton Jianlin Gong Stuart K Calderwood
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Methods in Molecular Biology
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Application of RNA-seq and Bioimaging Methods to Study Microbe-Microbe Interactions and Their Effects on Biofilm Formation and Gene Expression.
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2018-01-01
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Lars Jelsbak Claus Sternberg
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Cristina Isabel Amador
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Methods in Molecular Biology
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Laser Capture Microdissection-Based RNA-Seq of Barley Grain Tissues.
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2018-01-01
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Martin Mascher
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Ronny Brandt Johannes Thiel
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Methods in Molecular Biology
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Genome-Wide circRNA Profiling from RNA-seq Data.
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2018-01-01
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Pedro Miura
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Daphne A Cooper Mariela Cortés-López
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Methods in Molecular Biology
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RNA-Seq Analysis of the Transcriptome of Leaf Senescence in Tobacco.
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2018-01-01
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Yongfeng Guo
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Wei Li
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Methods in Molecular Biology
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netSmooth: Network-smoothing based imputation for single cell RNA-seq.
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2018-01-03
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Altuna Akalin
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Jonathan Ronen
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F1000Research
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RNAseq analysis of α-proteobacterium Gluconobacter oxydans 621H.
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2018-01-06
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Tino Polen Björn Usadel Michael Bott Jörn Kalinowski
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Angela Kranz Tobias Busche Alexander Vogel
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BMC Genomics
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Integrative approach using liver and duodenum RNA-Seq data identifies candidate genes and pathways associated with feed efficiency in pigs.
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2018-01-11
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Yuliaxis Ramayo-Caldas Klaus Wimmers David Torrallardona
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Maria Ballester Juan Pablo Sánchez Olga González-Rodríguez Manuel Revilla Henry Reyer Raquel Quintanilla
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Scientific Reports
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Transcriptome Analysis Based on RNA-Seq in Understanding Pathogenic Mechanisms of Diseases and the Immune System of Fish: A Comprehensive Review.
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2018-01-15
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Gokhlesh Kumar
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Arun Sudhagar Mansour El-Matbouli
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International Journal of Molecular Sciences
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A general and flexible method for signal extraction from single-cell RNA-seq data.
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2018-01-18
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Jean-Philippe Vert
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Davide Risso Fanny Perraudeau Svetlana Gribkova Sandrine Dudoit
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Nature Communications
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Observation weights to unlock bulk RNA-seq tools for zero inflation and single-cell applications
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2018-01-18
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Charlotte Soneson Michael I Love Mark D. Robinson Jean-Philippe Vert
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Koen Van den Berge Fanny Perraudeau Davide Risso Sandrine Dudoit Lieven Clement
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RNA-seq analysis reveals alternative splicing under salt stress in cotton, Gossypium davidsonii.
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2018-01-23
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Wangzhen Guo
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Guozhong Zhu Weixi Li Feng Zhang
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BMC Genomics
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Defining the earliest step of cardiovascular lineage segregation by single-cell RNA-seq.
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2018-01-25
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Xiaonan Wang
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Fabienne Lescroart Xionghui Lin Benjamin Swedlund Souhir Gargouri Adriana Sànchez-Dànes Victoria Moignard Christine Dubois Catherine Paulissen Sarah Kinston Cédric Blanpain
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Science
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Identification and visualisation of differential isoform expression in RNA-seq time series.
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2018-02-01
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Cristina Martí
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María José Nueda Jordi Martorell-Marugan Sonia Tarazona Ana Conesa
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Bioinformatics
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RNA-seq transcriptome analysis of breast cancer cell lines under shikonin treatment.
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2018-02-08
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Hung-Pin Tu
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Kuo-Hua Lin Ming-Yii Huang Wei-Chung Cheng Shu-Chi Wang Shih-Hua Fang Chia-Cheng Su Yung-Li Hung Po-Len Liu Chi-Shuo Chen Yu-Ting Wang Chia-Yang Li
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Scientific Reports
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RNA-Seq analysis during the life cycle of Cryptosporidium parvum reveals significant differential gene expression between proliferating stages in the intestine and infectious sporozoites.
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2018-02-09
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Christoph Lippuner Walter Basso Nicholas C Smith Peter Deplazes
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Chandra Ramakrishnan Marc W Schmid Michal Okoniewski Michael Hässig Adrian B Hehl
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International Journal for Parasitology
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De novo transcriptome analysis of Bagarius yarrelli (Siluriformes: Sisoridae) and the search for potential SSR markers using RNA-Seq.
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2018-02-09
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Min Du
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Na Li Baozhen Niu Yanhong Liu Dongjing You Defu Jiang Congquan Ruan Zhengquan Qin Taowen Song Wentao Wang
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PLOS ONE
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RNA-QC-chain: comprehensive and fast quality control for RNA-Seq data.
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2018-02-14
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Qian Zhou
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Xiaoquan Su Gongchao Jing Songlin Chen Kang Ning
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BMC Genomics
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Oasis 2: improved online analysis of small RNA-seq data.
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2018-02-14
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Stefan Bonn
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Raza-Ur Rahman Abhivyakti Gautam Jörn Bethune Abdul Sattar Maksims Fiosins Daniel Sumner Magruder Vincenzo Capece Orr Shomroni
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BMC Bioinformatics
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RNA-seq Reveals the Overexpression of IGSF9 in Endometrial Cancer.
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2018-02-14
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Zonggao Shi
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Chunyan Li Laura Tarwater Jun Li Yang Li William Kaliney Darshan S Chandrashekar M Sharon Stack
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Journal of oncology
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Mixed-species RNAseq analysis of human lymphoma cells adhering to mouse stromal cells identifies a core gene set that is also differentially expressed in the lymph node microenvironment of mantle cell lymphoma and chronic lymphocytic leukemia patien
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2018-02-15
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Johan Henriksson
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Gustav Arvidsson Birgitta Sander Anthony P Wright
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Haematologica
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Machine learning integration of rheumatoid arthritis synovial histology and RNAseq data identifies three disease subtypes.
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2018-02-22
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Dana E Orange
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Arthritis & Rheumatology
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MetaMap: An atlas of metatranscriptomic reads in human disease-related RNA-seq data
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2018-02-22
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Lukas Simon Fabian J. Theis
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Sebastian Karg Alexander J Westermann Marion Engel Ali HA Elbehery Burkhard Hense Matthias Heinig Li Deng
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Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation.
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2018-02-23
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Harold Swerdlow Andrew Butler Lionel B Ivashkiv William Stephenson
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Laura T Donlin Cristina Rozo Bernadette Bracken Ali Rashidfarrokhi Susan M Goodman Vivian P Bykerk Dana E Orange Robert B Darnell Rahul Satija
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Nature Communications
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Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications.
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2018-02-26
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Koen Van den Berge
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Fanny Perraudeau Charlotte Soneson Michael I Love Davide Risso Jean-Philippe Vert Mark D Robinson Sandrine Dudoit Lieven Clement
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Genome Biology
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SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer.
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2018-03-01
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Raffaele A. Calogero Marco Beccuti
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Francesca Cordero Maddalena Arigoni Riccardo Panero Elvio G Amparore Susanna Donatelli
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Bioinformatics
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First insight into the viral community of the cnidarian model metaorganism Aiptasia using RNA-Seq data.
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2018-03-01
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Christian R. Voolstra Jan D Brüwer
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PeerJ
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Single-Cell RNA-Seq of Mouse Dopaminergic Neurons Informs Candidate Gene Selection for Sporadic Parkinson Disease.
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2018-03-01
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A Jennifer Morton
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Paul W Hook Sarah A McClymont Gabrielle H Cannon William D Law Loyal A Goff Andrew S McCallion
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American Journal of Human Genetics
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Exponential scaling of single-cell RNA-seq in the past decade
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2018-03-01
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Valentine Svensson Sarah Teichmann
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Roser Vento-Tormo
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Nature Protocols
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Small RNA-seq analysis of circulating miRNAs to identify phenotypic variability in Friedreich's ataxia patients.
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2018-03-06
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Marta Seco-Cervera José Luis García-giménez
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Dayme González-Rodríguez José Santiago Ibáñez-Cabellos Lorena Peiró-Chova Federico V Pallardó
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Scientific Data
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An accurate and robust imputation method scImpute for single-cell RNA-seq data.
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2018-03-08
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Jingyi Jessica Li Wei Vivian Li
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Nature Communications
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Comprehensive Identification and Spatial Mapping of Habenular Neuronal Types Using Single-Cell RNA-Seq.
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2018-03-09
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Aviv Regev
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Shristi Pandey Karthik Shekhar Alexander F Schier
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Current Biology
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Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine Atherosclerosis.
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2018-03-15
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Ehsan Vafadarnejad Panagiota Arampatzi Antoine-Emmanuel Saliba Dennis Wolf Alma Zernecke
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Clément Cochain Pelisek Jaroslav Holger Winkels Klaus Ley
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Circulation Research
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BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data.
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2018-03-20
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Jens Wrammert Colin Havenar-Daughton
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Amit A Upadhyay Robert C Kauffman Amber N Wolabaugh Alice Cho Nirav B Patel Samantha M Reiss Reem A Dawoud Gregory K Tharp Iñaki Sanz Bali Pulendran Shane Crotty F Eun-Hyung Lee Steven E Bosinger
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Genome Medicine
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Author Correction: UClncR: Ultrafast and comprehensive long non-coding RNA detection from RNA-seq.
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2018-03-20
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Zhifu Sun
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Asha Nair Xianfeng Chen Naresh Prodduturi Junwen Wang Jean-Pierre Kocher
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Scientific Reports
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Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites
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2018-03-27
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Oliver Billker Matthew Berriman Ana Rita Gomes
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Adam J Reid Arthur M Talman Hayley M Bennett Mandy J Sanders Christopher J R Illingworth Mara Kn Lawniczak
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eLife
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QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data.
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2018-03-28
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Quaid D Morris
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Kevin C H Ha Benjamin J Blencowe
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Genome Biology
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Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq.
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2018-04-01
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Volker Hovestadt Christian Dorfer Angel M. Carcaboso Maria Martinez-Lage Mark W. Kieran Orit Rozenblatt-Rosen Aviv Regev Mariella G Filbin Christopher W Mount Nathan D Mathewson Michelle Monje Gad Getz
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Itay Tirosh McKenzie L Shaw Leah E Escalante Cyril Neftel Nelli Frank Kristine Pelton Christine M Hebert Christine Haberler Keren Yizhak Johannes Gojo Kristof Egervari Peter van Galen Dennis M Bonal Quang-De Nguyen Alexander Beck Claire Sinai Thomas Czech Liliana Goumnerova Cinzia Lavarino Jaume Mora Ravindra Mylvaganam Christina C Luo Andreas Peyrl Mara Popović Amedeo Azizi Tracy T Batchelor Matthew P Frosch Pratiti Bandopadhayay Rameen Beroukhim Gerhard Fritsch Kai W Wucherpfennig David N Louis Irene Slavc Keith L Ligon Todd R Golub Bradley E Bernstein Mario L Suvà
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Science
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Single-Cell RNA-Seq Reveals Transcriptional Heterogeneity in Latent and Reactivated HIV-Infected Cells.
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2018-04-01
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Angela Ciuffi Matthias Cavassini
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Monica Golumbeanu Sara Cristinelli Sylvie Rato Miguel Munoz Niko Beerenwinkel
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Cell Reports
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Identification of Hub Genes and Pathways in Zika Virus Infection Using RNA-Seq Data: A Network-Based Computational Approach.
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2018-04-02
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Sanathoi Gurumayum Rahul Brahma Mathavan Muthaiyan
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Leimarembi Devi Naorem Jeyakodi Gopal Amouda Venkatesan
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Viral Immunology
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RNA-Seq analysis validates the use of culture-derived Trypanosoma brucei and provides new markers for mammalian and insect life-cycle stages.
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2018-04-02
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Isabel Roditi
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Arunasalam Naguleswaran Nicholas Doiron
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BMC Genomics
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RNA sequencing (RNA-seq) reveals extremely low levels of reticulocyte-derived globin gene transcripts in peripheral blood from horses (Equus caballus) and cattle (Bos taurus)
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2018-04-04
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Kévin Rue-Albrecht David E. MacHugh
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Carolina N Correia Kirsten E McLoughlin Nicolas C Nalpas David A Magee John A Browne Stephen V. Gordon
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Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken
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2018-04-05
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Stephen J Bush Mark P Stevens
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Lucy Freem Amanda J MacCallum Jenny O'Dell Chunlei Wu Cyrus Afrasiabi Androniki Psifidi Jacqueline Smith Kim M Summers David A Hume
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A Beginner's Guide to Analysis of RNA-seq Data.
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2018-04-06
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Elizabeth T. Bartom
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Clarissa M Koch Stephen F Chiu Mahzad Akbarpour Ankit Bharat Karen M Ridge Deborah R Winter
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American Journal of Respiratory Cell and Molecular Biology
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A multitask clustering approach for single-cell RNA-seq analysis in Recessive Dystrophic Epidermolysis Bullosa.
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2018-04-09
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Cindy R Eide Jakub Tolar
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Huanan Zhang Catherine A A Lee Zhuliu Li John R Garbe Raphael Petegrosso Rui Kuang
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PLOS Computational Biology
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Massive mining of publicly available RNA-seq data from human and mouse.
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2018-04-10
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Avi Ma'ayan Moshe C Silverstein Alexander Lachmann
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Denis Torre Alexandra B Keenan Kathleen M Jagodnik Hoyjin J Lee Lily Wang
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Nature Communications
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Approximate inference of gene regulatory network models from RNA-Seq time series data.
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2018-04-11
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Thomas Thorne
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BMC Bioinformatics
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Sialome diversity of ticks revealed by RNAseq of single tick salivary glands.
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2018-04-13
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José M. Ribeiro Jan Perner
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Sára Kropáčková Petr Kopáček
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PLOS Neglected Tropical Diseases
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Complementary information on single nucleotide variants, INDELs and functional translocations can be obtained with RNAseq using different library preparations
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2018-04-14
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Raffaele A. Calogero Alessandro Weisz
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Riccardo Panero Maddalena Arigoni Martina Olivero Francesca Cordero Marco Beccuti Maria Flavia Direnzo
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RNA-Seq reveals the existence of a CDKN1C-E2F1-TP53 axis that is altered in human T-cell lymphoblastic lymphomas.
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2018-04-16
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Marcos Malumbres
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Pilar López-Nieva Pablo Fernández-Navarro Concepción Vaquero-Lorenzo María Villa-Morales Osvaldo Graña-Castro María Ángeles Cobos-Fernández José Luis López-Lorenzo Pilar Llamas Laura González-Sanchez Isabel Sastre Marina Pollan Javier Santos José Fernández-Piqueras
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BMC Cancer
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The Physcomitrella patens gene atlas project: large scale RNA-seq based expression data.
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2018-04-22
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Alessandro Alboresi Manuel Hiss Inés Ponce de León Daniel Lang Kerrie Barry
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Pierre-François Perroud Fabian B Haas Kristian K Ullrich Mojgan Amirebrahimi Roberto Bassi Sandrine Bonhomme Haodong Chen Juliet Coates Tomomichi Fujita Anouchka Guyon-Debast Junyan Lin Anna Lipzen Fabien Nogué Melvin J Oliver Ralph S Quatrano Catherine Rameau Bernd Reiss Ralf Reski Mariana Ricca Younousse Saidi Ning Sun Peter Szövényi Avinash Sreedasyam Jane Grimwood Gary Stacey Jeremy Schmutz Stefan A Rensing
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The Plant Journal
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A technical assessment of the porcine ejaculated spermatozoa for a sperm-specific RNA-seq analysis.
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2018-04-26
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Joan E Rodríguez-Gil Alex Clop Marta Gòdia
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Fabiana Quoos Mayer Julieta Nafissi Anna Castelló Armand Sánchez
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Systems Biology in Reproductive Medicine
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Biomarker Identification from RNA-Seq Data using a Robust Statistical Approach.
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2018-04-30
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Munirul Alam
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Zobaer Akond Md Nurul Haque Mollah
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Bioinformation
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Transcription Factor Co-expression Networks of Adipose RNA-Seq Data Reveal Regulatory Mechanisms of Obesity
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2018-05
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Haja N. Kadarmideen
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Ruta Skinkyte-Juskiene Lisette J A Kogelman
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Current Genomics
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Cnidarian Cell Type Diversity and Regulation Revealed by Whole-Organism Single-Cell RNA-Seq
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2018-05
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Arnau Sebé-Pedrós François Spitz
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Baptiste Saudemont Elad Chomsky Flora Plessier Marie-Pierre Mailhé Justine Renno Yann Loe-Mie Aviezer Lifshitz Zohar Mukamel Sandrine Schmutz Sophie Novault Patrick R.H. Steinmetz Amos Tanay Heather Marlow
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Cell
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RNentropy: an entropy-based tool for the detection of significant variation of gene expression across multiple RNA-Seq experiments.
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2018-05-01
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Ernesto Picardi
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Federico Zambelli Francesca Mastropasqua Anna Maria D'Erchia Graziano Pesole Giulio Pavesi
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Nucleic Acids Research
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Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis.
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2018-05-01
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Alicia Oshlack Nadia M Davidson
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GigaScience
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Improving the value of public RNA-seq expression data by phenotype prediction.
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2018-05-01
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Shannon Ellis Leonardo Collado-Torres Andrew E Jaffe Jeffrey T. Leek
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Nucleic Acids Research
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Evaluation of commercially available small RNASeq library preparation kits using low input RNA.
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2018-05-05
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Olivia Ziegler Elizabeth D Hutchins
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Ashish Yeri Amanda Courtright Kirsty Danielson Eric Alsop Elizabeth Carlson Michael Hsieh Avash Das Ravi V Shah Joel Rozowsky Saumya Das Kendall Van Keuren-Jensen
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BMC Genomics
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Transcriptome display during tilapia sex determination and differentiation as revealed by RNA-Seq analysis.
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2018-05-15
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Thomas D Kocher Deshou Wang
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Wenjing Tao Jinlin Chen Dejie Tan Jing Yang Lina Sun Jing Wei Matthew A Conte
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BMC Genomics
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A comparative study of RNA-Seq and microarray data analysis on the two examples of rectal-cancer patients and Burkitt Lymphoma cells.
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2018-05-16
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Tim Beißbarth
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Alexander Wolff Michaela Bayerlová Jochen Gaedcke Dieter Kube
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PLOS ONE
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The RNA-Seq-based high resolution gene expression atlas of chickpea (Cicer arietinum L.) reveals dynamic spatio-temporal changes associated with growth and development
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2018-05-16
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Vanika Garg
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Himabindu Kudapa Annapurna Chitikineni Rajeev K. Varshney
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Plant, Cell and Environment
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Analysis of the resistance mechanisms in sugarcane during Sporisorium scitamineum infection using RNA-seq and microscopy.
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2018-05-24
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Meredith D McNeil
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Shamsul A Bhuiyan Paul J Berkman Barry J Croft Karen S Aitken
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PLOS ONE
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Broad distribution spectrum from Gaussian to power law appears in stochastic variations in RNA-seq data.
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2018-05-29
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Atsushi J. Nagano
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Akinori Awazu Takahiro Tanabe Mari Kamitani Ayumi Tezuka
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Scientific Reports
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Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi.
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2018-05-30
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Michael Han Jens Keilwagen
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Frank Hartung Sven O Twardziok Jan Grau
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BMC Bioinformatics
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Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq.
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2018-05-30
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Kristyna Kupkova Karel Sedlar
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Pavlina Koscova Maryna Vasylkivska Barbora Branska Jan Kolek Petra Patakova Ivo Provaznik
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BMC Genomics
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Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database
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2018-06
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Luke Zappia Belinda Phipson Alicia Oshlack
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PLOS Computational Biology
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MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data.
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2018-06-01
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Lukas Simon Fabian J. Theis
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GigaScience
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Spatial transcriptomic survey of human embryonic cerebral cortex by single-cell RNA-seq analysis.
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2018-06-04
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Xiaoying Fan Ji Dong Suijuan Zhong Yuan Wei Qian Wu Liying Yan Jun Yong Le Sun Xiaoye Wang Yangyu Zhao Wei Wang Jie Yan Xiaoqun Wang Fuchou Tang
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Cell Research
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RNA-Seq reveals large quantitative differences between the transcriptomes of outbreak and non-outbreak locusts.
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2018-06-15
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Mohammed Bakkali
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Scientific Reports
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RNAseq analysis of hippocampal microglia after kainic acid-induced seizures.
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2018-06-20
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Long-Jun Wu Ukpong B Eyo Jason R. Richardson
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Dale B Bosco Jiaying Zheng Zhiyan Xu Jiyun Peng Ke Tang Cheng Yan Jun Huang Lijie Feng Gongxiong Wu Hui Wang
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Molecular Brain
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BioJupies: Automated Generation of Interactive Notebooks for RNA-seq Data Analysis in the Cloud
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2018-06-20
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Avi Ma'ayan
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Denis Torre Alexander Lachmann
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bcbioRNASeq: R package for bcbio RNA-seq analysis
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2018-06-20
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Michael J Steinbaugh Víctor Barrera
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Lorena Pantano Rory D. Kirchner Brad A. Chapman Mary E. Piper Meeta Mistry Radhika S. Khetani Kayleigh D. Rutherford Oliver Hofmann John N. Hutchinson Shannan Ho Sui
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F1000Research
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RNA-Seq analysis revealed genes associated with drought stress response in kabuli chickpea (Cicer arietinum L.).
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2018-06-28
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Rajeev Kumar Varshney Mahendar Thudi Vanika Garg
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Keyvan Mahdavi Mashaki Ali Asghar Nasrollahnezhad Ghomi Himabindu Kudapa Annapurna Chitikineni Khalil Zaynali Nezhad Ahad Yamchi Hasan Soltanloo
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PLOS ONE
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Predicting essential proteins based on RNA-Seq, subcellular localization and GO annotation datasets
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2018-07
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Hamido Fujita Aidong Zhang
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Xiujuan Lei Jie Zhao
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Knowledge-Based Systems
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Comparative transcriptome profiling of the human and mouse dorsal root ganglia: an RNA-seq-based resource for pain and sensory neuroscience research
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2018-07
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Tae Hoon Kim
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Pradipta Ray Andrew Torck Lilyana Quigley Andi Wangzhou Matthew Neiman Chandranshu Rao Tiffany Lam Ji-Young Kim Michael Q Zhang Gregory Dussor Theodore J Price
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SPAR: small RNA-seq portal for analysis of sequencing experiments.
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2018-07-01
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Alexandre Amlie-Wolf
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Pavel P Kuksa Živadin Katanic Otto Valladares Li-San Wang Yuk Yee Leung
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Nucleic Acids Research
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Clinker: visualizing fusion genes detected in RNA-seq data
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2018-07-01
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Alicia Oshlack Paul G Ekert Nadia M Davidson Ian J Majewski
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Breon M Schmidt Anthony D K Hawkins Ray Bartolo
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GigaScience
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Limitations of alignment-free tools in total RNA-seq quantification
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2018-07-03
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Claus O. Wilke Douglas C Wu
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Jun Yao Kevin S Ho Alan M Lambowitz
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BMC Genomics
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Guidelines for RNA-seq projects: applications and opportunities in non-model decapod crustacean species
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2018-07-03
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Guiomar Rotllant
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Tuan Viet Nguyen Hyungtaek Jung David Hurwood Peter Mather Tomer Ventura
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Hydrobiologia
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An Online Compendium of CHO RNA-Seq Data Allows Identification of CHO Cell Line-Specific Transcriptomic Signatures
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2018-07-05
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Helene Faustrup Kildegaard Mikael Rørdam Andersen
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Ankita Singh
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Biotechnology Journal
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Detection and removal of barcode swapping in single-cell RNA-seq data
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2018-07-10
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Jonathan A Griffiths John C Marioni
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Arianne C Richard Karsten Bach Aaron T L Lun
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Nature Communications
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RNASeq analysis of Aedes albopictus mosquitoes during chikungunya virus infection
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2018-07-11
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Prasad N Paradkar Ravikiran Vedururu
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Matthew J Neave Mary Tachedjian Paul R Gorry Jean-Bernard Duchemin
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RNA-seq analysis identifies different transcriptomic types and developmental trajectories of primary melanomas
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2018-07-11
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Paola Zigrino Janet Kelso Anja Bosserhoff
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Manfred Kunz Henry Löffler-Wirth Michael Dannemann Edith Willscher Gero Doose Tina Kottek Birgit Nickel Lydia Hopp Jenny Landsberg Steve Hoffmann Thomas Tüting Cornelia Mauch Jochen Utikal Mirjana Ziemer Hans-Joachim Schulze Michael Hölzel Alexander Roesch Susanne Kneitz Svenja Meierjohann Hans Binder Manfred Schartl
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Oncogene
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SLAM-ITseq: sequencing cell type-specific transcriptomes without cell sorting
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2018-07-11
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Stefan L Ameres Eric A Miska Wayo Matsushima
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Veronika A Herzog Tobias Neumann Katharina Gapp Johannes Zuber
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Development
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AltHapAlignR: improved accuracy of RNA-seq analyses through the use of alternative haplotypes
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2018-07-15
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Julian C Knight Peter Humburg
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Wanseon Lee Katharine Plant
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Bioinformatics
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Blue light induces a neuroprotective gene expression program in Drosophila photoreceptors
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2018-07-20
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Vikki M. Weake
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Hana Hall Jingqun Ma Sudhanshu Shekhar Walter D Leon-Salas
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BMC Neuroscience
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BraCeR: B-cell-receptor reconstruction and clonality inference from single-cell RNA-seq
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2018-07-31
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Sarah Teichmann
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Ida Lindeman Guy Emerton Lira Mamanova Omri Snir Krzysztof Polanski Shuo-Wang Qiao Ludvig M. Sollid Michael J. T. Stubbington
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Nature Methods
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RNA-Seq analysis of transcriptome responses in Atlantic cod (Gadus morhua) precision-cut liver slices exposed to benzo[a]pyrene and 17α-ethynylestradiol
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2018-08
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Xiaokang Zhang Eileen Marie Hanna Fekadu Yadetie Nello Blaser Anders Goksøyr
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Libe Aranguren-Abadía Marta Eide Morten Brun Inge Jonassen Odd André Karlsen
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Aquatic Toxicology
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Elysium: RNA-seq Alignment in the Cloud
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2018-08-02
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Alexander Lachmann Avi Ma'ayan
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Exploring parasite heterogeneity using single-cell RNA-seq reveals a gene signature among sexual stage Plasmodium falciparum parasites
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2018-08-07
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Rickard Sandberg Mats Wahlgren
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Mtakai Ngara Mia Palmkvist Sven Sagasser Daisy Hjelmqvist Åsa K Björklund Johan Ankarklev
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Experimental Cell Research
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Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken
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2018-08-07
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Stephen J Bush Mark P Stevens Kim M Summers
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Lucy Freem Amanda J MacCallum Jenny O'Dell Chunlei Wu Cyrus Afrasiabi Androniki Psifidi Jacqueline Smith David A Hume
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BMC Genomics
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DoGFinder: a software for the discovery and quantification of readthrough transcripts from RNA-seq
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2018-08-08
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Yuval Wiesel Niv Sabath
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BMC Genomics
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RNA-seq highlights parallel and contrasting patterns in the evolution of the nuclear genome of fully mycoheterotrophic plants
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2018-08-09
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Mikhail I. Schelkunov
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Aleksey A Penin Maria D Logacheva
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BMC Genomics
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Magic-BLAST, an accurate DNA and RNA-seq aligner for long and short reads
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2018-08-13
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Jean Thierry-Mieg
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Grzegorz M Boratyn Danielle Thierry-Mieg Ben Busby Thomas L Madden
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Comparative RNA-Seq analysis reveals a critical role for brassinosteroids in rose (Rosa hybrida) petal defense against Botrytis cinerea infection
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2018-08-20
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Zhao Zhang
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Xintong Liu Xiaoqian Cao Shaochuan Shi Na Zhao Dandan Li Peihong Fang Xi Chen Weicong Qi
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BMC Genetics
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RNAsik: A Pipeline for complete and reproducible RNA-seq analysis that runs anywhere with speed and ease
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2018-08-27
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Kirill Tsyganov Andrew J. Perry
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Stuart Kenneth Archer David Powell
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Journal of Open Source Software
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RNA-seq coupled to proteomic analysis reveals high sperm proteome variation between two closely related marine mussel species
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2018-09
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Mónica Carrera Andrés Pérez-Figueroa
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Mónica R. Romero Willie J. Swanson David O.F. Skibinski Angel P. Diz
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Journal of Proteomics
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Single-cell RNA-seq analysis identifies markers of resistance to targeted BRAF inhibitors in melanoma cell populations
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2018-09
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Molly Hammell
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Yu-Jui Ho Naishitha Anaparthy David Molik Grinu Mathew Toby Aicher Ami Patel James Hicks
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Genome Research
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ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes
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2018-09-01
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Sung-Huan Yu Konrad Förstner
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Jörg Vogel
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GigaScience
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RNA-seq analysis reveals different gene ontologies and pathways in rheumatoid arthritis and Kashin-Beck disease
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2018-09-05
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Xiong Guo Duan Chen
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Fangfang Yu Xiaodong Zhang Dandan Yao Gangquan Si Ying Gao Zongqiang Gao Farooq Umer
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International Journal of Rheumatic Diseases
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Genome-wide transcriptome analysis using RNA-Seq reveals a large number of differentially expressed genes in a transient MCAO rat model
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2018-09-05
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Vadim V Yuzhakov
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Lyudmila V Dergunova Ivan B Filippenkov Vasily V Stavchansky Alina E Denisova Sergey A Mozerov Leonid V Gubsky Svetlana A Limborska
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BMC Genomics
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Targeted enrichment outperforms other enrichment techniques and enables more multi-species RNA-Seq analyses
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2018-09-06
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Matthew Chung Silvia Libro Amol C Shetty Claire M. Fraser
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Laura Teigen Hong Liu Nikhil Kumar Xuechu Zhao Robin E Bromley Luke J Tallon Lisa Sadzewicz David A Rasko Scott G Filler Jeremy M Foster Michelle L Michalski Vincent M Bruno Julie C Dunning Hotopp
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Scientific Reports
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SAFE-clustering: Single-cell Aggregated (from Ensemble) clustering for single-cell RNA-seq data
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2018-09-08
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Michael I Love
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Yuchen Yang Ruth Huh Houston W Culpepper Yuan Lin Yun Li
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Bioinformatics
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AgriSeqDB: an online RNA-Seq database for functional studies of agriculturally relevant plant species
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2018-09-19
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Kathryn Unsworth Mathew G Lewsey James Whelan
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Andrew J Robinson Muluneh Tamiru Rachel Salby Clayton Bolitho Andrew Williams Simon Huggard Eva Fisch
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BMC Plant Biology
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scClustViz – Single-cell RNAseq cluster assessment and visualization
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2018-09-21
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Brendan T. Innes
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Gary D. Bader
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F1000Research
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RNA-seq analysis of gene expression changes during pupariation in Bactrocera dorsalis (Hendel) (Diptera: Tephritidae)
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2018-09-21
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Guy Smagghe
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Er-Hu Chen Qiu-Li Hou Wei Dou Dan-Dan Wei Yong Yue Rui-Lin Yang Shuai-Feng Yu Kristof De Schutter Jin-Jun Wang
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BMC Genomics
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Mixed-species RNA-seq for elucidation of non-cell-autonomous control of gene transcription
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2018-09-24
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Owen Dando
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Jing Qiu Paul S. Baxter Philip Hasel Samuel Heron T. Ian Simpson Giles E. Hardingham
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Nature Protocols
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Comparison of RNA-seq and microarray platforms for splice event detection using a cross-platform algorithm
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2018-09-25
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Angel Rubio
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Juan P Romero María Ortiz-Estévez Ander Muniategui Soraya Carrancio Fernando J de Miguel Fernando Carazo Luis M Montuenga Remco Loos Rubén Pío Matthew W B Trotter
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BMC Genomics
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Detection and Mitigation of Spurious Antisense RNA-seq Reads with RoSA
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2018-09-26
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Kimon Froussios Gordon G Simpson Nicholas Schurch Geoffrey J. Barton
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Kira Mourao Radoslaw Lukoszek Katarzyna MacKinnon Celine Duc
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MetaMap, an interactive webtool for the exploration of metatranscriptomic reads in human disease-related RNA-seq data
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2018-09-30
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Lukas Simon Fabian J. Theis
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George Tsitsiridis Philipp Angerer
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Screening for candidate genes related with histological microstructure, meat quality and carcass characteristic in pig based on RNA-seq data
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2018-10
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Kacper Żukowski Katarzyna Piórkowska Maria Oczkowicz Katarzyna Ropka-Molik
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Anna Bereta Mirosław Tyra Grzegorz Żak
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Asian-Australasian Journal of Animal Sciences
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Evaluation of the Expression of Genes Associated with Inflammation and Apoptosis in Androgenetic Alopecia by Targeted RNA-Seq
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2018-10
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Augusto Rojas-Martinez
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Lizeth Martinez-Jacobo Claudia I Ancer-Arellano Rocio Ortiz-Lopez Mauricio Salinas-Santander Cesar Daniel Villarreal-Villarreal Jesus Ancer-Rodriguez Bianka Camacho-Zamora Viviana Zomosa-Signoret Carlos E Medina-De la Garza Jorge Ocampo-Candiani
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Skin appendage disorders
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Small RNA-Seq reveals novel miRNAs shaping the transcriptomic identity of rat brain structures
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2018-10
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Alexandre Favereaux
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Anaïs Soula Mélissa Valere María-José López-González Vicky Ury-Thiery Alexis Groppi Marc Landry Macha Nikolski
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RNA-seq of macrophages of amoeboid or mesenchymal migratory phenotype due to specific structure of environment
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2018-10-02
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Ladislav Merta Daniel Rösel
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Vladimír Čermák Aneta Gandalovičová Jitka Fučíková Radek Špíšek Jan Brábek
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Scientific Data
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Isoform-Level Interpretation of High-Throughput Proteomics Data Enabled by Deep Integration with RNA-seq
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2018-10-05
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Nenad Sestan Mark Bender Gerstein
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Becky C Carlyle Robert R Kitchen Jing Zhang Rashaun S Wilson Tukiet T Lam Joel S Rozowsky Kenneth R Williams Nenad Sestan Angus C Nairn
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Journal of Proteome Research
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Improvements to the rice genome annotation through large-scale analysis of RNA-Seq and proteomics datasets
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2018-10-06
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Siqi Liu Zhe Ren
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Da Qi Pugh Nina Kai Li Bo Wen Ruo Zhou Shaohang Xu Andrew R. Jones
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Molecular & Cellular Proteomics
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Building gene regulatory networks from single-cell ATAC-seq and RNA-seq using Linked Self-Organizing Maps
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2018-10-09
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Ali Mortazavi Matthias Merkenschlager Jesper Tegnér David Gomez-Cabrero
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Camden Jansen Ricardo Ramirez Nicole El-Ali Ana Conesa
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Characterization of Critical Functions of Long Non-Coding RNAs and mRNAs in Rhabdomyosarcoma Cells and Mouse Skeletal Muscle Infected by 71 Using RNA-Seq
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2018-10-11
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Yuefei Jin
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Ying Li Chao Zhang Luwei Qin Dong Li Guangyuan Zhou Dejian Dang Shuaiyin Chen Tiantian Sun Rongguang Zhang Weidong Wu Yuanlin Xi Guangcai Duan
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Viruses
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Single cell RNA-seq reveals profound transcriptional similarity between Barrett's oesophagus and oesophageal submucosal glands
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2018-10-15
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Barbara Braden Richard Peter Owen Benjamin Schuster-Böckler Chris Ponting David T Severson Adam Bailey
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Michael Joseph White Robert Goldin Lai Mun Wang Carlos Ruiz-Puig Nicholas David Maynard Angie Green Paolo Piazza David Buck Mark Ross Middleton Xin Lu
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Nature Communications
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Affinity capture of polyribosomes followed by RNAseq (ACAPseq), a discovery platform for protein-protein interactions
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2018-10-22
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Mark F Sabbagh Amir Rattner Jeremy Nathans Philip M Smallwood
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Xi Peng Francesco Emiliani Hong Lei
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eLife
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Single-cell RNA-seq analysis reveals the platinum resistance gene COX7B and the surrogate marker CD63
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2018-10-26
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Nobuyuki Tanaka Kaneyasu Nishimura Juha Kere
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Shintaro Katayama Aparna Reddy Naoya Niwa Hiroshi Hongo Koichiro Ogihara Takeo Kosaka Ryuichi Mizuno Eiji Kikuchi Shuji Mikami Ayako Miyakawa Ernest Arenas Mototsugu Oya Per Uhlén
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Cancer Medicine
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Genome-wide RNA-seq analysis indicates that the DAG1 transcription factor promotes hypocotyl elongation acting on ABA, ethylene and auxin signaling
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2018-10-26
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Paola Vittorioso Anna Tramontano
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Riccardo Lorrai Francesco Gandolfi Alessandra Boccaccini Veronica Ruta Marco Possenti Paolo Costantino Rosalba Lepore
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Scientific Reports
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RNA-Seq transcriptomic profiling of primary murine microglia treated with LPS or LPS + IFNγ
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2018-10-31
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Jose M Vidal-taboada Alfonso Gerardo Garcia Diaz Barriga Carme Solà Josep Saura
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Marta Pulido-Salgado
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Scientific Reports
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Identifying deer antler uhrf1 proliferation and s100a10 mineralization genes using comparative RNA-seq
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2018-10-31
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Dai Fei Elmer Ker
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Dan Wang Rashmi Sharma Bin Zhang Ben Passarelli Norma Neff Chunyi Li William Maloney Stephen Quake Yunzhi Peter Yang
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Stem Cell Research & Therapy
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A semi-supervised deep learning method based on stacked sparse auto-encoder for cancer prediction using RNA-seq data
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2018-11
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Zongli Lin
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Yawen Xiao Jun Wu Xiaodong Zhao
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Computer Methods and Programs in Biomedicine
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Response of cell-wall composition and RNA-seq transcriptome to methyl-jasmonate in Brachypodium distachyon callus
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2018-11
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Louise V. Michaelson Jackie Freeman
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Lucy S Hyde Till K Pellny Rachael Simister Simon J McQueen-Mason Rowan A C Mitchell
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Planta
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Comparing RNA-Seq and microarray gene expression data in two zones of the root apex relevant to spaceflight
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2018-11
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Anna-Lisa Paul
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Aparna Krishnamurthy Robert J Ferl
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Applications in Plant Sciences
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Species-complex diversification and host-plant associations in Bemisia tabaci: A plant-defence, detoxification perspective revealed by RNA-Seq analyses
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2018-11
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Habibu Mugerwa Sharon van Brunschot Paul Visendi
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Osnat Malka Diego Santos-Garcia Ester Feldmesser Elad Sharon Renate Krause-Sakate Hélène Delatte Mitulkumar Patel Susan Seal John Colvin Shai Morin
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Molecular Ecology
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A fast detection of fusion genes from paired-end RNA-seq data
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2018-11-01
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Trung N. Vu
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Wenjiang Deng Quang Thinh Trac Stefano Calza Woochang Hwang Yudi Pawitan
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BMC Genomics
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Salt stress in the renal tubules is linked to TAL-specific expression of uromodulin and an upregulation of heat shock genes
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2018-11-01
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Alisha Aman Anna Dominiczak
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Lesley A Graham Desmond D Campbell Julian Augley Delyth Graham Martin W McBride Niall J Fraser Nicholas R Ferreri Sandosh Padmanabhan
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Physiological Genomics
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Analysis of Single-Cell RNA-Seq Identifies Cell-Cell Communication Associated with Tumor Characteristics
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2018-11-06
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Douglas A Lauffenburger
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Manu P Kumar Jinyan Du Georgia Lagoudas Yang Jiao Andrew Sawyer Daryl C Drummond Andreas Raue
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Cell Reports
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Identification of transcription factor genes involved in anthocyanin biosynthesis in carrot (Daucus carota L.) using RNA-Seq
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2018-11-08
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Miyako Kodama Henrik Brinch-Pedersen M Thomas P Gilbert
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Shrikant Sharma Inger Bæksted Holme Bjarne Joernsgaard Tsaneta Dzhanfezova Daniel Buchvaldt Amby Filipe Garrett Vieira Shanlin Liu
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BMC Genomics
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RNA-seq analysis reveals considerable genetic diversity and provides genetic markers saturating all chromosomes in the diploid wild wheat relative Aegilops umbellulata
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2018-11-08
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Shigeo Takumi
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Moeko Okada Kentaro Yoshida Ryo Nishijima Asami Michikawa Yuka Motoi Kazuhiro Sato
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BMC Plant Biology
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Evaluation of immune repertoire inference methods from RNA-seq data
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2018-11-09
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Xiaole Shirley Liu
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Xihao Hu Jian Zhang Jun S Liu Bo Li
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Nature Biotechnology
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Empirical assessment of the impact of sample number and read depth on RNA-Seq analysis workflow performance
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2018-11-14
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Charles C. Kim
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Alyssa Baccarella Claire R Williams Jay Z Parrish
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BMC Bioinformatics
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Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement
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2018-11-19
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Jens Preussner Sarah Teichmann Xi Chen Mario Looso Michail Yekelchyk Thomas Braun
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Guangshuai Jia Stefan Guenther Xuejun Yuan Carsten Kuenne Yonggang Zhou
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Nature Communications
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Hierarchical Clustering of DNA k-mer Counts in RNAseq Fastq Files Identifies Sample Heterogeneities
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2018-11-21
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Heiner Schaal Wolfgang Kaisers
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Holger Schwender
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International Journal of Molecular Sciences
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A Two-Cohort RNA-seq Study Reveals Changes in Endometrial and Blood miRNome in Fertile and Infertile Women
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2018-11-23
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Signe Altmäe
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Kadri Rekker Marina Suhorutshenko Maire Peters Juan F Martinez-Blanch Francisco M Codoñer Felipe Vilella Carlos Simón Andres Salumets Agne Velthut-Meikas
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Genes
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Comparative assessment shows the reliability of chloroplast genome assembly using RNA-seq
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2018-11-27
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Francisco Perfectti
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Carolina Osuna-Mascaró Rafael Rubio de Casas
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Scientific Reports
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A differential k-mer analysis pipeline for comparing RNA-Seq transcriptome and meta-transcriptome datasets without a reference
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2018-11-27
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Paul Visendi Nedeljka N. Rosic Chon-Kit Kenneth Chan Jacqueline Batley
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Michał T. Lorenc Meng Lin Paulina Kaniewska Brett J. Ferguson Peter M. Gresshoff David Edwards
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Functional and Integrative Genomics
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RNA-seq data from mature male gonads of marine mussels Mytilus edulis and M. galloprovincialis
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2018-12
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Andrés Pérez-Figueroa
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Angel P. Diz Mónica R. Romero Willie J. Swanson David O.F. Skibinski
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Data in Brief
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Quantitative RNAseq analysis of Ugandan KS tumors reveals KSHV gene expression dominated by transcription from the LTd downstream latency promoter
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2018-12
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Timothy M Rose
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A Gregory Bruce Serge Barcy Matt Fitzgibbon Lisa R Matsumoto Minako Ikoma Corey Casper Jackson Orem Warren Phipps
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PLOS Pathogens
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Comprehensive evaluation of RNA-seq analysis pipelines in diploid and polyploid species
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2018-12-01
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Margaret Staton
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Miriam Payá-Milans James W Olmstead Gerardo Nunez Timothy A Rinehart
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GigaScience
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Efficient and accurate detection of splice junctions from RNA-seq with Portcullis
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2018-12-01
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Gemy Kaithakottil Luca Venturini David Swarbreck
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Daniel Mapleson
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GigaScience
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Accuracy of RNAseq based SNP discovery and genotyping in Populusnigra
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2018-12-12
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Vincent Segura Odile Rogier
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Aurélien Chateigner Souhila Amanzougarene Marie-Claude Lesage-Descauses Sandrine Balzergue Véronique Brunaud José Caius Ludivine Soubigou-Taconnat Véronique Jorge
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BMC Genomics
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Genome-wide RNAseq study of the molecular mechanisms underlying microglia activation in response to pathological tau perturbation in the rTg4510 tau transgenic animal model
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2018-12-17
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Philip J Ebert
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Hong Wang Yupeng Li John W Ryder Justin T Hole David C Airey Hui-Rong Qian Benjamin Logsdon Alice Fisher Zeshan Ahmed Tracey K Murray Annalisa Cavallini Suchira Bose Brian J Eastwood David A Collier Jeffrey L Dage Bradley B Miller Kalpana M Merchant Michael J O'Neill Ronald B Demattos
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Molecular Neurodegeneration
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iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data
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2018-12-19
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Steven Ge
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Eun Wo Son Runan Yao
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BMC Bioinformatics
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A test metric for assessing single-cell RNA-seq batch correction
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2018-12-20
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Maren Büttner F. Alexander Wolf Fabian J. Theis Zhichao Miao Sarah Teichmann
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Nature Methods
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Identification and characterization of SSR, SNP and InDel molecular markers from RNA-Seq data of guar (Cyamopsis tetragonoloba, L. Taub.) roots
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2018-12-20
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Gursharn Singh Randhawa
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Omika Thakur
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BMC Genomics
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ddSeeker: a tool for processing Bio-Rad ddSEQ single cell RNA-seq data
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2018-12-24
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Angelo Di Leo
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Dario Romagnoli Giulia Boccalini Martina Bonechi Chiara Biagioni Paola Fassan Roberto Bertorelli Veronica De Sanctis Ilenia Migliaccio Luca Malorni Matteo Benelli
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BMC Genomics
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Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes
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2018-12-29
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Boas Pucker
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Samuel F Brockington
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BMC Genomics
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Androgen and Oestrogen Affect the Expression of Long Non-Coding RNAs During Phallus Development in a Marsupial
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2018-12-30
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Yu Chen Marilyn Renfree
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Yoko Kuroki Geoff Shaw Andrew J Pask Hongshi Yu Atsushi Toyoda Asao Fujiyama
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Non-coding RNA
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Screening human cell lines for viral infections applying RNA-Seq data analysis
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2019
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Hans Guenter Drexler Claudia Pommerenke
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Cord C Uphoff Sabine A Denkmann
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PLOS ONE
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LiBiNorm: an htseq-count analogue with improved normalisation of Smart-seq2 data and library preparation diagnostics
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2019
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Daniel Hebenstreit
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Nigel P Dyer Vahid Shahrezaei
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PeerJ
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Comparative STAT3-Regulated Gene Expression Profile in Renal Cell Carcinoma Subtypes
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2019
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Ashok Sharma
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Rebekah L Robinson Shan Bai Saleh Heneidi Tae Jin Lee Sai Karthik Kodeboyina Nikhil Patel Shruti Sharma
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Frontiers in Oncology
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Integrative Analysis of Transcriptome and GWAS Data to Identify the Hub Genes Associated With Milk Yield Trait in Buffalo
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2019
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Xiaoya Ma
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Tingxian Deng Aixin Liang Shasha Liang Xingrong Lu Anqin Duan Chunying Pang Guohua Hua Shenhe Liu Giuseppe Campanile Angela Salzano Bianca Gasparrini Gianluca Neglia Xianwei Liang Liguo Yang
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Frontiers in Genetics
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Fast and accurate differential transcript usage by testing equivalence class counts
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2019
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Marek Cmero Nadia M Davidson Alicia Oshlack
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F1000Research
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High-Depth RNA-Seq Data Sets for Studying Gene Expression Changes Mediated by Phase-Variable DNA Methyltransferases in Nontypeable Haemophilus influenzae
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2019-01
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Lauren O Bakaletz
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John M Atack Michael P Jennings
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Tissue culture and next-generation sequencing: A combined approach for detecting yam (Dioscorea spp.) viruses
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2019-01
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Moritz Bömer Paul Visendi
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Ajith I. Rathnayake Steven O. Sewe Juan Paolo A. Sicat Gonçalo Silva P. Lava Kumar Susan E. Seal
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Physiological and Molecular Plant Pathology
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Transcriptional and epigenetic profiling of nutrient-deprived cells to identify novel regulators of autophagy
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2019-01
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Mario Mauthe Michal Mokry
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Autophagy
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Palbociclib and Fulvestrant Act in Synergy to Modulate Central Carbon Metabolism in Breast Cancer Cells
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2019-01-02
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Caroline H Johnson Gary Siuzdak
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Benedikt Warth Amelia Palermo Nicholas J W Rattray Nathan V Lee Zhou Zhu Linh T Hoang Yuping Cai Anthony Mazurek Stephen Dann Todd VanArsdale Valeria R Fantin David Shields
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Metabolites
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Molecular signatures of multiple myeloma progression through single cell RNA-Seq
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2019-01-03
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Andre J van Wijnen
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Jin Sung Jang Ying Li Amit Kumar Mitra Lintao Bi Alexej Abyzov Linda B Baughn Brian Van Ness Vincent Rajkumar Shaji Kumar Jin Jen
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Blood Cancer Journal
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Differential expression feature extraction (DEFE) and its application in RNA-seq data analysis
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2019-01-03
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Youlian Pan
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Yifeng Li Ziying Liu Anuradha Surendra Lipu Wang Nora A. Foroud Ravinder K. Goyal Therese Ouellet Pierre R. Fobert
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A Hybrid Deep Clustering Approach for Robust Cell Type Profiling Using Single-cell RNA-seq Data: Supplementary Figures and Tables
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2019-01-04
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Dmitry Korkin Suhas Srinivasan
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Nathan T Johnson
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RNA-seq analysis of hepatic gene expression of common Pekin, Muscovy, mule and hinny ducks fed ad libitum or overfed
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2019-01-07
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Christian Diot
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Frédéric Hérault Magalie Houée-Bigot Elisabeth Baéza Olivier Bouchez Diane Esquerré Christophe Klopp
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BMC Genomics
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Methods for RNA Modification Mapping Using Deep Sequencing: Established and New Emerging Technologies
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2019-01-09
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Yuri Motorin Mark Helm
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Genes
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Stability of methods for differential expression analysis of RNA-seq data
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2019-01-11
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Zhen Pang
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Bingqing Lin
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BMC Genomics
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Dynamics of transcriptional regulation from total RNA-seq experiments: Supplemental Figures and Methods
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2019-01-14
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Mattia Pelizzola
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Mattia Furlan Stefano de Pretis Eugenia Galeota Michele Caselle
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Expression analysis of lung miRNAs responding to ovine VM virus infection by RNA-seq
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2019-01-18
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Martin Bilbao-Arribas
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Naiara Abendaño Endika Varela-Martínez Ramsés Reina Damián de Andrés Begoña M Jugo
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BMC Genomics
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Single-cell RNA-seq denoising using a deep count autoencoder
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2019-01-23
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Maria Mircea Lukas Simon Fabian J. Theis
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Gökcen Eraslan Nikola S Mueller
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Nature Communications
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RNA-seq of HaHV-1-infected abalones reveals a common transcriptional signature of Malacoherpesviruses
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2019-01-30
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Umberto Rosani
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Chang-Ming Bai Ya-Nan Li Shu-Min Zhang Lu-Sheng Xin Chong-Ming Wang
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Scientific Reports
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O157:H7 transcriptome datasets for comparison of RNA-seq and microarray platforms
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2019-02
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Nicola Holden
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Ewa Grabowiecka David Martin Louise Crozier
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Data in Brief
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Key role of SMN/SYNCRIP and RNA-Motif 7 in spinal muscular atrophy: RNA-Seq and motif analysis of human motor neurons
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2019-02-01
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Nereo Bresolin Andreina Bordoni
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Federica Rizzo Monica Nizzardo Shikha Vashisht Erika Molteni Valentina Melzi Michela Taiana Sabrina Salani Pamela Santonicola Elia Di Schiavi Monica Bucchia Irene Faravelli Giacomo Pietro Comi Uberto Pozzoli Stefania Corti
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Brain
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Transcriptomic analysis reveals adaptive strategies to chronic low nitrogen in Tibetan wild barley
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2019-02-11
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Guoping Zhang
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Xiaoyan Quan Jianbin Zeng Guang Chen
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BMC Plant Biology
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Dynamic inosinome profiles reveal novel patient stratification and gender-specific differences in glioblastoma
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2019-02-13
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Franco Locatelli
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Domenico Alessandro Silvestris Ernesto Picardi Valeriana Cesarini Bruno Fosso Nicolò Mangraviti Luca Massimi Maurizio Martini Graziano Pesole Angela Gallo
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Genome Biology
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Loss of Function in Escherichia coli Exposed to Environmentally Relevant Concentrations of Benzalkonium Chloride
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2019-02-15
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Gavin Humphreys Hitesh B Mistry Andrew J. McBain
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Sarah Forbes Nicola Morgan Alejandro Amézquita
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Applied and Environmental Microbiology
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gene signature identification from single-cell RNA-seq with hierarchical Poisson factorization
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2019-02-22
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David M. Blei
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Hanna Mendes Levitin Jinzhou Yuan Yim Ling Cheng Francisco Jr Ruiz Erin C Bush Jeffrey N Bruce Peter Canoll Antonio Iavarone Anna Lasorella Peter A Sims
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Molecular Systems Biology
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The role of the GATA transcription factor AreB in regulation of nitrogen and carbon metabolism in Aspergillus nidulans
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2019-03-01
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Piotr Węgleński
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Patrycja Chudzicka-Ormaniec Maria Macios Michał Koper Gareth D Weedall Mark X Caddick Agnieszka Dzikowska
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FEMS Microbiology Letters
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Physiological Expression of Ion Channel Receptors in Human Periodontal Ligament Stem Cells
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2019-03-06
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Emanuela Mazzon Placido Bramanti Oriana Trubiani
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Luigi Chiricosta Francesca Diomede
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Cells
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Prioritizing candidate genes for fertility in dairy cows using gene-based analysis, functional annotation and differential gene expression
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2019-03-29
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Mogens Sandø Lund
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Zexi Cai Bernt Guldbrandtsen Goutam Sahana
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BMC Genomics
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Identification of long non-coding RNAs expressed in knee and hip osteoarthritic cartilage
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2019-04
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Timothy E. Hardingham
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B Ajekigbe K Cheung Y Xu A J Skelton A Panagiotopoulos J Soul D J Deehan M J Barter D A Young
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Osteoarthritis and Cartilage
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Large-scale in-silico identification of a tumor-specific antigen pool for targeted immunotherapy in triple-negative breast cancer
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2019-04-02
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Nicolas Wentzensen
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Jessica Kaufmann Titus J Brinker Niels Grabe
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Oncotarget
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RNA-sequencing across three matched tissues reveals shared and tissue-specific gene expression and pathway signatures of COPD
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2019-04-02
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Kimberly Glass
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Jarrett D Morrow Robert P Chase Margaret M Parker Minseok Seo Miguel Divo Caroline A Owen Peter Castaldi Dawn L DeMeo Edwin K Silverman Craig P Hersh
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Respiratory Research
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Mapping the transcriptional diversity of genetically and anatomically defined cell populations in the mouse brain
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2019-04-12
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Ken Sugino Erin Clark Anton Schulmann Yasuyuki Shima Lihua Wang David L Hunt Bryan M Hooks Tränkner D Jayaram Chandrashekar Serge Picard Andrew L. Lemire Nelson Spruston Adam W. Hantman Sacha B. Nelson
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eLife
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Ryūtō: network-flow based transcriptome reconstruction
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2019-04-16
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Peter F. Stadler
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Thomas Gatter
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BMC Bioinformatics
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Gene expression changes associated with the evolutionary loss of a metabolic trait: lack of lipogenesis in parasitoids
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2019-04-23
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Jacintha Ellers
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Mark Lammers Ken Kraaijeveld Janine Mariën
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BMC Genomics
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Leukodystrophy-associated mutations down-regulate the RNA polymerase III transcript and important regulatory RNA
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2019-05-03
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Benoit Coulombe
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Karine Choquet Diane Forget Elisabeth Meloche Marie-Josée Dicaire Geneviève Bernard Adeline Vanderver Raphael Schiffmann Marc R Fabian Martin Teichmann Bernard Brais Claudia L Kleinman
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Journal of Biological Chemistry
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Transcriptomics data of 11 species of yeast identically grown in rich media and oxidative stress conditions
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2019-05-03
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William R Blevins
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Lucas B Carey M Mar Albà
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BMC Research Notes
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Model-Based Methods for Transcript Expression-Level Quantification in RNA-Seq
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Zhaohui Steve Qin
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Zhaonan Sun Han Wu Yu Zhu
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