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scholarly article[edit]

Article publication date author author name string published in
Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. 2008-05-18 Jürg Bähler
Ian Goodhead
Valerie Wood
Brian T Wilhelm
Samuel Marguerat
Stephen Watt
Falk Schubert
Christopher J Penkett
Jane Rogers
Jürg Bähler
Nature
The transcriptional landscape of the yeast genome defined by RNA sequencing 2008-06-06 Mark Bender Gerstein Ugrappa Nagalakshmi
Zhong Wang
Karl Waern
Chong Shou
Debasish Raha
Michael Snyder
Science
RNA-Seq: a revolutionary tool for transcriptomics 2009-01 Mark Bender Gerstein Zhong Wang
Michael Snyder
Nature Reviews Genetics
TopHat: discovering splice junctions with RNA-Seq 2009-05-01 Steven Salzberg
Lior Pachter
Cole Trapnell Bioinformatics
RNA-seq: from technology to biology. 2009-10-27 Jürg Bähler Samuel Marguerat
Jürg Bähler
Cellular and Molecular Life Sciences
Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome. 2009-11-18 Cynthia Sharma
Jörg Vogel
Marco Albrecht
Richard Reinhardt
Thomas Rudel
Nucleic Acids Research
An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data 2009-12-11 Daniel Ramsköld
Rickard Sandberg
Eric T Wang
Christopher B Burge
PLOS Computational Biology
Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs. 2009-12-30 Kathryn J Boor
Martin Wiedmann
Haley F Oliver
Renato H Orsi
Lalit Ponnala
Uri Keich
Wei Wang
Qi Sun
Samuel W Cartinhour
Melanie J Filiatrault
BMC Genomics
Differential expression analysis for sequence count data 2010 Simon Anders
Wolfgang Huber
Genome Biology
Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved elements 2010 Sandro Banfi
Elia Stupka
Vincenzo Alessandro Gennarino
Remo Sanges
Danilo Licastro
Francesca Petrera
BMC Genomics
Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing. 2010-01-01 Vincent Plagnol
Graham Heap
Charles Mein
David A van Heel
Richard Dobson
Lude Franke
Jennie H M Yang
Kate Downes
Barry C Healy
Karen A Hunt
Nicholas Bockett
Patrick C Dubois
Thomas J Albert
Matthew J Rodesch
David G Clayton
John A Todd
Human Molecular Genetics
New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq. 2010-02-04 Thomas D Otto
Arnab Pain
Chris Newbold
Matthew Berriman
Ulrike Böhme
Daniel Wilinski
Sammy Assefa
Thomas M Keane
Louis R Sarry
Ulrike Böhme
Jacob Lemieux
Bart Barrell
Matthew Berriman
Manuel Llinás
Molecular Microbiology
Gene ontology analysis for RNA-seq: accounting for selection bias. 2010-02-04 Alicia Oshlack
Matthew Wakefield
Gordon K Smyth
Matthew D Young Genome Biology
Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments. 2010-02-11 Marie-Laure Yaspo Hugues Richard
Marcel H Schulz
Marc Sultan
Asja Nürnberger
Sabine Schrinner
Daniela Balzereit
Emilie Dagand
Axel Rasche
Hans Lehrach
Martin Vingron
Stefan A Haas
Marie-Laure Yaspo
Nucleic Acids Research
RNA-Seq analysis to capture the transcriptome landscape of a single cell. 2010-02-25 Azim Surani Fuchou Tang
Catalin Barbacioru
Ellen Nordman
Bin Li
Nanlan Xu
Vladimir I Bashkirov
Kaiqin Lao
Nature Protocols
The primary transcriptome of the major human pathogen Helicobacter pylori 2010-03-11 Peter F. Stadler
Jörg Vogel
Kristin Reiche
Fabien Darfeuille
Cynthia Sharma
Jörg Hackermüller
Steve Hoffmann
Jérémy Reignier
Sven Findeiss
Alexandra Sittka
Sandrine Chabas
Richard Reinhardt
Nature
Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. 2010-03-19 Qiye Li
Guojie Zhang
Wang Jun
Jun Wang
Guangwu Guo
Xueda Hu
Yong Zhang
Ruiqiang Li
Ruhong Zhuang
Zhike Lu
Zengquan He
Xiaodong Fang
Li Chen
Wei Tian
Yong Tao
Karsten Kristiansen
Xiuqing Zhang
Songgang Li
Huanming Yang
Jian Wang
Genome Research
Integrative analysis of the melanoma transcriptome 2010-04 Eric Lander
Chad Nusbaum
Carrie Sougnez
Andreas Gnirke
Gad Getz
Kristian Cibulskis
Wendy Winckler
Reinhard Dummer
Liuda Ziaugra
Michael F Berger
Joshua Z Levin
Krishna Vijayendran
Andrey Sivachenko
Xian Adiconis
Jared Maguire
Laura A Johnson
James Robinson
Roel G Verhaak
Robert C Onofrio
Elisabeth Laine
Jordi Barretina
David E Fisher
Matthew Meyerson
David B Jaffe
Stacey B Gabriel
Levi A Garraway
Genome Research
mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus 2010-04-01 Stéphane Audic
Chantal Abergel
Jean-Michel Claverie
Julie Poulain
Pascal Hingamp
Matthieu Legendre
Olivier Poirot
Virginie Seltzer
Deborah Byrne
Audrey Lartigue
Magali Lescot
Alain Bernadac
Genome Research
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation 2010-05 Steven Salzberg
Lior Pachter
Cole Trapnell
Brian A Williams
Geo Pertea
Ali Mortazavi
Gordon Kwan
Marijke J van Baren
Barbara J Wold
Nature Biotechnology
Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis. 2010-05-01 Azim Surani Fuchou Tang
Catalin Barbacioru
Siqin Bao
Caroline Lee
Ellen Nordman
Xiaohui Wang
Kaiqin Lao
Cell Stem Cell
Screening the human exome: a comparison of whole genome and whole transcriptome sequencing. 2010-05-28 Elizabeth T Cirulli Abanish Singh
Kevin V Shianna
Dongliang Ge
Jason P Smith
Jessica M Maia
Erin L Heinzen
James J Goedert
David B Goldstein
Center for HIV/AIDS Vaccine Immunology (CHAVI)
Genome Biology
Transcriptome and targetome analysis in MIR155 expressing cells using RNA-seq 2010-06-28 Dale Hedges Guorong Xu
Claire Fewell
Christopher Taylor
Nan Deng
Dale Hedges
Xia Wang
Kun Zhang
Michelle Lacey
Haitao Zhang
Qinyan Yin
Jennifer Cameron
Zhen Lin
Dongxiao Zhu
Erik K Flemington
RNA
RNA-seq analysis of sulfur-deprived Chlamydomonas cells reveals aspects of acclimation critical for cell survival. 2010-06-29 David Casero David González-Ballester
Shawn Cokus
Matteo Pellegrini
Sabeeha S Merchant
Arthur R Grossman
The Plant Cell
An integrative approach to genomic introgression mapping. 2010-07-23 David L. Hyten Andrew J Severin
Gregory A Peiffer
Wayne W Xu
Bruna Bucciarelli
Jamie A O'Rourke
Yung-Tsi Bolon
David Grant
Andrew D Farmer
Gregory D May
Carroll P Vance
Randy C Shoemaker
Robert M Stupar
Plant Physiology
Recent advances in RNA sequence analysis 2010-08-19 Steven Salzberg F1000 biology reports
Transcribed dark matter: meaning or myth? 2010-08-25 Chris Ponting T Grant Belgard Human Molecular Genetics
Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq. 2010-09-01 Gavin Sherlock
Sadie L Marjani
Vincent M Bruno
Zhong Wang
Ghia M Euskirchen
Jeffrey Martin
Michael Snyder
Genome Research
High-throughput sequencing and clinical microbiology: progress, opportunities and challenges. 2010-09-16 Nicholas J Loman
Mark Pallen
Charles W Penn Current Opinion in Microbiology
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. 2010-09-19 Christoph Bock
Peggy Farnham
David Haussler
Junchen Gu
Mattia Pelizzola
Ryan Lister
R Alan Harris
Ting Wang
Cristian Coarfa
Raman P Nagarajan
Chibo Hong
Sara L Downey
Brett E Johnson
Shaun D Fouse
Allen Delaney
Yongjun Zhao
Adam Olshen
Tracy Ballinger
Xin Zhou
Kevin J Forsberg
Lorigail Echipare
Henriette O'Geen
Yuanxin Xi
Charles B Epstein
Bradley E Bernstein
R David Hawkins
Bing Ren
Wen-Yu Chung
Hongcang Gu
Andreas Gnirke
Michael Q Zhang
Joseph R Ecker
Wei Li
Robert A Waterland
Alexander Meissner
Marco A Marra
Martin Hirst
Aleksandar Milosavljevic
Joseph F Costello
Nature Biotechnology
Single molecule sequencing with a HeliScope genetic analysis system 2010-10-01 John F Thompson Kathleen E Steinmann Current protocols in molecular biology
Analysis of next-generation genomic data in cancer: accomplishments and challenges 2010-10-15 Elaine Mardis Li Ding
Michael C Wendl
Daniel C Koboldt
Human Molecular Genetics
Analysis and design of RNA sequencing experiments for identifying isoform regulation 2010-11-07 Edoardo M Airoldi Yarden Katz
Eric T Wang
Christopher B Burge
Nature Methods
Defining the transcriptome and proteome in three functionally different human cell lines. 2010-12-01 Cajsa Algenäs Emma Lundberg
Linn Fagerberg
Daniel Klevebring
Ivan Matic
Tamar Geiger
Juergen Cox
Cajsa Algenäs
Joakim Lundeberg
Matthias Mann
Mathias Uhlen
Molecular Systems Biology
A high-resolution comparative map of porcine chromosome 4 (SSC4). 2010-12-01 Lawrence B. Schook J-G Ma
T-C Chang
H Yasue
A D Farmer
J A Crow
K Eyer
H Hiraiwa
T Shimogiri
S N Meyers
J E Beever
E F Retzel
C W Beattie
W-S Liu
Animal Genetics
Analysis of transcript and protein overlap in a human osteosarcoma cell line. 2010-12-02 Mathias Uhlén Daniel Klevebring
Linn Fagerberg
Emma Lundberg
Olof Emanuelsson
Mathias Uhlén
Joakim Lundeberg
BMC Genomics
Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome 2010-12-22 Ayelet T. Lamm Michael R Stadler
Huibin Zhang
Jonathan I Gent
Andrew Z Fire
Genome Research
miR-191 regulates mouse erythroblast enucleation by down-regulating Riok3 and Mxi1. 2010-12-31 Johan Flygare Lingbo Zhang
Piu Wong
Bing Lim
Harvey F Lodish
Genes & Development
Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples 2011 Celina Sanchez Rivers
Zora Modrusan
Brock A Peters
Serban Nacu
Wenlin Yuan
Zhengyan Kan
Deepali Bhatt
Jeremy Stinson
Kenneth Jung
Somasekar Seshagiri
Thomas D Wu
BMC Medical Genomics
Thousands of Novel Transcripts Identified in Mouse Cerebrum, Testis, and ES Cells Based on ribo-minus RNA Sequencing 2011 Songnian Hu Wanfei Liu
Yuhui Zhao
Peng Cui
Qiang Lin
Feng Ding
Chengqi Xin
Xinyu Tan
Shuhui Song
Jun Yu
Frontiers in Genetics
Transcriptome profiling of chemosensory appendages in the malaria vector Anopheles gambiae reveals tissue- and sex-specific signatures of odor coding 2011 Laurence Zwiebel R Jason Pitts
David C Rinker
Patrick L Jones
Antonis Rokas
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
Steven Laing
Frank Jackson
Michael Quail
Robin Beech
John S Gilleard
PLoS ONE
The post-apoptotic fate of RNAs identified through high-throughput sequencing of human hair 2011 Benjamin Yu Gloria K Lefkowitz
Anandaroop Mukhopadhyay
Christopher Cowing-Zitron
PLoS ONE
ENCODE whole-genome data in the UCSC genome browser (2011 update) 2011-01 David Haussler
Venkat S Malladi
Angie S. Hinrichs
Donna Karolchik
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
Hiram Clawson
Ann S Zweig
Vanessa Kirkup
Pauline A Fujita
Brooke Rhead
Kayla E Smith
Andy Pohl
Robert M Kuhn
W James Kent
Nucleic Acids Research
Insights into global mechanisms and disease by gene expression profiling. 2011-01-01 Hubert Hackl
J Rainer
Ana Dopazo
Fátima Sánchez-Cabo
Zlatko Trajanoski
Methods in Molecular Biology
Identification of fusion genes in breast cancer by paired-end RNA-sequencing. 2011-01-19 Olli-Pekka Kallioniemi
Anne-Lise Borresen-Dale
Sara Kangaspeska
Vesa Hongisto
Kristine Kleivi
Henrik Edgren
Astrid Murumagi
Sara Kangaspeska
Daniel Nicorici
Vesa Hongisto
Kristine Kleivi
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
Michal Janitz Journal of Neurochemistry
Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array 2011-01-21 Shikai Liu
Eric Peatman
Huseyin Kucuktas
Ludmilla Kaltenboeck
Shaolin Wang
Zunchun Zhou
Jianguo Lu
Fanyue Sun
Hong Liu
Yanliang Jiang
Huseyin Kucuktas
Ludmilla Kaltenboeck
Zhanjiang Liu
BMC Genomics
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. 2011-01-31 Hendrik Marks
Yu Gao
Stoyan G Petkov
Tino Klein
Rodrigo S Garcia
Henk Stunnenberg
Poul Hyttel
Stem Cell Research
Transcriptome-wide sequencing reveals numerous APOBEC1 mRNA-editing targets in transcript 3' UTRs 2011-02 Nina Papavasiliou 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 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
Rebecca Cullum Respirology
Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-seq. 2011-02-08 Michael Eisen Susan E Lott
Jacqueline E Villalta
Gary P Schroth
Shujun Luo
Leath A Tonkin
PLOS Biology
Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes. 2011-02-15 Peggy Farnham 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 Marcus Kinsella
Olivier Harismendy
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
Solabomi A Ogun
Steven A Howell
Ellen Knuepfer
Deirdre A Cunningham
Zhengyao Xu
PLOS Pathogens
ACT: aggregation and correlation toolbox for analyses of genome tracks. 2011-02-23 Joel Rozowsky Justin Jee
Kevin Y Yip
Lucas Lochovsky
Robert Bjornson
Guoneng Zhong
Zhengdong Zhang
Yutao Fu
Jie Wang
Zhiping Weng
Mark Gerstein
Bioinformatics
MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers 2011-03-17 Louis M Staudt Christian Steidl
Sohrab P Shah
Bruce W Woolcock
Lixin Rui
Masahiro Kawahara
Pedro Farinha
Nathalie A Johnson
Yongjun Zhao
Adele Telenius
Susana Ben Neriah
Andrew McPherson
Barbara Meissner
Ujunwa C Okoye
Arjan Diepstra
Anke van den Berg
Mark Sun
Gillian Leung
Steven J Jones
Joseph M Connors
David G Huntsman
Kerry J Savage
Lisa M Rimsza
Douglas E Horsman
Ulrich Steidl
Marco A Marra
Randy D Gascoyne
Nature
Developmental changes in transcriptional profiles. 2011-03-30 Gad Shaulsky William F Loomis Development, Growth and Differentiation
RNA-Seq analysis in mutant zebrafish reveals role of U1C protein in alternative splicing regulation. 2011-04-05 Vladimir Benes
Gunnar Rätsch
Tanja Dorothe Rösel
Lee-Hsueh Hung
Jan Medenbach
Katrin Donde
Stefan Starke
Albrecht Bindereif
The EMBO Journal
Network-guided analysis of genes with altered somatic copy number and gene expression reveals pathways commonly perturbed in metastatic melanoma. 2011-04-08 Stylianos Antonarakis
Christian Iseli
Carlo Rivolta
Ioannis Xenarios
Jacques S. Beckmann
Armand Valsesia
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
PLoS ONE
Systems biology approach in Chlamydomonas reveals connections between copper nutrition and multiple metabolic steps. 2011-04-15 David Casero Madeli Castruita
Steven J Karpowicz
Janette Kropat
Astrid Vieler
Scott I Hsieh
Weihong Yan
Shawn Cokus
Joseph A Loo
Christoph Benning
Matteo Pellegrini
Sabeeha S Merchant
The Plant Cell
Contribution of Hfq to photooxidative stress resistance and global regulation in Rhodobacter sphaeroides. 2011-04-27 Cynthia Sharma
Jörg Vogel
Gabriele Klug
Bork A Berghoff
Jens Glaeser
Monica Zobawa
Friedrich Lottspeich
Molecular Microbiology
The sensitivity of massively parallel sequencing for detecting candidate infectious agents associated with human tissue 2011-05-13 Curtis A. Suttle
Jan M Friedman
Richard A Moore
René L Warren
J Douglas Freeman
Julia A Gustavsen
Caroline Chénard
Yongjun Zhao
Robert A Holt
PLoS ONE
The zebrafish transcriptome during early development. 2011-05-24 Juha Kere
Outi Hovatta
Liselotte Vesterlund
Hong Jiao
Per Unneberg
Outi Hovatta
BMC Developmental Biology
RNA sequencing reveals two major classes of gene expression levels in metazoan cells. 2011-06-07 Sarah Teichmann
Alexander van Oudenaarden
Muxin Gu
Varodom Charoensawan
Daniel Hebenstreit
Miaoqing Fang
Molecular Systems Biology
Poly (A)+ transcriptome assessment of ERBB2-induced alterations in breast cell lines. 2011-06-22 Dirce Carraro
Emmanuel Dias-Neto
Helena Brentani
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
Renata Pasqualini
Ricardo Renzo Brentani
PLoS ONE
Deterministic and stochastic allele specific gene expression in single mouse blastomeres 2011-06-23 Azim Surani Fuchou Tang
Catalin Barbacioru
Ellen Nordman
Siqin Bao
Caroline Lee
Xiaohui Wang
Brian B Tuch
Edith Heard
Kaiqin Lao
PLoS ONE
Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq 2011-07 Sten Linnarsson
Peter Lönnerberg
Saiful Islam
Una Kjällquist
Annalena Moliner
Pawel Zajac
Jian-Bing Fan
Peter Lönnerberg
Sten Linnarsson
Genome Research
De novo assembly of expressed transcripts and global analysis of the Phalaenopsis aphrodite transcriptome. 2011-07-19 Ya-Ting Chao Chun-lin Su
Yao-Chien Alex Chang
Wan-Chieh Chen
Chun-Yi Chen
Ann-Ying Lee
Kee Tuan Hwa
Ming-Che Shih
Plant and Cell Physiology
Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression 2011-07-31 John R. Prensner
Qi Cao
Irfan Asangani
Nallasivam Palanisamy
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
Nature Biotechnology
AlleleSeq: analysis of allele-specific expression and binding in a network framework. 2011-08-02 Yong Kong
Alexej Abyzov
Joel Rozowsky
Mark Rubin
Jing Wang
Pedro Alves
Debasish Raha
Arif Harmanci
Jing Leng
Robert Bjornson
Naoki Kitabayashi
Nitin Bhardwaj
Michael Snyder
Mark Gerstein
Molecular Systems Biology
Synthetic spike-in standards for RNA-seq experiments. 2011-08-04 Thomas R. Gingeras Lichun Jiang
Felix Schlesinger
Carrie A Davis
Yu Zhang
Renhua Li
Marc Salit
Brian Oliver
Genome Research
TopHat-Fusion: an algorithm for discovery of novel fusion transcripts 2011-08-11 Steven Salzberg Daehwan Kim Genome Biology
Genome-Wide Gene Expression Profiling of Nucleus Accumbens Neurons Projecting to Ventral Pallidum Using both Microarray and Transcriptome Sequencing 2011-08-12 Robert W. Williams Hao Chen
Zhimin Liu
Suzhen Gong
Xingjun Wu
William L Taylor
Shannon G Matta
Burt M Sharp
Frontiers in Neuroscience
Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma 2011-08-18 Martin Hirst
Yaron Butterfield
Angela Brooks-Wilson
Eric Y Zhao
Malachi Griffith
Andrew Mungall
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
Nature
The disequilibrium of nucleosomes distribution along chromosomes plays a functional and evolutionarily role in regulating gene expression 2011-08-19 Songnian Hu Peng Cui
Qiang Lin
Lingfang Zhang
Feng Ding
Chengqi Xin
Daoyong Zhang
Fanglin Sun
Jun Yu
PLoS ONE
Bioaccumulation and effects of CdTe/CdS quantum dots on Chlamydomonas reinhardtii - nanoparticles or the free ions? 2011-08-25 Rute F. Domingos Dana F Simon
Charles Hauser
Kevin J Wilkinson
Environmental Science & Technology
SpliceTrap: a method to quantify alternative splicing under single cellular conditions. 2011-09-06 W. Richard McCombie Jie Wu
Martin Akerman
Shuying Sun
Adrian R Krainer
Michael Q Zhang
Bioinformatics
wapRNA: a web-based application for the processing of RNA sequences. 2011-09-06 Songnian Hu Wenming Zhao
Wanfei Liu
Dongmei Tian
Bixia Tang
Yanqing Wang
Caixia Yu
Rujiao Li
Yunchao Ling
Jiayan Wu
Shuhui Song
Bioinformatics
Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals. 2011-09-25 Vincent Lynch Robert D Leclerc
Gemma May
Günter P Wagner
Nature Genetics
Genome-wide transcriptome analysis in murine neural retina using high-throughput RNA sequencing. 2011-10-01 Ece D. Gamsiz
Eric M Morrow
Qing Ouyang
Michael Schmidt
Shailender Nagpal
Genomics
The role of CYP3A4 mRNA transcript with shortened 3'-untranslated region in hepatocyte differentiation, liver development, and response to drug induction. 2011-10-13 Steven N. Hart Dan Li
Roger Gaedigk
J Steven Leeder
Xiao-bo Zhong
Molecular Pharmacology
Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster. 2011-10-23 Thomas R. Gingeras
Jay Shendure
David Sturgill
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
Nature Genetics
Identification of gene fusion transcripts by transcriptome sequencing in BRCA1-mutated breast cancers and cell lines 2011-10-27 Anne Vincent-Salomon Kevin C H Ha
Emilie Lalonde
Lili Li
Luca Cavallone
Rachael Natrajan
Maryou B Lambros
Costas Mitsopoulos
Jarle Hakas
Iwanka Kozarewa
Kerry Fenwick
Chris J Lord
Alan Ashworth
Mark Basik
Jorge S Reis-Filho
Jacek Majewski
William D Foulkes
BMC Medical Genomics
RNA-Seq reveals an integrated immune response in nucleated erythrocytes. 2011-10-27 Laia Ribas
Joan C Balasch
Simon Mackenzie
Steven B. Roberts
Nerea Roher
Davinia Morera
Carmen Doñate
Agnes Callol
Sebastian Boltaña
Giles Goetz
Frederick W Goetz
PLoS ONE
The transcriptome of the reference potato genome Solanum tuberosum Group Phureja clone DM1-3 516R44. 2011-10-28 Giovanni Giuliano Alicia N Massa
Kevin L Childs
Haining Lin
Glenn J Bryan
C Robin Buell
PLoS ONE
RNA-Seq reveals genotype-specific molecular responses to water deficit in eucalyptus 2011-11-02 Christophe Plomion Emilie Villar
Christophe Klopp
Céline Noirot
Evandro Novaes
Matias Kirst
Jean-Marc Gion
BMC Genomics
Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain. 2011-11-06 Adam Ameur Ammar Zaghlool
Jonatan Halvardson
Anna Wetterbom
Ulf Gyllensten
Lucia Cavelier
Lars Feuk
Nature Structural & Molecular Biology
Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq. 2011-11-08 Ming Hu
Zhaohui Steve Qin
Yu Zhu
Jeremy M G Taylor
Jun S Liu
Bioinformatics
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
Ru Huang
Markus Jaritz
Philipp Guenzl
Ido M Tamir
Thorsten Klampfl
Hendrik G Stunnenberg
Denise P Barlow
Florian M Pauler
PLoS ONE
Identification of new viral genes and transcript isoforms during Epstein-Barr virus reactivation using RNA-Seq. 2011-11-16 Melody Baddoo
Dale Hedges
Monica Concha
Xia Wang
Subing Cao
Melody Baddoo
Claire Fewell
Zhen Lin
William Hulme
Dale Hedges
Jane McBride
Erik K Flemington
Journal of Virology
Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. 2011-11-22 Aviv Regev
Eivind Valen
Albin Sandelin
John L. Rinn
Andrea Pauli
Michael F Lin
Manuel Garber
Nadine L Vastenhouw
Joshua Z Levin
Lin Fan
Aviv Regev
Alexander F Schier
Genome Research
RNA-Seq and find: entering the RNA deep field. 2011-11-22 Lior Pachter Adam Roberts Genome Medicine
Estimation of alternative splicing variability in human populations. 2011-11-23 Roderic Guigó i Serra
Michael Sammeth
Mar Gonzàlez-Porta
Miquel Calvo
Genome Research
Cell walls of developing wheat starchy endosperm: comparison of composition and RNA-Seq transcriptome. 2011-11-28 Paola Tosi
J Paul Knox
Till K Pellny
Alison Lovegrove
Jackie Freeman
Christopher G Love
Peter R Shewry
Rowan A C Mitchell
Plant Physiology
RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.). 2011-12-02 Jérôme Salse Caroline Pont
Florent Murat
Carole Confolent
Sandrine Balzergue
Genome Biology
Protein identification using customized protein sequence databases derived from RNA-Seq data. 2011-12-14 David Tabb Xiaojing Wang
Robbert J C Slebos
Dong Wang
Patrick J Halvey
Daniel C Liebler
Bing Zhang
Journal of Proteome Research
Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis 2011-12-22 Desmond G. Higgins
Geraldine Butler
Alessandro Guida
Claudia Lindstädt
Sarah L Maguire
Chen Ding
Nicola J Corton
Matthew Berriman
BMC Genomics
Characterization of a highly conserved histone related protein, Ydl156w, and its functional associations using quantitative proteomic analyses. 2011-12-22 Laurence Florens Joshua M Gilmore
Mihaela E Sardiu
Swaminathan Venkatesh
Brent Stutzman
Allison Peak
Chris W Seidel
Jerry L Workman
Michael P Washburn
Molecular & Cellular Proteomics
Cytoskeleton remodeling and alterations in smooth muscle contractility in the bovine jejunum during nematode infection. 2011-12-28 Steven G Schroeder Robert W Li Functional and Integrative Genomics
Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas. 2011-12-29 Steven B. Roberts Mackenzie R Gavery Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics
Isoform diversity and regulation in peripheral and central neurons revealed through RNA-Seq 2012 John L. Bixby
Vance P. Lemmon
Jessica K Lerch
Frank Kuo
Dario Motti
Richard Morris
PLoS ONE
Genes associated with MUC5AC expression in small airway epithelium of human smokers and non-smokers 2012 Jacqueline Salit Guoqing Wang
Zhibo Xu
Rui Wang
Mohammed Al-Hijji
Yael Strulovici-Barel
Ann E Tilley
Jason G Mezey
Ronald G Crystal
BMC Medical Genomics
The transcriptional landscape of the deep-sea bacterium Photobacterium profundum in both a toxR mutant and its parental strain 2012 Andrea Telatin Stefano Campanaro
Fabio De Pascale
Riccardo Schiavon
Douglas H Bartlett
Giorgio Valle
BMC Genomics
Computational analysis of noncoding RNAs 2012 Manolis Kellis
Stefan Washietl
Sebastian Will
David A. Hendrix
Loyal A. Goff
John L. Rinn
Bonnie Berger
Wiley interdisciplinary reviews. RNA
Tcf7 is an important regulator of the switch of self-renewal and differentiation in a multipotential hematopoietic cell line 2012 Mark Bender Gerstein
Vincent Schulz
Jia Qian Wu
Montrell Seay
Manoj Hariharan
David Tuck
Jin Lian
Jiang Du
Minyi Shi
Zhijia Ye
Michael P Snyder
Sherman Weissman
PLOS Genetics
RNA-seq analysis reveals different dynamics of differentiation of human dermis- and adipose-derived stromal stem cells 2012 Sten Linnarsson Kersti Jääger
Saiful Islam
Pawel Zajac
Sten Linnarsson
Toomas Neuman
PLoS ONE
Stable gene targeting in human cells using single-strand oligonucleotides with modified bases 2012 George M Church Xavier Rios
Adrian W Briggs
Danos Christodoulou
Josh M Gorham
Jonathan G Seidman
PLoS ONE
Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data 2012 Jean-Baptiste Veyrieras Jean-Baptiste Veyrieras
Daniel J Gaffney
Joseph K Pickrell
Yoav Gilad
Matthew Stephens
Jonathan K Pritchard
PLoS ONE
DBTSS: DataBase of Transcriptional Start Sites progress report in 2012 2012-01 Sumio Sugano Riu Yamashita
Yutaka Suzuki
Kenta Nakai
Nucleic Acids Research
Retinal transcriptome profiling by directional next-generation sequencing using 100 ng of total RNA. 2012-01-01 Anand Swaroop Matthew J Brooks
Harsha Karur Rajasimha
Methods in Molecular Biology
Defining the molecular profile of planarian pluripotent stem cells using a combinatorial RNAseq, RNA interference and irradiation approach. 2012-01-01 Jordi Solana Damian Kao
Yuliana Mihaylova
Farah Jaber-Hijazi
Sunir Malla
Ray Wilson
Aziz Aboobaker
Genome Biology
Genome-wide mapping of nucleosome occupancy, histone modifications, and gene expression using next-generation sequencing technology. 2012-01-01 Gangqing Hu Gang Wei
Kairong Cui
Keji Zhao
Methods in Enzymology
Direct isolation and RNA-seq reveal environment-dependent properties of engrafted neural stem/progenitor cells. 2012-01-01 Yasuyuki Ohkawa
Kazu Kobayakawa
Seiji Okada
Hiromi Kumamaru
Hirokazu Saiwai
Hisakata Yamada
Kensuke Kubota
Koichi Akashi
Hideyuki Okano
Yukihide Iwamoto
Nature Communications
Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution. 2012-01-03 Robert K. Bradley Jason Merkin
Nicole J Lambert
Christopher B Burge
PLOS Biology
PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data. 2012-01-04 Zemin Ning Yanju Zhang
Eric-Wubbo Lameijer
Peter A C 't Hoen
P Eline Slagboom
Kai Ye
Bioinformatics
IQSeq: integrated isoform quantification analysis based on next-generation sequencing. 2012-01-06 Andrea Sboner Jiang Du
Jing Leng
Lukas Habegger
Drew McDermott
Mark Gerstein
PLoS ONE
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. 2012-01-11 Melody Baddoo Zhen Lin
Adriane Puetter
Joseph Coco
Guorong Xu
Michael J Strong
Xia Wang
Claire Fewell
Melody Baddoo
Christopher Taylor
Erik K Flemington
Journal of Virology
The architecture and ppGpp-dependent expression of the primary transcriptome of Salmonella Typhimurium during invasion gene expression. 2012-01-17 Cynthia Sharma Vinoy K Ramachandran
Neil Shearer
Jobin J Jacob
Arthur Thompson
BMC Genomics
MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data. 2012-01-20 Zhi-xiang Lu Shihao Shen
Juw Won Park
Jian Huang
Kimberly A Dittmar
Qing Zhou
Russ P Carstens
Yi Xing
Nucleic Acids Research
Application of RNA-Seq transcriptome analysis: CD151 is an Invasion/Migration target in all stages of epithelial ovarian cancer. 2012-01-24 Sergio Marchini
Robert Fruscio
Maurizio D'Incalci
Rebecca A Mosig
Li Lin
Emir Senturk
Hardik Shah
Fei Huang
Peter Schlosshauer
Samantha Cohen
Ravi Sachidanandam
Peter Dottino
John A Martignetti
Journal of Ovarian Research
A powerful method for transcriptional profiling of specific cell types in eukaryotes: laser-assisted microdissection and RNA sequencing. 2012-01-26 Philip Rosenstiel
Ueli Grossniklaus
Marc W Schmid
Anja Schmidt
Ulrich C Klostermeier
Matthias Barann
Ueli Grossniklaus
PLoS ONE
Pepitome: evaluating improved spectral library search for identification complementarity and quality assessment. 2012-01-27 David Tabb Surendra Dasari
Matthew C Chambers
Misti A Martinez
Kristin L Carpenter
Amy-Joan L Ham
Lorenzo J Vega-Montoto
Journal of Proteome Research
Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. 2012-01-28 Davis J McCarthy
Gordon K Smyth
Yunshun Chen Nucleic Acids Research
Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae). 2012-02-01 W. Richard McCombie
Norman J Wickett
Michael R McKain
Yeting Zhang
Saravanaraj Ayyampalayam
Mark W Chase
J Chris Pires
Claude W dePamphilis
Jim Leebens-Mack
American Journal of Botany
Spt4 is selectively required for transcription of extended trinucleotide repeats. 2012-02-01 Yijuang Chern 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
Cell
The Pseudomonas aeruginosa transcriptome in planktonic cultures and static biofilms using RNA sequencing. 2012-02-03 Andreas Dötsch Denitsa Eckweiler
Monika Schniederjans
Ariane Zimmermann
Vanessa Jensen
Maren Scharfe
Robert Geffers
Susanne Häussler
PLoS ONE
Genome-wide transcriptional profiling of appressorium development by the rice blast fungus Magnaporthe oryzae. 2012-02-09 Nick Talbot Darren M Soanes
Apratim Chakrabarti
Konrad H Paszkiewicz
Angus L Dawe
PLOS Pathogens
Nuclear matrix factor hnRNP U/SAF-A exerts a global control of alternative splicing by regulating U2 snRNP maturation. 2012-02-09 Changwei Shao
Jie Huang
Yi Zhang
Rui Xiao
Peng Tang
Bo Yang
Yu Zhou
Hairi Li
Hui Sun
Xiang-Dong Fu
Molecular Cell
Genome-wide analysis of STAT3 binding in vivo predicts effectors of the anti-inflammatory response in macrophages. 2012-02-09 Andrew Paul Hutchins Stéphane Poulain
Diego Miranda-Saavedra
Blood
Specific and sensitive mRNA biomarkers for the identification of skin in 'touch DNA' evidence. 2012-02-09 Cordula Haas E Hanson
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Forensic Science International: Genetics
Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. 2012-02-12 Wang Jun
Bertrand Chin-Ming Tan
Zhiyu Peng
Yanbing Cheng
Lin Kang
Zhijian Tian
Yuankun Zhu
Wenwei Zhang
Yu Liang
Xueda Hu
Xuemei Tan
Jing Guo
Zirui Dong
Yan Liang
Li Bao
Nature Biotechnology
Uterine gene expression in the live-bearing lizard, Chalcides ocellatus, reveals convergence of squamate reptile and mammalian pregnancy mechanisms 2012-02-14 Dan L. Warren Matthew C Brandley
Rebecca L Young
Michael B Thompson
Günter P Wagner
Genome Biology and Evolution
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. 2012-02-17 Eric Peatman Chao Li
Yu Zhang
Ruijia Wang
Jianguo Lu
Samiran Nandi
Sriprakash Mohanty
Jeffery Terhune
Zhanjiang Liu
Fish and Shellfish Immunology
RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings. 2012-02-21 Jian-Hua Mao
Wang Jun
Jun Wang
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
Huanming Yang
Yinghao Sun
Cell Research
FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads. 2012-02-29 Angelo Valleriani Gong Zhang
Ivan Fedyunin
Sebastian Kirchner
Chuanle Xiao
Zoya Ignatova
Nucleic Acids Research
Characterization and differential expression analysis of complete coding sequences of Vitis vinifera L. sirtuin genes. 2012-03-03 Giacomo Morreale M Cucurachi
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Plant Physiology and Biochemistry
The human pancreatic islet transcriptome: expression of candidate genes for type 1 diabetes and the impact of pro-inflammatory cytokines. 2012-03-08 Gerton Lunter
Izortze Santin
Michael Sammeth
Miriam Cnop
Lorella Marselli
Piero Marchetti
Décio L Eizirik
Thomas Bouckenooghe
Guy Bottu
Giorgia Sisino
Mariana Igoillo-Esteve
Fernanda Ortis
Maikel L Colli
Jenny Barthson
Luc Bouwens
Linda Hughes
Lorna Gregory
Mark I McCarthy
PLOS Genetics
HnRNP L and L-like cooperate in multiple-exon regulation of CD45 alternative splicing. 2012-03-08 Vladimir Benes
Gunnar Rätsch
Hans-Martin Jäck
Marco Preussner
Silke Schreiner
Lee-Hsueh Hung
Martina Porstner
Albrecht Bindereif
Nucleic Acids Research
Application of the whole-transcriptome shotgun sequencing approach to the study of Philadelphia-positive acute lymphoblastic leukemia. 2012-03-09 Annalisa Lonetti
Giovanni Malerba
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P Garagnani
A Vitale
S Soverini
F Pane
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Blood Cancer Journal
An Interspecies Regulatory Network Inferred from Simultaneous RNA-seq of Candida albicans Invading Innate Immune Cells. 2012-03-12 Sascha Brunke
Karl Kuchler
Lanay Tierney
Jörg Linde
Sebastian Müller
Juan Camilo Molina
Bernhard Hube
Ulrike Schöck
Reinhard Guthke
Frontiers in Microbiology
Transcriptome landscape of the human placenta 2012-03-27 Zhi-xiang Lu Jinsil Kim
Keyan Zhao
Peng Jiang
Jinkai Wang
Jeffrey C Murray
Yi Xing
BMC Genomics
RNA-Seq analysis uncovers transcriptomic variations between morphologically similar in vivo- and in vitro-derived bovine blastocysts 2012-03-28 Francisco Peñagaricano Ashley M Driver
Wen Huang
Khawaja R Ahmad
Katie S Hackbart
Milo C Wiltbank
Hasan Khatib
BMC Genomics
Comparative analyses of H3K4 and H3K27 trimethylations between the mouse cerebrum and testis. 2012-04-01 Songnian Hu Peng Cui
Wanfei Liu
Yuhui Zhao
Qiang Lin
Daoyong Zhang
Feng Ding
Chengqi Xin
Zhang Zhang
Shuhui Song
Fanglin Sun
Jun Yu
Genomics Proteomics and Bioinformatics
Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity. 2012-04-01 Ellen V. Rothenberg Jingli A Zhang
Ali Mortazavi
Brian A Williams
Barbara J Wold
Cell
A zinc-finger-family transcription factor, AbVf19, is required for the induction of a gene subset important for virulence in Alternaria brassicicola. 2012-04-01 Igor V Grigoriev Akhil Srivastava
Robin A Ohm
Lindsay Oxiles
Fred Brooks
Christopher B Lawrence
Yangrae Cho
Molecular Plant-Microbe Interactions
Identification of shortened 3' untranslated regions from expression arrays. 2012-04-01 Andrei Zinovyev
Loredana Martignetti
Emmanuel Barillot
Journal of Bioinformatics and Computational Biology
Computational inference of mRNA stability from histone modification and transcriptome profiles 2012-04-10 Yong Zhang Chengyang Wang
Rui Tian
Qian Zhao
Han Xu
Clifford A Meyer
Cheng Li
X Shirley Liu
Nucleic Acids Research
RNA-SeQC: RNA-seq metrics for quality control and process optimization 2012-04-25 Gad Getz
Wendy Winckler
David S DeLuca
Joshua Z Levin
Andrey Sivachenko
Timothy Fennell
Marc-Danie Nazaire
Chris Williams
Michael Reich
Bioinformatics
Transcriptome profiling of the intoxication response of Tenebrio molitor larvae to Bacillus thuringiensis Cry3Aa protoxin 2012-04-25 Ana Conesa
Diana Huestis
Brenda Oppert
Scot E Dowd
Pascal Bouffard
Lewyn Li
Marcé D Lorenzen
Michelle Toutges
Jeremy Marshall
Jeff Fabrick
Cris Oppert
Juan Luis Jurat-Fuentes
PLoS ONE
Concordant signaling pathways produced by pesticide exposure in mice correspond to pathways identified in human Parkinson's disease 2012-05-01 Olivier Elemento Seema Gollamudi
Ashu Johri
Noel Y Calingasan
Lichuan Yang
M Flint Beal
PLoS ONE
Transcriptome characterization by RNA-seq unravels the mechanisms of butyrate-induced epigenomic regulation in bovine cells. 2012-05-15 Weizhong Li Sitao Wu
Robert W Li
Cong-Jun Li
PLoS ONE
Transcriptome sequencing of and microarray development for a Helicoverpa zea cell line to investigate in vitro insect cell-baculovirus interactions 2012-05-18 Lars K. Nielsen Quan Nguyen
Robin W Palfreyman
Leslie C L Chan
Steven Reid
PLoS ONE
Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns 2012-05-24 Anders Krogh
Wang Jun
Johannes Waage
Joachim Weischenfeldt
Bo Torben Porse
Geng Tian
Jing Zhao
Inge Damgaard
Janus Schou Jakobsen
Karsten Kristiansen
Genome Biology
Transcriptomic signatures of attachment, NF-κB suppression and IFN stimulation in the catfish gill following columnaris bacterial infection. 2012-06-02 Eric Peatman Fanyue Sun
Chao Li
Shikai Liu
Yanliang Jiang
Zunchun Zhou
Zhanjiang Liu
Developmental and Comparative Immunology
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
Martin Hemberg
Jesse M Gray
Scott Kuersten
Michael E Greenberg
Nucleic Acids Research
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
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
Detecting differential usage of exons from RNA-seq data 2012-06-21 Alejandro Reyes
Simon Anders
Wolfgang Huber
Genome Research
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
Cell
FusionFinder: a software tool to identify expressed gene fusion candidates from RNA-Seq data. 2012-06-27 Richard W Francis
Denise Anderson
Alex H. Beesley
Katherine Thompson-Wicking
Kim W Carter
Ursula R Kees
PLoS ONE
SAVoR: a server for sequencing annotation and visualization of RNA structures 2012-07 Otto Valladares
Fan Li
Paul Ryvkin
Daniel M Childress
Brian D Gregory
Li-San Wang
Nucleic Acids Research
Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions 2012-07-01 Gioacchino Natoli Dev M Bhatt
Amy Pandya-Jones
Ann-Jay Tong
Iros Barozzi
Michelle M Lissner
Douglas L Black
Stephen T Smale
Cell
Paired-end sequencing of Fosmid libraries by Illumina. 2012-07-16 Gad Getz Louise J S Williams
Diana G Tabbaa
Na Li
Aaron M Berlin
Terrance P Shea
Iain Maccallum
Michael S Lawrence
Yotam Drier
Sarah K Young
David B Jaffe
Chad Nusbaum
Andreas Gnirke
Genome Research
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 Brenton R. Graveley Joseph D Coolon
Kraig R Stevenson
C Joel McManus
Patricia J Wittkopp
Cell Reports
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
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 Sarah W Satola
Emily K Crispell
Timothy D Read
Antimicrobial Agents and Chemotherapy
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 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
RNA-Seq provides new insights in the transcriptome responses induced by the carcinogen benzo[a]pyrene. 2012-08-13 Stan Gaj Joost van Delft
Stan Gaj
Matthias Lienhard
Marcus W Albrecht
Alexander Kirpiy
Karen Brauers
Sandra Claessen
Daneida Lizarraga
Hans Lehrach
Ralf Herwig
Jos Kleinjans
Toxicological Sciences
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
Glenn F King
Emily S W Wong
David Morgenstern
Ehtesham Mofiz
Sara Gombert
Katrina M Morris
Peter Temple-Smith
Camilla M Whittington
Wesley C Warren
Katherine Belov
Molecular & Cellular Proteomics
Research resource: RNA-Seq reveals unique features of the pancreatic β-cell transcriptome. 2012-08-21 Michael McManus Gregory M Ku
Hail Kim
Ian W Vaughn
Matthew J Hangauer
Chang Myung Oh
Michael S German
Molecular Endocrinology
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
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
Marianna Fasoli
Sara Zenoni
Lorenzo Farina
Anita Zamboni
Andrea Porceddu
Luca Venturini
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 Thasso Griebel
Benedikt Zacher
Paolo Ribeca
Emanuele Raineri
Vincent Lacroix
Michael Sammeth
Nucleic Acids Research
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
Edward M Marcotte
Jeffrey M Gross
Developmental Biology
Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production. 2012-09-11 Todd P Michael Chongyuan Luo
David J Sidote
Yi Zhang
Randall A Kerstetter
Eric Lam
The Plant Journal
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
Mihoko Kato Proceedings of the National Academy of Sciences of the United States of America
High-resolution transcriptome of human macrophages. 2012-09-21 Joachim Schultze Marc Beyer
Michael R Mallmann
Jia Xue
Andrea Staratschek-Jox
Daniela Vorholt
Wolfgang Krebs
Daniel Sommer
Jil Sander
Christina Mertens
Andrea Nino-Castro
Susanne V Schmidt
PLoS ONE
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
Dual lineage-specific expression of Sox17 during mouse embryogenesis. 2012-10-01 Momoko Yoshimoto
Mark A. Magnuson
Eunyoung Choi
Marine R C Kraus
Laurence A Lemaire
Sasidhar Vemula
Leah A Potter
Elisabetta Manduchi
Christian J Stoeckert
Anne Grapin-Botton
Stem Cells
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
Hiroaki Yamasaki
Scott I Hsieh
Lital N Adler
Steven J Karpowicz
Steven G Clarke
Joseph A Loo
Sabeeha S Merchant
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
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 Julien Rougeot
Anne Coléno-Costes
Jean-Michel Gibert
Frédérique Peronnet
Stéphane Le Crom
Suk Min Jang
Augustin de Vanssay
Tahar Bouceba
Neel B Randsholt
Emmanuèle Mouchel-Vielh
Sébastien Bloyer
PLOS Genetics
Faster-X evolution of gene expression in Drosophila 2012-10-11 Richard P Meisel John H Malone
Andrew G Clark
PLOS Genetics
Identification of hundreds of novel UPF1 target transcripts by direct determination of whole transcriptome stability. 2012-10-12 Naoto Imamachi
Hidenori Tani
Kazi Abdus Salam
Rena Mizutani
Kenichi Ijiri
Takuma Irie
Tetsushi Yada
Yutaka Suzuki
Nobuyoshi Akimitsu
RNA Biology
The proteome of copper, iron, zinc, and manganese micronutrient deficiency in Chlamydomonas reinhardtii. 2012-10-13 Eugen Urzica
David Casero
Matteo Pellegrini
Scott I Hsieh
Madeli Castruita
Davin Malasarn
Jonathan Erde
M Dudley Page
Hiroaki Yamasaki
Sabeeha S Merchant
Joseph A Loo
Molecular & Cellular Proteomics
A bioinformatics approach for integrated transcriptomic and proteomic comparative analyses of model and non-sequenced anopheline vectors of human malaria parasites. 2012-10-17 Gerhard G Thallinger
Antonis Rokas
David R. Colquhoun
Jürgen Hartler
Jesus Martinez-Barnetche
Ceereena Ubaida Mohien
Derrick K Mathias
John G Gibbons
Jennifer S Armistead
Maria C Rodriguez
Mario Henry Rodriguez
Nathan J Edwards
David R Graham
Rhoel R Dinglasan
Molecular & Cellular Proteomics
Molecular aspects of mucin biosynthesis and mucus formation in the bovine cervix during the periestrous period. 2012-10-23 Paul A McGettigan
Jane A Irwin
Alan Baird
Katarzyna Pluta
Colm J Reid
John A Browne
Tharmala Tharmalingam
Anthony Corfield
Brendan J Loftus
Alexander C O Evans
Stephen D Carrington
Physiological Genomics
Transcription factor Amr1 induces melanin biosynthesis and suppresses virulence in Alternaria brassicicola 2012-10-25 Igor V Grigoriev Yangrae Cho
Akhil Srivastava
Robin A Ohm
Christopher B Lawrence
Koon-Hui Wang
Sharadchandra P Marahatta
PLOS Pathogens
Identification of PADI2 as a potential breast cancer biomarker and therapeutic target. 2012-10-30 Obi Griffith
Venkataraman Subramanian
John L McElwee
Sunish Mohanan
Heike C Breuer
Lynne J Anguish
Brian D Cherrington
Ashley M Palmer
Louise R Howe
Corey P Causey
Paul R Thompson
Joe W Gray
Scott A Coonrod
BMC Cancer
Interaction of cyclin-dependent kinase 12/CrkRS with cyclin K1 is required for the phosphorylation of the C-terminal domain of RNA polymerase II 2012-11 Jerry F. Tien
Malachi Griffith
Gregg B Morin
S-W Grace Cheng
Michael A Kuzyk
Annie Moradian
Taka-Aki Ichu
Vicky C-D Chang
Sarah E Vollett
Marco A Marra
Molecular and Cellular Biology
Age-related changes of gene expression in the neocortex: preliminary data on RNA-Seq of the transcriptome in three functionally distinct cortical areas. 2012-11-01 Dean Palejev
Flora M. Vaccarino
Oksana Yu Naumova
Natalia V Vlasova
Maria Lee
Sergei Yu Rychkov
Olga N Babich
Elena L Grigorenko
Development and Psychopathology
Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote 2012-11-05 Shikai Liu
Eric Peatman
Geoff Waldbieser
Huseyin Kucuktas
Yu Zhang
Zunchun Zhou
Geoff Waldbieser
Fanyue Sun
Jianguo Lu
Jiaren Zhang
Yanliang Jiang
Hao Zhang
Xiuli Wang
K V Rajendran
Lester Khoo
Huseyin Kucuktas
Zhanjiang Liu
BMC Genomics
Novel BRD4-NUT fusion isoforms increase the pathogenic complexity in NUT midline carcinoma. 2012-11-05 Adrian K. Charles
Alex H. Beesley
K Thompson-Wicking
R W Francis
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K W Carter
M B Phillips
U R Kees
Oncogene
DiffSplice: the genome-wide detection of differential splicing events with RNA-seq. 2012-11-15 D. Neil Hayes 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
Nucleic Acids Research
An RNA-seq-based gene expression profiling of radiation-induced tumorigenic mammary epithelial cells. 2012-12-04 Songnian Hu Lina Ma
Linghu Nie
Jing Liu
Bing Zhang
Shuhui Song
Min Sun
Jin Yang
Yadong Yang
Xiangdong Fang
Yongliang Zhao
Jun Yu
Genomics Proteomics and Bioinformatics
A histone deacetylase adjusts transcription kinetics at coding sequences during Candida albicans morphogenesis. 2012-12-06 Alexander Stark Denes Hnisz
Anaïs F Bardet
Clarissa J Nobile
Andriy Petryshyn
Walter Glaser
Ulrike Schöck
Karl Kuchler
PLOS Genetics
The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells. 2012-12-06 Wolf Reik Stefanie Seisenberger
Simon Andrews
Felix Krueger
Julia Arand
Jörn Walter
Fátima Santos
Christian Popp
Bernard Thienpont
Wendy Dean
Molecular Cell
Chromatin is an ancient innovation conserved between Archaea and Eukarya. 2012-12-13 Corey Nislow
Gary D. Bader
Ron Ammar
Dax Torti
Kyle Tsui
Marinella Gebbia
Tanja Durbic
Guri Giaever
eLife
Circular RNAs are abundant, conserved, and associated with ALU repeats. 2012-12-18 Norman E. Sharpless William R Jeck
Jessica A Sorrentino
Kai Wang
Michael K Slevin
Christin E Burd
Jinze Liu
William F Marzluff
RNA
HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency. 2012-12-20 Jeremy Luban Federico A Santoni
Jessica Guerra
Retrovirology
Whole-genome DNA/RNA sequencing identifies truncating mutations in RBCK1 in a novel Mendelian disease with neuromuscular and cardiac involvement 2013 Cecilia Kim
Hakon Hakonarson
Kai Wang
Jonathan Bradfield
Yunfei Guo
Elina Toskala
Frederick G Otieno
Cuiping Hou
Kelly Thomas
Christopher Cardinale
Gholson J Lyon
Ryan Golhar
Genome Medicine
Molecular and cellular mechanisms of neutral lipid accumulation in diatom following nitrogen deprivation 2013 Hong-Ye Li 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
Biotechnology for Biofuels
"A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids" 2013 Jennifer Ann Harikrishna Mark W Davey
Ranganath Gudimella
Lee Wan Sin
Norzulaani Khalid
Johan Keulemans
BMC Genomics
RNA-Seq profiling of spinal cord motor neurons from a presymptomatic SOD1 ALS mouse 2013 Arthur L. Horwich Urmi Bandyopadhyay
Justin Cotney
Maria Nagy
Sunghee Oh
Jing Leng
Milind Mahajan
Shrikant Mane
Wayne A Fenton
James P Noonan
PLoS ONE
Integrative approach reveals composition of endoparasitoid wasp venoms 2013 Todd A Schlenke
Nathan T Mortimer
James Taylor
Jeremy Goecks
James A Mobley
Gregory J Bowersock
PLoS ONE
Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy 2013 Majid Kazemian Qiong Cheng
Hannah Pham
Charles Blatti
Susan E Celniker
Scot A Wolfe
Michael H Brodsky
Saurabh Sinha
PLOS Genetics
Putative sugar transporters of the mustard leaf beetle Phaedon cochleariae: their phylogeny and role for nutrient supply in larval defensive glands 2013 Wilhelm Boland Magdalena Stock
René R Gretscher
Marco Groth
Simone Eiserloh
Antje Burse
PLoS ONE
High occurrence of functional new chimeric genes in survey of rice chromosome 3 short arm genome sequences 2013-01-01 Rod A. Wing Chengjun Zhang
Jun Wang
Nicholas C Marowsky
Manyuan Long
Chuanzhu Fan
Genome Biology and Evolution
Transcriptome sequencing of neonatal thymic epithelial cells. 2013-01-01 Claude Perreault Charles St-Pierre
Sylvie Brochu
Juan Ruiz Vanegas
Maude Dumont-Lagacé
Sébastien Lemieux
Scientific Reports
Dual functions of TAF7L in adipocyte differentiation. 2013-01-08 Michael Eisen
Ivan Grubisic
Tommy Kaplan
Haiying Zhou
Yan Li
Zhengjian Zhang
P Jeremy Wang
Robert Tjian
eLife
Transcriptome sequencing (RNA-Seq) of human endobronchial biopsies: asthma versus controls. 2013-01-11 Frank Baas Ching Yong Yick
Aeilko H Zwinderman
Peter W Kunst
Katrien Grünberg
Thais Mauad
Annemiek Dijkhuis
Elisabeth H Bel
René Lutter
Peter J Sterk
European Respiratory Journal
ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution. 2013-01-12 Raymond Wan Jing-Woei Li
Chi-Shing Yu
Ngai Na Co
Nathalie Wong
Ting-Fung Chan
Bioinformatics
Conserved gene regulatory function of the carboxy-terminal domain of dictyostelid C-module-binding factor. 2013-01-25 Gernot Glöckner Anika Schmith
Marco Groth
Josephine Ratka
Sara Gatz
Thomas Spaller
Oliver Siol
Thomas Winckler
Eukaryotic Cell
Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data 2013-01-28 John C Marioni Jong Kyoung Kim Genome Biology
Contribution of copy number variants involving nonsense-mediated mRNA decay pathway genes to neuro-developmental disorders. 2013-01-31 Jozef Gécz
Lam S Nguyen
Hyung-Goo Kim
Jill A Rosenfeld
Yiping Shen
James F Gusella
Yves Lacassie
Lawrence C Layman
Lisa G Shaffer
Human Molecular Genetics
puma 3.0: improved uncertainty propagation methods for gene and transcript expression analysis. 2013-02-05 Magnus Rattray Xuejun Liu
Zhenzhu Gao
Li Zhang
BMC Bioinformatics
Expression profile of ectopic olfactory receptors determined by deep sequencing. 2013-02-06 Hanns Hatt
Günter Gisselmann
Caroline Flegel
Stavros Manteniotis
Sandra Osthold
Hanns Hatt
Günter Gisselmann
PLoS ONE
FUS regulates genes coding for RNA-binding proteins in neurons by binding to their highly conserved introns. 2013-02-06 Zissimos Mourelatos
Manolis Maragkakis
Panagiotis Alexiou
Tadashi Nakaya
Alexandra Chang
RNA
SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data. 2013-02-14 Wang Jun
Wenlong Jia
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
Genome Biology
mRNA expression, splicing and editing in the embryonic and adult mouse cerebral cortex. 2013-02-17 Dagmar Galter
David N Hauser
Allissa A Dillman
J Raphael Gibbs
Michael A Nalls
Melissa K McCoy
Iakov N Rudenko
Mark R Cookson
Nature Neuroscience
EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. 2013-02-21 Christina Kendziorski 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
Bioinformatics
Perturbations of Plasmodium Puf2 expression and RNA-seq of Puf2-deficient sporozoites reveal a critical role in maintaining RNA homeostasis and parasite transmissibility. 2013-02-27 Scott E. Lindner
Sebastian A. Mikolajczak
Ashley M Vaughan
Wonjong Moon
Brad R Joyce
William J Sullivan
Stefan H I Kappe
Cellular Microbiology
SplicingCompass: differential splicing detection using RNA-seq data. 2013-02-28 Roland Eils Moritz Aschoff
Agnes Hotz-Wagenblatt
Karl-Heinz Glatting
Matthias Fischer
Rainer König
Bioinformatics
Epstein - Barr virus transforming protein LMP-1 alters B cells gene expression by promoting accumulation of the oncoprotein ΔNp73α 2013-03 Florence Le Calvez-Kelm
Birke Bartosch
Evelyne Manet
Hector Hernandez-Vargas
Rosita Accardi
Ikbal Fathallah
Henri Gruffat
Giuseppe Mariggiò
Catherine Voegele
James McKay
Bakary S Sylla
Massimo Tommasino
PLOS Pathogens
RNA-Seq analysis discloses early senescence and nucleolar dysfunction triggered by Tdp1α depletion in Medicago truncatula. 2013-03-06 Anca Macovei
Daniela Carbonera
Alma Balestrazzi
Mattia Donà
Massimo Confalonieri
Andrea Minio
Marco Biggiogera
Armando Buttafava
Elena Raimondi
Massimo Delledonne
Lorenzo Ventura
Maria Elisa Sabatini
Giorgio Giraffa
Journal of Experimental Botany
Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema. 2013-03-07 Bianca Habermann
Elly M Tanaka
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
PLOS Computational Biology
Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR). 2013-03-08 Jasmine Jacob-Hirsch 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
RNA
Proteogenomic analysis of human colon carcinoma cell lines LIM1215, LIM1899, and LIM2405. 2013-03-13 Susan Fanayan Joshua T Smith
Ling Y Lee
Fangfei Yan
Michael Snyder
William S Hancock
Edouard Nice
Journal of Proteome Research
CathaCyc, a metabolic pathway database built from Catharanthus roseus RNA-Seq data. 2013-03-14 Stephane Rombauts
Kirsi-Marja Oksman-Caldentey
Alex Van Moerkercke
Michele Fabris
Jacob Pollier
Gino J E Baart
Ghulam Hasnain
Heiko Rischer
Johan Memelink
Kirsi-Marja Oksman-Caldentey
Alain Goossens
Plant and Cell Physiology
Isolation of Blastomyces dermatitidis yeast from lung tissue during murine infection for in vivo transcriptional profiling 2013-03-14 Christina A Cuomo Amber J Marty
Marcel Wüthrich
John C Carmen
Thomas D Sullivan
Bruce S Klein
Gregory M Gauthier
Fungal Genetics and Biology
TDP-43 high throughput screening analyses in neurodegeneration: advantages and pitfalls. 2013-03-14 Emanuele Buratti
Maurizio Romano
Francisco E Baralle Molecular and Cellular Neuroscience
Interpretation, stratification and evidence for sequence variants affecting mRNA splicing in complete human genome sequences. 2013-03-14 Peter K. Rogan
Paul I Costea
Ben C Shirley
Eliseos J Mucaki
Tyson Whitehead
Pelin Akan
Genomics Proteomics and Bioinformatics
Identification of novel exons and transcripts by comprehensive RNA-Seq of horn cancer transcriptome in Bos indicus. 2013-03-14 Subhash J Jakhesara
Chaitanya G. Joshi
Prakash G Koringa Journal of Biotechnology
A multifaceted study of Pseudomonas aeruginosa shutdown by virulent podovirus LUZ19. 2013-03-19 Rob Lavigne Elke Lecoutere
Jeroen Wagemans
William Cenens
Abram Aertsen
Liliane Schoofs
Bart Landuyt
Jan Paeshuyse
Maurice Scheer
Max Schobert
Pieter-Jan Ceyssens
mBio
Investigation of radiation-induced transcriptome profile of radioresistant non-small cell lung cancer A549 cells using RNA-seq 2013-03-22 Namshin Kim Hee Jung Yang
Ki Moon Seong
HyeSook Youn
BuHyun Youn
PLoS ONE
Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation 2013-03-24 Wang Jun
Junyi Wang
Klaus Mayer
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
Thomas Wicker
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
Huanming Yang
Xu Liu
Zhonghu He
Long Mao
Nature
RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome. 2013-03-25 Alicia Oshlack
Nadia M Davidson
Craig A. Smith
Katie L Ayers
Diana Demiyah
Kelly N Roeszler
Frank Grützner
Andrew H Sinclair
Genome Biology
Development of strategies for SNP detection in RNA-seq data: application to lymphoblastoid cell lines and evaluation using 1000 Genomes data 2013-03-26 Michael Gill
Elaine M Kenny
Richard Anney
Derek W. Morris
Aiden Corvin
Emma M Quinn
Paul Cormican
Matthew Hill
PLoS ONE
Predicting long non-coding RNAs using RNA sequencing. 2013-03-27 Chris Ponting
Nicholas E Ilott
Methods
Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq. 2013-03-28 Jon Jerlström-Hultqvist Oscar Franzén
Elin Einarsson
Johan Ankarklev
Marcela Ferella
Björn Andersson
Staffan G Svärd
PLOS Computational Biology
Spatial transcriptional profile of the chick and mouse endocardial cushions identify novel regulators of endocardial EMT in vitro. 2013-04-01 Daniel M DeLaughter Daniel M DeLaughter
Danos C Christodoulou
Jamille Y Robinson
Christine E Seidman
H Scott Baldwin
J G Seidman
Joey V Barnett
Journal of Molecular and Cellular Cardiology
Frogs and estivation: transcriptional insights into metabolism and cell survival in a natural model of extended muscle disuse. 2013-04-02 Craig E. Franklin Beau D Reilly
David I Schlipalius
Rebecca L Cramp
Paul R Ebert
Physiological Genomics
New insights into Chlamydomonas reinhardtii hydrogen production processes by combined microarray/RNA-seq transcriptomics. 2013-04-03 Patrick May
Alexander Goesmann
Jörg Toepel
Maike Illmer-Kephalides
Sebastian Jaenicke
Jasmin Straube
Olaf Kruse
Plant Biotechnology Journal
Comparative RNA-Seq and microarray analysis of gene expression changes in B-cell lymphomas of Canis familiaris. 2013-04-04 Noel Monks 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
PLoS ONE
Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro. 2013-04-08 Amanda J Lohan
Kévin Rue-Albrecht
Karsten Hokamp
Brendan Loftus
Eamonn Gormley
David E. MacHugh
Stephen V. Gordon
Nicolas C Nalpas
Stephen D E Park
David A Magee
Maria Taraktsoglou
John A Browne
Kevin M Conlon
Kate E Killick
BMC Genomics
Characterization of FUS mutations in amyotrophic lateral sclerosis using RNA-Seq. 2013-04-08 Marka van Blitterswijk Eric T Wang
Brad A Friedman
Pamela J Keagle
Patrick Lowe
Ashley Lyn Leclerc
Leonard H van den Berg
David E Housman
Jan H Veldink
John E Landers
PLoS ONE
Accurate detection of differential RNA processing. 2013-04-12 Oliver Stegle
Gunnar Rätsch
Philipp Drewe
Lisa Hartmann
André Kahles
Regina Bohnert
Andreas Wachter
Karsten Borgwardt
Nucleic Acids Research
Evolution of the eye transcriptome under constant darkness in Sinocyclocheilus cavefish 2013-04-23 Ingo Braasch Fanwei Meng
Jennifer B Phillips
Xiwen Lin
Tom Titus
Chunguang Zhang
John H Postlethwait
Molecular Biology and Evolution
A model based criterion for gene expression calls using RNA-seq data. 2013-04-25 Vincent Lynch Günter P Wagner
Koryu Kin
Theory in Biosciences
Transcriptome analysis of Japanese pear (Pyrus pyrifolia Nakai) flower buds transitioning through endodormancy. 2013-04-26 Songling Bai Takanori Saito
Daisuke Sakamoto
Akiko Ito
Hiroshi Fujii
Takaya Moriguchi
Plant and Cell Physiology
RNA-Seq reveals expression signatures of genes involved in oxygen transport, protein synthesis, folding, and degradation in response to heat stress in catfish. 2013-04-30 Shikai Liu
Eric Peatman
Huseyin Kucuktas
Ludmilla Kaltenboeck
Xiuli Wang
Fanyue Sun
Jiaren Zhang
Jianbin Feng
Hong Liu
K V Rajendran
Luyang Sun
Yu Zhang
Yanliang Jiang
Ludmilla Kaltenboeck
Huseyin Kucuktas
Zhanjiang Liu
Physiological Genomics
Glucocorticoid-induced changes in gene expression of airway smooth muscle in patients with asthma. 2013-05-01 Frank Baas
Kees Fluiter
Ching Yong Yick
Aeilko H Zwinderman
Peter W Kunst
Katrien Grünberg
Thais Mauad
Elisabeth H Bel
René Lutter
Peter J Sterk
American Journal of Respiratory and Critical Care Medicine
Transcription factors that convert adult cell identity are differentially polycomb repressed 2013-05-01 Sean Eddy Fred P Davis PLoS ONE
Functional transcriptomic analysis of the role of MAB-5/Hox in Q neuroblast migration in Caenorhabditis elegans 2013-05-04 Stuart J Macdonald Joel V Tamayo
Mahekta Gujar
Erik A Lundquist
BMC Genomics
Research resource: small RNA-seq of human granulosa cells reveals miRNAs in FSHR and aromatase genes. 2013-05-09 Agne Velthut
Madis Metsis
Andres Salumets
Jaak Simm
Timo Tuuri
Juha S Tapanainen
Molecular Endocrinology
Differences in gastric carcinoma microenvironment stratify according to EBV infection intensity: implications for possible immune adjuvant therapy. 2013-05-09 Melody Baddoo Michael J Strong
Guorong Xu
Joseph Coco
Carl Baribault
Dass S Vinay
Michelle R Lacey
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
Erik K Flemington
PLOS Pathogens
Global detection and identification of developmental stage specific transcripts in mouse brain using subtractive cross-screening algorithm. 2013-05-12 Zhixiang Zuo Yi Lv
Xiao Xu
Genomics
Mapping the RNA-Seq trash bin: unusual transcripts in prokaryotic transcriptome sequencing data. 2013-05-13 Peter F. Stadler
David Langenberger
Gero Doose
Maria Alexis
Rebecca Kirsch
Sven Findeiß
Rainer Machné
Mario Mörl
Steve Hoffmann
RNA Biology
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. 2013-05-15 Tesfaye Wubet
Martin Schädler
Mika T Tarkka
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
Stefan Scheu
Silvia D Schrey
Ivo Grosse
François Buscot
New Phytologist
Comparative analysis of RNA sequencing methods for degraded or low-input samples. 2013-05-19 Aviv Regev
Rahul Satija
Nathalie Pochet
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
Aviv Regev
Joshua Z Levin
Nature Methods
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 2013-05-21 Guillaume Blanc Janet M Rowe
David D Dunigan
James R Gurnon
Yuannan Xia
James L Van Etten
Virology
Genome wide proteomics of ERBB2 and EGFR and other oncogenic pathways in inflammatory breast cancer. 2013-05-22 Gil Omenn
Susan Fanayan
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
Journal of Proteome Research
Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing 2013-05-22 Ryan D Morin
Andrew Mungall
Steven Jones
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
Blood
A comprehensive analysis of the effects of the deaminase AID on the transcriptome and methylome of activated B cells. 2013-05-26 Nina Papavasiliou Eric L Fritz
Brad R Rosenberg
Kenneth Lay
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Nature Immunology
Identification of the zebrafish maternal and paternal transcriptomes 2013-05-29 James Cuthbert Smith Steven A Harvey
Ian Sealy
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Transcriptome sequencing (RNA-seq) analysis of the effects of metal nanoparticle exposure on the transcriptome of Chlamydomonas reinhardtii. 2013-05-31 Rute F. Domingos
William Zerges
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Applied and Environmental Microbiology
The gene desert mammary carcinoma susceptibility locus Mcs1a regulates Nr2f1 modifying mammary epithelial cell differentiation and proliferation 2013-06 Christina Kendziorski Bart M G Smits
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PLOS Genetics
Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica 2013-06 Chad Nusbaum
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PLOS Genetics
A meta-analysis of the genomic and transcriptomic composition of complex life. 2013-06-06 John Mattick Ganqiang Liu
Ryan J Taft
Cell Cycle
Discovery of diversity in xylan biosynthetic genes by transcriptional profiling of a heteroxylan containing mucilaginous tissue. 2013-06-07 Jacob K Jensen Nathan Johnson
Curtis G Wilkerson
Frontiers in Plant Science
ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells. 2013-06-21 Avi Ma'ayan Huilei Xu
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Global transcriptome profiles of Camellia sinensis during cold acclimation 2013-06-22 Qiong-Yi Zhao Xin-Chao Wang
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BMC Genomics
Evaluating the impact of sequencing depth on transcriptome profiling in human adipose 2013-06-24 Jane Ferguson Yichuan Liu
Chenyi Xue
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Brian Gregory
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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
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BMC Bioinformatics
Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation. 2013-07-01 Sayan Mukherjee Dina Hafez
Ting Ni
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Uwe Ohler
Bioinformatics
Classification of topological domains based on gene expression and regulation. 2013-07-01 Nadav Ahituv Jingjing Zhao
Hongbo Shi
Genome
Exonuclease hDIS3L2 specifies an exosome-independent 3'-5' degradation pathway of human cytoplasmic mRNA 2013-07-03 Andrzej Dziembowski
Rafal Tomecki
Torben Heick Jensen
Michal Lubas
Christian K Damgaard
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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
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Biology Direct
Identification of genes critical for resistance to infection by West Nile virus using RNA-Seq analysis. 2013-07-08 Sebastian Kurscheid
Ruth R Montgomery
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Vincent Bruno
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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
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Journal of Translational Medicine
Male-biased genes in catfish as revealed by RNA-Seq analysis of the testis transcriptome. 2013-07-12 Shikai Liu
Ludmilla Kaltenboeck
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Ludmilla Kaltenboeck
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PLoS ONE
Senescence-associated lncRNAs: senescence-associated long noncoding RNAs. 2013-07-14 Kevin G. Becker Kotb Abdelmohsen
Amaresh Panda
Min-Ju Kang
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Roza Selimyan
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Aging Cell
Proteogenomic database construction driven from large scale RNA-seq data. 2013-07-17 Vineet Bafna Sunghee Woo
Seong Won Cha
Gennifer Merrihew
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Clark Guest
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Journal of Proteome Research
CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes 2013-07-18 Jennifer Doudna Luke A Gilbert
Matthew H Larson
Leonardo Morsut
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Gloria A Brar
Sandra E Torres
Noam Stern-Ginossar
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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
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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
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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
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The Plant Cell
Enhanced expression of codon optimized interferon gamma in CHO cells. 2013-07-19 Dong-Yup Lee Bevan Kai-Sheng Chung
Faraaz N K Yusufi
Mariati
Yuansheng Yang
Journal of Biotechnology
Replication protein A subunit 3 and the iron efficiency response in soybean. 2013-07-22 Di Cook Sarah E Atwood
Jamie A O'Rourke
Gregory A Peiffer
Tengfei Yin
Mahbubul Majumder
Chunquan Zhang
Silvia R Cianzio
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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
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
Christian Bendixen
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
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Molecular Immunology
Differential programming of B cells in AID deficient mice 2013-07-29 Bas van Steensel Marc A Hogenbirk
Marinus R Heideman
Arno Velds
Paul C M van den Berk
Ron M Kerkhoven
Heinz Jacobs
PLoS ONE
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
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Luoping Zhang
Roel Vermeulen
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Stephen M Rappaport
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Martyn T Smith
Environmental and Molecular Mutagenesis
The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line 2013-08-01 Jay Shendure
Joshua N Burton
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Nature
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
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Lucie Mieuzet
Béatrice Ségurens
Jean-Christophe Simon
PLOS Genetics
BlackOPs: increasing confidence in variant detection through mappability filtering. 2013-08-08 Charles M. Perou Christopher R Cabanski
Matthew D Wilkerson
Matthew Soloway
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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
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BMC Genomics
Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons. 2013-08-12 Cameron Brennan J Zachary Sanborn
Sofie R Salama
Mia Grifford
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Cancer Research
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
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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
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Prabhakar Rajan
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Mark Davis
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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
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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
Shaohua Fan
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Carmelo Fruciano
Molecular Ecology
Profiling microRNA expression in bovine alveolar macrophages using RNA-seq. 2013-08-24 Daniel G. Bradley Peter Vegh
Amir B K Foroushani
David A Magee
Matthew S McCabe
John A Browne
Nicolas C Nalpas
Kevin M Conlon
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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
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Breakpoint features of genomic rearrangements in neuroblastoma with unbalanced translocations and chromothripsis. 2013-08-26 Isabelle Janoueix-Lerosey
Valérie Combaret
Valentina Boeva
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
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Olivier Delattre
PLoS ONE
Remodeling of membrane lipids in iron-starved Chlamydomonas. 2013-08-27 David Casero Eugen I Urzica
Astrid Vieler
Anne Hong-Hermesdorf
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Sean D Gallaher
Janette Kropat
Matteo Pellegrini
Christoph Benning
Sabeeha S Merchant
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
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PLoS ONE
SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization 2013-08-31 Shintaro Katayama
Juha Kere
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Virpi Töhönen
Sten Linnarsson
Bioinformatics
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
Anja Hemschemeier
Bensheng Liu
Christoph Benning
Matteo Pellegrini
Sabeeha S Merchant
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
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Paul A Guerette
Shawn Hoon
Manfred Raida
Admir Masic
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Vincent H B Ho
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Abdon Pena-Francesch
Gavin Z Tay
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Nature Biotechnology
U1 small nuclear ribonucleoprotein complex and RNA splicing alterations in Alzheimer's disease. 2013-09-10 Yuxin Li
Drew R Jones
Hao Wu
Bing Bai
Chadwick M Hales
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Yair Gozal
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Qiangwei Xia
Duc M Duong
Craig Street
Gloria Cantero
Dongmei Cheng
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Howard D Rees
Li Lin
Keith E Szulwach
Marla Gearing
Elliott J Mufson
David A Bennett
Thomas J Montine
Nicholas T Seyfried
Thomas S Wingo
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Proceedings of the National Academy of Sciences of the United States of America
Androgen receptor signaling regulates DNA repair in prostate cancers. 2013-09-11 Deyou Zheng William R Polkinghorn
Joel S Parker
Man X Lee
Elizabeth M Kass
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Brett S Carver
Yu Chen
Philip A Watson
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Sho Fujisawa
Alexander G Goglia
Anuradha Gopalan
Haley Hieronymus
John Wongvipat
Peter T Scardino
Michael J Zelefsky
Maria Jasin
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Simon N Powell
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Cancer Discovery
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. 2013-09-15 Ann-Christine Syvänen
Michael Sammeth
Tuuli Lappalainen
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Seyed Yahya Anvar
Jeroen F J Laros
Henk P J Buermans
Olof Karlberg
Mathias Brännvall
GEUVADIS Consortium
Johan T den Dunnen
Gert-Jan B van Ommen
Ivo G Gut
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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 Adam Z Rosenthal
Xinning Zhang
Kaitlyn S Lucey
Elizabeth A Ottesen
Vikas Trivedi
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Proceedings of the National Academy of Sciences of the United States of America
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
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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 Michael J Strong
Tina O'Grady
Zhen Lin
Guorong Xu
Melody Baddoo
Chris Parsons
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Christopher M Taylor
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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
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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
Philip Brennecke
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Nature Methods
Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria. 2013-09-30 Margaret F Romine Ronald C Taylor
Bobbie-Jo M Webb Robertson
Lye Meng Markillie
Margrethe H Serres
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Joshua T Aldrich
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Integrative Biology
Human housekeeping genes, revisited 2013-10 Eli Eisenberg Erez Y. Levanon Trends in Genetics
Evaluation of the effectiveness of semen storage and sperm purification methods for spermatozoa transcript profiling 2013-10 Russ Hauser Shihong Mao
Robert J Goodrich
Steven M Schrader
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Systems Biology in Reproductive Medicine
RNA-Seq analysis of Citrus reticulata in the early stages of Xylella fastidiosa infection reveals auxin-related genes as a defense response. 2013-10-03 Luciano T. Kishi Carolina M Rodrigues
Alessandra A de Souza
Marco A Takita
Marcos A Machado
BMC Genomics
Transcriptome comparison of human neurons generated using induced pluripotent stem cells derived from dental pulp and skin fibroblasts 2013-10-03 Deyou Zheng
John J. Foxe
Jian Chen
Mingyan Lin
Erika Pedrosa
Anastasia Hrabovsky
Reed Carroll
Herbert M Lachman
PLoS ONE
Transcriptomics of the rice blast fungus Magnaporthe oryzae in response to the bacterial antagonist Lysobacter enzymogenes reveals candidate fungal defense response genes 2013-10-03 Bradley I. Hillman Sandra M Mathioni
Nrupali Patel
Bianca Riddick
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Jeffrey L Caplan
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Vidhyavathi Raman
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PLoS ONE
Function of lncRNAs and approaches to lncRNA-protein interactions. 2013-10-05 Hanjiang Fu Juanjuan Zhu
Yongge Wu
Xiaofei Zheng
Science in China. Series C: Life Sciences
In vitro grown pollen tubes of Nicotiana alata actively synthesise a fucosylated xyloglucan. 2013-10-08 Edwin R. Lampugnani
Ed Newbigin
Isabel E Moller
Andrew Cassin
Daniel F Jones
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Sunil Ratnayake
Cherie T Beahan
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PLoS ONE
Towards the integration, annotation and association of historical microarray experiments with RNA-seq 2013-10-09 Michael A Bauer Shweta S Chavan
Erich A Peterson
Christoph J Heuck
Donald J Johann
BMC Bioinformatics
Host-Mycobacterium avium subsp. paratuberculosis interactome reveals a novel iron assimilation mechanism linked to nitric oxide stress during early infection. 2013-10-10 Srinand Sreevatsan Elise A Lamont
Wayne W Xu
BMC Genomics
Histoplasma yeast and mycelial transcriptomes reveal pathogenic-phase and lineage-specific gene expression profiles. 2013-10-10 Chad Rappleye Jessica A Edwards
Chenxi Chen
Megan M Kemski
Jinnan Hu
Thomas K Mitchell
BMC Genomics
Transcriptome comparison between porcine subcutaneous and intramuscular stromal vascular cells during adipogenic differentiation. 2013-10-10 Hongkui Wei Shuzhong Jiang
Tongxing Song
Yang Yang
Jian Peng
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PLoS ONE
Modeling the next generation sequencing sample processing pipeline for the purposes of classification. 2013-10-11 Charles D. Johnson Noushin Ghaffari
Mohammadmahdi R Yousefi
Ivan Ivanov
Edward R Dougherty
BMC 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
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
PLoS ONE
Profiling the molecular mechanism of fullerene cytotoxicity on tumor cells by RNA-seq. 2013-10-12 Marco Gerdol
Alberto Pallavicini
Marianna Lucafò
Gianni Sava
Sabrina Pacor
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Maurizio Prato
Toxicology
Ribosomal protein S6 mRNA is a biomarker upregulated in multiple sclerosis, downregulated by interferon treatment, and affected by season. 2013-10-14 Peter M. Visscher
Mark Slee
Joseph E. Powell
Grant W. Montgomery
Grant P Parnell
Prudence N Gatt
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Malgorzata Krupa
Jeannette Lechner-Scott
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Multiple Sclerosis Journal
Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network 2013-10-16 Marcel E. Dinger
John Mattick
Animesh Ray
Shaojie Zhang
Jian-Liang Li
Joseph Mazar
Cuncong Zhong
Geoffrey J Faulkner
Subramaniam S Govindarajan
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Scientific Reports
A novel intra-U1 snRNP cross-regulation mechanism: alternative splicing switch links U1C and U1-70K expression. 2013-10-17 Ekaterina E Khrameeva Tanja Dorothe Rösel-Hillgärtner
Lee-Hsueh Hung
Patrick Le Querrec
Mikhail S Gelfand
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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. 2013-10-17 Liming Xiong
Shoudong Zhang
Tao Chen
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PLOS Genetics
Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032 2013-10-19 Alfred Pühler Almut Mentz
Armin Neshat
Katharina Pfeifer-Sancar
Christian Rückert
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BMC Genomics
Quantitative assessment of single-cell RNA-sequencing methods. 2013-10-20 Barbara Treutlein
Piero Dalerba
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Nature Methods
HAMR: high-throughput annotation of modified ribonucleotides. 2013-10-22 Otto Valladares Paul Ryvkin
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Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe. 2013-10-23 Monika Gullerova
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RNA
Parallel deep transcriptome and proteome analysis of zebrafish larvae 2013-10-24 Christiaan V. Henkel Magnus Palmblad
Ron P Dirks
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BMC Research Notes
Integrated transcriptomic and proteomic analysis of the global response of Wolbachia to doxycycline-induced stress. 2013-10-24 Alistair C. Darby A Christina Gill
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The ISME Journal
IMG 4 version of the integrated microbial genomes comparative analysis system. 2013-10-27 Natalia Ivanova
Nikos Kyrpides
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I-Min A Chen
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Nucleic Acids Research
Differential expression of olfactory genes in the southern house mosquito and insights into unique odorant receptor gene isoforms. 2013-10-28 Walter S Leal Young-Moo Choo
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Proceedings of the National Academy of Sciences of the United States of America
A unified model for yeast transcript definition. 2013-10-29 Harm van Bakel
Corey Nislow
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Genome Research
Identification of molecular tumor markers in renal cell carcinomas with TFE3 protein expression by RNA sequencing. 2013-11-01 Mark Rubin Dorothee Pflueger
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Neoplasia
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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Molecular Plant-Microbe Interactions
Systematic evaluation of spliced alignment programs for RNA-seq data 2013-11-03 Jennifer Harrow
Roderic Guigó i Serra
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Nature Methods
Assessment of transcript reconstruction methods for RNA-seq. 2013-11-03 Timothy John Phillip Hubbard
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RGASP Consortium Nature Methods
Dysregulation of synaptogenesis genes antecedes motor neuron pathology in spinal muscular atrophy. 2013-11-04 Anna Maria Pinto
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Proceedings of the National Academy of Sciences of the United States of America
Serotonergic neuron regulation informed by in vivo single-cell transcriptomics. 2013-11-05 Tamas Bartfai Jennifer M Spaethling
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FASEB Journal
Surfing transcriptomic landscapes. A step beyond the annotation of chromosome 16 proteome. 2013-11-05 Miguel Marcilla
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Carmen González-Tejedo
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Journal of Proteome Research
Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation. 2013-11-07 Alexander van Oudenaarden Juan R Alvarez-Dominguez
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Blood
Distinct splice variants and pathway enrichment in the cell-line models of aggressive human breast cancer subtypes 2013-11-07 Gil Omenn Rajasree Menon
Hogune Im
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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 2013-11-08 Hanns Hatt
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PLoS ONE
Deletion of Asxl1 results in myelodysplasia and severe developmental defects in vivo 2013-11-11 Jinfeng Liu
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Journal of Experimental Medicine
Efficient cellular fractionation improves RNA sequencing analysis of mature and nascent transcripts from human tissues. 2013-11-13 Adam Ameur Ammar Zaghlool
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BMC Biotechnology
Mapping genetic modifiers of survival in a mouse model of Dravet syndrome. 2013-11-14 Jennifer A Kearney A R Miller
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Genes, Brain and Behavior
Early T helper cell programming of gene expression in human 2013-11-15 Riitta Lahesmaa Soile Tuomela Seminars in Immunology
Resolving chromosome-centric human proteome with translating mRNA analysis: a strategic demonstration. 2013-11-15 Yizhi Cui
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Journal of Proteome Research
Proteogenomic analysis reveals unanticipated adaptations of colorectal tumor cells to deficiencies in DNA mismatch repair. 2013-11-18 Daniel C. Liebler Patrick J Halvey
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Cancer Research
Global bidirectional transcription of the Epstein-Barr virus genome during reactivation. 2013-11-20 Melody Baddoo Tina O'Grady
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Journal of Virology
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
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Roderic Guigó i Serra
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Genome Research
Assessment of myometrial transcriptome changes associated with spontaneous human labour by high-throughput RNA-seq. 2013-11-22 Jonathan D. Moore
Andrew M Blanks
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Experimental Physiology
Characterization of the human ESC transcriptome by hybrid sequencing. 2013-11-26 Harm van Bakel
Renee Reijo Pera
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Proceedings of the National Academy of Sciences of the United States of America
An infection-relevant transcriptomic compendium for Salmonella enterica Serovar Typhimurium. 2013-12-01 Carsten Kröger
Shabarinath Srikumar
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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. 2013-12-02 Anand Swaroop Sharda P Yadav
Hong Hao
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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. 2013-12-02 Morten Thaysen-Andersen
Susan Fanayan
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Joshua T Smith
Mark S Baker
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William S Hancock
Journal of Proteome Research
The Clostridium small RNome that responds to stress: the paradigm and importance of toxic metabolite stress in C. acetobutylicum 2013-12-04 Blake Meyers Keerthi P Venkataramanan
Shawn W Jones
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BMC Genomics
Simultaneous transcriptional profiling of bacteria and their host cells 2013-12-04 Claire M. Fraser
Naomi Sengamalay
Marcus C. Chibucos
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Todd Creasy
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PLoS ONE
Vespucci: a system for building annotated databases of nascent transcripts. 2013-12-04 Terry Gaasterland Karmel A Allison
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Nucleic Acids Research
A platform independent RNA-Seq protocol for the detection of transcriptome complexity. 2013-12-05 Graziano Pesole
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Marcella Attimonelli
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BMC Genomics
Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. 2013-12-05 Jens Nielsen
Mathias Uhlén
Jenny Ottosson Takanen
Cristina Al-Khalili Szigyarto
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Caroline Kampf
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Cristina Al-Khalili Szigyarto
Marie Skogs
Jenny Ottosson Takanen
Holger Berling
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Frida Danielsson
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Asa Sivertsson
Kalle von Feilitzen
Mattias Forsberg
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Molecular & Cellular Proteomics
Fermentation stage-dependent adaptations of Bacillus licheniformis during enzyme production. 2013-12-06 Sandra Wiegand Birgit Voigt
Dirk Albrecht
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Microbial Cell Factories
ETV6-NTRK3 is a common chromosomal rearrangement in radiation-associated thyroid cancer. 2013-12-10 Tetiana Bogdanova Rebecca J Leeman-Neill
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Cancer
Transcriptome changes in the porcine endometrium during the preattachment phase. 2013-12-12 Ulbrich SE Anastazia Samborski
Alexander Graf
Stefan Krebs
Barbara Kessler
Myriam Reichenbach
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Biology of Reproduction
Studying Culicoides vectors of BTV in the post-genomic era: resources, bottlenecks to progress and future directions. 2013-12-17 Daniel Lawson
Paul J Kersey
Dana Nayduch
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Virus Research
Combining DGE and RNA-sequencing data to identify new polyA+ non-coding transcripts in the human genome 2013-12-18 Eric Rivals Nicolas Philippe
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Alban Mancheron
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Nucleic Acids Research
Comprehensive analysis of transcriptome variation uncovers known and novel driver events in T-cell acute lymphoblastic leukemia 2013-12-19 Iwona Wlodarska Zeynep Kalender Atak
Valentina Gianfelici
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Frank Speleman
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PLOS Genetics
An overview of gene expression dynamics during early ovarian folliculogenesis: specificity of follicular compartments and bi-directional dialog. 2013-12-19 Sylvain Foissac Agnes Bonnet
Cedric Cabau
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Julien Sarry
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Florent Woloszyn
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BMC Genomics
Differential transcriptome analysis of glandular and filamentous trichomes in Artemisia annua 2013-12-20 Alain Goossens Sandra S A Soetaert
Christophe M F Van Neste
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BMC Plant Biology
Quantitative single-cell RNA-seq with unique molecular identifiers. 2013-12-22 Sten Linnarsson
Peter Lönnerberg
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Nature Methods
Lsh regulates LTR retrotransposon repression independently of Dnmt3b function. 2013-12-24 Colin A. Semple Donncha S Dunican
Hazel A Cruickshanks
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Tracey Davey
Robert J Arceci
John Greally
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Richard R Meehan
Genome Biology
Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors. 2013-12-24 Laura Elnitski Zhenqing Ye
Zhong Chen
Xun Lan
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Nucleic Acids Research
Mycorrhizal phosphate uptake pathway in maize: vital for growth and cob development on nutrient poor agricultural and greenhouse soils. 2013-12-26 Jan Jansa Martin Willmann
Nina Gerlach
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Frontiers in Plant Science
Nutritional impacts on gene expression in the surface mucosa of blue catfish (Ictalurus furcatus). 2013-12-28 Eric Peatman Chao Li
Benjamin H Beck
Developmental and Comparative Immunology
Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. 2013-12-30 Jean-Jack M Riethoven Yong Ding
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Michael Fromm
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BMC Plant Biology
Deep RNA sequencing reveals hidden features and dynamics of early gene transcription in Paramecium bursaria chlorella virus 1 2014 Jean-Jack M Riethoven
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PLoS ONE
De novo assembly and characterization of the transcriptome of the toxic dinoflagellate Karenia brevis 2014 Lisa Campbell Darcie E Ryan
Alan E Pepper
BMC Genomics
Comparative analysis and modeling of the severity of steatohepatitis in DDC-treated mouse strains 2014 Helmut Denk
Hans Lehrach
Marie-Laure Yaspo
Christina Grimm
Vikash Pandey
Marc Sultan
Karl Kashofer
Meryem Ralser
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Julia Starmann
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Hendrik Hache
Holger Sültmann
Michael Trauner
Kurt Zatloukal
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PLoS ONE
Genetics of gene expression in CNS 2014 Robert W. Williams Ashutosh K Pandey International Review of Neurobiology
Zinc finger transcription factors displaced SREBP proteins as the major Sterol regulators during Saccharomycotina evolution 2014-01 Sarah L Maguire
Geraldine Butler
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PLOS Genetics
Correlating histone modification patterns with gene expression data during hematopoiesis. 2014-01-01 Gangqing Hu Keji Zhao Methods in Molecular Biology
Domestic dogs and cancer research: a breed-based genomics approach. 2014-01-01 Elaine Ostrander Brian W Davis ILAR Journal
Topographical transcriptome mapping of the mouse medial ganglionic eminence by spatially resolved RNA-seq. 2014-01-01 Sten Linnarsson
Peter Lönnerberg
Sabrina Zechel
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Carlos F Ibáñez
Sten Linnarsson
Genome Biology
Developmental analysis of spliceosomal snRNA isoform expression. 2014-01-01 Zhipeng Lu A Gregory Matera G3
Deep sequencing of small chromatin-associated RNA: bioinformatic analysis. 2014-01-01 Sarah Diermeier
Gernot Längst
Methods in Molecular Biology
Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells. 2014-01-01 Daniel Ramsköld
Rickard Sandberg
Qiaolin Deng
Björn Reinius
Science
edgeR for differential RNA-seq and ChIP-seq analysis: an application to stem cell biology. 2014-01-01 Mark D. Robinson Olga Nikolayeva Methods in Molecular Biology
Full-length RNA-seq from single cells using Smart-seq2. 2014-01-02 Omid R Faridani
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Nature Protocols
Variable suites of non-effector genes are co-regulated in the type III secretion virulence regulon across the Pseudomonas syringae phylogeny. 2014-01-02 Marc T Nishimura
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PLOS Pathogens
RNA-Seq analysis of the toxicant-induced transcriptome of the marine diatom, Ceratoneis closterium. 2014-01-04 Philippe Moncuquet Sharon E Hook
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Marine Genomics
Differential protein occupancy profiling of the mRNA transcriptome. 2014-01-13 Markus Landthaler Markus Schueler
Mathias Munschauer
Lea Haarup Gregersen
Ana Finzel
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Christoph Dieterich
Genome Biology
Production of RNA for transcriptomic analysis from mouse spinal cord motor neuron cell bodies by laser capture microdissection. 2014-01-13 Arthur L. Horwich Urmi Bandyopadhyay
Wayne A Fenton
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Journal of Visualized Experiments
GuavaH: a compendium of host genomic data in HIV biology and disease. 2014-01-15 Paul J. McLaren
Angela Ciuffi
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Retrovirology
Transcriptome analysis of alternative splicing events regulated by SRSF10 reveals position-dependent splicing modulation. 2014-01-17 Wenwu Wu
James L. Manley
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Nucleic Acids Research
A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis 2014-01-17 Lior Pachter
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Nucleic Acids Research
Set5 and Set1 cooperate to repress gene expression at telomeres and retrotransposons. 2014-01-17 Sean R Collins Glòria Mas Martín
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Epigenetics
ALEA: a toolbox for allele-specific epigenomics analysis. 2014-01-21 Mohammad M Karimi Hamid Younesy
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Bioinformatics
RNA-Seq analysis provides insights for understanding photoautotrophic polyhydroxyalkanoate production in recombinant Synechocystis Sp. 2014-01-22 Kumar Sudesh Nyok-Sean Lau
Choon Pin Foong
Yukio Kurihara
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PLoS ONE
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. 2014-01-28 Christine Orengo James R Perkins
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Molecular Pain
The RNA-binding protein hnRNPLL induces a T cell alternative splicing program delineated by differential intron retention in polyadenylated RNA. 2014-01-29 Anselm Enders Vicky Cho
Yan Mei
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Genome Biology
RNA-seq analysis of host and viral gene expression highlights interaction between varicella zoster virus and keratinocyte differentiation. 2014-01-30 Judith Breuer Meleri Jones
Inga R Dry
Dan Frampton
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PLOS Pathogens
bwtool: a tool for bigWig files. 2014-01-30 Miguel Beato del Rosal Andy Pohl Bioinformatics
A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events 2014-01-31 Matthew Meyerson Angela N Brooks
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Marcin Imielinski
Gordon Saksena
Chandra Sekhar Pedamallu
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Mara Rosenberg
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PLoS ONE
Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. 2014-02-01 Naama Elefant
Hadas Keren-Shaul
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Science
SOX9: a stem cell transcriptional regulator of secreted niche signaling factors. 2014-02-01 Deyou Zheng Meelis Kadaja
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Genes & Development
The Cryptococcus neoformans transcriptome at the site of human meningitis. 2014-02-04 Yuan Chen Dena L Toffaletti
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mBio
Dormancy within Staphylococcus epidermidis biofilms: a transcriptomic analysis by RNA-seq. 2014-02-07 Rui Vitorino
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Applied Microbiology and Biotechnology
Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia. 2014-02-13 Ana Conesa
Corey Nislow
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Fungal Genetics and Biology
Dynamic recruitment of amino acid transporters to the insect/symbiont interface. 2014-02-16 John P. McCutcheon Rebecca P Duncan
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Molecular Ecology
Ammonium induces differential expression of methane and nitrogen metabolism-related genes in Methylocystis sp. strain SC2. 2014-02-18 Werner Liesack Bomba Dam
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Environmental Microbiology
Transcriptomic analysis reveals key regulators of mammogenesis and the pregnancy-lactation cycle. 2014-02-19 Songnian Hu YuanYuan Zhou
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Science in China. Series C: Life Sciences
Context-selective death of acute myeloid leukemia cells triggered by the novel hybrid retinoid-HDAC inhibitor MC2392. 2014-02-24 Dante Rotili
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Cancer Research
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 Yupeng Luo
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PLoS ONE
AnaLysis of Expression on human chromosome 21, ALE-HSA21: a pilot integrated web resource. 2014-02-25 Claudia Angelini
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Metabolic reprogramming during purine stress in the protozoan pathogen Leishmania donovani 2014-02-27 Jessica L Martin
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PLOS Pathogens
The path to triacylglyceride obesity in the sta6 strain of Chlamydomonas reinhardtii. 2014-02-28 Sean D Gallaher
Taylor L Weiss
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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 2014-02-28 Stephan Schmitz-Esser
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Frontiers in Microbiology
Transcriptome profiling of human hippocampus dentate gyrus granule cells in mental illness 2014-03-04 Eric Haugen R Kohen
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Translational Psychiatry
Differential transcriptomic analysis by RNA-Seq of GSNO-responsive genes between Arabidopsis roots and leaves. 2014-03-04 Juan C Begara-Morales
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Plant and Cell Physiology
Relaxed functional constraints on triplicate α-globin gene in the bank vole suggest a different evolutionary history from other rodents. 2014-03-05 Jeremy Searle S Marková
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The human testis-specific proteome defined by transcriptomics and antibody-based profiling. 2014-03-05 Linn Fagerberg D Djureinovic
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Molecular Human Reproduction
Overexpression of molecular chaperone genes in nucleomorph genomes. 2014-03-06 Patrick J. Keeling Yoshihisa Hirakawa
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Molecular Biology and Evolution
RNA- and antibody-based profiling of the human proteome with focus on chromosome 19. 2014-03-12 Linn Fagerberg
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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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Lung Cancer
Lacking alignments? The next-generation sequencing mapper segemehl revisited. 2014-03-13 Peter F. Stadler Christian Otto
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Bioinformatics
The human liver-specific proteome defined by transcriptomics and antibody-based profiling. 2014-03-19 Jens Nielsen
Linn Fagerberg
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FASEB Journal
The characteristic direction: a geometrical approach to identify differentially expressed genes. 2014-03-21 Avi Ma'ayan Neil R Clark
Kevin S Hu
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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
Inès Zouari
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BMC Genomics
spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data. 2014-03-23 Albin Sandelin
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BMC Bioinformatics
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. 2014-03-23 John L. Rinn Cole Trapnell
Davide Cacchiarelli
Jonna Grimsby
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Nature Biotechnology
RNA-seq analysis identifies an intricate regulatory network controlling cluster root development in white lupin 2014-03-25 Oliver Berkowitz
James Whelan
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BMC Genomics
De novo transcriptome analysis of Hevea brasiliensis tissues by RNA-seq and screening for molecular markers 2014-03-26 Luiz Gonzaga Paula de Almeida Leonardo Rippel Salgado
Daniela Martins Koop
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BMC Genomics
Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing. 2014-03-27 Hideya Kawaji
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Genome Research
HDAC-regulated myomiRs control BAF60 variant exchange and direct the functional phenotype of fibro-adipogenic progenitors in dystrophic muscles. 2014-03-28 Janet Rossant
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Differential meta-analysis of RNA-seq data from multiple studies 2014-03-29 Florence Jaffrézic Andrea Rau
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BMC Bioinformatics
Odorant and gustatory receptors in the tsetse fly Glossina morsitans morsitans 2014-04 Daniel Masiga George F O Obiero
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PLOS Neglected Tropical Diseases
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Bioinformatics
Genome-wide transcriptomic responses of the seagrasses Zostera marina and Nanozostera noltii under a simulated heatwave confirm functional types. 2014-04-03 Erich Bornberg-Bauer Susanne U Franssen
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Marine Genomics
LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq. 2014-04-07 Daniel C. Jeffares
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Genome Research
Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-Seq and ESTs. 2014-04-10 Gordon G Simpson
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PLoS ONE
Widespread use of non-productive alternative splice sites in Saccharomyces cerevisiae 2014-04-10 Matteo Pellegrini Tadashi Kawashima
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PLOS Genetics
Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq 2014-04-13 Doug Brownfield
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Nature
VDR primary targets by genome-wide transcriptional profiling. 2014-04-13 Graziano Pesole
Matteo Pallocca
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The Journal of Steroid Biochemistry and Molecular Biology
Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans. 2014-04-14 Gavin Sherlock Dale Muzzey
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Genome Research
Comparative genomic and transcriptomic analysis of wangiella dermatitidis, a major cause of phaeohyphomycosis and a model black yeast human pathogen 2014-04-16 Christina A Cuomo Zehua Chen
Diego A Martinez
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Transcriptome profiling to identify genes involved in pathogenicity of Valsa mali on apple tree. 2014-04-16 Zhiyuan Yin Xiwang Ke
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Fungal Genetics and Biology
Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation. 2014-04-17 Alexander Idnurm
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PLOS Genetics
Colorectal cancer cell lines are representative models of the main molecular subtypes of primary cancer. 2014-04-22 Diego Arango
Walter Bodmer
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Clare Sloggett
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Cancer Research
The cytochrome P450 genes of channel catfish: their involvement in disease defense responses as revealed by meta-analysis of RNA-Seq data sets. 2014-04-27 David Robert Nelson
Geoff Waldbieser
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Biochimica et Biophysica Acta
An improved genome release (version Mt4.0) for the model legume Medicago truncatula. 2014-04-27 Haibao Tang
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BMC Genomics
Microfluidic single-cell whole-transcriptome sequencing. 2014-04-29 Liang Zhao
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Proceedings of the National Academy of Sciences of the United States of America
From genome to function by studying eQTLs. 2014-05-04 Lude Franke Harm-Jan Westra Biochimica et Biophysica Acta
A new class of protein cancer biomarker candidates: differentially expressed splice variants of ERBB2 (HER2/neu) and ERBB1 (EGFR) in breast cancer cell lines 2014-05-05 Gil Omenn Yuanfang Guan
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Journal of Proteomics
De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum. 2014-05-12 Paul J Kersey
Arnaud Kerhornou
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PLoS ONE
Facile functional analysis of insect odorant receptors expressed in the fruit fly: validation with receptors from taxonomically distant and closely related species. 2014-05-13 Walter S Leal Carlos Ueira-Vieira
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Cellular and Molecular Life Sciences
Identification of a radiation sensitivity gene expression profile in primary fibroblasts derived from patients who developed radiotherapy-induced fibrosis. 2014-05-13 Jason Li Helen B Forrester
Trevor Leong
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Radiotherapy and Oncology
Expression profiling of the wheat pathogen Zymoseptoria tritici reveals genomic patterns of transcription and host-specific regulatory programs 2014-05-14 Tiffany Hsu
Ronny Kellner
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Genome Biology and Evolution
Network topology-based detection of differential gene regulation and regulatory switches in cell metabolism and signaling 2014-05-16 Roland Eils
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Gunnar Schramm
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BMC Systems Biology
A SUF Fe-S cluster biogenesis system in the mitochondrion-related organelles of the anaerobic protist Pygsuia. 2014-05-22 Laura Eme
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Current Biology
Oak root response to ectomycorrhizal symbiosis establishment: RNA-Seq derived transcript identification and expression profiling 2014-05-23 Bruno M Vieira
Octávio S. Paulo
Filipa Monteiro
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PLoS ONE
Time-resolved gene expression profiling during reprogramming of C/EBPα-pulsed B cells into iPS cells 2014-05-27 Bruno Di Stefano Samuel Collombet
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Scientific Data
Transcription of nuclear organellar DNA in a model plant system. 2014-05-27 David L. Adelson Dong Wang
Zhipeng Qu
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Jeremy N Timmis
Genome Biology and Evolution
SHP2 regulates chondrocyte terminal differentiation, growth plate architecture and skeletal cell fates 2014-05-29 Margot Bowen Ugur M Ayturk
Kyle C Kurek
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PLOS Genetics
Down-regulation of AUXIN RESPONSE FACTORS 6 and 8 by microRNA 167 leads to floral development defects and female sterility in tomato 2014-06 Jason Reed Ning Liu
Shan Wu
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Journal of Experimental Botany
Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation. 2014-06-01 Harri Lähdesmäki Tarmo Äijö
Vincent Butty
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Bioinformatics
Genome-wide identification of long intergenic noncoding RNA genes and their potential association with domestication in pigs. 2014-06-02 David M. Irwin Zhong-Yin Zhou
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Genome Biology and Evolution
The combination of transcriptomics and informatics identifies pathways targeted by miR-204 during neurogenesis and axon guidance. 2014-06-03 Remo Sanges
David A van Heel
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Nucleic Acids Research
RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri. 2014-06-06 Nicholas Thomson Marta Vergara-Irigaray
Maria C Fookes
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BMC Genomics
An optimized method for the extraction of bacterial mRNA from plant roots infected with Escherichia coli O157:H7. 2014-06-10 Robert W Jackson Ashleigh Holmes
Louise Birse
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Frontiers in Microbiology
Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. 2014-06-11 Nir Friedman
Aviv Regev
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Raktima Raychowdhury
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Nature
RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells. 2014-06-13 Jessica Lasky-Su Blanca E Himes
Xiaofeng Jiang
Peter Wagner
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PLoS ONE
The Aux/IAA gene rum1 involved in seminal and lateral root formation controls vascular patterning in maize (Zea mays L.) primary roots. 2014-06-13 Nina Opitz
Frank Hochholdinger
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Journal of Experimental Botany
A chemical potentiator of copper-accumulation used to investigate the iron-regulons of Saccharomyces cerevisiae. 2014-06-15 Ehmke Pohl
Nigel Robinson
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Molecular Microbiology
Transcriptomic landscape of prophase I sunflower male meiocytes. 2014-06-16 Octavio Martínez Nathalia M V Flórez-Zapata
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Frontiers in Plant Science
Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum 2014-06-17 W. Richard McCombie
Clícia Grativol
Felipe Rodrigues da Silva
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Marcelo Bertalan
Adhemar Zerlotini Neto
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The Plant Journal
The Chlamydomonas genome project: a decade on. 2014-06-17 David Goodstein
Jane Grimwood
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Trends in Plant Science
Adolescent mouse takes on an active transcriptomic expression during postnatal cerebral development 2014-06-18 Songnian Hu Wei Xu
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Genomics Proteomics and Bioinformatics
RNA-Seq for the identification of novel Mediator transcripts in endothelial progenitor cells. 2014-06-19 Valerio Costa
Concetta Schiano
Claudio Napoli
Monica Rienzo
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Gene
Epigenetic regulation by chromatin activation mark H3K4me3 in primate progenitor cells within adult neurogenic niche 2014-06-20 Richard Sandstrom
Eric Haugen
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Scientific Reports
RNA-binding protein RBM20 represses splicing to orchestrate cardiac pre-mRNA processing. 2014-06-24 Markus Landthaler
Nikolaus Rajewsky
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Journal of Clinical Investigation
A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package. 2014-06-27 Jia Meng Zhiliang Lu
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Profile of whole blood gene expression following immune stimulation in a wild passerine 2014-06-27 Peeter Hõrak
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BMC Genomics
Building the sugarcane genome for biotechnology and identifying evolutionary trends. 2014-06-30 Hélène Bergès Nathalia de Setta
Cláudia Barros Monteiro-Vitorello
Cushla Jane Metcalfe
Guilherme Marcelo Queiroga Cruz
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Roberta Alvares Campos
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Tatiana Caroline Silveira Corrêa
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Mariane de Mendonça Vilela
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BMC Genomics
The coding and noncoding architecture of the Caulobacter crescentus genome 2014-07 Bo Zhou
Jared M Schrader
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Gene-Wei Li
Keren Lasker
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PLOS Genetics
Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing 2014-07-01 Aviv Regev
Rahul Satija
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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 Haiyan Huang
Peter J Bickel
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Genome Research
Comprehensive high-throughput RNA sequencing analysis reveals contamination of multiple nasopharyngeal carcinoma cell lines with HeLa cell genomes. 2014-07-02 Melody Baddoo Michael J Strong
Melody Baddoo
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Journal of Virology
Novel bioinformatics method for identification of genome-wide non-canonical spliced regions using RNA-Seq data. 2014-07-03 Gil Omenn Yongsheng Bai
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PLoS ONE
Status of duckweed genomics and transcriptomics. 2014-07-04 Wenqin Wang J Messing Plant Biology
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
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Parasites & Vectors
Comparative Analysis of Glycogene Expression in Different Mouse Tissues Using RNA-Seq Data 2014-07-09 Vivekanand Jha
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International Journal of Genomics
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 Jun Hou
Zwier M A Groothuismink
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Antiviral Research
Apomictic and sexual germline development differ with respect to cell cycle, transcriptional, hormonal and epigenetic regulation. 2014-07-10 Christian Sailer
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PLOS Genetics
Expression pattern of immunoglobulin superfamily members in the silkworm, Bombyx mori. 2014-07-11 Moli Huang Lei He
Guangli Cao
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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
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Anja Paschold
Caroline Marcon
Ho Man Tang
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Robert B Meeley
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Wesley Bruce
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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
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Yaran Yang
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SigFuge: single gene clustering of RNA-seq reveals differential isoform usage among cancer samples 2014-07-16 Charles M. Perou
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Nucleic Acids Research
Differential gene expression in the respiratory tree of the sea cucumber Apostichopus japonicus during aestivation. 2014-07-16 Kenneth B. Storey Ye Zhao
Hongsheng Yang
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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
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New Phytologist
Bioinformatic exploration of RIO protein kinases of parasitic and free-living nematodes. 2014-07-17 Pasi K. Korhonen
Neil D. Young
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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 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
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E H Bel
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P J Sterk
Allergy
Genome-wide characterization of light-regulated genes in Neurospora crassa. 2014-07-21 Jeremy Zucker Cheng Wu
Fei Yang
Kristina M Smith
Matthew Peterson
Rigzin Dekhang
Ying Zhang
Erin L Bredeweg
Chandrashekara Mallappa
Xiaoying Zhou
Anna Lyubetskaya
Jeffrey P Townsend
James E Galagan
Michael Freitag
Jay C Dunlap
Deborah Bell-Pedersen
Matthew S Sachs
G3
A new dataset of spermatogenic vs. oogenic transcriptomes in the nematode Caenorhabditis elegans. 2014-07-24 Marco A Ortiz Daniel Noble
Elena P Sorokin
Judith Kimble
G3
Transcriptome Analysis of the Human Striatum in Tourette Syndrome. 2014-07-24 Gianfilippo Coppola
Dean Palejev
Flora M. Vaccarino
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
Rekin's Janky
Annelien Verfaillie
Hana Imrichová
Bram Van de Sande
Laura Standaert
Valerie Christiaens
Gert Hulselmans
Koen Herten
Marina Naval Sanchez
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 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
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
Rohan G T Lowe
Andrew Cassin
Bethany L Clark
Thierry Rouxel
Barbara J Howlett
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
Christopher S Bland
Auinash Kalsotra
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 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 Jörg Vogel
Alexander Westermann
Antoine-Emmanuel Saliba
Stanislaw A. Gorski
Nucleic Acids Research
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
In vivo mRNA profiling of uropathogenic Escherichia coli from diverse phylogroups reveals common and group-specific gene expression profiles 2014-08-05 Susanne Häussler Piotr Bielecki
Uthayakumar Muthukumarasamy
Denitsa Eckweiler
Agata Bielecka
Sarah Pohl
Ansgar Schanz
Ute Niemeyer
Tonio Oumeraci
Nils von Neuhoff
Jean-Marc Ghigo
mBio
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 Marc Sultan
Vyacheslav Amstislavskiy
Thomas Risch
Moritz Schuette
Simon Dökel
Meryem Ralser
Daniela Balzereit
Hans Lehrach
Marie-Laure Yaspo
BMC Genomics
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
Dhanisha J Jhaveri
Vikki M Marshall
Denis C Bauer
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 Huw B Thomas
Robert J Moots
Steven W Edwards
Rheumatology
Functional expression of dental plaque microbiota. 2014-08-14 Andrew I. Su Scott N Peterson
Tobias Meissner
Erik Snesrud
Ana C Ong
Nicholas J Schork
Walter A Bretz
Frontiers in cellular and infection microbiology
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
H3S28 phosphorylation is a hallmark of the transcriptional response to cellular stress. 2014-08-18 Karl Mechtler 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
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 Catherine Meplan
Sushma N Grellscheid
John C Mathers
Tom B L Kirkwood
John E Hesketh
Daryl P Shanley
RNA
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 M Vied
Yuting Wang
Alexandre A S F Raposo
David Feng
Frontiers in Neuroscience
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
Hyun-Jin Yang
Yi-Sheng Chang
Jung-Woong Kim
Matthew Brooks
Emily Y Chew
Wai T Wong
Robert N Fariss
Rivka A Rachel
Tiziana Cogliati
Haohua Qian
Investigative Ophthalmology & Visual Science
DNA copy number evolution in Drosophila cell lines 2014-08-28 Maurizio Gatti
Brenton R. Graveley
Teresa M Przytycka
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
Genome Biology
Assessing the clinical use of clear cell renal cell carcinoma molecular subtypes identified by RNA expression analysis. 2014-08-28 Richard W. Joseph Jeanette E Eckel-Passow
Daniel A Igel
Daniel J Serie
Thai H Ho
John C Cheville
Alexander S Parker
Urologic Oncology
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 2014-09 Lei Li
Konrad Förstner
Dagmar Krysciak
Jessica Grote
Mariita Rodriguez Orbegoso
Christian Utpatel
Christel Schmeisser
Hari B Krishnan
Wolfgang R Streit
Applied and Environmental Microbiology
Using heterogeneity of the patient-derived xenograft model to identify the chemoresistant population in ovarian cancer 2014-09-01 Britt K. Erickson
David A Schneider
Zachary C Dobbin
Ashwini A Katre
Adam D Steg
Monjri M Shah
Ronald D Alvarez
Michael G Conner
Dongquan Chen
Charles N Landen
Oncotarget
miR-155 induced transcriptome changes in the MCF-7 breast cancer cell line leads to enhanced mitogen activated protein kinase signaling 2014-09-01 Melody Baddoo Elizabeth C Martin
Adrienne E Krebs
Hope E Burks
Steven Elliott
Melody Baddoo
Bridgette M Collins-Burow
Erik K Flemington
Matthew E Burow
Genes & Cancer
Genome-wide interrogation of longitudinal FEV1 in children with asthma 2014-09-01 Hae Kyung Im Kehua Wu
Eric R Gamazon
Hae Kyung Im
Paul Geeleher
Steven R White
Julian Solway
George L Clemmer
Scott T Weiss
Kelan G Tantisira
Nancy J Cox
Mark J Ratain
R Stephanie Huang
American Journal of Respiratory and Critical Care Medicine
RNA-seq reveals aurora kinase-driven mTOR pathway activation in patients with sarcomatoid metastatic renal cell carcinoma. 2014-09-02 Tommy Tong 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
Jeremy O Jones
Molecular Cancer Research
Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer. 2014-09-04 Giorgio Inghirami Francesco Abate
Sakellarios Zairis
Elisa Ficarra
Andrea Acquaviva
Chris H Wiggins
Veronique Frattini
Anna Lasorella
Antonio Iavarone
Giorgio Inghirami
Raul Rabadan
BMC Systems Biology
Genome-wide binding and transcriptome analysis of human farnesoid X receptor in primary human hepatocytes. 2014-09-08 Yaping Fang Le Zhan
Hui-Xin Liu
Bo Kong
Yuqi He
Xiao-Bo Zhong
Jianwen Fang
Yu-Jui Yvonne Wan
Grace L Guo
PLoS ONE
Expression of antisense small RNAs in response to stress in Pseudomonas aeruginosa. 2014-09-11 Søren Molin María Gómez-Lozano
Rasmus L Marvig
Monica V L Tulstrup
BMC Genomics
Using normalization to resolve RNA-Seq biases caused by amplification from minimal input. 2014-09-16 Christiaan V. Henkel Eirill Ager-Wick
Trude M Haug
Finn-Arne Weltzien
Physiological Genomics
Understanding gene regulatory mechanisms by integrating ChIP-seq and RNA-seq data: statistical solutions to biological problems. 2014-09-17 Claudia Angelini
Valerio Costa
Claudia Angelini
Valerio Costa
Frontiers in cell and developmental biology
Clonal variation in interferon response determines the outcome of oncolytic virotherapy in mouse CT26 colon carcinoma model. 2014-09-18 Seppo Ylä-Herttuala J J Ruotsalainen
M U Kaikkonen
M Niittykoski
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
Gene Therapy
Nontemplated nucleotide additions distinguish the small RNA composition in cells from exosomes. 2014-09-18 Bauke Ylstra
Michael Hackenberg
Nicoletta Zini
Jaap M Middeldorp
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
Cell Reports
A comprehensive transcriptomic analysis of infant and adult mouse ovary. 2014-09-20 Songnian Hu Linlin Pan
Wei Gong
Yuanyuan Zhou
Xiaonuan Li
Jun Yu
Genomics Proteomics and Bioinformatics
Rule-based integration of RNA-Seq analyses tools for identification of novel transcripts. 2014-09-22 Avik Datta Harshal Inamdar
Sunitha Manjari K
Rajendra Joshi
Journal of Bioinformatics and Computational Biology
Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi. 2014-09-23 Robert M. Waterhouse
Gareth L. Maslen
Daniel Lawson
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
Genome Biology
Rare occurrence of EGFRvIII deletion in head and neck squamous cell carcinoma. 2014-09-23 Arun Khattri
Zhixiang Zuo
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
Everett E Vokes
Tanguy Y Seiwert
Oral Oncology
CO2 exposure at pressure impacts metabolism and stress responses in the model sulfate-reducing bacterium Desulfovibrio vulgaris strain Hildenborough. 2014-09-25 Matthew J. Marshall 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
Frontiers in Microbiology
Open-access synthetic spike-in mRNA-seq data for cancer gene fusions. 2014-09-30 Valérie Montel 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
BMC Genomics
Global transcriptome analysis of Al-induced genes in an Al-accumulating species, common buckwheat (Fagopyrum esculentum Moench). 2014-09-30 Naoki Yamaji Kengo Yokosho
Jian Feng Ma
Plant and Cell Physiology
A comparison of sperm RNA-seq methods 2014-10 Russ Hauser Shihong Mao
Edward Sendler
Robert J Goodrich
Stephen A Krawetz
Systems Biology in Reproductive Medicine
Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta. 2014-10-01 Reedik Mägi
Andres Metspalu
Ene Reimann
Kristiina Rull
Jaak Vilo
Lili Milani
Andres Salumets
Tauno Metsalu
Triin Viltrop
Airi Tiirats
Balaji Rajashekar
Sulev Kõks
Ganesh Acharya
Purusotam Basnet
Maire Peters
Kadri Haller-Kikkatalo
Epigenetics
How deep is enough in single-cell RNA-seq? 2014-10-01 Yanyi Huang Aaron M Streets Nature Biotechnology
Detection of very long antisense transcripts by whole transcriptome RNA-Seq analysis of Listeria monocytogenes by semiconductor sequencing technology. 2014-10-06 Stefanie Wehner
Ramakanth Madhugiri
Gopala K Mannala
Xiaoxing Qing
Trinad Chakraborty
Mobarak A Mraheil
Torsten Hain
Manja Marz
PLoS ONE
Role for LSM genes in the regulation of circadian rhythms. 2014-10-06 Lauren J. Francey Soledad Perez-Santángelo
Estefanía Mancini
Ruben Gustavo Schlaen
Ariel Chernomoretz
John B Hogenesch
Marcelo J Yanovsky
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 2014-10-07 Vimal Rawat Ranu Sharma
C G Suresh
PLoS ONE
Comparative transcriptomics and metabolomics in a rhesus macaque drug administration study. 2014-10-08 Jessica C Kissinger
Jeremy Debarry
Karan Uppal
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
Frontiers in cell and developmental biology
Gene expression plasticity resulting from parental leaf damage in Mimulus guttatus. 2014-10-08 Lena Hileman Jack M Colicchio
Patrick J Monnahan
John K Kelly
New Phytologist
Argonaute-1 binds transcriptional enhancers and controls constitutive and alternative splicing in human cells. 2014-10-13 Eduardo Eyras
Eneritz Agirre
Matías Blaustein
Gwendal Dujardin
Federico Pelisch
Juan Valcárcel
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
Reinhard Lührmann
Alberto R Kornblihtt
Proceedings of the National Academy of Sciences of the United States of America
trieFinder: an efficient program for annotating Digital Gene Expression (DGE) tags. 2014-10-13 Matthew C LaFave
Shawn M. Burgess
Gabriel Renaud
Jin Liang
Tyra G Wolfsberg
BMC Bioinformatics
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. 2014-10-13 Chenghua Li Xiumei Zhang
Pengjuan Zhang
Ye Li
Chunhua Jin
Weiwei Zhang
Developmental and Comparative Immunology
Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis. 2014-10-15 Ross C Hardison
Christapher S Morrissey
Mitchell J Weiss
Weisheng Wu
Cheryl A Keller
Tejaswini Mishra
Maxim Pimkin
Gerd A Blobel
Genome Research
Defining the genome-wide role of CRE1 during carbon catabolite repression in Trichoderma reesei using RNA-Seq analysis. 2014-10-18 Rafael Silva-Rocha Amanda Cristina Campos Antoniêto
Lílian dos Santos Castro
Gabriela Felix Persinoti
Roberto Nascimento Silva
Fungal Genetics and Biology
Transcriptomic portrait of human Mesenchymal Stromal/Stem Cells isolated from bone marrow and placenta. 2014-10-19 Javier De Las Rivas
Fermin Sanchez-Guijo
Beatriz Roson-Burgo
Consuelo Del Cañizo
BMC Genomics
Comparative proteomic and transcriptomic profile of Staphylococcus epidermidis biofilms grown in glucose-enriched medium. 2014-10-19 Gerald B Pier
Manuel Vilanova
Nuno Cerca
Rui Vitorino
Virginia Carvalhais
Angela França
Talanta
CHD8 regulates neurodevelopmental pathways associated with autism spectrum disorder in neural progenitors 2014-10-21 Nicholas Katsanis
Manolis Kellis
Stephen J Haggarty
Serkan Erdin
Michael E. Talkowski
Aarathi Sugathan
Marta Biagioli
Christelle Golzio
Ian Blumenthal
Poornima Manavalan
Ashok Ragavendran
Harrison Brand
Diane Lucente
Judith Miles
Steven D Sheridan
Alexei Stortchevoi
James F Gusella
Proceedings of the National Academy of Sciences of the United States of America
Gene expression associated with intersterility in Heterobasidion. 2014-10-22 Mårten Lind
Malin Elfstrand
Magnus Karlsson
Jan Stenlid
M A Van der Nest
Å Olson
K Dalman
M Brandström-Durling
B D Wingfield
Fungal Genetics and Biology
Gene expression patterns and sequence polymorphisms associated with mosquito resistance to Bacillus thuringiensis israelensis toxins 2014-10-23 Aurélie Bonin
Stéphane Reynaud
Laurence Despres
Jean-Philippe David
Guillaume Tetreau
Renaud Stalinski
Margot Paris
Vincent Navratil
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. 2014-10-27 Martin J. Simard Alexandra Dallaire
Sophie Proulx
Michel Lebel
BMC Genomics
Transcriptional adaptations during long-term persistence of Staphylococcus aureus in the airways of a cystic fibrosis patient. 2014-10-29 Boyke Bunk Nadine Windmüller
Anika Witten
Desirée Block
Cathrin Spröer
Barbara C Kahl
Alexander Mellmann
International Journal of Medical Microbiology
Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential. 2014-10-31 Igor V Grigoriev 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
Proceedings of the National Academy of Sciences of the United States of America
BCOR-CCNB3 fusions are frequent in undifferentiated sarcomas of male children. 2014-10-31 Stephen F Sarabia
Alexander J. Lazar
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
Modern Pathology
Widespread intron retention in mammals functionally tunes transcriptomes 2014-11 Ulrich Braunschweig
Thomas Gonatopoulos-Pournatzis
Babak Alipanahi
Nuno L Barbosa-Morais
Manuel Irimia
Qun Pan
Emil N Nachman
Brendan Frey
Benjamin J Blencowe
Genome Research
Tissue-specific mtDNA abundance from exome data and its correlation with mitochondrial transcription, mass and respiratory activity. 2014-11-01 Carmela Gissi
Graziano Pesole
Matteo Chiara
Anna Maria D'Erchia
Ernesto Picardi
Anna Atlante
Gemma Gadaleta
Giulio Pavesi
Caterina De Virgilio
Caterina Manzari
Francesca Mastropasqua
Gian Marco Prazzoli
David Horner
Aurelio Reyes
Elisabetta Sbisà
Apollonia Tullo
Mitochondrion
Transcriptomic analysis across nasal, temporal, and macular regions of human neural retina and RPE/choroid by RNA-Seq 2014-11-05 Alex H Wagner
Adam P. DeLuca
Arlene Drack
Budd A. Tucker
Todd E. Scheetz
Robert F. Mullins
Edwin M. Stone
S Scott Whitmore
Shemin Zeng
Terry A Braun
Experimental Eye Research
Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state 2014-11-07 Christopher J. Lengner
Rudolf Jaenisch
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
eLife
Investigating the molecular underpinnings underlying morphology and changes in carbon partitioning during tension wood formation in Eucalyptus. 2014-11-12 Shawn D Mansfield Eshchar Mizrachi
Victoria J Maloney
Janine Silberbauer
Charles A Hefer
Dave K Berger
Alexander A Myburg
New Phytologist
Functional diversity of carbohydrate-active enzymes enabling a bacterium to ferment plant biomass. 2014-11-13 Jean Weissenbach Magali Boutard
Tristan Cerisy
Pierre-Yves Nogue
Adriana Alberti
Marcel Salanoubat
Andrew C Tolonen
PLOS Genetics
Transcriptomic and physiological insights into the robustness of long filamentous cells of Methanosaeta harundinacea, prevalent in upflow anaerobic sludge blanket granules. 2014-11-14 Songnian Hu Liguang Zhou
Haiying Yu
Guomin Ai
Bo Zhang
Xiuzhu Dong
Applied and Environmental Microbiology
Construction and assessment of individualized proteogenomic databases for large-scale analysis of nonsynonymous single nucleotide variants. 2014-11-17 Boris Macek Karsten Krug
Sasa Popic
Alejandro Carpy
Christoph Taumer
Proteomics
Genome-wide analysis of the omega-3 fatty acid desaturase gene family in Gossypium 2014-11-18 Daniel Ilut 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
BMC Plant Biology
Omics profiles used to evaluate the gene expression of Exiguobacterium antarcticum B7 during cold adaptation. 2014-11-18 Vivian H. Pellizari
Adriano M C Pimenta
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
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BMC Genomics
IsoSCM: improved and alternative 3' UTR annotation using multiple change-point inference. 2014-11-18 Pedro Miura Sol Shenker
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Expression of human skin-specific genes defined by transcriptomics and antibody-based profiling 2014-11-19 Mathias Uhlén
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Journal of Histochemistry & Cytochemistry
DB-AT: a 2015 update to the Full-parasites database brings a multitude of new transcriptomic data for apicomplexan parasites. 2014-11-20 Tabea G Kischka
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Nucleic Acids Research
Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing. 2014-11-24 Sten Linnarsson
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Nature Neuroscience
Promiscuous mRNA splicing under the control of AIRE in medullary thymic epithelial cells. 2014-11-25 Rhodri Ceredig Peter Keane
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Bioinformatics
Natural genetic variation impacts expression levels of coding, non-coding, and antisense transcripts in fission yeast 2014-11-28 Jürg Bähler
María Rodríguez-López
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Molecular Systems Biology
The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease 2014-12 Kerstin Lindblad-Toh
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Nature Biotechnology
Development of novel filtering criteria to analyze RNA-sequencing data obtained from the murine ocular lens during embryogenesis 2014-12-01 Melinda K Duncan Abby L Manthey
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Genomics Data
Genotet: An Interactive Web-based Visual Exploration Framework to Support Validation of Gene Regulatory Networks. 2014-12-01 Christoph Hafemeister Bowen Yu
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IEEE Transactions on Visualization and Computer Graphics
Transcriptome structure variability in Saccharomyces cerevisiae strains determined with a newly developed assembly software. 2014-12-01 Laura Treu Alessandro Sardu
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BMC Genomics
Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress. 2014-12-02 Nedeljka N. Rosic
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BMC Genomics
QuASAR: quantitative allele-specific analysis of reads. 2014-12-04 Xiaoquan Wen
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Bioinformatics
Direct and indirect consequences on gene expression of a thyroid hormone receptor alpha 1 mutation restricted to Sertoli cells. 2014-12-08 Gabriel Livera Fabrice Chatonnet
Betty Fumel
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Molecular Reproduction and Development
Dynamic changes in the cardiac methylome during postnatal development. 2014-12-09 Mark Ziemann
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FASEB Journal
An epigenomic roadmap to induced pluripotency reveals DNA methylation as a reprogramming modulator. 2014-12-10 Thomas Bleazard
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Nature Communications
RNA-seq analysis of broiler liver transcriptome reveals novel responses to high ambient temperature. 2014-12-10 Carl J Schmidt Derrick J Coble
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BMC Genomics
High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies 2014-12-11 Aviv Regev
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Raktima Raychowdhury
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Cell
The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data 2014-12-16 Richard Weinshilboum Xiaojia Tang
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Nucleic Acids Research
Regulation of the KNOX-GA gene module induces heterophyllic alteration in North American lake cress. 2014-12-16 Hitoshi Sakakibara
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The Plant Cell
Recurrent PRDM10 gene fusions in undifferentiated pleomorphic sarcoma. 2014-12-16 Fredrik Mertens Jakob Hofvander
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Clinical Cancer Research
Evaluation and validation of a robust single cell RNA-amplification protocol through transcriptional profiling of enriched lung cancer initiating cells. 2014-12-17 Luca Roz Dominic G Rothwell
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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. 2014-12-18 Chris Ponting
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BMC Cancer
Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference. 2014-12-18 Delphine Potier
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Marina Naval Sanchez
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Cell Reports
Genome-wide analysis of the human p53 transcriptional network unveils a lncRNA tumour suppressor signature. 2014-12-19 Maite Huarte Yolanda Sánchez
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Nature Communications
plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants. 2014-12-23 Peter F. Stadler
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Frontiers in Plant Science
RNA-seq profiling of small numbers of Drosophila neurons. 2014-12-26 Michael Rosbash
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Methods in Enzymology
Considerations for RNA-seq analysis of circadian rhythms. 2014-12-26 Gregory R Grant Jiajia Li
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Methods in Enzymology
Identification of RNA polymerase III-transcribed Alu loci by computational screening of RNA-Seq data. 2014-12-29 Silvia Fustinoni
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Nucleic Acids Research
Β-catenin-dependent control of positional information along the AP body axis in planarians involves a teashirt family member. 2014-12-31 Gilbert Weidinger Hanna Reuter
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Cell Reports
Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties 2015 Eshita Mutt
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BMC Plant Biology
ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines 2015 Fabian Amman
Florian Eggenhofer
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F1000Research
Ixodes scapularis and Ixodes ricinus tick cell lines respond to infection with tick-borne encephalitis virus: transcriptomic and proteomic analysis 2015 Margarita Villar
José de la Fuente
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Sabine Weisheit
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Parasites & Vectors
From Insect to Man: Photorhabdus Sheds Light on the Emergence of Human Pathogenicity 2015 Helge Bode Geraldine Mulley
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PLoS ONE
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
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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
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Walter E Hitzler PLoS ONE
Global Gene Expression Profiling through the Complete Life Cycle of Trypanosoma vivax 2015 Matthew Berriman
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PLOS Neglected Tropical Diseases
RNA-Seq Analysis of Human Trigeminal and Dorsal Root Ganglia with a Focus on Chemoreceptors 2015 Janine Altmüller
Hanns Hatt
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PLoS ONE
Whole Body Melanoma Transcriptome Response in Medaka 2015 Manfred Schartl Manfred Schartl
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PLoS ONE
OperomeDB: A Database of Condition-Specific Transcription Units in Prokaryotic Genomes 2015 Sarath Chandra Janga Kashish Chetal
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BioMed Research International
Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli 2015-01-01 Thorsten Bischler
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Journal of Bacteriology
The transcription factor Nerfin-1 prevents reversion of neurons into neural stem cells 2015-01-01 Anthony T. Papenfuss Francesca Froldi
Milan Szuperak
Chen-Fang Weng
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Genes & Development
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
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Journal of Alzheimer's Disease
Characterization of the Olfactory Receptors Expressed in Human Spermatozoa 2015-01-01 Hanns Hatt
Günter Gisselmann
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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
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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
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RNA Biology
Integrative genome-wide analysis of the determinants of RNA splicing in kidney renal clear cell carcinoma. 2015-01-01 Oliver Stegle Kjong-Van Lehmann
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Gunnar Rätsch
Pacific Symposium on Biocomputing
Analysis of alternative splicing events in custom gene datasets by AStalavista. 2015-01-01 Sylvain Foissac
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Methods in Molecular Biology
Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data. 2015-01-05 Åslaug Helland Lynnette Fernandez-Cuesta
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Reinhard Buettner
Jürgen Wolf
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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 Kaiwei Liang
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Molecular and Cellular Biology
iRNA-seq: computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data 2015-01-06 Susanne Mandrup Jesper Grud Skat Madsen
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Nucleic Acids Research
Astrovirus VA1/HMO-C: an increasingly recognized neurotropic pathogen in immunocompromised patients 2015-01-07 Vincent Plagnol
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Clinical Infectious Diseases
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
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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
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Molecular Systems Biology
Deep sequencing of the murine olfactory receptor neuron transcriptome. 2015-01-15 Hanns Hatt
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PLoS ONE
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
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Cerebral Cortex
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
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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
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Biology of Reproduction
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
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Elisa Sugliano
Maurizio Marconi
Raffaele De Francesco
Jens Geginat
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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
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ACS Nano
Computational and analytical challenges in single-cell transcriptomics. 2015-01-28 Sarah Teichmann
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Nature Reviews Genetics
The transcriptional stress response of Candida albicans to weak organic acids. 2015-01-29 Norman Pavelka
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G3
The avian transcriptome response to malaria infection 2015-01-29 Olof Hellgren
Gediminas Valkiūnas
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Molecular Biology and Evolution
RNA-seq SSRs and small RNA-seq SSRs: new approaches in cancer biomarker discovery. 2015-01-30 Arghavan Alisoltani Arghavan Alisoltani
Hossein Fallahi
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Gene
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
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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 Jonathan Krell
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Claudia Carissimi
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The Lancet
Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers. 2015-02-02 Laura Clarke
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Genome Research
Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling. 2015-02-02 Jens Nielsen Pouyan Ghaffari
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Scientific Reports
The genomic landscape of phaeochromocytoma. 2015-02-02 Stephen B. Fox
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The Journal of Pathology
Comparison of larval and adult Drosophila astrocytes reveals stage-specific gene expression profiles 2015-02-04 Yanmei Huang Fanny S Ng
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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 Hyun-Jin Yang
Rinki Ratnapriya
Tiziana Cogliati
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Progress in Retinal and Eye Research
Regulatory small RNAs from the 3' regions of bacterial mRNAs. 2015-02-09 Jörg Vogel
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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
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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
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Physiological Genomics
Distinct Transcriptomic Features are Associated with Transitional and Mature B-Cell Populations in the Mouse Spleen. 2015-02-11 Daria Salyakina Eden Kleiman
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Frontiers in Immunology
Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. 2015-02-12 Je Hyuk Lee
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Nature Protocols
The herbicide linuron inhibits cholesterol biosynthesis and induces cellular stress responses in brown trout. 2015-02-12 Eduarda M. Santos
Tamsyn M Uren Webster
Mandy H Perry Environmental Science & Technology
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 Peter Deplazes Adrian B Hehl
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BMC Genomics
Differential RNA-seq of Vibrio cholerae identifies the VqmR small RNA as a regulator of biofilm formation 2015-02-17 Cynthia Sharma
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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 Jessica Nordlund
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Clinical epigenetics
Aging-like changes in the transcriptome of irradiated microglia 2015-02-17 Matthew D Li
Steven A. Sloan
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Glia
Molecular characterization and transcriptome analysis of orange head Chinese cabbage (Brassica rapa L. ssp. pekinensis). 2015-02-17 Barry J Pogson Junxiang Zhang
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Planta
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads 2015-02-18 Steven Salzberg
Mihaela Pertea
Geo M Pertea
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Nature Biotechnology
RNA Seq analysis of the Eimeria tenella gametocyte transcriptome reveals clues about the molecular basis for sexual reproduction and oocyst biogenesis 2015-02-18 Peter Deplazes Robert A Walker
Philippa A Sharman
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Michal Okoniewski
Ramon M Eichenberger
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BMC Genomics
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
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Peter Lönnerberg
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Jens Hjerling-Leffler
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Science
The lncRNA DRAIC/PCAT29 Locus Constitutes a Tumor-Suppressive Nexus. 2015-02-20 Anindya Dutta
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Molecular Cancer Research
A transcriptome derived female-specific marker from the invasive Western mosquitofish (Gambusia affinis). 2015-02-23 Manfred Schartl
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PLoS ONE
Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs. 2015-02-23 John Mattick
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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. 2015-02-23 Vivek Krishnakumar Xingtan Zhang
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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 Wentao Yang
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Developmental and Comparative Immunology
RNA-Seq: Improving Our Understanding of Retinal Biology and Disease. 2015-02-26 Eric A Pierce Michael H Farkas
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Cold Spring Harbor Perspectives in Medicine
Exon Skipping Is Correlated with Exon Circularization. 2015-02-26 Steven Kelly
Argyris Papantonis
Chris Greenman
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Journal of Molecular Biology
The landscape of long noncoding RNAs in the human transcriptome 2015-03 John R. Prensner Matthew K Iyer
Yashar S Niknafs
Rohit Malik
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Nature Genetics
Open pipelines for integrated tumor genome profiles reveal differences between pancreatic cancer tumors and cell lines 2015-03 James Taylor Jeremy Goecks
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Cancer Medicine
Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators. 2015-03-03 Steven A. Sloan Qinghong Yan
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Proceedings of the National Academy of Sciences of the United States of America
Discovery of putative small non-coding RNAs from the obligate intracellular bacterium Wolbachia pipientis. 2015-03-04 Jean Popovici
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PLoS ONE
Activation of an endogenous retrovirus-associated long non-coding RNA in human adenocarcinoma. 2015-03-05 Gregg B Morin Ewan A Gibb
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Genome Medicine
PATZ1 Is a DNA Damage-Responsive Transcription Factor That Inhibits p53 Function. 2015-03-09 Wilfried Ellmeier Nazli Keskin
Emre Deniz
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Molecular and Cellular Biology
Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing. 2015-03-09 Lars K. Nielsen
Anton J. Enright
John Mattick
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Nature Methods
DNA methylation dynamics at imprinted genes during bovine pre-implantation embryo development. 2015-03-10 Niamh Forde
Alan M O'Doherty
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BMC Developmental Biology
Cyclic GMP balance is critical for malaria parasite transmission from the mosquito to the mammalian host 2015-03-17 Sebastian A. Mikolajczak Viswanathan Lakshmanan
Matthew E Fishbaugher
Bob Morrison
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mBio
Transcriptomic profiling of linolenic acid-responsive genes in ROS signaling from RNA-seq data in Arabidopsis. 2015-03-17 Juan C Begara-Morales
Francisco J. Corpas
Capilla Mata-Pérez
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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 Mayada Achour
Stéphanie Le Gras
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Human Molecular Genetics
Immunoglobulin transcript sequence and somatic hypermutation computation from unselected RNA-seq reads in chronic lymphocytic leukemia. 2015-03-18 Albert de la Chapelle James S Blachly
Amy S Ruppert
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Proceedings of the National Academy of Sciences of the United States of America
Gene expression dosage regulation in an allopolyploid fish 2015-03-19 Maria Manuela Coelho I Matos
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PLoS ONE
GLI2 inhibition abrogates human leukemia stem cell dormancy. 2015-03-21 John McPherson Anil Sadarangani
Gabriel Pineda
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Ifat Geron
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Journal of Translational Medicine
Alternative polyadenylation allows differential negative feedback of human miRNA miR-579 on its host gene ZFR. 2015-03-23 Ludwig Christian Hinske Pedro A F Galante
Elisabeth Limbeck
Patrick Möhnle
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PLoS ONE
SplicePie: a novel analytical approach for the detection of alternative, non-sequential and recursive splicing. 2015-03-23 Annemieke Aartsma-Rus Irina Pulyakhina
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Nucleic Acids Research
Discovery of molecular markers to discriminate corneal endothelial cells in the human body. 2015-03-25 Masahito Yoshihara
Hideya Kawaji
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Susumu Hara
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FANTOM consortium
Yoshihide Hayashizaki
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PLoS ONE
Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols. 2015-03-26 Michael Eisen
Peter A Combs
PeerJ
Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels 2015-03-27 Cisca Wijmenga Patrick Deelen
Daria V Zhernakova
Mark de Haan
Marijke van der Sijde
Marc Jan Bonder
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Kristin M Abbott
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Richard J Sinke
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Genome Medicine
The Listeria monocytogenes strain 10403S BioCyc database. 2015-03-28 Teresa M Bergholz
Kathryn J Boor
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Renato H Orsi Database
UV irradiation responses in Giardia intestinalis. 2015-03-28 Karin Troell Elin Einarsson
Staffan G Svärd
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Experimental Parasitology
The Solanum commersonii Genome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives 2015-04 Toni Gabaldón
Riccardo Aiese Cigliano
Walter Sanseverino
Salvador Capella-Gutierrez
Riccardo Aversano
James M Bradeen
Felice Contaldi
Maria Raffaella Ercolano
Valentina Grosso
Massimo Iorizzo
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Luciano Xumerle
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The Plant Cell
Methyl-CpG Binding Protein 2 Regulates Microglia and Macrophage Gene Expression in Response to Inflammatory Stimuli. 2015-04-01 Jonathan Kipnis
Tajie H. Harris
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Geoffrey T Norris
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Immunity
p53 Enables metabolic fitness and self-renewal of nephron progenitor cells 2015-04-01 Melody Baddoo Yuwen Li
Jiao Liu
Wencheng Li
Aaron Brown
Melody Baddoo
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Thomas Carroll
Leif Oxburgh
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Development
EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments. 2015-04-05 Christina Kendziorski Ning Leng
Yuan Li
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Bioinformatics
Characterization of the transcriptome of nascent hair cells and identification of direct targets of the Atoh1 transcription factor 2015-04-08 Andrew K. Groves
Huda Zoghbi
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Journal of Neuroscience
Genome-wide analysis of the family 1 glycosyltransferases in cotton. 2015-04-08 Juan Huang Juan Huang
Chaoyou Pang
Shuli Fan
Meizhen Song
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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. 2015-04-08 Alicia Oshlack
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Biology of Reproduction
New basal cell carcinoma susceptibility loci. 2015-04-09 Laufey Tryggvadottir
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Nature Communications
New signaling pathways govern the host response to C. albicans infection in various niches. 2015-04-09 Jacques Ravel
Jennifer Schwartz
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Genome Research
Allelic Imbalance Is a Prevalent and Tissue-Specific Feature of the Mouse Transcriptome. 2015-04-09 Bernhard Payer
David Colognori
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Genetics
Spatial reconstruction of single-cell gene expression data. 2015-04-13 Aviv Regev
Rahul Satija
Jeffrey A Farrell
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Nature Biotechnology
Asymmetric transcript discovery by RNA-seq in C. elegans blastomeres identifies neg-1, a gene important for anterior morphogenesis. 2015-04-13 Erin Osborne
Bob Goldstein
Jay C Zhang
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PLOS Genetics
Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum. 2015-04-13 Gad Shaulsky Rafael David Rosengarten
Balaji Santhanam
Danny Fuller
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William F Loomis
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BMC Genomics
ChIP-Seq and RNA-Seq analyses identify components of the Wnt and Fgf signaling pathways as Prep1 target genes in mouse embryonic stem cells. 2015-04-13 Miguel Torres
Hans-Jörg Warnatz
Marie-Laure Yaspo
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PLoS ONE
Evaluation of two statistical methods provides insights into the complex patterns of alternative polyadenylation site switching 2015-04-14 Yonggui Fu Jie Li
Rui Li
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PLoS ONE
NMD3 regulates both mRNA and rRNA nuclear export in African trypanosomes via an XPOI-linked pathway. 2015-04-14 Paul Capewell
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Nucleic Acids Research
Identification of candidate mimicry proteins involved in parasite-driven phenotypic changes 2015-04-15 Nadia Aubin-Horth Francois Olivier Hebert
Luke Phelps
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Parasites & Vectors
Widespread exon skipping triggers degradation by nuclear RNA surveillance in fission yeast 2015-04-16 Jürg Bähler Danny A Bitton
Sophie R Atkinson
Charalampos Rallis
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Genome Research
SF3B1 association with chromatin determines splicing outcomes. 2015-04-16 Arnab Datta Nir Kfir
Galit Lev-Maor
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Cell Reports
First description of small proteins encoded by spRNAs in Methanosarcina mazei strain Gö1. 2015-04-16 Ruth Schmitz-Streit Daniela Prasse
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Biochimie
PGTools: A Software Suite for Proteogenomic Data Analysis and Visualization. 2015-04-17 Sean M. Grimmond Shivashankar H Nagaraj
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Journal of Proteome Research
Transcriptomics-based analysis using RNA-Seq of the coconut (Cocos nucifera) leaf in response to yellow decline phytoplasma infection. 2015-04-18 Mark Ziemann Naghmeh Nejat
David M Cahill
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Molecular Genetics and Genomics
edgeRun: an R package for sensitive, functionally relevant differential expression discovery using an unconditional exact test. 2015-04-21 Winston Hide
Rory Kirchner
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Bioinformatics
Hepatitis D Virus Infection of Mice Expressing Human Sodium Taurocholate Co-transporting Polypeptide 2015-04-22 Wenhui Li
Jianhua Sui
Wenhui He
Bijie Ren
Fengfeng Mao
Zhiyi Jing
Yunfei Li
Yang Liu
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PLOS Pathogens
Individual genome sequencing identified a novel enhancer element in exon 7 of the CSFR1 gene by shift of expressed allele ratios. 2015-04-22 Ekaterina E Khrameeva S Zhenilo
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Gene
Imprinted expression in cystic embryoid bodies shows an embryonic and not an extra-embryonic pattern 2015-04-24 Christoph Bock
Sylvia Knapp
Josef M Penninger
Tomasz M Kulinski
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Philipp M Guenzl
Daniel Wenzel
Daniel Andergassen
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Paul Datlinger
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Developmental Biology
PtaRHE1, a Populus tremula × Populus alba RING-H2 protein of the ATL family, has a regulatory role in secondary phloem fibre development. 2015-04-25 Wout Boerjan Fabien Baldacci-Cresp
Jihad Moussawi
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Rebecca Van Acker
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Julie Candiracci
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Gerd Bossinger
Françoise Laurans
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The Plant Journal
Tet3 regulates synaptic transmission and homeostatic plasticity via DNA oxidation and repair 2015-04-27 Guo-Li Ming
Hongjun Song
Huimei Yu
Yijing Su
Jaehoon Shin
Chun Zhong
Junjie U Guo
Yi-Lan Weng
Fuying Gao
Daniel H Geschwind
Giovanni Coppola
Nature Neuroscience
High-performance probes for light and electron microscopy 2015-04-27 Gerald M. Rubin
Megan E Williams
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Brian P. English
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Timothy J Stasevich
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Ronak Patel
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Loren L Looger
Nature Methods
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. 2015-04-29 Melody Baddoo Subing Cao
Walter Moss
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Monica Concha
Michael J Strong
Xia Wang
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Melody Baddoo
Kun Zhang
Claire Fewell
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Yan Dong
Erik K Flemington
Journal of Virology
Oviduct-Embryo Interactions in Cattle: Two-Way Traffic or a One-Way Street? 2015-04-29 Niamh Forde
Thomas E. Spencer
Alfonso Gutierrez-Adan
Gregory W Burns
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Peadar Ó Gaora
Urban Besenfelder
Vitezslav Havlicek
Patrick Lonergan
Dimitrios Rizos
Biology of Reproduction
Coronary Artery Disease Associated Transcription Factor TCF21 Regulates Smooth Muscle Precursor Cells That Contribute to the Fibrous Cap 2015-05 Thomas Quertermous
Sylvia T Nurnberg
Ivan Carcamo-Oribe
Michelle D Tallquist
Lars Maegdefessel
Ulf Hedin
Karen Cheng
Azad Raiesdana
Ramendra Kundu
Clint L Miller
Juyong B Kim
Komal Arora
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Nikhil Tellakula
Vivek Nanda
Nikitha Murthy
William A Boisvert
Ljubica Perisic
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PLOS Genetics
Mutant U2AF1 Expression Alters Hematopoiesis and Pre-mRNA Splicing In Vivo. 2015-05-01 Sean D McGrath
Malachi Griffith
Timothy A. Graubert
Cara Lunn Shirai
James N Ley
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Justin Tibbitts
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Eric J Duncavage
Theresa Okeyo-Owuor
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Vincent Magrini
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Cancer Cell
Perturbations of heart development and function in cardiomyocytes from human embryonic stem cells with trisomy 21. 2015-05-01 Stylianos Antonarakis
Outi Hovatta
Laura Sartiani
Alexis Bosman
Audrey Letourneau
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Flavio Ronzoni
Rostyslav Kuziakiv
Virpi Tohonen
Marco Zucchelli
Federico Santoni
Michel Guipponi
Biljana Dumevska
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Stem Cells
Telomere dysfunction drives aberrant hematopoietic differentiation and myelodysplastic syndrome. 2015-05-01 Marianna D'Anca
Matteo Marchesini
Paola Storti
Simona Colla
Marcos Estecio
Nicola Giuliani
Lynda Chin
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Derrick Sek Tong Ong
Yamini Ogoti
Matteo Marchesini
Nipun A Mistry
Karen Clise-Dwyer
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Marcos Estecio
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Philip Jones
Laurence J N Cooper
Han Liang
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Cancer Cell
Identification of genes involved in the phosphate metabolism in Cryptococcus neoformans. 2015-05-05 Yu Kanesaki Akio Toh-e
Misako Ohkusu
Hao-Man Li
Kiminori Shimizu
Azusa Takahashi-Nakaguchi
Toru Gonoi
Susumu Kawamoto
Hirofumi Yoshikawa
Masafumi Nishizawa
Fungal Genetics and Biology
MIsoMine: a genome-scale high-resolution data portal of expression, function and networks at the splice isoform level in the mouse 2015-05-07 Gil Omenn Hong-Dong Li
Yuanfang Guan
Database
Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species. 2015-05-07 Igor Ulitsky Hadas Hezroni
David Koppstein
Matthew G Schwartz
Alexandra Avrutin
David P Bartel
Cell Reports
Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea. 2015-05-08 Gustavo Rodriguez-Esteban
Emili Salo
Josep F. Abril
Alejandro González-Sastre
José Ignacio Rojo-Laguna
BMC Genomics
Combining GWAS and RNA-Seq Approaches for Detection of the Causal Mutation for Hereditary Junctional Epidermolysis Bullosa in Sheep. 2015-05-08 Gwenola Tosser-Klopp Aroa Suárez-Vega
Beatriz Gutiérrez-Gil
Julio Benavides
Valentín Perez
Gwenola Tosser-Klopp
Christophe Klopp
Stephen J Keennel
Juan José Arranz
PLoS ONE
Gene expression associated with white syndromes in a reef building coral, Acropora hyacinthus. 2015-05-09 Mikhail Matz Rachel M Wright
Galina V Aglyamova
Eli Meyer
BMC Genomics
Contrasting host-pathogen interactions and genome evolution in two generalist and specialist microsporidian pathogens of mosquitoes. 2015-05-13 Christina A Cuomo Christopher A Desjardins
Neil D Sanscrainte
Jonathan M Goldberg
David Heiman
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Qiandong Zeng
Hiten D Madhani
James J Becnel
Nature Communications
GermlncRNA: a unique catalogue of long non-coding RNAs and associated regulations in male germ cell development. 2015-05-17 Tin-Lap Lee Alfred Chun-Shui Luk
Huayan Gao
Sizhe Xiao
Jinyue Liao
Daxi Wang
Jiajie Tu
Owen M Rennert
Wai-Yee Chan
Database
Splice variants and regulatory networks associated with host resistance to the intestinal worm Cooperia oncophora in cattle. 2015-05-18 Steven G Schroeder
Weizhong Li
Cong-Jun Li
Robert W Li
Sitao Wu
Veterinary Parasitology
Chlamydomonas reinhardtii cells adjust the metabolism to maintain viability in response to atrazine stress. 2015-05-19 Marta Esperanza
Marta Seoane
Concepción Herrero
Carmen Rioboo
Ángeles Cid
Aquatic Toxicology
Effect of ovarian hormones on the healthy equine uterus: a global gene expression analysis. 2015-05-20 Neil D. Young
Natali Krekeler
Christina D Marth
Lisa Y Glenton
Drew M Noden
Glenn F Browning
Reproduction, Fertility and Development
Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations 2015-05-21 Chris Ponting
Caroline Oedekoven
Fernando J Calero-Nieto
Florian Buettner
Iain C Macaulay
David Kent
Fabian J. Theis
Nicola K Wilson
Mona Shehata
Manuel Sánchez Castillo
Evangelia Diamanti
Reiner Schulte
Thierry Voet
Carlos Caldas
John Stingl
Anthony R Green
Berthold Göttgens
Cell Stem Cell
Alzheimer disease (AD) specific transcription, DNA methylation and splicing in twenty AD associated loci 2015-05-21 Margaret A. Pericak-Vance Crystal Humphries
Martin A Kohli
Patrice Whitehead
Deborah C Mash
John Gilbert
Molecular and Cellular Neuroscience
Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus agalactiae 2015-05-30 Isabelle Rosinski-Chupin
Patrick Trieu-Cuot
Elisabeth Sauvage
Odile Sismeiro
Adrien Villain
Violette Da Cunha
Marie-Elise Caliot
Marie-Agnès Dillies
Philippe Bouloc
Marie-Frédérique Lartigue
Philippe Glaser
BMC Genomics
Functionally defined therapeutic targets in diffuse intrinsic pontine glioma 2015-06 Wenchao Sun 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
Maryam Fouladi
Matthew N Svalina
Nicholas Wang
Cynthia Hawkins
Javad Nazarian
Marta M Alonso
Eric H Raabe
Esther Hulleman
Paul T Spellman
Xiao-Nan Li
Charles Keller
Ranadip Pal
Jacques Grill
Michelle Monje
Nature Medicine
FourCSeq: analysis of 4C sequencing data. 2015-06-01 Yad Ghavi-Helm
Wolfgang Huber
Simon Anders
Felix A Klein
Tibor Pakozdi
Eileen E M Furlong
Bioinformatics
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
Deepti Jain
Tejaswini Mishra
Belinda M Giardine
Cheryl A Keller
Susan Magargee
Christine M Dorman
Maria Long
Genomics Data
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
Transcriptional landscape of trans-kingdom communication between Candida albicans and Streptococcus gordonii. 2015-06-04 Sophie Shaw
Howard F. Jenkinson
L C Dutton
K H Paszkiewicz
R J Silverman
P R Splatt
A H Nobbs
R J Lamont
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Oral Microbiology and Immunology
Defective pollen wall contributes to male sterility in the male sterile line 1355A of cotton. 2015-06-05 Daojun Yuan Yuanlong Wu
Ling Min
Zancheng Wu
Li Yang
Longfu Zhu
Xiyan Yang
Xiaoping Guo
Xianlong Zhang
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 Sayantan Bose
Zhenmao Wan
Ambrose Carr
Abbas H Rizvi
Gregory Vieira
Dana Pe'er
Peter A Sims
Genome Biology
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 Junqiang Ye
Nadine Beetz
Sean O'Keeffe
Juan Carlos Tapia
Lindsey Macpherson
Weisheng V. Chen
Eric N. Olson
Tom Maniatis
Proceedings of the National Academy of Sciences of the United States of America
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
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 E. Sharpless Xiaobei Zhao
Anyou Wang
Vonn Walter
Nirali M Patel
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
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
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
ArcA Controls Metabolism, Chemotaxis, and Motility Contributing to the Pathogenicity of Avian Pathogenic Escherichia coli. 2015-06-22 Eve Syrkin Wurtele Fengwei Jiang
Chunxia An
Yinli Bao
Xuefeng Zhao
Robert L Jernigan
Andrew Lithio
Dan Nettleton
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 Zhili Zhou
Huancheng Ma
Kevin Lin
Youjie Zhao
Zhi Xiong
Liuyang Wang
Bin Tian
Evolutionary Bioinformatics
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
Eeva-Mari Jouhilahti
Tiina Skoog
Shintaro Katayama
H Annika Siitonen
Kristo Nuutila
Mari H Tervaniemi
Jyrki Vuola
Anna Johnsson
Peter Lönnerberg
Sten Linnarsson
Outi Elomaa
Esko Kankuri
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
Wang Jun
Jun Wang
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
Jo Vandesompele
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
Zhiyu Peng
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
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
Björn M Hallström
Fredrik Ponten
Alistair R R Forrest
Fantom Consortium
Yoshihide Hayashizaki
Mathias Uhlén
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 Charles Walther
Jakob Hofvander
Jenny Nilsson
Linda Magnusson
Henryk A Domanski
Johnbosco Tayebwa
Leona A Doyle
Christopher D M Fletcher
Fredrik Mertens
Laboratory Investigation
Phylogenetic analysis and expression profiling of the pattern recognition receptors: Insights into molecular recognition of invading pathogens in Manduca sexta 2015-07 Xiaolong Cao Xiufeng Zhang
Yan He
Ramesh T Gunaratna
Yun-ru Chen
Gary Blissard
Michael R Kanost
Haobo Jiang
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 Spiro P Pantazatos
Stuart J Andrews
Jane Dunning-Broadbent
Jiuhong Pang
Yung-Yu Huang
Peter L Nagy
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 Benjamin P Towler
Sandra C Viegas
Patricia Apura
Joseph A Waldron
Sarah K Smalley
Cecilia M Arraiano
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
Cytoplasmic LSM-1 protein regulates stress responses through the insulin/IGF-1 signaling pathway in Caenorhabditis elegans 2015-07-06 Denis Dupuy Eric Cornes
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
Julián Cerón
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
Tungsten-induced carcinogenesis in human bronchial epithelial cells. 2015-07-08 Steven Shen
Maria Antonietta Zoroddu
Freda Laulicht
Jason Brocato
Laura Cartularo
Joshua Vaughan
Feng Wu
Thomas Kluz
Hong Sun
Betul Akgol Oksuz
Massimiliano Peana
Serenella Medici
Maria Antonietta Zoroddu
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
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
Alan E Hoban
Fergus Shanahan
Gerard Clarke
Marcus J Claesson
Timothy G Dinan
John F Cryan
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
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
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 Sunniva Stordal Bjørklund
Vessela N Kristensen
Michael Seiler
Surendra Kumar
Grethe I Grenaker Alnæs
Yao Ming
John Kerrigan
Bjørn Naume
Ravi Sachidanandam
Gyan Bhanot
Anne-Lise Børresen-Dale
Shridar Ganesan
BMC Cancer
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
Deborah I Scheffer
Anna Morgan
Mariateresa Di Stazio
Diego Vozzi
Teresa Nutile
Maria P Concas
Ginevra Biino
Lisa Nolan
Aileen Bahl
Anu Loukola
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
Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data. 2015-07-23 Mihaela Zavolan
Andreas R Gruber
Alexander Kanitz
Foivos Gypas
Andreas R Gruber
Georges Martin
Genome Biology
Identifying new sex-linked genes through BAC sequencing in the dioecious plant Silene latifolia. 2015-07-25 Alex Widmer N Blavet
H Blavet
A Muyle
J Käfer
R Cegan
C Deschamps
N Zemp
S Mousset
S Aubourg
R Bergero
D Charlesworth
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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 Rossukon Kaewkhaw
Koray Dogan Kaya
Matthew Brooks
Kohei Homma
Jizhong Zou
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 Gillian O'Hurley
Christer Busch
Linn Fagerberg
Björn M Hallström
Charlotte Stadler
Anna Tolf
Emma Lundberg
Jochen M Schwenk
Karin Jirström
Anders Bjartell
William M Gallagher
Mathias Uhlén
Fredrik Pontén
PLoS ONE
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
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Rachael M DeRita
Max Rothschild
Chris Ashwell
Michael E Persia
Cell Stress & Chaperones
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
ROTS: reproducible RNA-seq biomarker detector-prognostic markers for clear cell renal cell cancer. 2015-08-11 Laura L. Elo Fatemeh Seyednasrollah
Krista Rantanen
Panu Jaakkola
Nucleic Acids Research
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
Lost in Translation: Pitfalls in Deciphering Plant Alternative Splicing Transcripts. 2015-08-18 Andrea Barta John W S Brown
Craig G Simpson
Yamile Marquez
Geoffrey M Gadd
Maria Kalyna
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
Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms 2015-08-19 Mihaela Pertea Tsung-Cheng Chang
Sungyul Lee
Steven L Salzberg
Joshua T Mendell
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
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
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
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
Chromatin features, RNA polymerase II and the comparative expression of lens genes encoding crystallins, transcription factors, and autophagy mediators 2015-08-28 Deyou Zheng Jian Sun
Shira Rockowitz
Daniel Chauss
Ping Wang
Marc Kantorow
Ales Cvekl
Molecular Vision
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
Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses 2015-09-02 Aviv Regev
Rahul Satija
Roi Avraham
Nathan Haseley
Douglas Brown
Cristina Penaranda
Humberto B Jijon
John J Trombetta
Alex K Shalek
Ramnik J Xavier
Aviv Regev
Deborah T Hung
Cell
HiCdat: a fast and easy-to-use Hi-C data analysis tool. 2015-09-03 Ueli Grossniklaus Marc W Schmid
Stefan Grob
Ueli Grossniklaus
BMC Bioinformatics
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
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
Systematic identification of factors for provirus silencing in embryonic stem cells 2015-09-09 George Q. Daley Bin Xia Yang
Chadi A El Farran
Hong Chao Guo
Tao Yu
Hai Tong Fang
Hao Fei Wang
Sharon Schlesinger
Yu Fen Samantha Seah
Germaine Yen Lin Goh
Suat Peng Neo
Yinghui Li
Matthew C Lorincz
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 Laurianne Bessière
Anne-Laure Todeschini
Sandrine Caburet
Sabine Sarnacki
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
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
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
RNA-seq analysis of Pichia anomala reveals important mechanisms required for survival at low pH 2015-09-16 Jens Nielsen
Verena Siewers
Eugene Fletcher
Amir Feizi
SungSoo Kim
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 Itziar Frades
Kibrom B Abreha
Åsa Lankinen
Erik Andreasson
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
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
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
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
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
De novo transcriptome profiling of highly purified human lymphocytes primary cells 2015-09-29 Sergio Abrignani
Massimiliano Pagani
Grazisa Rossetti
Raoul J P Bonnal
Valeria Ranzani
Alberto Arrigoni
Serena Curti
Ilaria Panzeri
Paola Gruarin
Scientific Data
Functional Impact and Evolution of a Novel Human Polymorphic Inversion That Disrupts a Gene and Creates a Fusion Transcript. 2015-10-01 Tõnu Esko Marta Puig
David Castellano
Lorena Pantano
Carla Giner-Delgado
David Izquierdo
Magdalena Gayà-Vidal
José Ignacio Lucas-Lledó
Chikashi Terao
Fumihiko Matsuda
Mario Cáceres
PLOS Genetics
Prdm12 specifies V1 interneurons through cross-repressive interactions with Dbx1 and Nkx6 genes in Xenopus. 2015-10-01 Carine Van Lint
Benoît Van Driessche
Aurore Thélie
Simon Desiderio
Julie Hanotel
Ian Quigley
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
Alessandra Pierani
Michael Schubert
Jane E Johnson
Christopher R Kintner
Tomas Pieler
Kristine A Henningfeld
Eric J Bellefroid
Claude Van Campenhout
Development
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
Aviv Regev
Genome Research
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
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
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
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
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
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
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
Rolf I Skotheim
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
Puneet Paul
Mario Selymesi
Anida Mesihovic
Klaus-Dieter Scharf
Wolfram Weckwerth
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 Mikhail G Dozmorov
Nicolas Dominguez
Krista Bean
Susan R Macwana
Virginia Roberts
Edmund Glass
Judith A James
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
Bjarne Johannessen
Sharmini Alagaratnam
Sen Zhao
Marthe Løvf
Anne C Bakken
Merete Hektoen
Anita Sveen
Ragnhild A Lothe
Rolf I Skotheim
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
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
Nina Opitz
Caroline Marcon
Anja Paschold
Andrew Lithio
Ronny Brandt
Hans-Peter Piepho
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
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
Decay-Initiating Endoribonucleolytic Cleavage by RNase Y Is Kept under Tight Control via Sequence Preference and Sub-cellular Localisation. 2015-10-16 Peter Redder Vanessa Khemici
Julien Prados
Patrick Linder
PLOS Genetics
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
Ryan Demeter
Vincent Magrini
Varinder Jeet
Anja Rockstroh
Stephen McPherson
John Lai
Nenad Bartonicek
Jiyuan An
Jyotsna Batra
Melanie L Lehman
Colleen C Nelson
Molecular and Cellular Endocrinology
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
Laura Fontrodona
David Aristizábal-Corrales
Silvia Torres
Eric Cornes
Francisco J García-Rodríguez
Xènia Serrat
David González-Knowles
Montserrat Porta-De-La-Riva
Julián Cerón
RNA
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 Andrew D Bolton
Yasunobu Murata
Rory Kirchner
Sung-Yon Kim
Andrew Young
Tru Dang
Yuchio Yanagawa
Martha Constantine-Paton
Cell Reports
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
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
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
P. Wesseling
Myron G Best
Nik Sol
Irsan Kooi
Jihane Tannous
Bart A Westerman
François Rustenburg
Pepijn Schellen
Heleen Verschueren
Edward Post
Jan Koster
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
Paulina Kaniewska
Edmund Yew Siang Ling
David Edwards
Ove Hoegh-Guldberg
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
A high-throughput RNA-seq approach to profile transcriptional responses 2015-10-29 Xiaoquan Wen
Francesca Luca
G A Moyerbrailean
G O Davis
C T Harvey
D Watza
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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
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 Feng Zhang
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
Molecular Cell
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
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
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
Karsten Kristiansen
Xiuqing Zhang
Yingrui Li
Huanming Yang
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
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
Yuji Tanaka
Robin Andersson
Yoshihide Hayashizaki
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
Javed K Manesia
Zhuofei Xu
Dorien Broekaert
Guy Eelen
Thomas Vanwelden
Steve Stegen
Alberto Pascual-Montano
Geert Carmeliet
Peter Carmeliet
Satish Khurana
Stem Cell Research
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
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
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
Sabina Bajda
Robert Greenhalgh
Ralf Nauen
Luc Tirry
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 Chao Wang
Nir Yosef
Jellert Gaublomme
Chuan Wu
Youjin Lee
Clary B Clish
Jim Kaminski
Sheng Xiao
Gerd Meyer Zu Horste
Mathias Pawlak
Yasuhiro Kishi
Nicole Joller
Katarzyna Karwacz
Chen Zhu
Maria Ordovas-Montanes
Asaf Madi
Ivo Wortman
Toru Miyazaki
Raymond A Sobel
Hongkun Park
Aviv Regev
Vijay K Kuchroo
Cell
Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity. 2015-11-18 Pier Paolo Pandolfi
Aviv Regev
Rahul Satija
Jellert T Gaublomme
Nir Yosef
Youjin Lee
Rona S Gertner
Li V Yang
Chuan Wu
Tak Mak
Alex K Shalek
Vijay K Kuchroo
Hongkun Park
Aviv Regev
Cell
Deciphering the molecular adaptation of the king scallop (Pecten maximus) to heat stress using transcriptomics and proteomics. 2015-11-23 Romain Lavaud
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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
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Cell Reports
Analysis of nucleosome positioning landscapes enables gene discovery in the human malaria parasite Plasmodium falciparum. 2015-11-25 Evelien M. Bunnik Xueqing Maggie Lu
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BMC Genomics
Different mechanisms of resistance modulate sulfite tolerance in wine yeasts. 2015-11-28 Chiara Nadai
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Applied Microbiology and Biotechnology
Bromodomain Proteins Contribute to Maintenance of Bloodstream Form Stage Identity in the African Trypanosome 2015-12 Nina Papavasiliou Danae Schulz
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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
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BMC Genomics
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
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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
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Plant Physiology
Phenotypic Heterogeneity Affects Stenotrophomonas maltophilia K279a Colony Morphotypes and β-Lactamase Expression 2015-12-02 Konrad Förstner
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Frontiers in Microbiology
Transcriptome profiling of two Iberian freshwater fish exposed to thermal stress. 2015-12-04 Maria Manuela Coelho Tiago Filipe Jesus
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Journal of Thermal Biology
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
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Genome Biology and Evolution
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
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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
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Journal of Virology
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
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Fish and Shellfish Immunology
Transcriptional, post-transcriptional and chromatin-associated regulation of pri-miRNAs, pre-miRNAs and moRNAs. 2015-12-15 Laure Bally-Cuif Chirag Nepal
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Nucleic Acids Research
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
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Osteoarthritis and Cartilage
Lin28A Binds Active Promoters and Recruits Tet1 to Regulate Gene Expression 2015-12-16 Guo-Li Ming
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Molecular Cell
Characterization and Comparative Analysis of the Milk Transcriptome in Two Dairy Sheep Breeds using RNA Sequencing 2015-12-18 Gwenola Tosser-Klopp Aroa Suárez-Vega
Beatriz Gutiérrez-Gil
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Scientific Reports
Integration of electrophysiological recordings with single-cell RNA-seq data identifies neuronal subtypes 2015-12-21 Sten Linnarsson János Fuzik
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Nature Biotechnology
Single-cell transcriptomes reveal characteristic features of human pancreatic islet cell types 2015-12-21 Christoph Bock
Johanna Klughammer
Ekaterine Berishvili
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EMBO Reports
Human cerebral organoids recapitulate gene expression programs of fetal neocortex development 2015-12-22 Svante Pääbo
Farhath Badsha
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Proceedings of the National Academy of Sciences of the United States of America
Multidimensional Genome-wide Analyses Show Accurate FVIII Integration by ZFN in Primary Human Cells 2015-12-22 Ajit Johnson Nirmal
Jaichandran Sivalingam
Sebastian Maurer-Stroh
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Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis. 2015-12-23 Jeremy Chien Wei Zhang
Jae-Woong Chang
Lilong Lin
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PLOS Computational Biology
Chromatin and RNA Maps Reveal Regulatory Long Noncoding RNAs in Mouse. 2015-12-28 Miguel Beato del Rosal
Marc A Marti-Renom
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Molecular and Cellular Biology
Simultaneous transcriptional profiling of Leishmania major and its murine macrophage host cell reveals insights into host-pathogen interactions. 2015-12-29 Héctor Corrada Bravo
Najib El-sayed
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BMC Genomics
Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. 2015-12-30 Mark D. Robinson
Michael I Love
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Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq 2015-12-31 Ricardo DeMarco
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PLOS Neglected Tropical Diseases
Single-Cell Genomics for Virology 2016 Amalio Telenti Angela Ciuffi
Sylvie Rato
Viruses
Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla 2016 Samuel O Purvine Peter H Waltman
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PLoS ONE
5'-Hydroxymethylcytosine Precedes Loss of CpG Methylation in Enhancers and Genes Undergoing Activation in Cardiomyocyte Maturation 2016 Rolf Backofen David K Kranzhöfer
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PLoS ONE
Identification of Ice Plant (Mesembryanthemum crystallinum L.) MicroRNAs Using RNA-Seq and Their Putative Roles in High Salinity Responses in Seedlings 2016 Won Cheol Yim
John Cushman
Chih-Pin Chiang
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Miwa Ohnishi
Tetsuro Mimura
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Frontiers in Plant Science
Fish-T1K (Transcriptomes of 1,000 Fishes) Project: large-scale transcriptome data for fish evolution studies 2016 Byrappa Venkatesh
Yu Huang
Jose V. Lopez
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Keith A. Crandall
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Identifying stably expressed genes from multiple RNA-Seq data sets 2016 Jeff H. Chang Bin Zhuo
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Loss of neurogenesis in Hydra leads to compensatory regulation of neurogenic and neurotransmission genes in epithelial cells. 2016-01-01 Brigitte Galliot Y Wenger
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Utility of next-generation RNA-sequencing in identifying chimeric transcription involving human endogenous retroviruses. 2016-01-01 Finn Skou Pedersen Martin Sokol
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Acta Pathologica et Microbiologica Scandinavica
Using RNA-seq for Analysis of Differential Gene Expression in Fungal Species. 2016-01-01 Geraldine Butler Can Wang
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Methods in Molecular Biology
Genome-Wide Identification of Alternative Polyadenylation Events Using 3'T-Fill. 2016-01-01 Vicent Pelechano Stefan Wilkening
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Methods in Molecular Biology
A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages. 2016-01-06 Paul C. Blainey
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Nature Communications
Tunable protein synthesis by transcript isoforms in human cells 2016-01-06 Jennifer Doudna
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eLife
OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data 2016-01-06 Christina Kendziorski Ning Leng
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HTLV-1 bZIP Factor Impairs Anti-viral Immunity by Inducing Co-inhibitory Molecule, T Cell Immunoglobulin and ITIM Domain (TIGIT). 2016-01-06 Yuichi Mitobe
Masao Matsuoka
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PLOS Pathogens
Ribosomal protein genes are highly enriched among genes with allele-specific expression in the interspecific F1 hybrid catfish. 2016-01-08 Eric Peatman Ailu Chen
Ruijia Wang
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Molecular Genetics and Genomics
Direct and Absolute Quantification of over 1800 Yeast Proteins via Selected Reaction Monitoring. 2016-01-10 Robert J. Beynon Craig Lawless
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Molecular & Cellular Proteomics
A trans-acting Variant within the Transcription Factor RIM101 Interacts with Genetic Background to Determine its Regulatory Capacity. 2016-01-11 Robin Dowell Timothy Read
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PLOS Genetics
Mitochondrial iron chelation ameliorates cigarette smoke-induced bronchitis and emphysema in mice. 2016-01-11 John Quackenbush
Kristen T Rooney
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Nature Medicine
Corrigendum: Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression 2016-01-11 John C Marioni Jong Kyoung Kim
Aleksandra A Kolodziejczyk
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Nature Communications
RNA-Seq identifies SPGs as a ventral skeletal patterning cue in sea urchins. 2016-01-11 Evan S Bardot Michael L Piacentino
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The power and promise of RNA-seq in ecology and evolution. 2016-01-12 Michael A. Black
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Erica V Todd Molecular Ecology
Genome-wide transcriptome analysis of soybean primary root under varying water-deficit conditions. 2016-01-15 Trupti Joshi
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BMC Genomics
Dosage Compensation in the African Malaria Mosquito Anopheles gambiae. 2016-01-18 Graham Rose
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Genome Biology and Evolution
IL-36R signalling activates intestinal epithelial cells and fibroblasts and promotes mucosal healing in vivo. 2016-01-18 Stefan Wirtz Kristina Scheibe
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Dual RNA-seq unveils noncoding RNA functions in host–pathogen interactions 2016-01-20 Konrad Förstner
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Nature
Using high-throughput sequencing transcriptome data for INDEL detection: challenges for cancer drug discovery. 2016-01-20 Gabriel Wajnberg Fabio Passetti Expert Opinion on Drug Discovery
Identification of novel noncoding transcripts in telomerase-negative yeast using RNA-seq. 2016-01-20 David Zappulla Rachel O Niederer
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Scientific Reports
Cross-platform normalization of microarray and RNA-seq data for machine learning applications 2016-01-21 Casey S. Greene Jeffrey A Thompson
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PeerJ
Hepatic transcriptomic and metabolic responses of hybrid striped bass (Morone saxatilis×Morone chrysops) to acute and chronic hypoxic insult. 2016-01-21 Eric Peatman Benjamin H Beck
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Social defeat leads to changes in the endocannabinoid system: An overexpression of calreticulin and motor impairment in mice. 2016-01-24 Vincenzo Di Marzo J Tomas-Roig
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Behavioural Brain Research
Highly efficient lipid production in the green alga Parachlorella kessleri: draft genome and transcriptome endorsed by whole-cell 3D ultrastructure 2016-01-25 Masahira Hattori Shuhei Ota
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Biotechnology for Biofuels
A survey of best practices for RNA-seq data analysis 2016-01-26 Ana Conesa
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Genome Biology
DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments. 2016-01-27 Jie Yao Feinan Wu
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Journal of Visualized Experiments
Gene expression under thermal stress varies across a geographical range expansion front. 2016-01-28 Rachael Y. Dudaniec
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Molecular Ecology
RiboGalaxy: A browser based platform for the alignment, analysis and visualization of ribosome profiling data. 2016-01-29 Vimalkumar Velayudhan
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RNA Biology
Proteomic and Genomic Analyses of the Rvb1 and Rvb2 Interaction Network upon Deletion of R2TP Complex Components 2016-02-01 Laurence Florens Mahadevan Lakshminarasimhan
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Molecular & Cellular Proteomics
Transcriptome Analysis of Murine Olfactory Sensory Neurons during Development Using Single Cell RNA-Seq. 2016-02-02 Hanns Hatt
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Chemical Senses
Cancer-associated SF3B1 mutations affect alternative splicing by promoting alternative branchpoint usage. 2016-02-04 Sophie Piperno-Neumann
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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
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Scientific Reports
Erratum to: Dynamics of gene silencing during X inactivation using allele-specific RNA-seq. 2016-02-05 Hendrik Marks Hindrik H D Kerstens
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Genome Biology
New insights into the Plasmodium vivax transcriptome using RNA-Seq. 2016-02-09 Bruce Russell
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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
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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
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Scientific Reports
Selective amplification and sequencing of cyclic phosphate-containing RNAs by the cP-RNA-seq method. 2016-02-11 Yohei Kirino Shozo Honda
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Nature Protocols
Expression Profiling of Macrophages Reveals Multiple Populations with Distinct Biological Roles in an Immunocompetent Orthotopic Model of Lung Cancer 2016-02-12 Vinod Yadav
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Journal of Immunology
Single-cell transcriptome analysis of endometrial tissue. 2016-02-13 Juha Kere
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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
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Oncotarget
Extreme Hypoxic Conditions Induce Selective Molecular Responses and Metabolic Reset in Detached Apple Fruit. 2016-02-16 Leonardo Tenori Dubravka Cukrov
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Frontiers in Plant Science
Classification of low quality cells from single-cell RNA-seq data 2016-02-17 Aleksandra A Kolodziejczyk
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Genome Biology
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
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The Plant Cell
Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons 2016-02-18 Jennifer Erwin Suguna Rani Krishnaswami
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Nature Protocols
Hemocytome: deep sequencing analysis of mosquito blood cells in Indian malarial vector Anopheles stephensi. 2016-02-22 Rajnikant Dixit Tina Thomas
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RNA-seq analysis of clinical-grade osteochondral allografts reveals activation of early response genes. 2016-02-22 A. Noelle Larson Yang Lin
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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
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Nucleic Acids Research
Enhancer methylation dynamics contribute to cancer plasticity and patient mortality. 2016-02-23 Yankel Gabet Rachel E Bell
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Genome Research
Nitric oxide release from nitro-fatty acids in Arabidopsis roots. 2016-02-24 Francisco J. Corpas Capilla Mata-Pérez
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Isolation of the protein and RNA content of active sites of transcription from mammalian cells. 2016-02-25 Argyris Papantonis
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Nature Protocols
Transcriptional signature induced by a metastasis-promoting c-Src mutant in a human breast cell line. 2016-02-26 Mathias Heikenwalder Felix Broecker
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FEBS Journal
TRX-1 Regulates SKN-1 Nuclear Localization Cell Non-autonomously in Caenorhabditis elegans. 2016-02-26 Peter Swoboda
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Genetics
Overlapping cell population expression profiling and regulatory inference in C. elegans. 2016-02-29 Arjun Raj Joshua Burdick
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Expression Analysis Highlights AXL as a Candidate Zika Virus Entry Receptor in Neural Stem Cells 2016-03 Carmen Sandoval-Espinosa Tomasz J. Nowakowski
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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
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Journal of Virology
Genome-Wide Profiles of Extra-cranial Malignant Rhabdoid Tumors Reveal Heterogeneity and Dysregulated Developmental Pathways. 2016-03-01 Andrew Mungall Hye-Jung E Chun
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Transcriptional profiling of subcutaneous adipose tissue in Italian Large White pigs divergent for backfat thickness. 2016-03-01 Paolo Zambonelli E Gaffo
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Animal Genetics
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
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Scientific Reports
De novo assembly and comparative transcriptome analysis of Euglena gracilis in response to anaerobic conditions 2016-03-03 Takanori Maruta
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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
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Genome Biology and Evolution
Early alterations on photosynthesis-related parameters in Chlamydomonas reinhardtii cells exposed to atrazine: A multiple approach study. 2016-03-04 Marta Seoane
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Genomic and transcriptomic analysis of the streptomycin-dependent Mycobacterium tuberculosis strain 18b. 2016-03-05 Jérémie Piton Andrej Benjak
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Spermatogenesis Drives Rapid Gene Creation and Masculinization of the X Chromosome in Stalk-Eyed Flies (Diopsidae). 2016-03-06 Josephine A Reinhardt
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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 Vieira
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PLoS ONE
Comparative analysis of human and mouse transcriptomes of Th17 cell priming. 2016-03-07 Brigitta Stockinger Soile Tuomela
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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
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Engineering EMT using 3D micro-scaffold to promote hepatic functions for drug hepatotoxicity evaluation. 2016-03-09 Chenyu Huang Jingyu Wang
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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
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PLoS ONE
Gene expression changes in damaged osteoarthritic cartilage identify a signature of non-chondrogenic and mechanical responses 2016-03-10 Jean-Marc Schwartz S L Dunn
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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
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Integrating RNA-seq and ChIP-seq data to characterize long non-coding RNAs in Drosophila melanogaster 2016-03-11 Fang-Hua Chu
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BMC Genomics
The Ess/Type VII secretion system of Staphylococcus aureus shows unexpected genetic diversity. 2016-03-11 Catriona P Harkins Ben Warne
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miR2118-triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species. 2016-03-12 Francois Sabot
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Transcriptional profiling of Klebsiella pneumoniae defines signatures for planktonic, sessile and biofilm-dispersed cells 2016-03-15 Damien Balestrino Cyril Guilhen
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BMC Genomics
Exploring the surfaceome of Ewing sarcoma identifies a new and unique therapeutic target 2016-03-15 Lucy F Stead
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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
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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
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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
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Genes, Chromosomes and Cancer
Genome-wide analysis of dorsal and ventral transcriptomes of the Xenopus laevis gastrula. 2016-03-23 Edward M. De Robertis Yi Ding
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Developmental Biology
Role of miRNAs and alternative mRNA 3'-end cleavage and polyadenylation of their mRNA targets in cardiomyocyte hypertrophy. 2016-03-23 Traude H. Beilharz
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Biochimica et Biophysica Acta
Transcriptomic and epigenomic characterization of the developing bat wing. 2016-03-28 Nicola Illing Walter L Eckalbar
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Nature Genetics
Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes. 2016-03-29 Roberto Galizi
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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
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Nature Communications
Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants. 2016-03-31 Igor V Grigoriev
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BMC Genomics
Transcriptome Analysis of Differentially Expressed Genes Provides Insight into Stolon Formation in Tulipa edulis 2016-03-31 Qiaosheng Guo Yuanyuan Miao
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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
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq 2016-04-01 Aviv Regev
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Science
Near-optimal probabilistic RNA-seq quantification. 2016-04-04 Lior Pachter
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Comparison of syncytiotrophoblast generated from human embryonic stem cells and from term placentas 2016-04-05 Yoel Sadovsky Shinichiro Yabe
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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 Sophie Petropoulos
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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
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Cancer Research
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 Yukio Nakamura
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Refined Pichia pastoris reference genome sequence. 2016-04-12 Ruth Birner-Gruenberger Lukas Sturmberger
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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
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Beyond comparisons of means: understanding changes in gene expression at the single-cell level. 2016-04-15 John C Marioni Catalina A Vallejos
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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
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EBioMedicine
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
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Infection and Immunity
Nuclear RNA-seq of single neurons reveals molecular signatures of activation 2016-04-19 Carolyn O'Connor
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Nature Communications
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
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Molecular Ecology
Trisomy 21 Alters DNA Methylation in Parent-of-Origin-Dependent and -Independent Manners. 2016-04-21 Bruna Lancia Zampieri
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PLoS ONE
Dysregulation of miRNA-9 in a Subset of Schizophrenia Patient-Derived Neural Progenitor Cells 2016-04-21 Manuel Mattheisen
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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
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International Journal for Parasitology
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
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PLoS ONE
Survey of cryptic unstable transcripts in yeast. 2016-04-26 Robin Dowell Jessica M Vera BMC Genomics
A spectrum of CodY activities drives metabolic reorganization and virulence gene expression in Staphylococcus aureus. 2016-04-26 Nicholas R Waters David J Samuels
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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
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Genome Biology
CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. 2016-04-28 Aviv Regev Tamar Hashimshony
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Genome Biology
RNA-sequencing study of peripheral blood monocytes in chronic periodontitis 2016-05-01 Melody Baddoo
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Wishbone identifies bifurcating developmental trajectories from single-cell data. 2016-05-02 Dana Pe'er Manu Setty
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Nature Biotechnology
Characterization of novel Bovine Leukemia Virus (BLV) antisense transcripts by deep sequencing reveals constitutive expression in tumors and transcriptional interaction with viral microRNAs. 2016-05-03 Anne Van den Broeke
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Candidate gene networks and blood biomarkers of methamphetamine-associated psychosis: an integrative RNA-sequencing report. 2016-05-10 Dan J. Stein
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Targeting super-enhancer-associated oncogenes in oesophageal squamous cell carcinoma. 2016-05-10 Ling-Wen Ding
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Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation 2016-05-12 Tapio Lönnberg
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Genome Biology
An updated human snoRNAome. 2016-05-12 Mihaela Zavolan
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Nucleic Acids Research
The transcriptome of mouse central nervous system myelin. 2016-05-13 Sudhir Thakurela
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Scientific Reports
Polycomb repressive complex 1 controls uterine decidualization. 2016-05-16 Artem Barski
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Scientific Reports
Molecular Mechanisms of Malignant Transformation by Low Dose Cadmium in Normal Human Bronchial Epithelial Cells. 2016-05-17 Steven Shen Laura Cartularo
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PLoS ONE
De Novo Sequencing and Transcriptome Analysis of Pleurotus eryngii subsp. tuoliensis (Bailinggu) Mycelia in Response to Cold Stimulation. 2016-05-17 Songnian Hu Yong-Ping Fu
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The Proteasome Stress Regulon Is Controlled by a Pair of NAC Transcription Factors in Arabidopsis. 2016-05-18 Richard D Vierstra Nicholas P Gladman
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Identification of new regulators of embryonic patterning and morphogenesis in Xenopus gastrulae by RNA sequencing. 2016-05-18 David K. Crossman Ivan K Popov
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Developmental Biology
Group II mGluRs suppress hyperexcitability in mouse and human nociceptors. 2016-05-21 Pradipta R Ray Steve Davidson
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Identification of host genes leading to West Nile virus encephalitis in mice brain using RNA-seq analysis. 2016-05-23 Mukesh Kumar Mahdi Belcaid
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Scientific Reports
Comparative transcriptomics of stickleback immune gene responses upon infection by two helminth parasites, Diplostomum pseudospathaceum and Schistocephalus solidus. 2016-05-23 Erich Bornberg-Bauer David Haase
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Zoology
Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts 2016-05-26 Lior Pachter Vasilis Ntranos
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Genome Biology
Hsf1 and Hsp90 orchestrate temperature-dependent global transcriptional remodelling and chromatin architecture in Candida albicans. 2016-05-26 Christina A Cuomo Michelle D Leach
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Nature Communications
An atlas of gene expression and gene co-regulation in the human retina. 2016-05-27 Luisa Cutillo
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Nucleic Acids Research
Landscape of tumor-infiltrating T cell repertoire of human cancers 2016-05-30 Nir Hacohen Bo Li
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Nature Genetics
The IL-4/STAT6 signaling axis establishes a conserved microRNA signature in human and mouse macrophages regulating cell survival via miR-342-3p 2016-05-31 Cei Abreu-Goodger Zsolt Czimmerer
Tamas Varga
Mate Kiss
Cesaré Ovando Vázquez
Quang Minh Doan-Xuan
Dominik Rückerl
Sudhir Gopal Tattikota
Xin Yan
Zsuzsanna S Nagy
Bence Daniel
Szilard Poliska
Attila Horvath
Gergely Nagy
Eva Varallyay
Matthew N Poy
Judith E Allen
Zsolt Bacso
Laszlo Nagy
Genome Medicine
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 2016-05-31 Darren Wong R Lopez Gutierrez
N Dimopoulos
G A Gambetta
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BMC Genomics
Diversity of ABC transporter genes across the plant kingdom and their potential utility in biotechnology. 2016-05-31 Gane Ka-Shu Wong
Michael Melkonian
Caroline Rempe
Thomas S Lane
Jack Davitt
Margaret E Staton
Yanhui Peng
Douglas Edward Soltis
Michael Melkonian
Michael Deyholos
James H Leebens-Mack
Mark Chase
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
BMC Biotechnology
Sex differences in DNA methylation and expression in zebrafish brain: a test of an extended 'male sex drive' hypothesis. 2016-05-31 Julia A. Horsfield
Shinichi Nakagawa
Aniruddha Chatterjee
Malgorzata Lagisz
Euan J Rodger
Li Zhen
Peter A Stockwell
Elizabeth J Duncan
Justin Jeyakani
Sinnakaruppan Mathavan
Yuichi Ozaki
Gene
ZFP57 maintains the parent-of-origin-specific expression of the imprinted genes and differentially affects non-imprinted targets in mouse embryonic stem cells 2016-06-01 Kristian Helin
Marco Cammisa
Gaetano Verde
Aditya Sankar
Vincenzo Riso
Harpreet Kukreja
Zahra Anvar
Angela Sparago
Basilia Acurzio
Shraddha Lad
Enza Lonardo
Robert Feil
Annalisa Fico
Claudia Angelini
Giovanna Grimaldi
Andrea Riccio
Nucleic Acids Research
Identification of interleukin genes in Pogona vitticeps using a de novo transcriptome assembly from RNA-seq data. 2016-06-02 Janine E. Deakin
Kristine Hardy
Alexie Papanicolaou
Stephen D. Sarre
Alexandra Livernois
Renae Domaschenz
Arthur Georges
Sudha Rao
Tariq Ezaz
Immunogenetics
Insights into the transcriptional and translational mechanisms of linear organellar chromosomes in the box jellyfish Alatina alata (Cnidaria: Medusozoa: Cubozoa) 2016-06-06 Allen Collins Ehsan Kayal
Bastian Bentlage
RNA Biology
Genome-wide imputation study identifies novel HLA locus for pulmonary fibrosis and potential role for auto-immunity in fibrotic idiopathic interstitial pneumonia. 2016-06-07 Mark Lathrop
Diana Zelenika
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
Naftali Kaminski
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
Diana Zelenika
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
BMC Genetics
Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq 2016-06-08 Moritz Mall
Barbara Treutlein
Qian Yi Lee
J Gray Camp
Winston Koh
Seyed Ali Mohammad Shariati
Sopheak Sim
Norma F Neff
Jan M Skotheim
Marius Wernig
Stephen R Quake
Nature
Reduced Expression of Histone Methyltransferases KMT2C and KMT2D Correlates with Improved Outcome in Pancreatic Ductal Adenocarcinoma 2016-06-08 Frances R Balkwill
Jun Wang
Claude Chelala
Joshua B N Dawkins
Eleni Maniati
James A Heward
Lola Koniali
Hemant M Kocher
Sarah A Martin
Jude Fitzgibbon
Richard P Grose
Cancer Research
Transcriptomic analysis illuminates genes involved in chlorophyll synthesis after nitrogen starvation in Acaryochloris sp. CCMEE 5410. 2016-06-09 Gautam Dantas Aki Yoneda
Bruce J Wittmann
Jeremy D King
Robert E Blankenship
Photosynthesis Research
Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research 2016-06-11 Anand Swaroop Vijender Chaitankar
Gökhan Karakülah
Rinki Ratnapriya
Felipe O Giuste
Matthew J Brooks
Progress in Retinal and Eye Research
Evolutionary origin and functional divergence of totipotent cell homeobox genes in eutherian mammals 2016-06-13 Juan A. Bernal
Ferdinand Marlétaz
Ignacio Maeso
Thomas L Dunwell
Manuel Irimia
Chris D R Wyatt
Borbála Vető
Shan Quah
Peter W H Holland
BMC Biology
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
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 V. Biankin
John P Neoptolemos
Paola Martinelli
Enrique Carrillo-de Santa Pau
Trevor Cox
Bruno Sainz
Nelson Dusetti
William Greenhalf
Lorenzo Rinaldi
Eithne Costello
Paula Ghaneh
Núria Malats
Markus Büchler
Juan Iovanna
Francisco X Real
Gut
Hypoxia-related microRNA-210 is a diagnostic marker for discriminating osteoblastoma and osteosarcoma. 2016-06-21 Anne-Marie Cleton-Jansen Scott M Riester
Jorge Torres-Mora
Amel Dudakovic
Emily T Camilleri
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
Annalise N Larson
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
Hanns Hatt
Oncotarget
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
Sarah Ayling
Daniel Barrell
Valery Curwen
Fergal J Martin
Michael Schuster
Y Amy Tang
Jan-Hinnerk Vogel
Simon White
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 Mara Maldotti
Danny Incarnato
Francesco Neri
Anna Krepelova
Stefania Rapelli
Francesca Anselmi
Caterina Parlato
Giulia Basile
Daniela Dettori
Salvatore Oliviero
Biochimica et Biophysica Acta
Integrating transcriptome and proteome profiling: Strategies and applications. 2016-06-25 Dhirendra Kumar Gourja Bansal
Ankita Narang
Trayambak Basak
Tahseen Abbas
Debasis Dash
Proteomics
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 J Bonder
Lude Franke
Koen F Dekkers
Roderick C Slieker
Jenny van Dongen
Rick Jansen
Maarten van Iterson
Matthijs H Moed
Michiel van Galen
Hailiang Mei
Leonard H van den Berg
Joris Deelen
Diana van Heemst
Albert Hofman
Jouke J Hottenga
Carla J H van der Kallen
Casper G Schalkwijk
Coen D A Stehouwer
Ettje F Tigchelaar
Alexandra Zhernakova
Peter A C 't Hoen
Joyce van Meurs
Dorret I Boomsma
Marleen M J van Greevenbroek
Jan H Veldink
BIOS Consortium
Erik W van Zwet
P Eline Slagboom
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
Kaarel Krjutškov
Paula Hakala
Anna-Elina Lehesjoki
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
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
Malachi Griffith
Obi L Griffith
Matthew J Christopher
Jeffery M Klco
Avinash Ramu
Tamara L Lamprecht
Alex H Wagner
Robert Lesurf
Jasreet Hundal
Jin Zhang
Nicholas C Spies
David E Larson
Sharon E Heath
Catrina Fronick
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 Katarzyna B Hooks
Samina Naseeb
Steven Parker
Daniela Delneri
Genetics
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
Helene Thygesen
Walter Gregory
David R Westhead
Pim J French
Martin J Van Den Bent
Sean E Lawler
Molecular Oncology
The synovial microenvironment of osteoarthritic joints alters RNA-seq expression profiles of human primary articular chondrocytes. 2016-07-01 A. 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
Transcriptome sequencing reveals aberrant alternative splicing in Huntington's disease. 2016-07-04 Maurice A Curtis Lan Lin
Juw Won Park
Shyam Ramachandran
Yida Zhang
Yu-Ting Tseng
Shihao Shen
Henry J Waldvogel
Richard L M Faull
Juan C Troncoso
Olga Pletnikova
Christopher A Ross
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 Gitte H Bruun
Thomas K Doktor
Jonas Borch-Jensen
Akio Masuda
Adrian R Krainer
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 Aroa Suárez-Vega
Beatriz Gutiérrez-Gil
Christophe Klopp
Gwenola Tosser-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 Mélanie A C Ikeh
Stavroula L Kastora
Alison M Day
Carmen M Herrero-de-Dios
Emma Tarrant
Kevin J Waldron
A Peter Banks
Judith M Bain
David Lydall
Elizabeth A Veal
Donna M MacCallum
Lars P Erwig
Alistair J P Brown
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
Functional characterization of the 12p12.1 renal cancer-susceptibility locus implicates BHLHE41. 2016-07-07 Mitchell Machiela Pierre Bigot
Leandro M Colli
Lea Jessop
Timothy A Myers
Julie Carrouget
Sarah Wagner
David Roberson
Caroline Eymerit
Daniel Henrion
Stephen J Chanock
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 Michael J Strong
Eugene Blanchard
Zhen Lin
Cindy A Morris
Melody Baddoo
Christopher M Taylor
Marcus L Ware
Erik K Flemington
Acta neuropathologica communications
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
Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNA-Seq. 2016-07-14 Barbara Treutlein
Thomas C. Südhof
Marc V Fuccillo
Ozgun Gokce
Geoff Stanley
Norma F Neff
Gray J Camp
Robert C Malenka
Patrick E Rothwell
Stephen R Quake
Cell Reports
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
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
Frauke Zipp
Esther Witsch
Journal of Neuroimmune Pharmacology
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 K. Varshney
Wei Chen
Qiuming Yao
Gunvant B Patil
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
Contextual fear conditioning induces differential alternative splicing. 2016-07-19 Ted Abel Shane G Poplawski
Lucia Peixoto
Giulia S Porcari
Mathieu E Wimmer
Anna G McNally
Keiko Mizuno
K Peter Giese
Snehajyoti Chatterjee
John N Koberstein
Davide Risso
Terence P Speed
Neurobiology of Learning and Memory
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 Dominik P Waluk
Gila Zur
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
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 M. Blüher A Weingarten
L Turchetti
K Krohn
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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
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
Aviv Regev
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
Yuichi Morozumi
Fayçal Boussouar
Minjia Tan
Mahya Jamshidikia
Gozde Colak
Huang He
Litong Nie
Carlo Petosa
Maud de Dieuleveult
Sandrine Curtet
Anne-Laure Vitte
Clothilde Rabatel
Alexandra Debernardi
Els Verhoeyen
Anouk Emadali
Norbert Schweifer
Davide Gianni
Marta Gut
Philippe Guardiola
Sophie Rousseaux
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
Victoria Hore
Alfonso Buil
Julian Knight
Mark I McCarthy
Nature Genetics
Epigenetic remodeling regulates transcriptional changes between ovarian cancer and benign precursors 2016-08-01 John Quackenbush
Emily MacDuffie
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
JCI insight
Identification and Validation of PCAT14 as Prognostic Biomarker in Prostate Cancer. 2016-08-01 Marcin Cieślik 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
Neoplasia
142 Genetic and Nongenetic Determinants of Cellular Architecture in IDH1-Mutant Oligodendrogliomas and Astrocytomas Using Single-Cell Transcriptome Analysis. 2016-08-01 Aviv Regev
Itay Tirosh
Andrew Sean Venteicher
Itay Tirosh
Christine Hebert
Leah Escalante
Robert L Martuza
Brian V Nahed
William T Curry
Daniel P Cahill
Bradley Bernstein
David N Louis
Aviv Regev
Mario Suva
Neurosurgery
Strong down-regulation of glycophorin genes: A host defense mechanism against rotavirus infection. 2016-08-01 Alberto Gómez-Carballa Antonio Salas
Guillermo Marco-Puche
Juan Carlos Triviño
Miriam Cebey-López
Irene Rivero-Calle
Lucía Vilanova-Trillo
Carmen Rodríguez-Tenreiro
José Gómez-Rial
Federico Martinón-Torres
Infection, Genetics and Evolution
Optimized design and analysis of preclinical intervention studies in vivo 2016-08-02 Jukka Westermarck Teemu D Laajala
Mikael Jumppanen
Riikka Huhtaniemi
Vidal Fey
Amanpreet Kaur
Matias Knuuttila
Eija Aho
Riikka Oksala
Sari Mäkelä
Matti Poutanen
Tero Aittokallio
Scientific Reports
The (in)complete organelle genome: exploring the use and nonuse of available technologies for characterizing mitochondrial and plastid chromosomes. 2016-08-02 David Roy Smith Matheus Sanitá Lima
Laura C Woods
Matthew W Cartwright
Molecular Ecology Resources
Hierarchical RNA Processing Is Required for Mitochondrial Ribosome Assembly. 2016-08-03 Oliver Rackham 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
Nils-Göran Larsson
Aleksandra Filipovska
Cell Reports
microRNA-132/212 deficiency enhances Aβ production and senile plaque deposition in Alzheimer's disease triple transgenic mice. 2016-08-03 Maxime P Vallée
Sébastien S. Hébert
Julia Hernandez-Rapp
Sara Rainone
Claudia Goupil
Véronique Dorval
Pascal Y Smith
Martine Saint-Pierre
Emmanuel Planel
Arnaud Droit
Frédéric Calon
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Scientific Reports
Modulatory Effects of Sex Steroids Progesterone and Estradiol on Odorant Evoked Responses in Olfactory Receptor Neurons. 2016-08-05 Hanns Hatt
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PLoS ONE
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). 2016-08-05 Michael A. Skinner Efstathios S Giotis
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Veterinary Research
RNA-seq analysis identifies key long non-coding RNAs connected to the pathogenesis of alcohol-associated head and neck squamous cell carcinoma. 2016-08-08 Jessica Wang-Rodriguez Vicky Yu
Pranav Singh
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Oncology Letters
Spliced synthetic genes as internal controls in RNA sequencing experiments. 2016-08-08 Lars K. Nielsen
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Nature Methods
Transcriptional Profiling of Cultured, Embryonic Epicardial Cells Identifies Novel Genes and Signaling Pathways Regulated by TGFβR3 In Vitro. 2016-08-09 Daniel M DeLaughter Daniel M DeLaughter
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PLoS ONE
Ordered chromatin changes and human X chromosome reactivation by cell fusion-mediated pluripotent reprogramming. 2016-08-10 Tatyana B Nesterova
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Nature Communications
Metronomic cyclophosphamide activation of anti-tumor immunity: tumor model, mouse host, and drug schedule dependence of gene responses and their upstream regulators. 2016-08-11 David J Waxman Junjie Wu
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BMC Cancer
Comparative transcriptome profiling of resistant and susceptible rice genotypes in response to the seedborne pathogen Fusarium fujikuroi. 2016-08-11 Davide Spadaro Slavica Matić
Paolo Bagnaresi
Chiara Biselli
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BMC Genomics
Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta. 2016-08-11 Robert M. Waterhouse
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Insect Biochemistry and Molecular Biology
Peromyscus transcriptomics: Understanding adaptation and gene expression plasticity within and between species of deer mice. 2016-08-12 Jason Munshi-South Jonathan L Richardson Seminars in Cell & Developmental Biology
Proteolysis-a characteristic of tumor-initiating cells in murine metastatic breast cancer. 2016-08-16 Marie Follo
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Oncotarget
Critical re-evaluation of neuroglobin expression reveals conserved patterns among mammals. 2016-08-16 Thorsten Burmester Andrej Fabrizius
Daniel Andre
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Neuroscience
The Spectrum and Regulatory Landscape of Intestinal Innate Lymphoid Cells Are Shaped by the Microbiome. 2016-08-17 Hadas Keren-Shaul Meital Gury-BenAri
Christoph A Thaiss
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Assaf Weiner
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Cell
Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm. 2016-08-17 Christina Kendziorski Li-Fang Chu
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Genome Biology
Integrative Genomics Outlines a Biphasic Glucose Response and a ChREBP-RORγ Axis Regulating Proliferation in β Cells. 2016-08-17 Jens Juul Holst
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Cell Reports
C. elegans Stress-Induced Sleep Emerges from the Collective Action of Multiple Neuropeptides. 2016-08-17 Han Wang
Erich M Schwarz
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Current Biology
Paternal chronic colitis causes epigenetic inheritance of susceptibility to colitis. 2016-08-19 Ole Ammerpohl Markus Tschurtschenthaler
Priyadarshini Kachroo
Femke-Anouska Heinsen
Timon Erik Adolph
Malte Christoph Rühlemann
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Scientific Reports
RNA-sequencing of a mouse-model of spinal muscular atrophy reveals tissue-wide changes in splicing of U12-dependent introns. 2016-08-23 Brage Storstein Andresen Thomas Koed Doktor
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Nucleic Acids Research
Identification of novel regulators of developmental hematopoiesis using Endoglin regulatory elements as molecular probes. 2016-08-23 Rahul Roychoudhuri
Jason Wong
Rabab Nasrallah
Eva M Fast
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Roshana Thambyrajah
Ashwin Unnikrishnan
Julie Thoms
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Thomas Willnow
Bertie Göttgens
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Blood
An integrative transcriptomic atlas of organogenesis in human embryos. 2016-08-24 Dave Gerrard Andrew A Berry
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eLife
Genomewide Association Study of African Children Identifies Association of SCHIP1 and PDE8A with Facial Size and Shape. 2016-08-25 Washington Mio
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Joanne B Cole
Mange Manyama
Emmanuel Kimwaga
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Tracey M Ferrara
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Washington Mio
Michaela Prochazkova
Trevor Williams
Hong Li
Kenneth L Jones
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PLOS Genetics
DNA Methylation Profiling of Uniparental Disomy Subjects Provides a Map of Parental Epigenetic Bias in the Human Genome 2016-08-25 Karin Buiting Ricky S Joshi
Paras Garg
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Thomas Eggermann
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American Journal of Human Genetics
Expression dynamics, relationships, and transcriptional regulations of diverse transcripts in mouse spermatogenic cells 2016-08-25 Bo Wen Xiwen Lin
Miao Han
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RNA Biology
Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach 2016-08-26 Feixiong Cheng
Bairong Shen
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BMC Systems Biology
Inferring expressed genes by whole-genome sequencing of plasma DNA. 2016-08-29 Peter Ulz
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Nature Genetics
Characterization of non-olfactory GPCRs in human sperm with a focus on GPR18 2016-08-30 Janine Altmüller
Hanns Hatt
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Caroline Flegel
Felix Vogel
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Hanns Hatt
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Scientific Reports
Chromatin recruitment of activated AMPK drives fasting response genes co-controlled by GR and PPARα. 2016-08-30 Bart Staels
Réjane Paumelle
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Sandrine Caron
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Lode De Cauwer
Jonathan Thommis
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Nucleic Acids Research
A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor. 2016-08-31 John C Marioni
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Induction of Activating Transcription Factor 3 Is Associated with Cisplatin Responsiveness in Non-Small Cell Lung Carcinoma Cells. 2016-09-01 Theodore J Perkins Jair Bar
Mohamed S Hasim
Tabassom Baghai
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Neoplasia
Signaling transcript profile of the asexual intraerythrocytic development cycle of Plasmodium falciparum induced by melatonin and cAMP. 2016-09-01 Andrei Rozanski Wânia Rezende Lima
Giulliana Tessarin-Almeida
Kleber S Parreira
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Genes & Cancer
ANGIOGENES: knowledge database for protein-coding and noncoding RNA genes in endothelial cells. 2016-09-01 Stefanie Dimmeler
Tyler Weirick
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David John
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Scientific Reports
Mammary Tumor-Associated RNAs Impact Tumor Cell Proliferation, Invasion, and Migration. 2016-09-01 Sarah Diermeier Kung-Chi Chang
Susan M Freier
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Cell Reports
Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos. 2016-09-01 Sten Linnarsson Sophie Petropoulos
Daniel Edsgärd
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Qiaolin Deng
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Cell
A full-body transcriptome and proteome resource for the European common carp. 2016-09-02 Hans J Jansen
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BMC Genomics
Pro-invasive Effect of Proto-oncogene PBF Is Modulated by an Interaction with Cortactin. 2016-09-07 Vicki E Smith Rachel J Watkins
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Hannah R Nieto
Ujjal Mallick
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The Journal of Clinical Endocrinology and Metabolism
TNIP2 is a Hub Protein in the NF-κB Network with Both Protein and RNA Mediated Interactions. 2016-09-08 Gaye L Hattem
Michael P. Washburn
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Molecular & Cellular Proteomics
Condition-dependent co-regulation of genomic clusters of virulence factors in the grapevine trunk pathogen Neofusicoccum parvum. 2016-09-08 Dario Cantu Mélanie Massonnet
Abraham Morales-Cruz
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Molecular Plant Pathology
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
Matthias Barann
Thomas Wieland
Suzana Ezquina
Marc R Friedländer
Manuel A Rivas
Anna Esteve-Codina
GEUVADIS Consortium
Tim M Strom
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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
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Proceedings of the National Academy of Sciences of the United States of America
Zinc finger protein 407 overexpression upregulates PPAR target gene expression and improves glucose homeostasis in mice. 2016-09-13 Dave Bridges
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Li Wang
Erin J Stephenson
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American Journal of Physiology - Endocrinology and Metabolism
MdMyb93 is a regulator of suberin deposition in russeted apple fruit skins. 2016-09-15 Marc Boutry Sylvain Legay
Gea Guerriero
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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 Feng Wang
JongDae Shin
Jeremy M Shea
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eLife
Transcriptomic profiles of the upper olfactory rosette in cultured and wild Senegalese sole (Solea senegalensis) males. 2016-09-20 Elvira Fatsini
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Single-Cell Transcriptomics Bioinformatics and Computational Challenges 2016-09-21 Lana Garmire Olivier B. Poirion
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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
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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
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Cyrielle Hou
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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
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Archives of Microbiology
A Global Analysis of the Polygalacturonase Gene Family in Soybean (Glycine max). 2016-09-22 Fanjiang Kong Feifei Wang
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PLoS ONE
Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms. 2016-09-22 Cornelia M. van Duijn
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Dorret I Boomsma
BIOS consortium
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Genome Biology
A perspective on single cell behavior during infection 2016-09-22 Roi Avraham Deborah T Hung Gut microbes
Pre-mRNA splicing repression triggers abiotic stress signaling in plants. 2016-09-24 Stefan T Arold
Sahar Alshareef
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The Plant Journal
Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development 2016-09-26 Svante Pääbo
Farhath Badsha
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eLife
Protein C receptor (PROCR) is a negative regulator of Th17 pathogenicity. 2016-09-26 Aviv Regev Yasuhiro Kishi
Takaaki Kondo
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Journal of Experimental Medicine
Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq. 2016-09-26 Rickard Sandberg Björn Reinius
Jeff E Mold
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Nature Genetics
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
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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
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PLoS ONE
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
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Stem Cells Translational Medicine
Downregulation of sphingosine kinase-1 induces protective tumor immunity by promoting M1 macrophage response in melanoma. 2016-09-30 Nathalie Andrieu-Abadie Marguerite Mrad
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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
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PLOS Neglected Tropical Diseases
Profiling of adhesive-related genes in the freshwater cnidarian Hydra magnipapillata by transcriptomics and proteomics. 2016-10-01 Peter Ladurner Marcelo Rodrigues
Thomas Ostermann
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Biofouling
Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells. 2016-10-01 Sten Linnarsson
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Cell
Correlation of an epigenetic mitotic clock with cancer risk 2016-10-03 Diana Kuh
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Genome Biology
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
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Molecular Psychiatry
Ethylene responsive transcription factor ERF109 retards PCD and improves salt tolerance in plant 2016-10-06 Sherif Edris Ahmed Bahieldin
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Magdy A Al-Kordy
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BMC Plant Biology
Discovering Single Nucleotide Polymorphisms Regulating Human Gene Expression Using Allele Specific Expression from RNA-seq Data. 2016-10-07 Sagiv Shifman
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Genetics
The Molecular Circuit Regulating Tooth Development in Crocodilians. 2016-10-07 A Abdelhamid S Tsai
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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 Margareta D Pisarska
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Erica T Wang
Aaron J Mackey
Stephen S Rich
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Yii-der I Chen
Mark O Goodarzi
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Prenatal Diagnosis
Transcriptomic alterations in Sitophilus zeamais in response to allyl isothiocyanate fumigation. 2016-10-11 Xing Zhang Chao Zhang
Zhiqing Ma
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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
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David A Wheeler
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Blood
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
Timothy L Fitzgerald
Jiri Stiller
Paul J Berkman
John M Manners
Robert J Henry
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 Agata Stryjewska
Ruben Dries
Tim Pieters
Griet Verstappen
Andrea Conidi
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Annick Francis
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Wilfred F J van IJcken
Geert Berx
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Stem Cells
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
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Journal of Molecular and Cellular Cardiology
Global analysis of pre-mRNA subcellular localization following splicing inhibition by spliceostatin A. 2016-10-17 Daisuke Kaida
Maxwell Burroughs
Rei Yoshimoto
Masaaki Furuno
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Shohei Noma
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Minoru Yoshida
RNA
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
Elise P Salerno
Davide Bedognetti
Donna H Deacon
Sofia M Shea
Joel Pinczewski
Joseph M Obeid
Ena Wang
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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
Emily Hodge
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Charlotte K Billington
Sangita K Bhaker
Ma'en Obeidat
Erik Melén
Simon K Merid
Caroline Swan
Catherine Gowland
Carl P Nelson
Ceri E Stewart
Charlotte E Bolton
Iain Kilty
Anders Malarstig
Stuart G Parker
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
Loris De Cecco
Tiziana Triulzi
Sandra Romero-Cordoba
Elda Tagliabue
Andrea Balsari
Cell Cycle
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
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 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 Miguel Jesus Nunes Ramos
João Lucas Coito
Joana Fino
Jorge Cunha
Helena Silva
Patrícia Gomes de Almeida
Maria Manuela Ribeiro Costa
Sara Amâncio
Margarida Rocheta
Plant Molecular Biology
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
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
Developmental transcriptome of resting cell formation in Mycobacterium smegmatis. 2016-10-26 Hans-Joachim Mollenkopf Mu-Lu Wu
Martin Gengenbacher
Jade C S Chung
Swaine Lin Chen
Stefan H E Kaufmann
Thomas Dick
BMC Genomics
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
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Jason E McDermott
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Galya Orr
ACS Nano
Single-Cell Analysis Reveals a Close Relationship between Differentiating Dopamine and Subthalamic Nucleus Neuronal Lineages. 2016-10-27 Malin Parmar Nigel Kee
Nikolaos Volakakis
Agnete Kirkeby
Lina Dahl
Helena Storvall
Sara Nolbrant
Laura Lahti
Åsa K Björklund
Linda Gillberg
Eliza Joodmardi
Rickard Sandberg
Thomas Perlmann
Cell Stem Cell
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
Andrew S Venteicher
Christine Hebert
Leah E Escalante
Anoop P Patel
Keren Yizhak
Jonathan M Fisher
Christopher Rodman
Christopher Mount
Mariella G Filbin
Cyril Neftel
Niyati Desai
Jackson Nyman
Benjamin Izar
Christina C Luo
Joshua M Francis
Aanand A Patel
Maristela L Onozato
Nicolo Riggi
Kenneth J Livak
Dave Gennert
Brian V Nahed
William T Curry
Robert L Martuza
Ravindra Mylvaganam
A John Iafrate
Matthew P Frosch
Todd R Golub
Miguel N Rivera
Gad Getz
Orit Rozenblatt-Rosen
Michelle Monje
Bradley E Bernstein
David N Louis
Aviv Regev
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
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 Jan Provazník
Jana Schrenková
Veronika Urbanová
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
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
Bingshu E Chen
Wei Xu
David N Reisman
Clinical Cancer Research
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
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Christine E Seidman
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
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
Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella. 2016-11-14 Jörg Vogel Antoine-Emmanuel Saliba
Lei Li
Alexander J Westermann
Silke Appenzeller
Daphne A C Stapels
Leon N Schulte
Sophie Helaine
Nature Microbiology
Patterns of Transposable Element Expression and Insertion in Cancer. 2016-11-16 Lavanya Rishishwar Evan A Clayton
Lu Wang
Jianrong Wang
John F McDonald
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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
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
Cell culture-based profiling across mammals reveals DNA repair and metabolism as determinants of species longevity 2016-11-22 Vera Gorbunova Siming Ma
Akhil Upneja
Andrzej Galecki
Yi-Miau Tsai
Charles F Burant
Sasha Raskind
Quanwei Zhang
Zhengdong D Zhang
Andrei Seluanov
Clary B Clish
Richard A Miller
Vadim N Gladyshev
eLife
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
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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
Tobias Gerber
Edith Willscher
Henry Loeffler-Wirth
Lydia Hopp
Dirk Schadendorf
Manfred Schartl
Ulf Anderegg
Gray Camp
Hans Binder
Manfred Kunz
Oncotarget
A comprehensive approach to expression of L1 loci. 2016-11-28 Melody Baddoo 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
Erik K Flemington
Victoria P Belancio
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
A SLM2 Feedback Pathway Controls Cortical Network Activity and Mouse Behavior. 2016-12-01 Gavin Clowry
David J Elliott
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
Mauro Santibanez-Koref
Silvia Middei
Claudio Sette
Yoseph Barash
Mark O Cunningham
Cell Reports
The Lair: a resource for exploratory analysis of published RNA-Seq data. 2016-12-01 Lior Pachter
Harold Pimentel
Pascal Sturmfels
Nicolas Bray
Páll Melsted
BMC Bioinformatics
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 Matthias Lienhard
Sabrina Grasse
Jana Rolff
Steffen Frese
Uwe Schirmer
Michael Becker
Stefan Börno
Bernd Timmermann
Lukas Chavez
Holger Sültmann
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
Atray Dixit
Oren Parnas
Biyu Li
Charles P Fulco
Livnat Jerby-Arnon
Nemanja D Marjanovic
Danielle Dionne
Tyler Burks
Britt Adamson
Thomas M Norman
Jonathan S Weissman
Cell
A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response. 2016-12-01 Aviv Regev Britt Adamson
Thomas M Norman
Marco Jost
Min Y Cho
James K Nuñez
Yuwen Chen
Jacqueline E Villalta
Luke A Gilbert
Max A Horlbeck
Marco Y Hein
Ryan A Pak
Andrew N Gray
Carol A Gross
Atray Dixit
Oren Parnas
Jonathan S Weissman
Cell
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
Tushar D Bhagat
Yiyu Zou
Shizheng Huang
Jihwan Park
Matthew B Palmer
Caroline Hu
Weijuan Li
Niraj Shenoy
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
Yuanxin Xi
Ryan McCarthy
Kendra Allton
Kadir C Akdemir
Lalit R Patel
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
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 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
Zhandong Liu
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 J Bonder
Jenny van Dongen
Yang Li
Rick Jansen
Marian Beekman
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
Jouke J Hottenga
Coen D A Stehouwer
Carla J H van der Kallen
Casper G Schalkwijk
Alexandra Zhernakova
Ettje F Tigchelaar
Niek de Klein
Joris Deelen
Diana van Heemst
Leonard H van den Berg
Albert Hofman
André G Uitterlinden
Marleen M J van Greevenbroek
Jan H Veldink
Dorret I Boomsma
P Eline Slagboom
Morris A Swertz
Aaron Isaacs
Joyce B J van Meurs
Bastiaan T Heijmans
Peter A C 't Hoen
Nature Genetics
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
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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
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 Victor L Jensen
Stephen Carter
Anna A W M Sanders
Chunmei Li
Julie Kennedy
Tiffany A Timbers
Jerry Cai
Noemie Scheidel
Ryan D Morin
Michel R Leroux
Oliver E Blacque
PLOS Genetics
Cardiac inflammation in genetic dilated cardiomyopathy caused by MYBPC3 mutation. 2016-12-09 Sakthivel Sadayappan
Anil G. Jegga
Thomas L Lynch
Mohamed Ameen Ismahil
Michael J Zilliox
Christian Troidl
Sumanth D Prabhu
Journal of Molecular and Cellular Cardiology
Prediction and prioritization of neoantigens: integration of RNA sequencing data with whole-exome sequencing. 2016-12-13 Osamu Ohara Takahiro Karasaki
Kazuhiro Nagayama
Hideki Kuwano
Jun-Ichi Nitadori
Masaaki Sato
Masaki Anraku
Akihiro Hosoi
Hirokazu Matsushita
Masaki Takazawa
Jun Nakajima
Kazuhiro Kakimi
Cancer Science
Identification of the RNA Pyrophosphohydrolase RppH of Helicobacter pylori and Global Analysis of Its RNA Targets. 2016-12-14 Thorsten Bischler Ping-Kun Hsieh
Marcus Resch
Quansheng Liu
Hock Siew Tan
Patricia L Foley
Anika Hartleib
Cynthia M Sharma
Joel G Belasco
Journal of Biological Chemistry
Characterization of a TUTase/RNase complex required for Drosophila gametogenesis. 2016-12-14 Jiayu Wen Ching-Jung Lin
Fernando Bejarano
Fuqu Hu
Diane Bortolamiol-Becet
Lijuan Kan
Piero Sanfilippo
Eric C Lai
RNA
SLICE: determining cell differentiation and lineage based on single cell entropy. 2016-12-19 Erik L Bao Minzhe Guo
Michael Wagner
Jeffrey A Whitsett
Yan Xu
Nucleic Acids Research
Limb patterning genes and heterochronic development of the emu wing bud. 2016-12-20 Alicia Oshlack
Nadia M Davidson
Craig A. Smith
Peter G Farlie
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Claire Hirst
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EvoDevo
Molecular mechanisms underlying active desalination and low water permeability in the esophagus of eels acclimated to seawater. 2016-12-21 Wataru Iwasaki Yoshio Takei
Marty K-S Wong
Supriya Pipil
Haruka Ozaki
Yutaka Suzuki
Makoto Kusakabe
American Journal of Physiology - Regulatory, Integrative and Comparative Physiology
Logic programming to infer complex RNA expression patterns from RNA-seq data. 2016-12-22 Stefanie Dimmeler
Yuliya Ponomareva
Tyler Weirick
Shizuka Uchida
Giuseppe Militello
David John
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Briefings in Bioinformatics
Stable Binding of the Conserved Transcription Factor Grainy Head to its Target Genes Throughout Drosophila melanogaster Development. 2016-12-22 Tommy Kaplan Markus Nevil
Eliana R Bondra
Katharine N Schulz
Melissa M Harrison
Genetics
ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery. 2016-12-23 Vivek Krishnakumar
Erik S Ferlanti
Jason R Miller
Matthew Vaughn
Sergio Contrino
Chia-Yi Cheng
Irina Belyaeva
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Christopher D Town
Agnes P Chan
Plant and Cell Physiology
Derivation of marker gene signatures from human skin and their use in the interpretation of the transcriptional changes associated with dermatological disorders 2016-12-23 Thomas Freeman Barbara B Shih
Ajit J Nirmal
Denis J Headon
Arne N Akbar
Neil A Mabbott
The Journal of Pathology
Alternative splicing in tomato pollen in response to heat stress. 2016-12-26 Enrico Schleiff Mario Keller
Yangjie Hu
Anida Mesihovic
Sotirios Fragkostefanakis
Stefan Simm
DNA Research
Succession of splicing regulatory elements determines cryptic 5΄ss functionality. 2016-12-29 Emanuele Buratti Anna-Lena Brillen
Katrin Schöneweis
Lara Walotka
Linda Hartmann
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Johannes Ptok
Wolfgang Kaisers
Gereon Poschmann
Kai Stühler
Stephan Theiss
Heiner Schaal
Nucleic Acids Research
Pathway Analysis and Omics Data Visualization Using Pathway Genome Databases: FragariaCyc, a Case Study. 2017-01-01 Pankaj Jaiswal Sushma Naithani
Pankaj Jaiswal
Methods in Molecular Biology
RNA-Seq investigations of human post-mortem trigeminal ganglia. 2017-01-01 Danielle Thierry-Mieg
Stephen J Raithel
Jean Thierry-Mieg
Danielle M LaPaglia
Matthew R Sapio
Peter D Burbelo
Danielle Thierry-Mieg
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Cephalalgia
Bioinformatics Pipeline for Transcriptome Sequencing Analysis. 2017-01-01 Thomas Derrien Sarah Djebali
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Methods in Molecular Biology
Understanding development and stem cells using single cell-based analyses of gene expression. 2017-01-01 Patrick Cahan Pavithra Kumar
Yuqi Tan
Development
Analysis of EBV Transcription Using High-Throughput RNA Sequencing. 2017-01-01 Melody Baddoo Tina O'Grady
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Erik K Flemington
Methods in Molecular Biology
Next-Generation Sequencing Analysis of Long Noncoding RNAs in CD4+ T Cell Differentiation. 2017-01-01 Sergio Abrignani Valeria Ranzani
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Methods in Molecular Biology
Simultaneous Transcriptional and Epigenomic Profiling from Specific Cell Types within Heterogeneous Tissues In Vivo 2017-01-01 Linus T-Y Tsai Hyun Cheol Roh
Anna Lyubetskaya
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Cell Reports
ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data. 2017-01-03 Roderic Guigó i Serra Bernardo Rodríguez-Martín
Emilio Palumbo
Santiago Marco-Sola
Thasso Griebel
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BMC Genomics
JACUSA: site-specific identification of RNA editing events from replicate sequencing data. 2017-01-03 Markus Landthaler Michael Piechotta
Emanuel Wyler
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Christoph Dieterich
BMC Bioinformatics
Blocking Tumor-Educated MSC Paracrine Activity Halts Osteosarcoma Progression. 2017-01-04 Sonia A. Melo
Roberta Bonafede
Anne-Marie Cleton-Jansen
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Clinical Cancer Research
In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways 2017-01-05 Konrad Förstner
Jörg Vogel
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Dylan Girodat
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Richard Reinhardt
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Molecular Cell
Mutations in EBF3 Disturb Transcriptional Profiles and Cause Intellectual Disability, Ataxia, and Facial Dysmorphism 2017-01-05 Kerstin Kutsche
Stéphane Bézieau
Sébastien Küry
Frederike Leonie Harms
Katta M. Girisha
Andrew A. Hardigan
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Malik Alawi
Ashwin Dalal
Lauren Brady
Mark Tarnopolsky
Lynne M. Bird
Sophia Ceulemans
Martina Bebin
Kevin M. Bowling
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Edward J. Lose
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Stéphane Bézieau
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Bertrand Isidor
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James R. Lupski
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Gregory M. Cooper
American Journal of Human Genetics
Mapping eQTLs with RNA-seq reveals novel susceptibility genes, non-coding RNAs and alternative-splicing events in systemic lupus erythematosus 2017-01-05 Amy L Roberts
Ana Viñuela
Kerrin S. Small
Christopher A Odhams
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Human Molecular Genetics
Single-cell transcriptomics of small microbial eukaryotes: limitations and potential. 2017-01-06 Karla B Heidelberg Zhenfeng Liu
Sarah K Hu
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The ISME Journal
Allele-specific wild-type TP53 expression in the unaffected carrier parent of children with Li-Fraumeni syndrome. 2017-01-09 Jeffrey S. Buzby Shirley A Williams
Lana Schaffer
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Cancer Genetics
Whole-Genome Sequencing of Invasion-Resistant Cells Identifies Laminin α2 as a Host Factor for Bacterial Invasion 2017-01-10 Victor Nizet Xander M van Wijk
Simon Döhrmann
Björn M Hallström
Shangzhong Li
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mBio
Long noncoding RNA repertoire in chicken liver and adipose tissue 2017-01-10 Hervé Acloque
Fabrice Legeai
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Thomas Derrien
Sandrine Lagarrigue
Christophe Klopp
Valentin Wucher
Diane Esquerré
Frédéric Lecerf
Colette Désert
Morgane Boutin
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Elisabetta Giuffra
Sarah Djebali
Sylvain Foissac
Genetics Selection Evolution
Nitro-fatty acids in plant signaling: New key mediators of nitric oxide metabolism. 2017-01-10 Francisco J. Corpas Capilla Mata-Pérez
Beatriz Sánchez-Calvo
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Juan C Begara-Morales
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Redox Biology
Hydrogel scaffolds promote neural gene expression and structural reorganization in human astrocyte cultures. 2017-01-11 Elba Serrano V Bleu Knight PeerJ
High variability of expression profiles of homeologous genes for Wnt, Hh, Notch, and Hippo signaling pathways in Xenopus laevis. 2017-01-12 Takayoshi Yamamoto
Yuuri Yasuoka
Takuya Nakayama
Tatsuo Michiue
Toshiyasu Goto
Takafumi Ikeda
Kei Nagura
Masanori Taira
Tsutomu Kinoshita
Developmental Biology
Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R 2017-01-14 Davis J McCarthy Kieran R Campbell
Aaron T L Lun
Quin F Wills
Bioinformatics
Transcriptional analysis of mating and pre-infection stages of the anther smut, Microbotryum lychnidis-dioicae. 2017-01-17 Christina A Cuomo Su San Toh
Zehua Chen
David J Schultz
Michael H Perlin
Microbiology
Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis 2017-01-18 Pär G Engström
Janne Lehtiö
Yafeng Zhu
Christian Tellgren-Roth
Charles D Baudo
John C Kennell
Sheng Sun
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Markus S Schröder
Anna Andersson
Tina Holm
Benjamin Sigurgeirsson
Guangxi Wu
Sundar Ram Sankaranarayanan
Rahul Siddharthan
Kaustuv Sanyal
Joakim Lundeberg
Björn Nystedt
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Nucleic Acids Research
Nematophagous fungus Arthrobotrys oligospora mimics olfactory cues of sex and food to lure its nematode prey. 2017-01-18 Erich M Schwarz
Yen-Ping Hsueh
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Paul W Sternberg
eLife
UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy 2017-01-18 Andreas Heger
Tom Smith
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Genome Research
Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization 2017-01-19 Lana Garmire Xun Zhu
Travers Ching
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PeerJ
Lemna minor plants chronically exposed to ionising radiation: RNA-seq analysis indicates a dose rate dependent shift from acclimation to survival strategies. 2017-01-22 Arne Van Hoeck Nele Horemans
Robin Nauts
May Van Hees
Hildegarde Vandenhove
Ronny Blust
Plant Science
Large-scale analysis of branchpoint usage across species and cell lines. 2017-01-24 Allison J Taggart
William G Fairbrother
Chien-Ling Lin
Barsha Shrestha
Claire Heintzelman
Seongwon Kim
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 2017-01-25 Matthew E Thornton Kathy A Schall
Mubina Isani
Kathleen A Holoyda
Xiaogang Hou
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BMC Genomics
Guanylate-binding protein 1 (GBP1) contributes to the immunity of human mesenchymal stromal cells against Toxoplasma gondii. 2017-01-25 Geoff Hide Aiping Qin
De-Hua Lai
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Sunxing Yan
Huimin Xia
Zhao-Rong Lun
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Proceedings of the National Academy of Sciences of the United States of America
Molecular phenotyping of multiple mouse strains under metabolic challenge uncovers a role for Elovl2 in glucose-induced insulin secretion. 2017-01-26 Céline Cruciani-Guglielmacci
Christophe Magnan
Lara Bellini
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
Robin Liechti
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
Ioannis Xenarios
Hervé Le Stunff
Bernard Thorens
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Molecular Metabolism
Profiling of human epigenetic regulators using a semi-automated real-time qPCR platform validated by next generation sequencing. 2017-01-27 Allan B. Dietz Amel Dudakovic
Martina Gluscevic
Christopher R Paradise
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Farzaneh Khani
Roman Thaler
Farah S Ahmed
Xiaodong Li
Gary S Stein
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Jennifer J Westendorf
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Gene
Regulation of miR-29b-1/a transcription and identification of target mRNAs in CHO-K1 cells. 2017-01-28 Justin L. Mott Penn Muluhngwi
Kirsten Richardson
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Molecular and Cellular Endocrinology
Comparative genomics of two jute species and insight into fibre biogenesis. 2017-01-30 Xuehua Wan Md Shahidul Islam
Jennifer A Saito
Emdadul Mannan Emdad
Borhan Ahmed
Mohammad Moinul Islam
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Quazi Md Mosaddeque Hossen
Md Zakir Hossain
Rasel Ahmed
Md Sabbir Hossain
Shah Md Tamim Kabir
Md Sarwar Alam Khan
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Rajnee Hasan
Nasima Aktar
Ummay Honi
Rahin Islam
Md Mamunur Rashid
Shaobin Hou
Taslima Haque
Muhammad Shafiul Azam
Mahdi Muhammad Moosa
Sabrina M Elias
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Niaz Mahmood
Md Shafiuddin
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Nusrat Sharmeen Shommu
Sharmin Jahan
Saroj Roy
Amlan Chowdhury
Ashikul Islam Akhand
Golam Morshad Nisho
Khaled Salah Uddin
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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
Nature Plants
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
Danitza Nébor
Ravi Sachidanandam
Mathieu Lajoie
Graham W Magor
Michael R Tallack
Michael J Landsberg
Joel P Mackay
Luke A Miles
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Andrew C Perkins
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
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Shiwen Xu
Oncotarget
USP39 Deubiquitinase Is Essential for KRAS Oncogene-driven Cancer. 2017-02-01 Víctor Quesada
Amaia Lujambio
Julia M Fraile
Eusebio Manchado
Diana Campos-Iglesias
Thomas R Webb
Scott W Lowe
Carlos López-Otín
José M P Freije
Journal of Biological Chemistry
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
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
Charles Y Chiu
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Complex Chronic Disease Study Group
Clinical Infectious Diseases
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
Discovery of new candidate genes for rheumatoid arthritis through integration of genetic association data with expression pathway analysis. 2017-02-02 Leonid Padyukov Klementy Shchetynsky
Lina-Marcella Diaz-Gallo
Lasse Folkersen
Aase Haj Hensvold
Anca Irinel Catrina
Louise Berg
Lars Klareskog
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
Kiel Nikolakakis
Jennifer Reed
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
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Elizabeth Montague
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John Choiniere
Natali Kolker
William S Hancock
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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 Nicolaas Van Renne
Armando Andres Roca Suarez
Francois H T Duong
Claire Gondeau
Diego Calabrese
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Amina Ababsa
Simonetta Bandiera
Tom Croonenborghs
Nathalie Pochet
Vito De Blasi
Patrick Pessaux
Tullio Piardi
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Atsushi Ono
Kazuaki Chayama
Masashi Fujita
Hidewaki Nakagawa
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Mirjam B Zeisel
Thomas F Baumert
Joachim Lupberger
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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
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Camilo E Fadul
Yolanda Sanchez
BMC Genomics
Expression map of a complete set of gustatory receptor genes in chemosensory organs of Bombyx mori. 2017-02-06 Qingyou Xia Huizhen Guo
Tingcai Cheng
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Liang Jiang
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Jianqiu Liu
Shenglong Li
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Keiko Kadono-Okuda
Kallare P Arunkumar
Jiaqi Wu
Hirohisa Kishino
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Rakesh K Seth
Karumathil P Gopinathan
Nicolas Montagné
Emmanuelle Jacquin-Joly
Marian R Goldsmith
Kazuei Mita
Insect Biochemistry and Molecular Biology
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
Reduced mitochondrial activity in colonocytes facilitates AMPKα2-dependent inflammation. 2017-02-09 Melody Baddoo Sandra Heller
Harrison M Penrose
Chloe Cable
Debjani Biswas
Hani Nakhoul
Erik Flemington
Susan E Crawford
Suzana D Savkovic
FASEB Journal
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
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Nature Methods
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
Variant discovery in the sheep milk transcriptome using RNA sequencing 2017-02-15 Gwenola Tosser-Klopp Aroa Suárez-Vega
Beatriz Gutiérrez-Gil
Christophe Klopp
Gwenola Tosser-Klopp
Juan José Arranz
BMC Genomics
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
Natalie A. Prow
Wayne A. Schroder
Jonathan J. Ellis
Helen E. Cumming
Linden J. Gearing
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Adam Taylor
Paul J. Hertzog
Linda Hueston
Roger Le Grand
Bing Tang
Thuy T. Le
Joy Gardner
Suresh Mahalingam
Phillip I. Bird
Andreas Suhrbier
PLOS Pathogens
Resolving host-pathogen interactions by dual RNA-seq. 2017-02-16 Jörg Vogel Alexander J Westermann
Lars Barquist
PLOS Pathogens
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
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
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
Rex Dunham
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
Shikai Liu
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
CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor. 2017-02-23 D Yap 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
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
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
Magnus Tobiasson
Hani Abdulkadir
Andreas Lennartsson
Ayla De Paepe
Mohsen Karimi
Kaarel Krjutskov
Michael Grövdal
Monika Jansson
Asmaa Ben Azenkoud
Lina Corddedu
Sören Lehmann
Karl Ekwall
Eva Hellström-Lindberg
Johanna Ungerstedt
Oncotarget
Conserved expression of transposon-derived non-coding transcripts in primate stem cells. 2017-02-28 Guillaume Bourque LeeAnn Ramsay
Maria C Marchetto
Maxime Caron
Shu-Huang Chen
Stephan Busche
Tony Kwan
Tomi Pastinen
Fred H Gage
BMC Genomics
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
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
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
William R Heath
Oliver Billker
Ashraful Haque
Sarah A Teichmann
Science immunology
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 Anne-Sophie Petitot
Tina Kyndt
Rana Haidar
Alexis Dereeper
Myriam Collin
Godelieve Gheysen
Diana Fernandez
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 Alfredo Ambrosone
Modi Roopin
Abuelmagd M Abdelmonem
Lisa-Maria Ackermann
Lucia Mattera
Mariateresa Allocca
Angela Tino
Markus Klapper
Wolfgang J Parak
Oren Levy
Claudia Tortiglione
Nanotoxicology
Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq. 2017-03-01 Daniel P Cahill
Itay Tirosh
Andrew S Venteicher
Christine Hebert
Keren Yizhak
Cyril Neftel
Mariella G Filbin
Volker Hovestadt
Leah E Escalante
McKenzie L Shaw
Christopher Rodman
Shawn M Gillespie
Danielle Dionne
Christina C Luo
Hiranmayi Ravichandran
Ravindra Mylvaganam
Christopher Mount
Maristela L Onozato
Brian V Nahed
Hiroaki Wakimoto
William T Curry
A John Iafrate
Miguel N Rivera
Matthew P Frosch
Todd R Golub
Priscilla K Brastianos
Gad Getz
Anoop P Patel
Michelle Monje
Orit Rozenblatt-Rosen
David N Louis
Bradley E Bernstein
Aviv Regev
Mario L Suvà
Science
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
Nathalie Dereuddre-Bosquet
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
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
The transcriptome of the avian malaria parasite Plasmodium ashfordi displays host-specific gene expression. 2017-03-07 Gediminas Valkiūnas
Elin Videvall
Charlie K Cornwallis
Dag Ahrén
Vaidas Palinauskas
Gediminas Valkiūnas
Olof Hellgren
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 Margaux Michel
Carina Demel
Benedikt Zacher
Björn Schwalb
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
Lea Weber
Klaudia Al-Refae
Juliane Ebbert
Peter Jägers
Janine Altmüller
Christian Becker
Stephan Hahn
Günter Gisselmann
Hanns Hatt
PLoS ONE
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
High-throughput sequencing reveals circular substrates for an archaeal RNA ligase. 2017-03-09 Roxane Lestini Hubert F Becker
Alice Héliou
Kamel Djaout
Mireille Regnier
Hannu Myllykallio
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
Brittany G Durgin
Olga A Cherepanova
Themistoclis Karaoli
Gabriel F Alencar
Yu-Qing Zhou
Michelle P Bendeck
Brant E Isakson
Gary K Owens
Jessica J Connelly
American Journal of Physiology - Heart and Circulatory Physiology
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
Richard Weinshilboum
Ravishankar K Iyer
Liewei Wang
Oncotarget
Lipid degradation promotes prostate cancer cell survival. 2017-03-11 Etienne Waelkens Harri M Itkonen
Michael Brown
Alfonso Urbanucci
Gregory Tredwell
Chung Ho Lau
Stefan Barfeld
Claire Hart
Ingrid J Guldvik
Mandeep Takhar
Hannelore V Heemers
Nicholas Erho
Katarzyna Bloch
Elai Davicioni
Rita Derua
James L Mohler
Noel Clarke
Johan V Swinnen
Hector C Keun
Ole P Rekvig
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Oncotarget
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 Amir Foroushani
Rupesh Agrahari
Roderick Docking
Linda Chang
Gerben Duns
Monika Hudoba
Aly Karsan
BMC Medical Genomics
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
Brendan R E Ansell
Louise Baker
Samantha J Emery
Malcolm J McConville
Aaron R Jex
Frontiers in Microbiology
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
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
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
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 Vladimir Yu Kiselev
Kristina Kirschner
Michael T Schaub
Tallulah Andrews
Andrew Yiu
Tamir Chandra
Kedar N Natarajan
Wolf Reik
Anthony R Green
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 Brett P Shiel
Nathan E Hall
Ira R Cooke
Jan M Strugnell
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
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
Alexander R Pico
Elke Grassman
Diana Nordling
Antonis K Hatzopoulos
Punam Malik
Jose A Cancelas
Carolyn Lutzko
Bruce J Aronow
Larsson Omberg
Scientific Data
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
Alexandra-Chloé Villani
Gary Reynolds
Siranush Sarkizova
Karthik Shekhar
James Fletcher
Morgane Griesbeck
Andrew Butler
Shiwei Zheng
Suzan Lazo
Laura Jardine
David Dixon
Emily Stephenson
Emil Nilsson
Ida Grundberg
David McDonald
Andrew Filby
Weibo Li
Philip L De Jager
Orit Rozenblatt-Rosen
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
Functional Enhancer Screening in Single Cells. 2017-04-01 Bas van Steensel Joris van Arensbergen Molecular Cell
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
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
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
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
Federica Rizzo
Agnese Ramirez
Claudia Compagnucci
Sabrina Salani
Valentina Melzi
Andreina Bordoni
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
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 Chenyi Xue
Xuan Zhang
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
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
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 Gregory Jacobson
Simon Muncaster
Koen Mensink
Maria Forlenza
Nick Elliot
Grant Broomfield
Beth Signal
Developmental and Comparative Immunology
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 Rhonda Bacher
Li-Fang Chu
Ning Leng
Audrey P Gasch
James A Thomson
Ron M Stewart
Michael Newton
Nature Methods
Prospective Isolation and Comparison of Human Germinal Matrix and Glioblastoma EGFR+ Populations with Stem Cell Properties. 2017-04-19 Roland H. Friedel
Rut Tejero
Jessica Tome-Garcia
German Nudelman
Raymund L Yong
Robert Sebra
Huaien Wang
Mary Fowkes
Margret Magid
Martin Walsh
Violeta Silva-Vargas
Elena Zaslavsky
Fiona Doetsch
Nadejda M Tsankova
Stem Cell Reports
Direct comparison of distinct naive pluripotent states in human embryonic stem cells. 2017-04-21 Dieter Deforce S Warrier
M Van der Jeught
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A Van Soom
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D I M De Coninck
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J Van de Sompele
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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 S Piras
Jonida Krate
Jason J Corneveaux
Geidy E Serrano
Lucia Sue
Thomas G Beach
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
IL-10 improves cardiac remodeling after myocardial infarction by stimulating M2 macrophage polarization and fibroblast activation. 2017-04-24 Merry L. Lindsey Mira Jung
Yonggang Ma
Rugmani Padmanabhan Iyer
Kristine Y DeLeon-Pennell
Andriy Yabluchanskiy
Michael R Garrett
Basic Research in Cardiology
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
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
Larissa A Martins
Maria F B de Melo Galletti
José M Ribeiro
André Fujita
Francisco B Costa
Marcelo B Labruna
Frontiers in cellular and infection microbiology
The landscape of BRAF transcript and protein variants in human cancer. 2017-04-28 Letizia Pitto
Alberto Mercatanti
Andrea Marranci
Zhijie Jiang
Marianna Vitiello
Elena Guzzolino
Laura Comelli
Samanta Sarti
Simone Lubrano
Cinzia Franchin
Ileabett Echevarría-Vargas
Andrea Tuccoli
Monica Evangelista
Paolo Sportoletti
Giorgio Cozza
Ettore Luzi
Enrico Capobianco
Jessie Villanueva
Giorgio Arrigoni
Giovanni Signore
Silvia Rocchiccioli
Nicholas Tsinoremas
Laura Poliseno
Molecular Cancer
Gene length and detection bias in single cell RNA sequencing protocols. 2017-04-28 Alicia Oshlack
Luke Zappia
Belinda Phipson
F1000Research
High-Resolution RNA Maps Suggest Common Principles of Splicing and Polyadenylation Regulation by TDP-43. 2017-05-01 Tomaž Curk Gregor Rot
Zhen Wang
Ina Huppertz
Miha Modic
Tina Lenče
Martina Hallegger
Nejc Haberman
Christian von Mering
Jernej Ule
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
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
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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
Jörg Schönheit
Amir Giladi
Eyal David
David Lara-Astiaso
Erika Lorenzo-Vivas
Louise Chappell-Maor
Josef Priller
Ido Amit
Immunity
HAND2 Target Gene Regulatory Networks Control Atrioventricular Canal and Cardiac Valve Development. 2017-05-01 Javier Lopez-Rios Frédéric Laurent
Ausra Girdziusaite
Julie Gamart
Iros Barozzi
Marco Osterwalder
Jennifer A Akiyama
Joy Lincoln
Aimée Zuniga
Rolf Zeller
Cell Reports
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
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Cell
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
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Joseph C Giacalone
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Kristin R Anfinson
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Megan J Riker
Maurine Neiman
Stem Cells Translational Medicine
Alternative TSSs are co-regulated in single cells in the mouse brain. 2017-05-11 Sten Linnarsson
Peter Lönnerberg
Kasper Karlsson
Peter Lönnerberg
Sten Linnarsson
Molecular Systems Biology
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
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Brain Research
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
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Oncogene
Isolation of tissues and preservation of RNA from intact, germinated barley grain. 2017-05-16 Oliver Berkowitz Natalie S Betts
Ruijie Liu
Helen M Collins
Birgitte Skadhauge
Christoph Dockter
Rachel A Burton
James Whelan
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
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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 Yasuaki Takada
Ryutaro Miyagi
Aya Takahashi
Toshinori Endo
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Transcriptomics technologies. 2017-05-18 Thomas Shafee
Rohan Lowe
Mark Bleackley
Neil Shirley
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PLOS Computational Biology
Cell fixation and preservation for droplet-based single-cell transcriptomics. 2017-05-19 Nikolaus Rajewsky Jonathan Alles
Nikos Karaiskos
Samantha D Praktiknjo
Stefanie Grosswendt
Philipp Wahle
Pierre-Louis Ruffault
Salah Ayoub
Luisa Schreyer
Anastasiya Boltengagen
Carmen Birchmeier
Robert Zinzen
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
Krüppel-like factors compete for promoters and enhancers to fine-tune transcription. 2017-05-24 Timothy L. Bailey
Melissa D Ilsley
Melissa D Ilsley
Kevin R Gillinder
Graham W Magor
Stephen Huang
Merlin Crossley
Andrew C Perkins
Nucleic Acids Research
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 Ida Henriksen
Christa Broholm
Maria Pedersen
Mathias Uhlén
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
Cholinergic neuron gene expression differences captured by translational profiling in a mouse model of Alzheimer's disease. 2017-05-25 Andrew R. Hesketh Paul M McKeever
TaeHyung Kim
Laura MacNair
Denise Miletic
Giorgio Favrin
Stephen G Oliver
Zhaolei Zhang
Peter St George-Hyslop
Janice Robertson
Neurobiology of Aging
Accurate characterization of the IFITM locus using MiSeq and PacBio sequencing shows genetic variation in Galliformes 2017-05-30 Paul Kellam Irene Bassano
Swee Hoe Ong
Nathan Lawless
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
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
Genome-Wide Target Analyses of Otx2 Homeoprotein in Postnatal Cortex 2017-05-31 Ryuichiro Nakato Akiko Sakai
Yiwei Ling
Xubin Hou
Norikazu Hara
Tomoya Iijima
Yuchio Yanagawa
Ryozo Kuwano
Shujiro Okuda
Katsuhiko Shirahige
Sayaka Sugiyama
Frontiers in Neuroscience
Ly6Chi Monocytes and Their Macrophage Descendants Regulate Neutrophil Function and Clearance in Acetaminophen-Induced Liver Injury. 2017-06-01 Metsada Pasmanik-Chor Nadine Graubardt
Milena Vugman
Odelia Mouhadeb
Gabriele Caliari
Metsada Pasmanik-Chor
Debby Reuveni
Ehud Zigmond
Eli Brazowski
Eyal David
Lousie Chappell-Maor
Steffen Jung
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
IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment. 2017-06-01 Aviv Regev
Itay Tirosh
Olga Troyanskaya
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
Tae-Gyun Kim
Ruiqi Huang
Judilyn Fuentes-Duculan
George X Song-Zhao
Nicholas Gulati
Michelle A Lowes
Sandra L King
Francisco J Quintana
Young-Suk Lee
James G Krueger
Kavita Y Sarin
Charles H Yoon
Levi Garraway
Aviv Regev
Alex K Shalek
Olga Troyanskaya
Niroshana Anandasabapathy
Cell
Bcl11b and combinatorial resolution of cell fate in the T-cell gene regulatory network. 2017-06-05 Ellen V. Rothenberg William J R Longabaugh
Weihua Zeng
Jingli A Zhang
Hiroyuki Hosokawa
Camden S Jansen
Long Li
Maile Romero-Wolf
Pentao Liu
Hao Yuan Kueh
Ali Mortazavi
Proceedings of the National Academy of Sciences of the United States of America
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
DNA methylation variations are required for epithelial-to-mesenchymal transition induced by cancer-associated fibroblasts in prostate cancer cells. 2017-06-05 Mattia Pelizzola C Pistore
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Oncogene
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 David K Y Lim
Holger Schuhmann
Skye R Thomas-Hall
Kenneth C K Chan
Taylor J Wass
Felipe Aguilera
T Catalina Adarme-Vega
Cristiana G O Dal'Molin
Glen J Thorpe
David Edwards
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
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 Elliott D Crouser
Evelyn Guirado Caceres
Mark W Julian
Audrey C Papp
Landon W Locke
Wolfgang Sadee
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
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
Mary E B McCulloch
Kim M Summers
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
Miriam Friedman-Einat
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
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
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
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Ganeshwaran H Mochida
James Irvine
Edmond G Lemire
Patricia Blakley
Christopher A Walsh
Genome Research
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
Katarzyna Malenczyk
Fatima Girach
Edit Szodorai
Petter Storm
Åsa Segerstolpe
Giuseppe Tortoriello
Robert Schnell
Jan Mulder
Erzsébet Borók
Fabiana Piscitelli
Vincenzo Di Marzo
Gábor Szabó
Rickard Sandberg
Gert Lubec
Ludwig Wagner
Leif Groop
Tibor Harkany
The EMBO Journal
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
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
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
Laura Huerta
Maria Keays
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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
Miles W Carroll
Sam Haldenby
Natasha Y Rickett
Bernadett Pályi
Isabel Garcia-Dorival
Xuan Liu
Gary Barker
Joseph Akoi Bore
Fara Raymond Koundouno
E Diane Williamson
Thomas R Laws
Romy Kerber
Daouda Sissoko
Nóra Magyar
Antonino Di Caro
Mirella Biava
Tom E Fletcher
Armand Sprecher
Lisa F P Ng
Laurent Rénia
N'faly Magassouba
Roman Wölfel
Kilian Stoecker
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 Michael Zimmermann
Maria Kogadeeva
Martin Gengenbacher
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
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
Transcriptional Profiling of Biofilm Regulators Identified by an Overexpression Screen in Saccharomyces cerevisiae. 2017-07-03 Aimée M Dudley Gareth A Cromie
Zhihao Tan
Michelle Hays
Amy Sirr
Eric W Jeffery
G3
Recessive mutation in EXOSC3 associates with mitochondrial dysfunction and pontocerebellar hypoplasia. 2017-07-04 Richard J Rodenburg Gudrun Schottmann
Sylvie Picker-Minh
Jana Marie Schwarz
Esther Gill
Werner Stenzel
Angela M Kaindl
Markus Schuelke
Mitochondrion
PLATINUM SENSITIVE 2 LIKE impacts growth, root morphology, seed set, and stress responses. 2017-07-05 Cathrine Lillo Amr R A Kataya
Maria T Creighton
Toga P Napitupulu
Christine Sætre
Behzad Heidari
Peter Ruoff
PLoS ONE
Defects in dosage compensation impact global gene regulation in the mouse trophoblast. 2017-07-06 Takashi Sado
Koji Nagao
Yuka Sakata
Yuko Hoki
Hiroyuki Sasaki
Chikashi Obuse
Development
Genome-Scale Model and Omics Analysis of Metabolic Capacities of Akkermansia muciniphila Reveal a Preferential Mucin-Degrading Lifestyle. 2017-07-07 Peter J. Schaap
Mark Davids
Noora Ottman
Maria Suarez-Diez
Sjef Boeren
Vitor A P Martins Dos Santos
Hauke Smidt
Clara Belzer
Willem M de Vos
Applied and Environmental Microbiology
Neat1 is a p53-inducible lincRNA essential for transformation suppression. 2017-07-11 Stephano S. Mello
Tetsuro Hirose
John L. Rinn
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
Genes & Development
A Case of AML Characterized by a Novel t(4;15)(q31;q22) Translocation That Confers a Growth-Stimulatory Response to Retinoid-Based Therapy. 2017-07-11 Francisco Vega
Kevin Petrie
Justin M Watts
Aymee Perez
Lutecia Pereira
Yao-Shan Fan
Geoffrey Brown
Ronan T Swords
Arthur Zelent
International Journal of Molecular Sciences
Multi-omics Analyses of Starvation Responses Reveal a Central Role for Lipoprotein Metabolism in Acute Starvation Survival in C. elegans. 2017-07-12 Nils Joakim Færgeman
Richard R Sprenger
Eva Bang Harvald
Kathrine Brændgaard Dall
Christer S Ejsing
Ronni Nielsen
Susanne Mandrup
Alejandro Brenes Murillo
Mark Larance
Anton Gartner
Angus I Lamond
Cell systems
Rapid recovery gene downregulation during excess-light stress and recovery in Arabidopsis. 2017-07-13 Aaron B Smith
Peter A Crisp
Diep R. Ganguly
Kevin D Murray
Ryan Lister
Justin O Borevitz
Barry J Pogson
Gonzalo M Estavillo
Iain R Searle
Ethan Ford
Ozren Bogdanović
Steven R Eichten
The Plant Cell
Widespread alternative exon usage in clinically distinct subtypes of Invasive Ductal Carcinoma 2017-07-17 Anne-Lise Børresen-Dale Sunniva Stordal Bjørklund
Anshuman Panda
Surendra Kumar
Michael Seiler
Doug Robinson
Jinesh Gheeya
Ming Yao
Grethe I Grenaker Alnæs
Deborah Toppmeyer
Margit Riis
Bjørn Naume
Anne-Lise Børresen-Dale
Vessela N Kristensen
Shridar Ganesan
Gyan Bhanot
Scientific Reports
Human iPSC Glial Mouse Chimeras Reveal Glial Contributions to Schizophrenia. 2017-07-18 Maiken Nedergaard
Steven A. Goldman
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
Paul J Tesar
Steven A Goldman
Cell Stem Cell
Deletion of the celA gene in Aspergillus nidulans triggers overexpression of secondary metabolite biosynthetic genes. 2017-07-20 Frank Maixner
Joseph Strauss
Michael Sulyok
Gea Guerriero
Lucia Silvestrini
Sylvain Legay
Jean-Francois Hausman
Scientific Reports
Gigaspora margarita with and without its endobacterium shows adaptive responses to oxidative stress. 2017-07-20 Paola Bonfante
Stefano Ghignone
Maria C de Pinto
Francesco Venice
Mara Novero
Alessandra Salvioli
Mycorrhiza
Cell wall modifications of two Arabidopsis thaliana ecotypes, Col and Sha, in response to sub-optimal growth conditions: An integrative study. 2017-07-20 Thierry Balliau
Christophe Dunand
Harold Duruflé
Vincent Hervé
Philippe Ranocha
Michel Zivy
Josiane Chourré
Hélène San Clemente
Vincent Burlat
Cécile Albenne
Sébastien Déjean
Elisabeth Jamet
Plant Science
Direct targets of pSTAT5 signalling in erythropoiesis. 2017-07-21 Andrew C Perkins Kevin R Gillinder
Hugh Tuckey
Charles C Bell
Graham W Magor
Stephen Huang
Melissa D Ilsley
PLoS ONE
Methylation of protein phosphatase 2A-Influence of regulators and environmental stress factors. 2017-07-25 Cathrine Lillo
Jodi Maple-Grødem
Maria T Creighton
Anna Kolton
Amr R A Kataya
Jodi Maple-Grødem
Irina O Averkina
Behzad Heidari
Plant, Cell and Environment
Dual RNA-Seq of Lysobacter capsici AZ78 - Phytophthora infestans interaction shows the implementation of attack strategies by the bacterium and unsuccessful oomycete defense responses. 2017-07-26 Paolo Sonego Selena Tomada
Marco Moretto
Kristof Engelen
Ilaria Pertot
Michele Perazzolli
Gerardo Puopolo
Environmental Microbiology
Advantages of RNA-seq compared to RNA microarrays for transcriptome profiling of anterior cruciate ligament tears. 2017-07-27 Eric Tycksen
Muhammad Farooq Rai
Linda J Sandell
Robert H Brophy
Journal of Orthopaedic Research
Comprehensive discovery of noncoding RNAs in acute myeloid leukemia cell transcriptomes. 2017-07-28 Sean D McGrath 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
Experimental Hematology
FOXA1 hypermethylation: link between parity and ER-negative breast cancer in African American women? 2017-07-29 Elisa V. Bandera 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
Christine B Ambrosone
Michael J Higgins
Breast Cancer Research and Treatment
Simultaneous epitope and transcriptome measurement in single cells. 2017-07-31 Harold Swerdlow
Christoph Hafemeister
Marlon Stoeckius
Brian Houck-Loomis
Rahul Satija
Peter Smibert
William Stephenson
Pratip K. Chattopadhyay
Nature Methods
Copper homeostasis networks in the bacterium Pseudomonas aeruginosa. 2017-07-31 Lorena Novoa-Aponte Julia Quintana
José M Argüello
Journal of Biological Chemistry
Comprehensive single-cell transcriptional profiling of a multicellular organism. 2017-08-01 Jay Shendure Junyue Cao
Jonathan S Packer
Vijay Ramani
Darren A Cusanovich
Chau Huynh
Riza Daza
Xiaojie Qiu
Choli Lee
Scott N Furlan
Frank J Steemers
Andrew Adey
Robert H Waterston
Cole Trapnell
Science
Impact of Alternative Splicing on the Human Proteome. 2017-08-01 John C Marioni
Vihandha O Wickramasinghe
Yansheng Liu
Alvis Brazma
Mar Gonzàlez-Porta
Sergio Santos
Ruedi Aebersold
Ashok R Venkitaraman
Cell Reports
SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation. 2017-08-01 Itoshi Nikaido Hirotaka Matsumoto
Hisanori Kiryu
Chikara Furusawa
Minoru S H Ko
Shigeru B H Ko
Norio Gouda
Tetsutaro Hayashi
Bioinformatics
Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation. 2017-08-01 Antonio Scialdone
John C Marioni
Hisham Mohammed
Irene Hernando-Herraez
Aurora Savino
Iain Macaulay
Carla Mulas
Tamir Chandra
Thierry Voet
Wendy Dean
Jennifer Nichols
Wolf Reik
Cell Reports
TREM2 Maintains Microglial Metabolic Fitness in Alzheimer's Disease. 2017-08-01 Tyler K Ulland
Susan Gilfillan
Yingyue Zhou
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
Herbert W Virgin
Emil R Unanue
Yaming Wang
Maxim N Artyomov
David M Holtzman
Marco Colonna
Cell
Human Astrocyte Maturation Captured in 3D Cerebral Cortical Spheroids Derived from Pluripotent Stem Cells. 2017-08-01 Steven A. Sloan Spyros Darmanis
Nina Huber
Themasap A Khan
Fikri Birey
Christine Caneda
Richard Reimer
Stephen R Quake
Ben A Barres
Sergiu P Paşca
Neuron
Whole transcriptome profiling of taste bud cells. 2017-08-08 Alexander Bachmanov Sunil K Sukumaran
Brian C Lewandowski
Yumei Qin
Ramana Kotha
Robert F Margolskee
Scientific Reports
Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation. 2017-08-08 Nadav Ahituv Ann H Ryu
Walter L Eckalbar
Anat Kreimer
Nir Yosef
Scientific Reports
Amiloride, An Old Diuretic Drug, Is a Potential Therapeutic Agent for Multiple Myeloma. 2017-08-08 Ramón García-Sanz Elizabeta A Rojas
Luis Antonio Corchete
Laura San-Segundo
Juan F Martínez-Blanch
Francisco M Codoñer
Teresa Paíno
Noemí Puig
María Victoria Mateos
Enrique M Ocio
Irena Misiewicz-Krzeminska
Norma C Gutiérrez
Clinical Cancer Research
Modeling Glaucoma: Retinal Ganglion Cells Generated from Induced Pluripotent Stem Cells of Patients with SIX6 Risk Allele Show Developmental Abnormalities. 2017-08-09 Pooja Teotia Matthew J Van Hook
Christopher S Wichman
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Michael A Hauser
Iqbal Ahmad
Stem Cells
Identification of competing endogenous RNAs of the tumor suppressor gene PTEN: A probabilistic approach. 2017-08-10 Pier Paolo Pandolfi Kourosh Zarringhalam
Yvonne Tay
Prajna Kulkarni
Assaf C Bester
Rahul V Kulkarni
Scientific Reports
Characterization of the human thyroid epigenome. 2017-08-14 Andrew Mungall
Steven Jones
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
Journal of Endocrinology
Mapping the mouse Allelome reveals tissue-specific regulation of allelic expression. 2017-08-14 Josef M Penninger
Christoph Bock
Quanah J Hudson
Daniel Andergassen
Christoph P Dotter
Daniel Wenzel
Verena Sigl
Philipp C Bammer
Markus Muckenhuber
Daniela Mayer
Tomasz M Kulinski
Hans-Christian Theussl
Denise P Barlow
Florian M Pauler
eLife
Heart morphogenesis gene regulatory networks revealed by temporal expression analysis. 2017-08-14 Jonathon T Hill Bradley Demarest
Megan Smith
Bushra Gorsi
H Joseph Yost
Development
Zygotic Genome Activation Occurs Shortly after Fertilization in Maize. 2017-08-16 Nicholas Putz Junyi Chen
Nadia G Krohn
Philipp Cyprys
Stefanie Sprunck
Julia C Engelmann
Thomas Dresselhaus
The Plant Cell
A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications. 2017-08-18 Tapio Lönnberg Ashraful Haque
Jessica Engel
Sarah A Teichmann
Genome Medicine
Itm2a silencing rescues lamin A mediated inhibition of 3T3-L1 adipocyte differentiation. 2017-08-18 Pavel V Baranov Stephanie J Davies
James Ryan
Patrick B F O'Connor
Elaine Kenny
Derek Morris
Rosemary O'Connor
Tommie V McCarthy
Adipocyte
Architecture and Dynamics of the Jasmonic Acid Gene Regulatory Network. 2017-08-21 Johanna Rhodes
Katherine J Denby
Richard Hickman
Marcel C Van Verk
Anja J H Van Dijken
Marciel Pereira Mendes
Irene A Vroegop-Vos
Lotte Caarls
Merel Steenbergen
Ivo Van der Nagel
Gert Jan Wesselink
Aleksey Jironkin
Adam Talbot
Michel De Vries
Robert C Schuurink
Corné M J Pieterse
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The Plant Cell
Transcriptional Analysis Allows Genome Reannotation and Reveals that Cryptococcus gattii VGII Undergoes Nutrient Restriction during Infection. 2017-08-23 Livia Kmetzsch Patrícia Aline Gröhs Ferrareze
Rodrigo Silva Araujo Streit
Patricia Ribeiro Dos Santos
Francine Melise Dos Santos
Rita Maria Cunha de Almeida
Augusto Schrank
Marilene Henning Vainstein
Microorganisms
New skin for the old RNA-Seq ceremony: the age of single-cell multi-omics. 2017-08-24 Itai Yanai Maayan Baron Genome Biology
Massively parallel single-nucleus RNA-seq with DroNc-seq. 2017-08-28 Aviv Regev
Kristin Ardlie
Naomi Habib
Inbal Avraham-Davidi
Anindita Basu
Tyler Burks
Karthik Shekhar
Matan Hofree
Sourav R Choudhury
François Aguet
Ellen Gelfand
David A Weitz
Orit Rozenblatt-Rosen
Feng Zhang
Nature Methods
An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms. 2017-08-30 Julia Ponomarenko
Javier Tapial
Ulrich Braunschweig
Antoni Hermoso
Miguel Manzanares
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
Julia Ponomarenko
Benjamin Blencowe
Manuel Irimia
Genome Research
Characterization and Genomic Localization of a SMAD4 Processed Pseudogene. 2017-08-31 Julian Weldon Adlard
David T. Bonthron
Ian M. Carr
Alexander Markham
Christopher M Watson
Nick Camm
Laura A Crinnion
Agne Antanaviciute
Ruth Charlton
The Journal of Molecular Diagnostics
Single-cell analyses to tailor treatments. 2017-09-01 Alex K. Shalek Mikael Benson Science Translational Medicine
Assessing the activity of nonsense-mediated mRNA decay in lung cancer. 2017-09-06 Zhenguo Zhang Meng Wang
Peiwei Zhang
Yufei Zhu
Xiangyin Kong
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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
Matthew N McCall
Mohammed Adil
Yin Lu
Christopher J Mitchell
Pamela Leal-Rojas
Jinchong Xu
Manoj Kumar
Ted M Dawson
Alexander S Baras
Dan E Arking
Kathleen H Burns
Akhilesh Pandey
Genome Research
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
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
Ilaria Iacobucci
Antonella Turchiano
Elisa Ficarra
Giulia Paciello
Federica Cattina
Enrica Imbrogno
Claudio Agostinelli
Pierluigi Zinzani
Giovanni Martinelli
Enrico Derenzini
Leukemia & Lymphoma
Regulatory network changes between cell lines and their tissues of origin. 2017-09-12 John Quackenbush
Cho-Yi Chen
Camila M Lopes-Ramos
Joseph N Paulson
Marieke L Kuijjer
Maud Fagny
John Platig
Abhijeet R Sonawane
Dawn L DeMeo
Kimberly Glass
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
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
Alice Lambolez
Mikiko Kojima
Yumiko Takebayashi
Jefri Heyman
Shunsuke Watanabe
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
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
Mary E B McCulloch
Iseabail L Farquhar
Rachel Young
Lucas Lefevre
Clare Pridans
Hiu G Tsang
Cyrus Afrasiabi
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Tom C Freeman
Kim M Summers
Alan L Archibald
PLOS Genetics
Pervasive, Genome-Wide Transcription in the Organelle Genomes of Diverse Plastid-Bearing Protists. 2017-09-21 David Roy Smith Matheus Sanitá Lima G3
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
Mirnovo: genome-free prediction of microRNAs from small RNA sequencing data and single-cells using decision forests. 2017-09-25 Anton J. Enright Dimitrios M Vitsios
Elissavet Kentepozidou
Leonor Quintais
Elia Benito-Gutiérrez
Stijn van Dongen
Matthew P Davis
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 Jannik Donner
Michael Reck
Boyke Bunk
Michael Jarek
Constantin Benjamin App
Jan P Meier-Kolthoff
Jörg Overmann
Rolf Müller
Andreas Kirschning
Irene Wagner-Döbler
mSphere
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
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
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
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
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
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
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
Boris V Krivoshiev
Katrien Sprangers
Ronny Blust
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
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
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
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
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
Cell Type-Specific Chromatin Signatures Underline Regulatory DNA Elements in Human Induced Pluripotent Stem Cells and Somatic Cells. 2017-10-13 Ning-Yi Shao 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
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
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
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. 2017-10-18 Moriah L. Szpara 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 Delong Li
Zhengang Miao
Shanshan Zhang
Wenxing Liang
Lin Liu
Biochimica et Biophysica Acta
Lipoprotein lipase reaches the capillary lumen in chickens despite an apparent absence of GPIHBP1. 2017-10-19 Haibo Jiang 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
André Bensadoun
Rosemary L Walzem
Richard I Kuo
Anne P Beigneux
Loren G Fong
Stephen G Young
JCI insight
Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium. 2017-10-19 Gina Chaput 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 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 Christopher A Odhams
Deborah S Cunninghame Graham
PLOS Genetics
Development of functional ectopic compound eyes in scarabaeid beetles by knockdown of orthodenticle. 2017-10-24 Eduardo E. Zattara Anna L M Macagno
Hannah A Busey
Armin P Moczek
Proceedings of the National Academy of Sciences of the United States of America
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 Sue A Krause
Aniruddha Pandit
Shireen A Davies
Julian A T Dow
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 Rafael M Martins
Cameron R Macpherson
Aurélie Claes
Christine Scheidig-Benatar
Hiroshi Sakamoto
Peter Preiser
Suchi Goel
Mats Wahlgren
Odile Sismeiro
Jean-Yves Coppée
Artur Scherf
Scientific Reports
Efficient protein production by yeast requires global tuning of metabolism. 2017-10-25 Jens Nielsen Mingtao Huang
Jichen Bao
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
Alterations in the host transcriptome in vitro following Rift Valley fever virus infection. 2017-10-30 Gustavo Palacios Chelsea Pinkham
Bibha Dahal
Cynthia L de la Fuente
Nicole Bracci
Brett Beitzel
Michael Lindquist
Aura Garrison
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 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 Canaan M Whitfield-Cargile
Kejun He
Ivan Ivanov
Jennifer S Goldsby
Ana Chamoun-Emanuelli
Laurie A Davidson
Robert S Chapkin
Scientific Reports
MicroRNAs promote skeletal muscle differentiation of mesodermal iPSC-derived progenitors. 2017-11-01 Maurilio Sampaolesi Giorgia Giacomazzi
Bryan Holvoet
Sander Trenson
Ellen Caluwé
Bojana Kravic
Hanne Grosemans
Álvaro Cortés-Calabuig
Christophe M Deroose
Stefan Janssens
Elizabeth McNally
Mattia Quattrocelli
Nature Communications
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
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Charissa de Bekker
Debra J. Skene
Michael E Hughes
Katherine C Abruzzi
Ravi Allada
Ron Anafi
Alaaddin Bulak Arpat
Gad Asher
Pierre Baldi
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
Francis J Doyle
Giles E Duffield
Jay C Dunlap
Kristin Eckel-Mahan
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
Martha Merrow
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
Aziz Sancar
Paolo Sassone-Corsi
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
Eric Erquan Zhang
Tomasz Zielinski
John B Hogenesch
Journal of Biological Rhythms
Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation. 2018-02-23 Harold Swerdlow
Andrew Butler
Lionel B Ivashkiv
William Stephenson
Laura T Donlin
Cristina Rozo
Bernadette Bracken
Ali Rashidfarrokhi
Susan M Goodman
Vivian P Bykerk
Dana E Orange
Robert B Darnell
Rahul Satija
Nature Communications
RNA-seq analysis reveals different gene ontologies and pathways in rheumatoid arthritis and Kashin-Beck disease 2018-09-05 Xiong Guo Fangfang Yu
Chen Duan
Xiaodong Zhang
Dandan Yao
Gangquan Si
Ying Gao
Zongqiang Gao
Farooq Umer
International Journal of Rheumatic Diseases
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