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scholarly article

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
H-DBAS: human-transcriptome database for alternative splicing: update 2010	2009-12-07	Takashi Gojobori Tadashi Imanishi	Jun-ichi Takeda Yutaka Suzuki Ryuichi Sakate Yoshiharu Sato Sumio Sugano	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 Stefan Haas Hans Lehrach	Hugues Richard Marcel H Schulz Marc Sultan Asja Nürnberger Sabine Schrinner Daniela Balzereit Emilie Dagand Axel Rasche Martin Vingron 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 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
In-depth transcriptome analysis reveals novel TARs and prevalent antisense transcription in human cell lines	2010-03-25	Daniel Klevebring	Magnus Bjursell Olof Emanuelsson Joakim Lundeberg	PLoS ONE
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 Jordi Barretina	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 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
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs	2010-05	Eric Lander	Guttman M Garber M Levin JZ Donaghey J Robinson J Adiconis X Fan L Koziol MJ Gnirke A Nusbaum C Rinn JL Regev A	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
Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing.	2010-10-29	Andrea Sboner Stéphane Terry Francesca Demichelis Mark Rubin	Dorothee Pflueger Lukas Habegger Raquel Esgueva Pei-Chun Lin Maria A Svensson Naoki Kitabayashi Benjamin J Moss Theresa Y MacDonald Xuhong Cao Terrence Barrette Ashutosh K Tewari Mark S Chee Arul M Chinnaiyan David S Rickman Mark B Gerstein	Genome Research
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 Daniel Klevebring Linn Fagerberg Ivan Matic	Emma Lundberg 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 Craig W. Beattie	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 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 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 Ujunwa C Okoye Pedro Farinha Anke van den Berg Steven Jones	Christian Steidl Sohrab P Shah Bruce W Woolcock Lixin Rui Masahiro Kawahara Nathalie A Johnson Yongjun Zhao Adele Telenius Susana Ben Neriah Andrew McPherson Barbara Meissner Arjan Diepstra Mark Sun Gillian Leung Joseph M Connors David G Huntsman Kerry J Savage Lisa M Rimsza Douglas E Horsman Ulrich Steidl Marco A Marra Randy D Gascoyne	Nature
Effects of nickel treatment on H3K4 trimethylation and gene expression.	2011-03-24	Stuart M. Brown Phillip R Smith	Kam-Meng Tchou-Wong Kathrin Kiok Zuojian Tang Thomas Kluz Adriana Arita Max Costa	PLoS ONE
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
Protocol dependence of sequencing-based gene expression measurements	2011-05-06	John F Thompson	Tal Raz Philipp Kapranov Doron Lipson Stan Letovsky Patrice M Milos	PLoS ONE
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
FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution.	2011-05-18	Wolfgang Hoeck	Huanying Ge Kejun Liu Todd Juan Fang Fang Matthew Newman	Bioinformatics
deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data.	2011-05-19	Malachi Griffith Gavin Ha	Andrew McPherson Fereydoun Hormozdiari Abdalnasser Zayed Ryan Giuliany Mark G F Sun Alireza Heravi Moussavi Janine Senz Nataliya Melnyk Marina Pacheco Marco A Marra Martin Hirst Torsten O Nielsen S Cenk Sahinalp David Huntsman Sohrab P Shah	PLOS Computational Biology
The zebrafish transcriptome during early development.	2011-05-24	Juha Kere Outi Hovatta Liselotte Vesterlund	Hong Jiao Per Unneberg Outi Hovatta	BMC Developmental Biology
Characterizing the impact of smoking and lung cancer on the airway transcriptome using RNA-Seq	2011-06	Frank Schembri Jennifer Beane Yuriy O Alekseyev Avrum Spira Marc E Lenburg Shawn Levy	Jessica Vick Christina Anderlind Adam Gower Joshua Campbell Lingqi Luo Xiao Hui Zhang Ji Xiao Shenglong Wang Pierre P Massion	Cancer Prevention Research
Proportion statistics to detect differentially expressed genes: a comparison with log-ratio statistics.	2011-06-07	Tracy L Bergemann	Jason Wilson	BMC Bioinformatics
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
PR-domain-containing Mds1-Evi1 is critical for long-term hematopoietic stem cell function.	2011-06-10	Subhash Juneja	Yi Zhang Sandra Stehling-Sun Kimberly Lezon-Geyda Lucie Coillard Gouri Chatterjee Charles A Wuertzer Fernando Camargo Archibald S Perkins	Blood
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
Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data.	2011-07-12	David Casero Matteo Pellegrini	David Lopez Shawn J Cokus Sabeeha S Merchant	BMC Bioinformatics
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
ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data.	2011-07-28	Tom Maniatis Brad Friedman		Genome Biology
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
FDM: a graph-based statistical method to detect differential transcription using RNA-seq data.	2011-08-08	Derek Y Chiang	Darshan Singh Christian F Orellana Yin Hu Corbin D Jones Yufeng Liu Jinze Liu Jan F Prins	Bioinformatics
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 Kevin J Wilkinson	Dana F Simon Charles Hauser	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 William D Foulkes	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	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 Kevin L. Childs	Alicia N Massa 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 Evandro Novaes	Emilie Villar Christophe Klopp Céline Noirot 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 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
Comparative analysis of human protein-coding and noncoding RNAs between brain and 10 mixed cell lines by RNA-Seq.	2011-11-30	Jian Luo	Geng Chen Kangping Yin Leming Shi Yuanzhang Fang Ya Qi Peng Li Bing He Mingyao Liu Tieliu Shi	PLoS ONE
EpiRegNet: constructing epigenetic regulatory network from high throughput gene expression data for humans.	2011-12-01	Jing Qin Junwen Wang	Lily Yan Wang Panwen Wang Mulin Jun Li Xiaowo Wang Michael Q Zhang	Epigenetics
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
X-chromosome hyperactivation in mammals via nonlinear relationships between chromatin states and transcription	2011-12-04	Ruslan I Sadreyev	Eda Yildirim Stefan F Pinter Jeannie T Lee	Nature Structural & Molecular Biology
Protein identification using customized protein sequence databases derived from RNA-Seq data.	2011-12-14	David Tabb Daniel C. Liebler	Xiaojing Wang Robbert J C Slebos Dong Wang Patrick J Halvey 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 Sarah L Maguire	Alessandro Guida Claudia Lindstädt 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 Swaminathan Venkatesh Michael P. Washburn	Joshua M Gilmore Mihaela E Sardiu Brent Stutzman Allison Peak Chris W Seidel Jerry L Workman	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
Adaptation of the black yeast Wangiella dermatitidis to ionizing radiation: molecular and cellular mechanisms	2012	Christina A Cuomo	Kelly L Robertson Anahita Mostaghim Carissa M Soto Nikolai Lebedev Robert F Bailey Zheng Wang	PLoS ONE
Isoform diversity and regulation in peripheral and central neurons revealed through RNA-Seq	2012	John L. Bixby Vance P. Lemmon Dario Motti	Jessica K Lerch Frank Kuo 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
Transcriptome analysis reveals strain-specific and conserved stemness genes in Schmidtea mediterranea	2012	Brenton R. Graveley	Alissa M Resch Dasaradhi Palakodeti Yi-Chien Lu Michael Horowitz	PLoS ONE
RNA-seq-based metatranscriptomic and microscopic investigation reveals novel metalloproteases of Neobodo sp. as potential virulence factors for soft tunic syndrome in Halocynthia roretzi	2012	Tae Sung Jung	Ho Bin Jang Young Kyu Kim Carmelo S Del Castillo Seong Won Nho In Seok Cha Seong Bin Park Mi Ae Ha Jun-Ichi Hikima Sung Jong Hong Takashi Aoki	PLoS ONE
GABAergic gene expression in postmortem hippocampus from alcoholics and cocaine addicts; corresponding findings in alcohol-naïve P and NP rats	2012	David Goldman	Mary-Anne Enoch Zhifeng Zhou Mitsuru Kimura Deborah C Mash Qiaoping Yuan	PLoS ONE
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
Gene expression profiling of liver cancer stem cells by RNA-sequencing	2012	Timothy Wan	David W Y Ho Zhen Fan Yang Kang Yi Chi Tat Lam Michael N P Ng Wan Ching Yu Joyce Lau Xiaoqi Wang Zhixiang Yan Hang Liu Yong Zhang Sheung Tat Fan	PLoS ONE
Nrac, a novel nutritionally-regulated adipose and cardiac-enriched gene	2012	Feng Gao Abdul B Abou-Samra	Ren Zhang Fayi Yao	PLoS ONE
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 Daniel J Gaffney	Jean-Baptiste Veyrieras 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
How to analyze gene expression using RNA-sequencing data.	2012-01-01	Daniel Ramsköld Rickard Sandberg	Ersen Kavak	Methods in Molecular Biology
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 Hideyuki Okano	Hiromi Kumamaru Hirokazu Saiwai Hisakata Yamada Kensuke Kubota Koichi Akashi 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
Next-generation sequencing identifies TGF-β1-associated gene expression profiles in renal epithelial cells reiterated in human diabetic nephropathy	2012-01-14	Peadar Ó Gaora Helen M Roche	Eoin P Brennan Melissa J Morine David W Walsh Sarah A Roxburgh Maja T Lindenmeyer Derek P Brazil Denise M Sadlier Clemens D Cohen GENIE Consortium Catherine Godson Finian Martin	Biochimica et Biophysica Acta
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 Jian Huang	Shihao Shen Juw Won Park 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	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 Susanne Häussler	Monika Schniederjans Ariane Zimmermann Vanessa Jensen Maren Scharfe Robert Geffers	PLoS ONE
Transcriptome analysis of the model protozoan, Tetrahymena thermophila, using Deep RNA sequencing.	2012-02-07	Miao Tian	Jie Xiong Xingyi Lu Zhemin Zhou Yue Chang Dongxia Yuan Zhigang Zhou Lei Wang Chengjie Fu Eduardo Orias Wei Miao	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 R Jucker J Ballantyne	Forensic Science International: Genetics
Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome.	2012-02-12	Jun Wang 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 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 M Busconi A Zanetti L Bavaresco C Fogher	Plant Physiology and Biochemistry
A new subtype of bone sarcoma defined by BCOR-CCNB3 gene fusion.	2012-03-04	Franck Tirode Olivier Delattre	Gaëlle Pierron Carlo Lucchesi Stéphanie Reynaud Stelly Ballet Sarah Cohen-Gogo Virginie Perrin Jean-Michel Coindre	Nature Genetics
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 Luciano Xumerle Alberto Ferrarini	I Iacobucci M Sazzini E Giacomelli A Ferrari C Papayannidis D Luiselli A Boattini P Garagnani A Vitale S Soverini F Pane M Baccarani M Delledonne G Martinelli	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
Characterization of the longissimus lumborum transcriptome response to adding propionate to the diet of growing Angus beef steers.	2012-03-27	Jennifer Thomson Cong-Jun Li	Ransom L Baldwin Robert W Li Brian J Bequette	Physiological 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
Identification of allele-specific alternative mRNA processing via transcriptome sequencing.	2012-03-29	Jae-Hyung Lee Guangdun Peng Xinshu Xiao	Gang Li Jae Hoon Bahn Zugen Chen Stanley F Nelson	Nucleic Acids Research
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
Spatial proximity and similarity of the epigenetic state of genome domains.	2012-04-04	Ekaterina E Khrameeva Gennady G Fedonin	Andrey A Mironov Philipp Khaitovich Mikhail S Gelfand	PLoS ONE
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
Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data.	2012-04-12	J Duitama	Pramod K Srivastava Ion I Măndoiu	BMC Genomics
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 Juan Luis Jurat-Fuentes	Brenda Oppert Scot E Dowd Pascal Bouffard Lewyn Li Marcé D Lorenzen Michelle Toutges Jeremy Marshall Jeff Fabrick Cris Oppert	PLoS ONE
Transcriptome sequencing revealed significant alteration of cortical promoter usage and splicing in schizophrenia.	2012-04-27	Xi Wang Murray J Cairns	Jing Qin Wu Natalie J Beveridge Paul A Tooney Rodney J Scott Vaughan J Carr	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
PhenoLink--a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains.	2012-05-04	Douwe Molenaar	Jumamurat R Bayjanov Vesela Tzeneva Roland J Siezen Sacha A F T van Hijum	BMC Genomics
RNA-Seq identifies SNP markers for growth traits in rainbow trout	2012-05-04	Timothy D Leeds	Mohamed Salem Roger L Vallejo Yniv Palti Sixin Liu Annas Sabbagh Caird E Rexroad Jianbo Yao	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 Robin William Palfreyman Quan Nguyen	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 Jun Wang Johannes Waage Joachim Weischenfeldt Bo Torben Porse Janus Schou Jakobsen	Geng Tian Jing Zhao Inge Damgaard Karsten Kristiansen	Genome Biology
Trehalose-enhanced isolation of neuronal sub-types from adult mouse brain.	2012-06-01	Piero Carninci	Alka Saxena Akiko Wagatsuma Yukihiko Noro Takenobu Kuji Atsuko Asaka-Oba Akira Watahiki Cecile Gurnot Michela Fagiolini Takao K Hensch	BioTechniques
Transcriptomic signatures of attachment, NF-κB suppression and IFN stimulation in the catfish gill following columnaris bacterial infection.	2012-06-02	Eric Peatman	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
Differential gene expression in tamoxifen-resistant breast cancer cells revealed by a new analytical model of RNA-Seq data	2012-07-23	Willard M. Freeman Kent Vrana	Kathryn J Huber-Keener Xiuping Liu Zhong Wang Yaqun Wang Song Wu Maricarmen D Planas-Silva Xingcong Ren Yan Cheng Yi Zhang Chang-Gong Liu Jin-Ming Yang Rongling Wu	PLoS ONE
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
Discovery and characterization of new transcripts from RNA-seq data in mouse CD4(+) T cells.	2012-08-04	Stéphane Poulain Andrew Paul Hutchins Hodaka Fujii	Diego Miranda-Saavedra	Genomics
Transcriptome profiling of resistant and susceptible Cavendish banana roots following inoculation with Fusarium oxysporum f. sp. cubense tropical race 4.	2012-08-05	Altus Viljoen	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 Hans Lehrach	Joost van Delft Stan Gaj Matthias Lienhard Marcus W Albrecht Alexander Kirpiy Karen Brauers Sandra Claessen Daneida Lizarraga 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
Detecting transcription of ribosomal protein pseudogenes in diverse human tissues from RNA-seq data	2012-08-21	Shaojie Zhang	Peter Tonner Vinodh Srinivasasainagendra Degui Zhi	BMC Genomics
Research resource: RNA-Seq reveals unique features of the pancreatic β-cell transcriptome.	2012-08-21	Michael McManus	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 Luca Venturini Lorenzo Farina	Marianna Fasoli Sara Zenoni Anita Zamboni Andrea Porceddu Manuele Bicego Alberto Ferrarini Massimo Delledonne Mario Pezzotti	The Plant Cell
A novel computational strategy to identify A-to-I RNA editing sites by RNA-Seq data: de novo detection in human spinal cord tissue	2012-09-05	Graziano Pesole Angela Gallo Ernesto Picardi	Federica Galeano Sara Tomaselli	PLoS ONE
Modelling and simulating generic RNA-Seq experiments with the flux simulator.	2012-09-07	Roderic Guigó i Serra Michael Sammeth	Thasso Griebel Benedikt Zacher Paolo Ribeca Emanuele Raineri Vincent Lacroix	Nucleic Acids Research
Id2a functions to limit Notch pathway activity and thereby influence the transition from proliferation to differentiation of retinoblasts during zebrafish retinogenesis.	2012-09-08	Taejoon Kwon Rosa A Uribe Jeffrey M Gross	Edward M Marcotte	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
Gene expression changes in a tumor xenograft by a pyrrole-imidazole polyamide.	2012-09-17	Georgi K Marinov	Jevgenij A Raskatov Nicholas G Nickols Amanda E Hargrove Barbara Wold Peter B Dervan	Proceedings of the National Academy of Sciences of the United States of America
Heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma cells	2012-09-18	Harri Lähdesmäki Vivek Anantharaman Lakshminarayanan Aravind Tarmo Aijö John Gagnon Xing Chang	Micah J Benson Tarmo Aijö Utz J Pape Juha-Pekka Pursiheimo Shalini Oberdoerffer X Shirley Liu Riitta Lahesmaa Anjana Rao	Proceedings of the National Academy of Sciences of the United States of America
Functional transcriptomics of a migrating cell in Caenorhabditis elegans.	2012-09-18	Erich M Schwarz Paul W. Sternberg	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 Andrea Nino-Castro	Marc Beyer Michael R Mallmann Jia Xue Andrea Staratschek-Jox Daniela Vorholt Wolfgang Krebs Daniel Sommer Jil Sander Christina Mertens Susanne V Schmidt	PLoS ONE
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 Anne Grapin-Botton	Eunyoung Choi Marine R C Kraus Laurence A Lemaire Sasidhar Vemula Leah A Potter Elisabetta Manduchi Christian J Stoeckert	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
Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript.	2012-10-23	Matteo Benelli Marco Severgnini Alberto Magi	Chiara Pescucci Giuseppina Marseglia Francesca Torricelli	Bioinformatics
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 Brendan Loftus	Katarzyna Pluta Colm J Reid John A Browne Tharmala Tharmalingam Anthony Corfield 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 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 A Stirnweiss E Ferrari M D Welch E Baker A R Murch A M Gout K W Carter M B Phillips U R Kees	Oncogene
Simultaneous RNA-seq analysis of a mixed transcriptome of rice and blast fungus interaction.	2012-11-06	Takeshi Itoh	Yoshihiro Kawahara Youko Oono Hiroyuki Kanamori Takashi Matsumoto Eiichi Minami	PLoS ONE
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
The AHL- and BDSF-dependent quorum sensing systems control specific and overlapping sets of genes in Burkholderia cenocepacia H111.	2012-11-20	Aurelien L Carlier Christian H Ahrens Ulrich Omasits Gabriella Pessi	Nadine Schmid Yinyue Deng Claudio Aguilar Alexander Grunau Lian-Hui Zhang Leo Eberl	PLoS ONE
High-throughput sequencing of the melanoma genome.	2012-11-22	Janet Kelso	Manfred Kunz Michael Dannemann	Experimental Dermatology
Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching.	2012-11-24	Charles Plessy Piero Carninci	Dave T P Tang Md Salimullah Ana Maria Suzuki Raffaella Calligaris Stefano Gustincich	Nucleic Acids Research
iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data	2012-11-29	Derek Y Chiang	Aziz M Mezlini Eric J M Smith Marc Fiume Orion Buske Gleb L Savich Sohrab Shah Sam Aparicio Anna Goldenberg Michael Brudno	Genome Research
Nuclear RNA sequencing of the mouse erythroid cell transcriptome	2012-11-29	Chih-Yu Chen Jennifer A. Mitchell Ieuan Clay Peter Fraser	David Umlauf Catherine A Moir Christopher H Eskiw Stefan Schoenfelder Lyubomira Chakalova Takashi Nagano	PLoS ONE
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 Felix Krueger Bernard Thienpont	Stefanie Seisenberger Simon Andrews Julia Arand Jörn Walter Fátima Santos Christian Popp 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 Differentiates Tumour and Host mRNA Expression Changes Induced by Treatment of Human Tumour Xenografts with the VEGFR Tyrosine Kinase Inhibitor Cediranib	2013	James R. Bradford	Matthew Farren Steve J Powell Sarah Runswick Susie L Weston Helen Brown Oona Delpuech Mark Wappett Neil R Smith T Hedley Carr Jonathan R Dry Neil J Gibson Simon T Barry	PLoS ONE
RNA-Seq profiling of spinal cord motor neurons from a presymptomatic SOD1 ALS mouse	2013	Arthur L. Horwich Justin Cotney	Urmi Bandyopadhyay 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
Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing	2013	Yinglong Chen	Yan Wang Liang Xu Hong Shen Yiqin Gong Cecilia Limera Liwang Liu	PLoS ONE
Connectivity Mapping for Candidate Therapeutics Identification Using Next Generation Sequencing RNA-Seq Data	2013	Philip D Dunne Darragh G McArt Shu-Dong Zhang	Jaine K Blayney Manuel Salto-Tellez Sandra Van Schaeybroeck Peter W Hamilton	PLoS ONE
Unique transcriptome patterns of the white and grey matter corroborate structural and functional heterogeneity in the human frontal lobe	2013	Michael Janitz Glenda Halliday	James D Mills Tomas Kavanagh Woojin S Kim Bei Jun Chen Yoshihiro Kawahara	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 René R Bodemann Marco Groth	Magdalena Stock 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
Comparative RNA-seq analysis of early-infected peach leaves by the invasive phytopathogen Xanthomonas arboricola pv. pruni.	2013-01-14	Joël F. Pothier A Patocchi	Didier Socquet-Juglard Tim Kamber Danilo Christen Cesare Gessler Brion Duffy	PLoS ONE
RNA-Seq data: a goldmine for organelle research.	2013-01-18	David Roy Smith		Briefings in functional genomics
Efficient and comprehensive representation of uniqueness for next-generation sequencing by minimum unique length analyses.	2013-01-18	Daniel Ramsköld Rickard Sandberg	Helena Storvall	PLoS ONE
Analysis of RNA-Seq data reveals involvement of JAK/STAT signalling during leg regeneration in the cricket Gryllus bimaculatus.	2013-01-23	Taro Nakamura	Tetsuya Bando Yoshiyasu Ishimaru Takuro Kida Yoshimasa Hamada Yuji Matsuoka Hideyo Ohuchi Sumihare Noji Taro Mito	Development
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 Günter Gisselmann	PLoS ONE
A high-dimensional, deep-sequencing study of lung adenocarcinoma in female never-smokers	2013-02-06	Wan Kyu Kim Namshin Kim	Sang Cheol Kim Yeonjoo Jung Jinah Park Sooyoung Cho Chaehwa Seo Jaesang Kim Pora Kim Jehwan Park Jihae Seo Jiwoong Kim Seongjin Park Insu Jang Jin Ok Yang Byungwook Lee Kyoohyoung Rho Yeonhwa Jung Juhee Keum Jinseon Lee Jungho Han Sangeun Kang Sujin Bae So-Jung Choi Sujin Kim Jong-Eun Lee Jhingook Kim Sanghyuk Lee	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	Jun Wang 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
Activity of a Py-Im polyamide targeted to the estrogen response element.	2013-02-26	Jerzy O Szablowski	Nicholas G Nickols Amanda E Hargrove Benjamin C Li Jevgenij A Raskatov Peter B Dervan	Molecular Cancer Therapeutics
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
WNT5A inhibits metastasis and alters splicing of Cd44 in breast cancer cells.	2013-03-06	David K. Crossman	Wen Jiang Elizabeth H Mitchell Philip Sohn Michael R Crowley Rosa Serra	PLoS ONE
RNA-seq reveals activation of both common and cytokine-specific pathways following neutrophil priming.	2013-03-06	Huw B Thomas Helen L Wright	Robert J Moots Steven W Edwards	PLoS ONE
Regulation of viral and cellular gene expression by Kaposi's sarcoma-associated herpesvirus polyadenylated nuclear RNA.	2013-03-06	Cyprian Rossetto Subhash C. Verma	Margaret Tarrant-Elorza Pravinkumar Purushothaman Gregory S Pari	Journal of Virology
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 Ling Yen Lee	Joshua T Smith 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 Michele Fabris Alex Van Moerkercke Jacob Pollier Johan Memelink Alain Goossens	Gino J E Baart Ghulam Hasnain Heiko Rischer	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	Jun Wang 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 Staffan G Svärd	Oscar Franzén Elin Einarsson Johan Ankarklev Marcela Ferella Björn Andersson	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 David I Schlipalius Paul R Ebert Rebecca L. Cramp	Beau D Reilly	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 Brad Friedman	Eric T Wang 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
Exome-based analysis for RNA epigenome sequencing data.	2013-04-14	Jia Meng	Xiaodong Cui Manjeet K Rao Yidong Chen Yufei Huang	Bioinformatics
Glycyrrhiza uralensis transcriptome landscape and study of phytochemicals.	2013-04-14	Keiichi Mochida Tetsuya Sakurai Carsten O Daub Toshiya Muranaka Kazuki Saito	Jordan A Ramilowski Satoru Sawai Hikaru Seki Takuhiro Yoshida	Plant and Cell Physiology
Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity	2013-04-17	Yohei Sasagawa Tetsutaro Hayashi Itoshi Nikaido Takeshi Imai Hiroki R Ueda	Hiroki Danno Kenichiro D Uno	Genome Biology
Characterization of differential transcript abundance through time during Nematostella vectensis development.	2013-04-19	Sarah Tulin Joel Smith Casey W. Dunn	Rebecca Rae Helm Stefan Siebert	BMC Genomics
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 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	Seaun 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 Michelle Lacey	Michael J Strong Guorong Xu Joseph Coco Carl Baribault Dass S Vinay Amy L Strong Teresa A Lehman Michael B Seddon Zhen Lin Monica Concha Melody Baddoo Marybeth Ferris Kenneth F Swan Deborah E Sullivan Matthew E Burow Christopher M Taylor 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 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 Thomas Tuschl	Eric L Fritz Brad R Rosenberg Kenneth Lay Aleksandra Mihailović F Nina Papavasiliou	Nature Immunology
Identification of the zebrafish maternal and paternal transcriptomes	2013-05-29	James Cuthbert Smith	Steven A Harvey Ian Sealy Ross Kettleborough Fruzsina Fenyes Richard White Derek Stemple	Development
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 Kevin J Wilkinson	Dana F Simon Charles Hauser Colin M Hutchins	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 Jill D Haag Anna I Rissman Deepak Sharma Ann Tran Alexi A Schoenborn Rachael C Baird Dan S Peiffer David Q Leinweber Matthew J Muelbl Amanda L Meilahn Mark R Eichelberg Ning Leng Manorama C John Patricia A Powers Caroline M Alexander Michael N Gould	PLOS Genetics
Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica	2013-06	Chad Nusbaum Carsten Russ Berend Snel Stephan Wawra Sucheta Tripathy Irene de Bruijn Michael F. Seidl Guido Van den Ackerveken Pieter van West Francine Govers Stan Oome Neil Horner Bernard Dumas	Rays H Y Jiang Brian J Haas Rodrigo Belmonte Lars Löbach James Christie Arnaud Bottin Vincent Bulone Sara M Díaz-Moreno Lin Fan Elodie Gaulin Laura J Grenville-Briggs Joshua Z Levin Marco Mammella Harold J G Meijer Paul Morris Stan Oome Andrew J Phillips David van Rooyen Elzbieta Rzeszutek Marcia Saraiva Chris J Secombes Joost H M Stassen Sean Sykes Herbert van den Berg Julio C Vega-Arreguin Sarah K Young Qiandong Zeng Javier Dieguez-Uribeondo Brett M Tyler	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
Cellular source and mechanisms of high transcriptome complexity in the mammalian testis.	2013-06-20	Anamaria Necsulea	Magali Soumillon Manuela Weier David Brawand Xiaolan Zhang Hongcang Gu Pauline Barthès Maria Kokkinaki Serge Nef Andreas Gnirke Martin Dym Bernard de Massy Tarjei S Mikkelsen Henrik Kaessmann	Cell Reports
ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells.	2013-06-21	Avi Ma'ayan Caroline Baroukh	Huilei Xu Ruth Dannenfelser Edward Y Chen Christopher M Tan Yan Kou Yujin E Kim Ihor R Lemischka	Database
Global transcriptome profiles of Camellia sinensis during cold acclimation	2013-06-22	Qiong-Yi Zhao	Xin-Chao Wang Chun-Lei Ma Zong-Hong Zhang Hong-Li Cao Yi-Meng Kong Chuan Yue Xin-Yuan Hao Liang Chen Jian-Qiang Ma Ji-Qiang Jin Xuan Li Ya-Jun Yang	BMC Genomics
Evaluating the impact of sequencing depth on transcriptome profiling in human adipose	2013-06-24	Jane Ferguson Muredach P. Reilly	Yichuan Liu Chenyi Xue Ian M Silverman Brian Gregory Mingyao Li	PLoS ONE
Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets	2013-06-28	W. Richard McCombie	Xiao Xu Yuanhao Zhang Jennie Williams Eric Antoniou Song Wu Wei Zhu Nicholas O Davidson Paula Denoya Ellen Li	BMC Bioinformatics
Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation.	2013-07-01	Sayan Mukherjee	Dina Hafez Ting Ni Jun Zhu 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 Rafał Tomecki Torben Heick Jensen Dominik Cysewski	Michal Lubas Christian K Damgaard	The EMBO Journal
RNaseIII and T4 polynucleotide Kinase sequence biases and solutions during RNA-seq library construction	2013-07-04	Claus O. Wilke	Changhoon Lee R Adron Harris Jason K Wall R Dayne Mayfield	Biology Direct
Identification of genes critical for resistance to infection by West Nile virus using RNA-Seq analysis.	2013-07-08	Sebastian Kurscheid Ruth R Montgomery Erol Fikrig	Feng Qian Lisa Chung Wei Zheng Vincent Bruno Roger P Alexander Zhong Wang Xiaomei Wang Hongyu Zhao Mark Gerstein Michael Snyder	Viruses
Clear cell renal cell carcinoma associated microRNA expression signatures identified by an integrated bioinformatics analysis.	2013-07-10	Wenying Yan	Jiajia Chen Daqing Zhang Wenyu Zhang Yifei Tang Lingchuan Guo Bairong Shen	Journal of Translational Medicine
Male-biased genes in catfish as revealed by RNA-Seq analysis of the testis transcriptome.	2013-07-12	Shikai Liu Ludmilla Kaltenboeck	Fanyue Sun Xiaoyu Gao Yanliang Jiang Dayan Perera Xiuli Wang Chao Li Luyang Sun Jiaren Zhang Ludmilla Kaltenboeck Rex Dunham Zhanjiang Liu	PLoS ONE
Senescence-associated lncRNAs: senescence-associated long noncoding RNAs.	2013-07-14	Kevin G. Becker	Kotb Abdelmohsen Amaresh Panda Min-Ju Kang Jason Xu Roza Selimyan Je-Hyun Yoon Jennifer L Martindale Supriyo De William H Wood Myriam Gorospe	Aging Cell
Proteogenomic database construction driven from large scale RNA-seq data.	2013-07-17	Vineet Bafna	Sunghee Woo Seong Won Cha Gennifer Merrihew Yupeng He Natalie Castellana Clark Guest Michael MacCoss	Journal of Proteome Research
CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes	2013-07-18	Jennifer Doudna Lei S Qi	Luke A Gilbert Matthew H Larson Leonardo Morsut Zairan Liu Gloria A Brar Sandra E Torres Noam Stern-Ginossar Onn Brandman Evan H Whitehead Wendell A Lim Jonathan S Weissman	Cell
Methylmercury exposure increases lipocalin related (lpr) and decreases activated in blocked unfolded protein response (abu) genes and specific miRNAs in Caenorhabditis elegans	2013-07-18	Natalia Vanduyn	Martina Rudgalvyte Vuokko Aarnio Liisa Heikkinen Juhani Peltonen Merja Lakso Richard Nass Garry Wong	Toxicology Letters
Using a periclinal chimera to unravel layer-specific gene expression in plants.	2013-07-19	James Abbott	Ioannis Filippis Rosa Lopez-Cobollo Sarah Butcher Gerard J Bishop	The Plant Journal
Gene networks and chromatin and transcriptional regulation of the phaseolin promoter in Arabidopsis.	2013-07-19	Lakshminarayan M. Iyer	Sabarinath Sundaram Sunee Kertbundit Eugene V Shakirov Lakshminarayan M Iyer Miloslav Jurícek Timothy C Hall	The Plant Cell
Enhanced expression of codon optimized interferon gamma in CHO cells.	2013-07-19	Dong-Yup Lee	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 John H Hill Steven A Whitham Randy C Shoemaker Michelle A Graham	Plant, Cell and Environment
Knockdown of CDKN1C (p57(kip2)) and PHLDA2 results in developmental changes in bovine pre-implantation embryos	2013-07-22	Francisco Peñagaricano Wen Huang	Ashley M Driver Jenna Kropp Hasan Khatib	PLoS ONE
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 Benjamin H Beck	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 Alan E Hubbard Luoping Zhang Roel Vermeulen Guilan Li Stephen M Rappaport Songnian Yin 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	Andrew Adey Jacob O Kitzman Joseph B Hiatt Alexandra P Lewis Beth K Martin Ruolan Qiu Choli Lee	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 Denis Roze Lucie Mieuzet Béatrice Ségurens Jean-Christophe Simon	PLOS Genetics
BlackOPs: increasing confidence in variant detection through mappability filtering.	2013-08-08	Charles M. Perou	Christopher R Cabanski Matthew D Wilkerson Matthew Soloway Joel S Parker Jinze Liu Jan F Prins J S Marron D Neil Hayes	Nucleic Acids Research
Genome-wide transcriptional response of Trichoderma reesei to lignocellulose using RNA sequencing and comparison with Aspergillus niger	2013-08-09	Stéphane Delmas Steven T. Pullan	Laure Ries Sunir Malla Martin J Blythe David B Archer	BMC Genomics
Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons.	2013-08-12	Cameron Brennan	J Zachary Sanborn Sofie R Salama Mia Grifford Tom Mikkelsen Suresh Jhanwar Sol Katzman Lynda Chin David Haussler	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 Dibyendu Kumar Fahong Yu Jeffrey B Jones James H Graham Frank F White Nian Wang	BMC Genomics
Next-generation sequencing of advanced prostate cancer treated with androgen-deprivation therapy.	2013-08-14	Owen J Sansom Chris Ponting Andreas Heger Ian Sudbery Imran Ahmad Joanne Edwards Hing Y Leung	Prabhakar Rajan M Eugenia M Villasevil Ernest Mui Janis Fleming Mark Davis David Sims Rhona M McMenemin Ian D Pedley	European Urology
Adaptive responses to glucose restriction enhance cell survival, antioxidant capability, and autophagy of the protozoan parasite Trichomonas vaginalis.	2013-08-17	Petrus Tang	Kuo-Yang Huang Yi-Ywan Margaret Chen Yi-Kai Fang Wei-Hung Cheng Chih-Chieh Cheng Yu-Chuen Chen Tiffany E Wu Fu-Man Ku Shih-Chieh Chen Rose Lin	Biochimica et Biophysica Acta
Shaping development through mechanical strain: the transcriptional basis of diet-induced phenotypic plasticity in a cichlid fish.	2013-08-19	Helen M Gunter Paolo Franchini Axel Meyer Carmelo Fruciano	Shaohua Fan Fan Xiong	Molecular Ecology
A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments.	2013-08-21	Pedro Puig	Mikel Esnaola David Gonzalez Robert Castelo Juan R Gonzalez	BMC Bioinformatics
Profiling microRNA expression in bovine alveolar macrophages using RNA-seq.	2013-08-24	Daniel G. Bradley Peter Vegh David J. Lynn David E. MacHugh Stephen V. Gordon	Amir B K Foroushani David A Magee Matthew S McCabe John A Browne Nicolas C Nalpas Kevin M Conlon	Veterinary Immunology and Immunopathology
Transcriptome analysis and SNP identification in SCC of horn in (Bos indicus) Indian cattle.	2013-08-24	Subhash J Jakhesara Chaitanya G. Joshi	Prakash G Koringa Vaibhav D Bhatt Anand B Patel Debabrata Dash	Gene
Complete mitochondrial genome of the medicinal mushroom Ganoderma lucidum	2013-08-26	Jianhui Zhang	Jianqin Li Haimei Chen Xiangdong Chen Jin Lan Chang Liu	PLoS ONE
Breakpoint features of genomic rearrangements in neuroblastoma with unbalanced translocations and chromothripsis.	2013-08-26	Isabelle Janoueix-Lerosey Valérie Combaret Valentina Boeva Emmanuel Barillot Olivier Delattre	Stéphanie Jouannet Romain Daveau Cécile Pierre-Eugène Alex Cazes Caroline Louis-Brennetot Gudrun Schleiermacher Sandrine Ferrand Gaëlle Pierron Alban Lermine Thomas Rio Frio Virginie Raynal Gilles Vassal	PLoS ONE
Remodeling of membrane lipids in iron-starved Chlamydomonas.	2013-08-27	David Casero	Eugen I Urzica Astrid Vieler Anne Hong-Hermesdorf M Dudley Page 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 Cunxian Chen	PLoS ONE
SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization	2013-08-31	Shintaro Katayama Juha Kere Sten Linnarsson	Virpi Töhönen Sten Linnarsson	Bioinformatics
Mining RNA-seq data for infections and contaminations.	2013-09-03	Caroline C Friedel	Thomas Bonfert Gergely Csaba Ralf Zimmer	PLoS ONE
RNA-Seq reveals infection-related gene expression changes in Phytophthora capsici.	2013-09-03	Xiao-Ren Chen	Yu-Ping Xing Yan-Peng Li Yun-Hui Tong Jing-You Xu	PLoS ONE
Trametes versicolor protein YZP activates regulatory B lymphocytes - gene identification through de novo assembly and function analysis in a murine acute colitis model.	2013-09-03	Fuu Sheu	Yen-Chou Kuan Ying-Jou Wu Chih-Liang Hung	PLoS ONE
Short-term feed deprivation alters immune status of surface mucosa in channel catfish (Ictalurus punctatus).	2013-09-04	Eric Peatman Lisa Liu	Chao Li Baofeng Su Benjamin H Beck	PLoS ONE
Copper response regulator1-dependent and -independent responses of the Chlamydomonas reinhardtii transcriptome to dark anoxia.	2013-09-06	David Casero Thomas Happe	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 Ali Miserez	Paul A Guerette Shawn Hoon Manfred Raida Admir Masic Fong T Wong Vincent H B Ho Kiat Whye Kong Melik C Demirel Abdon Pena-Francesch Gavin Z Tay Dawei Ding	Nature Biotechnology
Beta cell 5'-shifted isomiRs are candidate regulatory hubs in type 2 diabetes.	2013-09-09	Jeanette Baran-Gale	Emily E Fannin C Lisa Kurtz Praveen Sethupathy	PLoS ONE
U1 small nuclear ribonucleoprotein complex and RNA splicing alterations in Alzheimer's disease.	2013-09-10	Yuxin Li Drew R Jones Hao Wu Eric B Dammer	Bing Bai Chadwick M Hales Ping-Chung Chen Yair Gozal Jason J Fritz Xusheng Wang Qiangwei Xia Duc M Duong Craig Street Gloria Cantero Dongmei Cheng Zhiping Wu Ian Diner Craig J Heilman Howard D Rees Li Lin Keith E Szulwach Marla Gearing Elliott J Mufson David A Bennett Thomas J Montine Nicholas T Seyfried Thomas S Wingo Yi E Sun Peng Jin John Hanfelt Donna M Willcock Allan Levey James J Lah Junmin Peng	Proceedings of the National Academy of Sciences of the United States of America
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 Daniel E Spratt Phillip J Iaquinta Vivek K Arora Wei-Feng Yen Ling Cai Brett S Carver Yu Chen Philip A Watson Neel P Shah Sho Fujisawa Alexander G Goglia Anuradha Gopalan Haley Hieronymus John Wongvipat Peter T Scardino Michael J Zelefsky Maria Jasin Jayanta Chaudhuri Simon N Powell Charles L Sawyers	Cancer Discovery
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.	2013-09-15	Ann-Christine Syvänen Michael Sammeth Tuuli Lappalainen Xavier Estivill i Pallejà	Peter A C 't Hoen Marc R Friedländer Jonas Almlöf Irina Pulyakhina 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 Roderic Guigó Emmanouil T Dermitzakis	Nature Biotechnology
Localizing transcripts to single cells suggests an important role of uncultured deltaproteobacteria in the termite gut hydrogen economy	2013-09-16	Niles A. Pierce Xinning Zhang Vikas Trivedi	Adam Z Rosenthal Kaitlyn S Lucey Elizabeth A Ottesen Harry M T Choi Niles A Pierce Jared R Leadbetter	Proceedings of the National Academy of Sciences of the United States of America
Analysis of the host transcriptome from demyelinating spinal cord of murine coronavirus-infected mice.	2013-09-18	Fan Li	Ruth Elliott Isabelle Dragomir Ming Ming W Chua Brian D Gregory Susan R Weiss	PLoS ONE
Differentiating progressive from nonprogressive T1 bladder cancer by gene expression profiling: applying RNA-sequencing analysis on archived specimens.	2013-09-18	John Quackenbush	Xuanhui Sharron Lin Lan Hu Kirley Sandy Mick Correll Chin-Lee Wu William Scott McDougal	Urologic Oncology
Epstein-Barr virus and human herpesvirus 6 detection in a non-Hodgkin's diffuse large B-cell lymphoma cohort by using RNA sequencing.	2013-09-18	Melody Baddoo Tina O'Grady	Michael J Strong Zhen Lin Guorong Xu Melody Baddoo Chris Parsons Kun Zhang Christopher M Taylor Erik K Flemington	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 Mathias Uhlén	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 Jong Kyoung Kim Aleksandra A Kołodziejczyk Xiuwei Zhang Bianka Baying	Nature Methods
Next-generation sequence analysis of cancer xenograft models.	2013-09-26	Fernando J Rossello Kara L. Britt Richard W. Tothill Luciano G. Martelotto Jason Li Luigi Marchionni	Kieren D Marini Jeanette Falzon David M Thomas Craig D Peacock Samara Bennett Erwin Tantoso Tracey Brown Philip Chan D Neil Watkins	PLoS ONE
Taf7l cooperates with Trf2 to regulate spermiogenesis.	2013-09-30	Ke Zheng Ivan Grubisic Tommy Kaplan	Haiying Zhou Ying He P Jeremy Wang Robert Tjian	Proceedings of the National Academy of Sciences of the United States of America
Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria.	2013-09-30	Margaret F Romine Ronald Taylor	Bobbie-Jo M Webb Robertson Lye Meng Markillie Margrethe H Serres Bryan E Linggi Joshua T Aldrich Eric A Hill Mary S Lipton H Steven Wiley	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 Zhen Chen Stephen A Krawetz	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 James A Sweigard Kirk J Czymmek Jeffrey L Caplan Sridhara G Kunjeti Saritha Kunjeti Vidhyavathi Raman Donald Y Kobayashi Nicole M Donofrio	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 Poh Ling Koh Sunil Ratnayake Cherie T Beahan Sarah M Wilson Antony Bacic	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 Siwen Jiang	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	Sonia Zorzet Tatiana Da Ros Maurizio Prato	Toxicology
Use of a capture-based pathogen transcript enrichment strategy for RNA-Seq analysis of the Francisella tularensis LVS transcriptome during infection of murine macrophages.	2013-10-14	David M Brazel	Zachary W Bent Mary B Tran-Gyamfi Rachelle Y Hamblin Victoria A VanderNoot Steven S Branda	PLoS ONE
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 Fiona C McKay	Grant P Parnell Prudence N Gatt Stephen Schibeci Malgorzata Krupa Jeannette Lechner-Scott Simon Broadley Christopher Liddle Steve Vucic Graeme J Stewart David R Booth	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 Zhan Zhang Gavin Meredith Christopher Adams Ranjan J Perera	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 Albrecht Bindereif	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 Peng Cui Hao Chen Shahjahan Ali	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 Jörn Kalinowski	BMC Genomics
Quantitative assessment of single-cell RNA-sequencing methods.	2013-10-20	Barbara Treutlein Piero Dalerba	Angela R Wu Norma F Neff Tomer Kalisky Michael E Rothenberg Francis M Mburu Gary L Mantalas Sopheak Sim Michael F Clarke Stephen R Quake	Nature Methods
HAMR: high-throughput annotation of modified ribonucleotides.	2013-10-22	Otto Valladares	Paul Ryvkin Yuk Yee Leung Ian M Silverman Micah Childress Isabelle Dragomir Brian D Gregory Li-San Wang	RNA
Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe.	2013-10-23	Monika Gullerova Jürg Bähler Nicholas Jarvis Proudfoot	Margarita Schlackow Samuel Marguerat Jürg Bähler Radek Erban	RNA
Parallel deep transcriptome and proteome analysis of zebrafish larvae	2013-10-24	Christiaan V. Henkel	Magnus Palmblad Ron P Dirks Annemarie H Meijer André M Deelder Herman P Spaink	BMC Research Notes
Integrated transcriptomic and proteomic analysis of the global response of Wolbachia to doxycycline-induced stress.	2013-10-24	Alistair C. Darby Dong Xia	A Christina Gill Stuart D Armstrong Catherine S Hartley Jonathan M Wastling Benjamin L Makepeace	The ISME Journal
IMG 4 version of the integrated microbial genomes comparative analysis system.	2013-10-27	Natalia Ivanova Nikos Kyrpides Tanja Woyke Neha Varghese Konstantinos Billis	Victor M Markowitz I-Min A Chen Krishna Palaniappan Ken Chu Ernest Szeto Manoj Pillay Anna Ratner Jinghua Huang Marcel Huntemann Iain Anderson Konstantinos Mavromatis Amrita Pati	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 Pingxi Xu Cherre S B da Silva Carlos Ueira-Vieira	Proceedings of the National Academy of Sciences of the United States of America
Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps.	2013-10-29	Ross C Hardison Manolis Kellis	Ali Mortazavi Shirley Pepke Camden Jansen Georgi K Marinov Jason Ernst Richard M Myers Barbara J Wold	Genome Research
A unified model for yeast transcript definition.	2013-10-29	Harm van Bakel Corey Nislow Carl G de Boer	Kyle Tsui Joyce Li Quaid D Morris Jack F Greenblatt Timothy R Hughes	Genome Research
An integrated model of the transcriptome of HER2-positive breast cancer.	2013-11-01	Kevin J Thompson Xiaojia Tang Krishna R Kalari Richard W. Joseph Zhifu Sun	Brian M Necela Melissa Lau Jeanette E Eckel-Passow Jennifer M Kachergus S Keith Anderson Saurabh Baheti Jennifer M Carr Tiffany R Baker Poulami Barman Derek C Radisky Sarah A McLaughlin High-seng Chai Stephan Camille David Rossell Yan W Asmann E Aubrey Thompson Edith A Perez	PLoS ONE
Identification of molecular tumor markers in renal cell carcinomas with TFE3 protein expression by RNA sequencing.	2013-11-01	Mark Rubin	Dorothee Pflueger Andrea Sboner Martina Storz Jasmine Roth Eva Compérat Elisabeth Bruder Peter Schraml Holger Moch	Neoplasia
Global aspects of pacC regulation of pathogenicity genes in Colletotrichum gloeosporioides as revealed by transcriptome analysis.	2013-11-01	Michael Thon Serenella Sukno	Noam Alkan Xiangchun Meng Gilgi Friedlander Eli Reuveni Amir Sherman Robert Fluhr Dov Prusky	Molecular Plant-Microbe Interactions
Systematic evaluation of spliced alignment programs for RNA-seq data	2013-11-03	Jennifer Harrow Roderic Guigó i Serra Tamara Steijger Pär G Engström Gregory R Grant Gunnar Rätsch Nick Goldman Paul Bertone	Botond Sipos André Kahles Tim J Hubbard RGASP Consortium	Nature Methods
Assessment of transcript reconstruction methods for RNA-seq.	2013-11-03	Timothy John Phillip Hubbard Jennifer Harrow Felix Kokocinski Roderic Guigó i Serra Tamara Steijger Pär G Engström Josep F. Abril Paul Bertone	RGASP Consortium	Nature Methods
Dysregulation of synaptogenesis genes antecedes motor neuron pathology in spinal muscular atrophy.	2013-11-04	Anna Maria Pinto Christopher Dengler	Zhenxi Zhang Lili Wan Wei Wang Michael G Berg Isabela Oliva Larry N Singh Zhi Wei Gideon Dreyfuss	Proceedings of the National Academy of Sciences of the United States of America
Serotonergic neuron regulation informed by in vivo single-cell transcriptomics.	2013-11-05	Tamas Bartfai	Jennifer M Spaethling David Piel Hannah Dueck Peter T Buckley Jacqueline F Morris Stephen A Fisher Jaehee Lee Jai-Yoon Sul Junhyong Kim Sheryl G Beck James H Eberwine	FASEB Journal
Surfing transcriptomic landscapes. A step beyond the annotation of chromosome 16 proteome.	2013-11-05	Miguel Marcilla Cristina Ruiz-Romero Joan J Bech-Serra Oscar Gallardo Gorka Prieto Concha Gil Joaquín Abian Marta Mendes Irene Orera Noelia Dasilva Kerman Aloria María I Mora Manuel Fuentes	Víctor Segura Juan Alberto Medina-Aunon Salvador Martínez-Bartolomé Oreto Antúnez Jesús M Arizmendi Mikel Azkargorta Silvia Barceló-Batllori Jabier Beaskoetxea Francisco Blanco Mariana B Monteiro David Cáceres Francesc Canals Monserrat Carrascal José Ignacio Casal Felipe Clemente Nuria Colomé Paula Díaz Félix Elortza Patricia Fernández-Puente Severine I Gharbi Carmen González-Tejedo María Luisa Hernáez Manuel Lombardía Maria Lopez-Lucendo José M Mato Eliandre Oliveira Alberto Pascual-Montano Manuel M Sánchez del Pino Daniel Tabas-Madrid Maria L Valero Vital Vialas Joan Villanueva Juan Pablo Albar Fernando J Corrales	Journal of Proteome Research
Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation.	2013-11-07	Alexander van Oudenaarden Wenqian Hu Jiahai Shi	Juan R Alvarez-Dominguez Bingbing Yuan Staphany S Park Austin A Gromatzky Harvey F Lodish	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 Emma Yue Zhang Shiaw-Lin Wu Rui Chen Michael Snyder William S Hancock	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 Günter Gisselmann	Stavros Manteniotis Ramona Lehmann Caroline Flegel Felix Vogel Adrian Hofreuter Benjamin S P Schreiner Janine Altmüller Christian Becker Nicole Schöbel Günter Gisselmann	PLoS ONE
Deletion of Asxl1 results in myelodysplasia and severe developmental defects in vivo	2013-11-11	Jinfeng Liu Xinyang Zhao Eunhee Kim Omar Abdel-Wahab	Jie Gao Mazhar Adli Anwesha Dey Thomas Trimarchi Young Rock Chung Cem Kuscu Todd Hricik Delphine Ndiaye-Lobry Lindsay M Lafave Richard Koche Alan H Shih Olga A Guryanova Sheng Li Suveg Pandey Joseph Y Shin Leon Telis Parva K Bhatt Sebastien Monette Christopher E Mason Christopher Y Park Bradley E Bernstein Iannis Aifantis Ross L Levine	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 Linnea Nyberg Jonatan Halvardson Manfred Grabherr Lucia Cavelier Lars Feuk	BMC Biotechnology
Mapping genetic modifiers of survival in a mouse model of Dravet syndrome.	2013-11-14	Jennifer A Kearney	A R Miller N A Hawkins C E McCollom	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 Qing-Yu He Gong Zhang Tong Wang	Jiayong Zhong Jiahui Guo Zhipeng Chen Lijuan Yang	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 Xiaojing Wang Jing Wang Ajaz A Bhat Punita Dhawan Ming Li Bing Zhang Robbert J C Slebos	Cancer Research
Global analysis of differentially expressed genes and proteins in the wheat callus infected by Agrobacterium tumefaciens	2013-11-20	Dongwen Lv	Xiaohong Zhou Ke Wang Chengjun Wu Jiarui Li Pei Zhao Zhishan Lin Lipu Du Yueming Yan Xingguo Ye	PLoS ONE
Phenotypic and transcriptional fidelity of patient-derived colon cancer xenografts in immune-deficient mice	2013-11-20	Edus H Warren	Jeffrey Chou Matthew P Fitzgibbon Christie-Lynn L Mortales Andrea M H Towlerton Melissa P Upton Raymond S Yeung Martin W McIntosh	PLoS ONE
Global bidirectional transcription of the Epstein-Barr virus genome during reactivation.	2013-11-20	Melody Baddoo Tina O'Grady	Subing Cao Michael J Strong Monica Concha Xia Wang Sandra Splinter Bondurant Marie Adams Melody Baddoo Sudesh K Srivastav Zhen Lin Claire Fewell Qinyan Yin Erik K Flemington	Journal of Virology
DUX4 binding to retroelements creates promoters that are active in FSHD muscle and testis.	2013-11-21	Zizhen Yao Silvère M van der Maarel	Janet M Young Jennifer L Whiddon Bhavatharini Kasinathan Lauren Snider Linda N Geng Judit Balog Rabi Tawil Stephen J Tapscott	PLOS Genetics
Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia.	2013-11-21	Víctor Quesada Núria López-Bigas Alfonso Valencia Carlos López Otín Roderic Guigó i Serra Jean Monlong Panagiotis Papasaikas Simone Ecker Guillem Clot Sarah Djebali Pedro G Ferreira Rory Johnson Daniel Rico Gonzalo Gómez-López Xose S. Puente David G. Pisano María Rozman José I Martín-Subero Dolors Colomer Elias Campo	Pedro Jares Alejandra Martínez-Trillos Neus Villamor Abel González-Pérez David G Knowles Mónica López-Guerra Cristina Royo Maite Cazorla Magda Pinyol Marta Aymerich Marta Kulis David Tamborero Anaïs Gouin Julie Blanc Marta Gut Ivo Gut Armando López-Guillermo	Genome Research
RNA-seq reveals the RNA binding proteins, Hfq and RsmA, play various roles in virulence, antibiotic production and genomic flux in Serratia sp. ATCC 39006.	2013-11-22	Adam J Reid Joshua P Ramsay Laurent Gatto Lars Barquist	Nabil M Wilf Neil R Williamson Nicholas J Croucher Svenja S Hester David Goulding Kathryn S Lilley Robert A Kingsley Gordon Dougan George Pc Salmond	BMC Genomics
Assessment of myometrial transcriptome changes associated with spontaneous human labour by high-throughput RNA-seq.	2013-11-22	Jonathan D. Moore Andrew M Blanks	Yi-Wah Chan Hugo A van den Berg Siobhan Quenby	Experimental Physiology
Characterization of the human ESC transcriptome by hybrid sequencing.	2013-11-26	Harm van Bakel Renee Reijo Pera	Kin Fai Au Vittorio Sebastiano Pegah Tootoonchi Afshar Jens Durruthy Durruthy Lawrence Lee Brian A Williams Eric E Schadt Jason G Underwood Wing Hung Wong	Proceedings of the National Academy of Sciences of the United States of America
Transcriptional regulation of two conceptus interferon tau genes expressed in Japanese black cattle during peri-implantation period.	2013-11-27	So Nakagawa	Toshihiro Sakurai Min-Su Kim Hanako Bai Rulan Bai Junyou Li Kwan-Sik Min Atsushi Ideta Yoshito Aoyagi Kazuhiko Imakawa	PLoS ONE
An infection-relevant transcriptomic compendium for Salmonella enterica Serovar Typhimurium.	2013-12-01	Carsten Kröger Shabarinath Srikumar Kristian Händler Karsten Hokamp	Aoife Colgan Sathesh K Sivasankaran Disa L Hammarlöf Rocío Canals Joe E Grissom Tyrrell Conway Jay C D Hinton	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 Hyun-Jin Yang Marie-Audrey I Kautzmann Matthew Brooks Jacob Nellissery Bernward Klocke Martin Seifert	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 Mark Baker	Manveen K Sethi Joshua T Smith Nicolle H Packer 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 Kevin P McCormick Sridhara G Kunjeti Matthew T Ralston Eleftherios T Papoutsakis	BMC Genomics
Simultaneous transcriptional profiling of bacteria and their host cells	2013-12-04	Claire M. Fraser Naomi Sengamalay Marcus C. Chibucos Amol C Shetty	Michael S Humphrys Todd Creasy Yezhou Sun Elliott F Drabek Umar Farooq Naomi Sengamalay Sandy Ott Huizhong Shou Patrik M Bavoil Anup Mahurkar Garry S A Myers	PLoS ONE
Vespucci: a system for building annotated databases of nascent transcripts.	2013-12-04	Terry Gaasterland Minna U Kaikkonen Christopher K Glass	Karmel A Allison	Nucleic Acids Research
A platform independent RNA-Seq protocol for the detection of transcriptome complexity.	2013-12-05	Graziano Pesole Flaviana Marzano Mariano Francesco Caratozzolo Ivana Kurelac D D'Elia Anna Maria D'Erchia Flavio Licciulli Ernesto Picardi	Claudia Calabrese Marina Mangiulli Caterina Manzari Anna Maria Paluscio Sabino Liuni Marcella Attimonelli Giuseppe Gasparre Anna Maria Porcelli Elisabetta Sbisà Apollonia Tullo	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 Kalle von Feilitzen Linn Fagerberg Jan Mulder Mikael Huss Jochen Schwenk Jacob Odeberg Peter Nilsson Per Oksvold	Björn M Hallström Caroline Kampf Dijana Djureinovic Masato Habuka Simin Tahmasebpoor Angelika Danielsson Karolina Edlund Anna Asplund Evelina Sjöstedt Emma Lundberg Cristina Al-Khalili Szigyarto Marie Skogs Jenny Ottosson Takanen Holger Berling Hanna Tegel Cecilia Lindskog Frida Danielsson Adil Mardinoglu Asa Sivertsson Kalle von Feilitzen Mattias Forsberg Martin Zwahlen IngMarie Olsson Sanjay Navani Fredrik Ponten Mathias Uhlén	Molecular & Cellular Proteomics
Fermentation stage-dependent adaptations of Bacillus licheniformis during enzyme production.	2013-12-06	Sandra Wiegand Heiko Liesegang Rolf Daniel	Birgit Voigt Dirk Albrecht Johannes Bongaerts Stefan Evers Michael Hecker	Microbial Cell Factories
ETV6-NTRK3 is a common chromosomal rearrangement in radiation-associated thyroid cancer.	2013-12-10	Tetiana Bogdanova Mark P Little	Rebecca J Leeman-Neill Lindsey M Kelly Pengyuan Liu Alina V Brenner Viktoria N Evdokimova Maureen Hatch Liudmyla Y Zurnadzy Marina N Nikiforova Ning J Yue Miao Zhang Kiyohiko Mabuchi Mykola D Tronko Yuri E Nikiforov	Cancer
Next generation sequencing analysis of human platelet PolyA+ mRNAs and rRNA-depleted total RNA.	2013-12-11	Abdimajid Osman	Antheia Kissopoulou Jon Jonasson Tomas L Lindahl	PLoS ONE
Transcriptome changes in the porcine endometrium during the preattachment phase.	2013-12-12	Susanne E. Ulbrich	Anastazia Samborski Alexander Graf Stefan Krebs Barbara Kessler Myriam Reichenbach Horst-Dieter Reichenbach Stefan Bauersachs	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 Lee W Cohnstaedt Christopher Saski Mark Fife Simon Carpenter	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 Elias Bou Samra Anthony Boureux Alban Mancheron Florence Rufflé Qiang Bai John De Vos Thérèse Commes	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 Gert Hulselmans Zeynep Kalender Atak Kim De Keersmaecker Peter Vandenberghe Jan Cools Stein Aerts	Valentina Gianfelici Arun George Devasia Ellen Geerdens Nicole Mentens Sabina Chiaretti Kaat Durinck Anne Uyttebroeck Jacqueline Cloos Robin Foà Frank Speleman	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 Olivier Bouchez Julien Sarry Nathalie Marsaud Florent Woloszyn Philippe Mulsant Beatrice Mandon-Pepin	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 Mado L Vandewoestyne Steven R Head Filip C W Van Nieuwerburgh Dieter L D Deforce	BMC Plant Biology
Quantitative single-cell RNA-seq with unique molecular identifiers.	2013-12-22	Sten Linnarsson Peter Lönnerberg	Saiful Islam Amit Zeisel Simon Joost Gioele La Manno Pawel Zajac Maria Kasper Peter Lönnerberg Sten Linnarsson	Nature Methods
Divergent transcription is associated with promoters of transcriptional regulators.	2013-12-23	Marc Garibal Jean-Christophe Andrau Jean Imbert Salvatore Spicuglia	Cyrille Lepoivre Mohamed Belhocine Aurélie Bergon Aurélien Griffon Miriam Yammine Laurent Vanhille Joaquin Zacarias-Cabeza Frederic Koch Muhammad Ahmad Maqbool Romain Fenouil Beatrice Loriod Hélène Holota Marta Gut Ivo Gut Denis Puthier	BMC Genomics
Lsh regulates LTR retrotransposon repression independently of Dnmt3b function.	2013-12-24	Colin A. Semple	Donncha S Dunican Hazel A Cruickshanks Masako Suzuki Tracey Davey Robert J Arceci John Greally Ian R Adams 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 Zhong Chen	Zhenqing Ye Xun Lan Stephen Hara Benjamin Sunkel Tim H-M Huang Qianben Wang Victor X Jin	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 Benjamin Buer Aleksandra Polatajko Réka Nagy Eva Koebke René Flisch Marcel Bucher	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 Ning Liu Laetitia Virlouvet Michael Fromm Zoya Avramova	BMC Plant Biology
Transcriptomics reveal several gene expression patterns in the piezophile Desulfovibrio hydrothermalis in response to hydrostatic pressure	2014	Christian Tamburini	Amira Amrani Aurélie Bergon Hélène Holota Marc Garel Bernard Ollivier Jean Imbert Alain Dolla Nathalie Pradel	PLoS ONE
Melanocytes in the skin--comparative whole transcriptome analysis of main skin cell types	2014	Viljar Jaks Ene Reimann Q24546281 Eero Vasar Q16408409	Paula Reemann Sten Ilmjärv Orm Porosaar Helgi Silm	PLoS ONE
Deep RNA sequencing reveals hidden features and dynamics of early gene transcription in Paramecium bursaria chlorella virus 1	2014	Jean-Jack M Riethoven Guillaume Blanc David D. Dunigan	Michael Mozar Irina V Agarkova James R Gurnon Giane Yanai-Balser Janet M Rowe Yuannan Xia James L Van Etten	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 Vyacheslav Amstislavskiy Julia Starmann Ingrid Osprian Hendrik Hache Holger Sültmann Michael Trauner Kurt Zatloukal Christoph Wierling	PLoS ONE
Mining gene expression data for pollutants (dioxin, toluene, formaldehyde) and low dose of gamma-irradiation	2014	Darya Peregudova Alexey A. Dmitriev Sergey V Mylnikov Peter O Fedichev Nataliya Melnikova Anna V Kudryavtseva Mikhail V Shaposhnikov Alexey A Moskalev	Anastasia Snezhkina Valeria Kogan Ekaterina Plyusnina Leonid Uroshlev Sergey Plusnin	PLoS ONE
The SLE transcriptome exhibits evidence of chronic endotoxin exposure and has widespread dysregulation of non-coding and coding RNAs	2014	Angela M Yu Patrícia Costa Reis	Lihua Shi Zhe Zhang Wei Wang Zhi Wei Ehtisham Akhter Kelly Maurer Li Song Michelle Petri Kathleen E Sullivan	PLoS ONE
Establishment of highly tumorigenic human colorectal cancer cell line (CR4) with properties of putative cancer stem cells	2014	Iwao Ojima	Rebecca A Rowehl Stephanie Burke Agnieszka B Bialkowska Donald W Pettet Leahana Rowehl Ellen Li Eric Antoniou Yuanhao Zhang Roberto Bergamaschi Kenneth R Shroyer Galina I Botchkina	PLoS ONE
RNA-sequencing analysis of HepG2 cells treated with atorvastatin	2014	Daniel Sachse Jens P. Berg	Camilla Stormo Marianne K Kringen Robert Lyle Ole Kristoffer Olstad Armin P Piehler	PLoS ONE
The oncogenic MicroRNA Hsa-miR-155-5p targets the transcription factor ELK3 and links it to the hypoxia response	2014	Alain C Jung Bohdan Wasylyk	E Douglas Robertson Christine Wasylyk Tao Ye	PLoS ONE
Genetics of gene expression in CNS	2014	Robert W. Williams	Ashutosh K Pandey	International Review of Neurobiology
Towards a computational model of a methane producing archaeum	2014	Piyush Labhsetwar Zaida Luthey-Schulten	Joseph R Peterson Jeremy R Ellermeier Petra R A Kohler Ankur Jain Taekjip Ha William W Metcalf	Archaea
Zinc finger transcription factors displaced SREBP proteins as the major Sterol regulators during Saccharomycotina evolution	2014-01	Sarah L Maguire Geraldine Butler Theodore C White Kenneth H. Wolfe Jean-Marc Nicaud	Can Wang Linda M Holland François Brunel Cécile Neuvéglise Martin Zavrel	PLOS Genetics
CellFinder: a cell data repository	2014-01	Stefanie Seltmann Fritz Lekschas Mariana Lara Neves Harald Stachelscheid Nancy Mah Andreas Kurtz	Jean-Fred Fontaine Miguel A Andrade-Navarro Ulf Leser	Nucleic Acids Research
Isl1 and Pou4f2 form a complex to regulate target genes in developing retinal ganglion cells	2014-01-01	Xiuqian Mu	Renzhong Li Fuguo Wu Raili Ruonala Darshan Sapkota Zihua Hu	PLoS ONE
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 Pawel Zajac Peter Lönnerberg 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 Rickard Sandberg	Simone Picelli Asa K Björklund Gösta Winberg Sven Sagasser	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 Jeff H. Chang David A. Baltrus	Tatiana S Mucyn Scott Yourstone Abigail L Lind Surojit Biswas Jason S Cumbie Corbin D Jones Jeffery L Dangl Sarah R Grant	PLOS Pathogens
RNA-Seq analysis of the toxicant-induced transcriptome of the marine diatom, Ceratoneis closterium.	2014-01-04	Philippe Moncuquet	Sharon E Hook Hannah L Osborn Francesca Gissi Natalie A Twine Marc R Wilkins Merrin S Adams	Marine Genomics
The histone-H3K4-specific demethylase KDM5B binds to its substrate and product through distinct PHD fingers.	2014-01-09	Brian D Strahl	Brianna J Klein Lianhua Piao Yuanxin Xi Hector Rincon-Arano Scott B Rothbart Danni Peng Hong Wen Connie Larson Xi Zhang Xia Zheng Michael A Cortazar Pedro V Peña Anthony Mangan David L Bentley Mark Groudine Wei Li Xiaobing Shi Tatiana G Kutateladze	Cell Reports
Differential protein occupancy profiling of the mRNA transcriptome.	2014-01-13	Markus Landthaler	Markus Schueler Mathias Munschauer Lea Haarup Gregersen Ana Finzel Alexander Loewer Wei Chen 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 Maria Nagy	Journal of Visualized Experiments
GuavaH: a compendium of host genomic data in HIV biology and disease.	2014-01-15	Paul J. McLaren Angela Ciuffi Jacques Fellay	István Bartha Amalio Telenti	Retrovirology
The development of a high density linkage map for black tiger shrimp (Penaeus monodon) based on cSNPs.	2014-01-17	Matthew Baranski Nicholas A. Robinson	Gopalapillay Gopikrishna Vinaya Kumar Katneni Mudagandur S Shekhar Jayakani Shanmugakarthik Sarangapani Jothivel Chavali Gopal Pitchaiyappan Ravichandran Matthew Kent Mariann Arnyasi Alphis G Ponniah	PLoS ONE
Transcriptome analysis of alternative splicing events regulated by SRSF10 reveals position-dependent splicing modulation.	2014-01-17	Wenwu Wu James L. Manley	Xuexia Zhou Huang Li Yuanming Cheng Ning Wei Jie Zong Xiaoyan Feng Zhiqin Xie Dai Chen Hui Wang Ying Feng	Nucleic Acids Research
A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis	2014-01-17	Lior Pachter Harold Pimentel	Marilyn Parra Sherry Gee Dana Ghanem Xiuli An Jie Li Narla Mohandas John G Conboy	Nucleic Acids Research
Set5 and Set1 cooperate to repress gene expression at telomeres and retrotransposons.	2014-01-17	Sean R Collins Devin A King Ashby Morrison Or Gozani	Glòria Mas Martín Erin M Green Pablo E Garcia-Nieto Richard Alexander Nevan J Krogan	Epigenetics
ALEA: a toolbox for allele-specific epigenomics analysis.	2014-01-21	Mohammad M Karimi Torsten Möller Matthew C. Lorincz	Hamid Younesy Alireza Heravi-Moussavi Jeffrey B Cheng Joseph F Costello Steven J M Jones	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 Kumar Sudesh Minami Matsui	PLoS ONE
glbase: a framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data.	2014-01-24	Andrew Paul Hutchins	Ralf Jauch Mateusz Dyla Diego Miranda-Saavedra	Cell regeneration (London, England)
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 Matthias Kohl	Ana Antunes-Martins Margarita Calvo John Grist Werner Rust Ramona Schmid Tobias Hildebrandt Stephen B McMahon David L H Bennett	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 Arleen Sanny Stephanie Chan Edward M Bertram Andy Tan Christopher C Goodnow T Daniel Andrews	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 Manuraj Singh Ravinder K Kanda Michael B Yee Paul Kellam Michael Hollinshead Paul R Kinchington Edel A O'Toole	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 Mara Rosenberg	Angela N Brooks Peter S Choi Luc de Waal Tanaz Sharifnia Marcin Imielinski Gordon Saksena Chandra Sekhar Pedamallu Andrey Sivachenko Juliann Chmielecki Michael S Lawrence David S DeLuca Gad Getz	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 Franziska Paul Alexander Mildner Steffen Jung	Diego Adhemar Jaitin Ephraim Kenigsberg Hadas Keren-Shaul Naama Elefant Irina Zaretsky Nadav Cohen Amos Tanay Ido Amit	Science
SOX9: a stem cell transcriptional regulator of secreted niche signaling factors.	2014-02-01	Deyou Zheng Elaine Fuchs Maria Genander	Meelis Kadaja Brice E Keyes Mingyan Lin H Amalia Pasolli Lisa Polak Nicole Stokes	Genes & Development
The Cryptococcus neoformans transcriptome at the site of human meningitis.	2014-02-04	Yuan Chen David R. Boulware	Dena L Toffaletti Jennifer L Tenor Anastasia P Litvintseva Charles Fang Thomas G Mitchell Tami R McDonald Kirsten Nielsen Tihana Bicanic John R Perfect	mBio
Tissue-specific RNA-Seq in human evoked inflammation identifies blood and adipose LincRNA signatures of cardiometabolic diseases.	2014-02-06	Rachel L Ballantyne Muredach P. Reilly	Yichuan Liu Jane F Ferguson Chenyi Xue Ian M Silverman Sager J Gosai Jacquelyn Serfecz Michael P Morley Brian D Gregory Mingyao Li	Arteriosclerosis, Thrombosis, and Vascular Biology
Dormancy within Staphylococcus epidermidis biofilms: a transcriptomic analysis by RNA-seq.	2014-02-07	Rui Vitorino Gerald B Pier Manuel Vilanova	Virginia Carvalhais Angela França Filipe Cerca Nuno Cerca	Applied Microbiology and Biotechnology
ALS-associated mutation FUS-R521C causes DNA damage and RNA splicing defects.	2014-02-10	Erik D. Roberson James Shorter Eric J Huang	Haiyan Qiu Sebum Lee Yulei Shang Wen-Yuan Wang Kin Fai Au Sherry Kamiya Sami J Barmada Steven Finkbeiner Hansen Lui Caitlin E Carlton Amy A Tang Michael C Oldham Hejia Wang Anthony J Filiano Warren G Tourtellotte Bin Chen Li-Huei Tsai	Journal of Clinical Investigation
Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia.	2014-02-13	Ana Conesa Corey Nislow Eduardo Larriba José Martín-Nieto Luis V Lopez-Llorca	María D L A Jaime José Carbonell-Caballero Joaquín Dopazo	Fungal Genetics and Biology
Dynamic recruitment of amino acid transporters to the insect/symbiont interface.	2014-02-16	John P. McCutcheon Rebecca P. Duncan Filip Husník	James T Van Leuven Donald G Gilbert Liliana M Dávalos Alex C C Wilson	Molecular Ecology
Interaction of vitamin D with membrane-based signaling pathways	2014-02-18	María Jesús Larriba	José Manuel González-Sancho Félix Bonilla Alberto Muñoz	Frontiers in Physiology
Ammonium induces differential expression of methane and nitrogen metabolism-related genes in Methylocystis sp. strain SC2.	2014-02-18	Werner Liesack	Bomba Dam Somasri Dam Yongkyu Kim	Environmental Microbiology
Transcriptomic analysis reveals key regulators of mammogenesis and the pregnancy-lactation cycle.	2014-02-19	Songnian Hu	YuanYuan Zhou Wei Gong JingFa Xiao JiaYan Wu LinLin Pan XiaoNuan Li XuMin Wang WeiWei Wang Jun Yu	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 Yves Collette Angela Nebbioso Antonello Mai Hugues de Thé Mariarosaria Conte Sergio Valente Lucia Altucci	Floriana De Bellis Vincenzo Carafa Francesca Petraglia Filomena Matarese Kees-Jan Françoijs Julien Ablain Rèmy Castellano Armelle Goubard Amit Mandoli Joost H A Martens Hendrik G Stunnenberg	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 Chao Li Andrew Gascho Landis Guiling Wang James Stoeckel	PLoS ONE
AnaLysis of Expression on human chromosome 21, ALE-HSA21: a pilot integrated web resource.	2014-02-25	Claudia Angelini Valerio Costa Maria Rosaria Ambrosio	Margherita Scarpato Roberta Esposito Daniela Evangelista Marianna Aprile Alfredo Ciccodicola	Database
Metabolic reprogramming during purine stress in the protozoan pathogen Leishmania donovani	2014-02-27	Jessica L Martin Vladislav A Petyuk Kristin E Burnum Richard D. Smith	Phillip A Yates Radika Soysa Joshua F Alfaro Feng Yang Karl K Weitz David G Camp Phillip A Wilmarth Larry L David Gowthaman Ramasamy Peter J Myler Nicola S Carter	PLOS Pathogens
The path to triacylglyceride obesity in the sta6 strain of Chlamydomonas reinhardtii.	2014-02-28	Sean D Gallaher Taylor L Weiss David Casero Shannon L Johnson Matteo Pellegrini	Ursula Goodenough Ian Blaby Carrie Goodson Jae-Hyeok Lee Sabeeha S Merchant Robyn Roth Jannette Rusch Manmilan Singh James G Umen Tuya Wulan	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 Edward M Fox Aidan Coffey	Aidan Casey Edward M Fox Aidan Coffey Olivia McAuliffe Kieran Jordan	Frontiers in Microbiology
Transcriptome profiling of human hippocampus dentate gyrus granule cells in mental illness	2014-03-04	Eric Haugen	R Kohen A Dobra J H Tracy	Translational Psychiatry
Differential transcriptomic analysis by RNA-Seq of GSNO-responsive genes between Arabidopsis roots and leaves.	2014-03-04	Juan C Begara-Morales Francisco J. Corpas	Beatriz Sánchez-Calvo Francisco Luque María O Leyva-Pérez Marina Leterrier Juan B Barroso	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 Petr Kotlík	S Marková	Heredity
The human testis-specific proteome defined by transcriptomics and antibody-based profiling.	2014-03-05	Linn Fagerberg	D Djureinovic B Hallström A Danielsson C Lindskog M Uhlén F Pontén	Molecular Human Reproduction
Overexpression of molecular chaperone genes in nucleomorph genomes.	2014-03-06	Patrick J. Keeling	Yoshihisa Hirakawa Shigekatsu Suzuki John M Archibald Ken-ichiro Ishida	Molecular Biology and Evolution
RNA- and antibody-based profiling of the human proteome with focus on chromosome 19.	2014-03-12	Linn Fagerberg Mathias Uhlén Per Oksvold	Charlotte Stadler Åsa Sivertsson Martin Zwahlen Björn M Hallström Emma Lundberg Mathias Uhlén	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	Evgeny A Moskalev Judith Frohnauer Arno Dimmler Thomas Schubert Carsten Boltze Helmut König Florian Fuchs Horia Sirbu Ralf J Rieker Abbas Agaimy Arndt Hartmann Florian Haller	Lung Cancer
Lacking alignments? The next-generation sequencing mapper segemehl revisited.	2014-03-13	Peter F. Stadler	Christian Otto Steve Hoffmann	Bioinformatics
The human liver-specific proteome defined by transcriptomics and antibody-based profiling.	2014-03-19	Jens Nielsen Linn Fagerberg	Caroline Kampf Adil Mardinoglu Björn M Hallström Karolina Edlund Emma Lundberg Fredrik Pontén Mathias Uhlen	FASEB Journal
Genomics of CpG methylation in developing and developed zebrafish	2014-03-21	David M McGaughey	Hatice Ozel Abaan Ryan M Miller Peter A Kropp Lawrence C Brody	G3
The characteristic direction: a geometrical approach to identify differentially expressed genes.	2014-03-21	Avi Ma'ayan	Neil R Clark Kevin S Hu Axel S Feldmann Yan Kou Edward Y Chen Qiaonan Duan	BMC Bioinformatics
From root to fruit: RNA-Seq analysis shows that arbuscular mycorrhizal symbiosis may affect tomato fruit metabolism	2014-03-21	Matteo Chialva Paola Bonfante	Inès Zouari Alessandra Salvioli Mara Novero Laura Miozzi Gian Carlo Tenore Paolo Bagnaresi	BMC Genomics
spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.	2014-03-23	Albin Sandelin Kristoffer Vitting-Seerup Johannes Waage Bo Torben Porse		BMC Bioinformatics
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.	2014-03-23	John L. Rinn	Cole Trapnell Davide Cacchiarelli Jonna Grimsby Prapti Pokharel Shuqiang Li Michael Morse Niall J Lennon Kenneth J Livak Tarjei S Mikkelsen	Nature Biotechnology
RNA-seq analysis identifies an intricate regulatory network controlling cluster root development in white lupin	2014-03-25	Oliver Berkowitz James Whelan	David Secco Huixia Shou	BMC Genomics
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 Daniel Guariz Pinheiro Ronan Rivallan Vincent Le Guen Marisa Fabiana Nicolás Viviani Ribeiro Rocha Milena Magalhães Alexandra Lehmkuhl Gerber Antonio Figueira Júlio Cézar de Mattos Cascardo AnaTereza Ribeiro de Vasconcelos Wilson Araújo Silva Luiz Lehmann Coutinho Dominique Garcia	BMC Genomics
Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing.	2014-03-27	Hideya Kawaji Masayoshi Itoh Piero Carninci	Marina Lizio Mutsumi Kanamori-Katayama Ai Kaiho Hiromi Nishiyori-Sueki Jay W Shin Miki Kojima-Ishiyama Mitsuoki Kawano Mitsuyoshi Murata Noriko Ninomiya-Fukuda Sachi Ishikawa-Kato Sayaka Nagao-Sato Shohei Noma Yoshihide Hayashizaki Alistair R R Forrest FANTOM Consortium	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 Gianmaria Frigè Lorenzo Giordani Alberto Termanini Chiara Mozzetta Giovanna Borsellino	Valentina Saccone Silvia Consalvi Iros Barozzi Martina Sandoná Tammy Ryan Agustin Rojas-Muñoz Luca Madaro Pasquale Fasanaro Marco De Bardi Xin Sun Benoit G Bruneau Mark Mercola Saverio Minucci Pier Lorenzo Puri	Genes & Development
Differential meta-analysis of RNA-seq data from multiple studies	2014-03-29	Florence Jaffrézic	Andrea Rau Guillemette Marot Florence Jaffrézic	BMC Bioinformatics
Small regulatory RNAs in Archaea.	2014-03-31	L Randau Jörg Soppa	Julia Babski Lisa-Katharina Maier Ruth Heyer Katharina Jaschinski Daniela Prasse Dominik Jäger Ruth A Schmitz Anita Marchfelder	RNA Biology
Odorant and gustatory receptors in the tsetse fly Glossina morsitans morsitans	2014-04	Daniel Masiga Paul O. Mireji Alan Christoffels	George F O Obiero Steven R G Nyanjom Hugh M Robertson	PLOS Neglected Tropical Diseases
PRADA: pipeline for RNA sequencing data analysis	2014-04-01	Gad Getz	Wandaliz Torres-García Siyuan Zheng Andrey Sivachenko Rahulsimham Vegesna Qianghu Wang Rong Yao Michael F Berger John N Weinstein Roel G W Verhaak	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	Jenny Gu Gidon Winters Ann-Kathrin Huylmans Isabell Wienpahl Maximiliane Sparwel James A Coyer Jeanine L Olsen Thorsten B H Reusch	Marine Genomics
LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq.	2014-04-07	Daniel C. Jeffares Graeme C Smith Charalampos Rallis Jürg Bähler	Danny A Bitton Charalampos Rallis Graeme C Smith Yuan Y C Chen Sandra Codlin Samuel Marguerat Jürg Bähler	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 Nicholas Schurch Christian Cole Sara J Brown Geoffrey J. Barton	Alexander Sherstnev Junfang Song Céline Duc Kate G Storey W H Irwin McLean	PLoS ONE
Post-translational decrease in respiratory chain proteins in the Polg mutator mouse brain.	2014-04-10	David N Hauser	Allissa A Dillman Jinhui Ding Yan Li Mark R Cookson	PLoS ONE
Widespread use of non-productive alternative splice sites in Saccharomyces cerevisiae	2014-04-10	Matteo Pellegrini	Tadashi Kawashima Stephen Douglass Jason Gabunilas Guillaume F Chanfreau	PLOS Genetics
Mining of public sequencing databases supports a non-dietary origin for putative foreign miRNAs: underestimated effects of contamination in NGS.	2014-04-11	Juan Pablo Tosar Alfonso Cayota	Carlos Rovira Hugo Naya	RNA
Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq	2014-04-13	Doug Brownfield Barbara Treutlein	Angela R Wu Norma F Neff Gary L Mantalas F Hernan Espinoza Tushar J Desai Mark A Krasnow Stephen R Quake	Nature
VDR primary targets by genome-wide transcriptional profiling.	2014-04-13	Graziano Pesole Matteo Pallocca	Frauke Goeman Francesca De Nicola Paolo D'Onorio De Meo Berardino Elmi Tiziana Castrignanò Sabrina Strano Giovanni Blandino Maurizio Fanciulli Paola Muti	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 Jonathan S Weissman	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 Sharvari Gujja Sean M Sykes Qiandong Zeng Paul J Szaniszlo Zheng Wang	G3
Transcriptome profiling to identify genes involved in pathogenicity of Valsa mali on apple tree.	2014-04-16	Zhiyuan Yin	Xiwang Ke Na Song Qingqing Dai Ralf T Voegele Yangyang Liu Haiying Wang Xiaoning Gao Zhensheng Kang Lili Huang	Fungal Genetics and Biology
Structure and Function of Steroid Receptor RNA Activator Protein, the Proposed Partner of SRA Noncoding RNA	2014-04-17	Thomas Cech	David B McKay Linghe Xi Kristen K B Barthel	Journal of Molecular 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 Jason E. Stajich Christina A Cuomo Yuan Chen Gautam Chatterjee Kate L Ormerod Yen-Ping Hsueh James Fraser Tristan Rossignol Kaustuv Sanyal Guilhem Janbon Yong-Sun Bahn Steven Jones Piotr A Mieczkowski	Damien Paulet Edmond J Byrnes Vikas Yadav Nandita Mullapudi Chung-Chau Hon R Blake Billmyre François Brunel Weidong Chen Eve W L Chow Jean-Yves Coppée Anna Floyd-Averette Claude Gaillardin Kimberly J Gerik Jonathan Goldberg Sara Gonzalez-Hilarion Sharvari Gujja Joyce L Hamlin Giuseppe Ianiri Chinnappa D Kodira Lukasz Kozubowski Woei Lam Marco Marra Larry D Mesner Frédérique Moyrand Kirsten Nielsen Caroline Proux Jacqueline E Schein Sheng Sun Carolin Wollschlaeger Ian A Wood Qiandong Zeng Cécile Neuvéglise Carol S Newlon John R Perfect Jennifer K Lodge James W Kronstad Joseph Heitman Fred S Dietrich	PLOS Genetics
IKKα restoration via EZH2 suppression induces nasopharyngeal carcinoma differentiation.	2014-04-17	Eric W-F Lam	Min Yan Yan Zhang Bin He Jin Xiang Zi-feng Wang Fei-meng Zheng Jie Xu Ming-yuan Chen Yu-liang Zhu Hai-jun Wen Xiang-bo Wan Cai-feng Yue Na Yang Wei Zhang Jia-liang Zhang Jing Wang Yang Wang Lian-hong Li Yi-xin Zeng Mien-Chie Hung Quentin Liu	Nature Communications
Colorectal cancer cell lines are representative models of the main molecular subtypes of primary cancer.	2014-04-22	Diego Arango Walter Bodmer Oliver Sieber Robert N Jorissen Daniel D Buchanan	Dmitri Mouradov Clare Sloggett Christopher G Love Shan Li Antony W Burgess Robert L Strausberg Samuel Wormald Liam O'Connor Jennifer L Wilding David Bicknell Ian P M Tomlinson John M Mariadason	Cancer Research
Insights into the trypanosome-host interactions revealed through transcriptomic analysis of parasitized tsetse fly salivary glands.	2014-04-24	Michelle B O'Neill Thiago Luiz Alves e Silva Erich L Telleria Serap Aksoy	Joshua B Benoit Xin Zhao Amy F Savage Sandesh Regmi	PLOS Neglected Tropical Diseases
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	Jiaren Zhang Jun Yao Ruijia Wang Yu Zhang Shikai Liu Luyang Sun Yanliang Jiang Jianbin Feng Nannan Liu Geoff Waldbieser Zhanjiang Liu	Biochimica et Biophysica Acta
An improved genome release (version Mt4.0) for the model legume Medicago truncatula.	2014-04-27	Haibao Tang Vivek Krishnakumar Laurent Gentzbittel Kevin L. Childs	Shelby Bidwell Benjamin Rosen Agnes Chan Shiguo Zhou Mark Yandell Heidrun Gundlach Klaus F X Mayer David C Schwartz Christopher D Town	BMC Genomics
Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival.	2014-04-29	Spencer D. Martin Brad H Nelson	Scott D Brown Rene L Warren Ewan A Gibb John J Spinelli Robert A Holt	Genome Research
Microfluidic single-cell whole-transcriptome sequencing.	2014-04-29	Liang Zhao Yanyi Huang	Aaron M Streets Xiannian Zhang Chen Cao Yuhong Pang Xinglong Wu Liang Xiong Lu Yang Yusi Fu Fuchou Tang	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 Rajasree Menon	Journal of Proteomics
Characterization of a genetic mouse model of lung cancer: a promise to identify Non-Small Cell Lung Cancer therapeutic targets and biomarkers.	2014-05-06	Matteo Carrara Dario Livio Longo Elena Quaglino Manuela Iezzi Silvio Bicciato Raffaele A. Calogero Federica Cavallo	Federica Riccardo Maddalena Arigoni Genny Buson Elisa Zago Alessandra Fiore Simona Nuzzo Patrizia Nanni Lorena Landuzzi	BMC Genomics
De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum.	2014-05-12	Paul J Kersey Arnaud Kerhornou Sushma Naithani Dan Bolser Gerard Lazo	Samuel E Fox Matthew Geniza Mamatha Hanumappa Chris Sullivan Justin Preece Vijay K Tiwari Justin Elser Jeffrey M Leonard Abigail Sage Cathy Gresham Fiona McCarthy Pankaj Jaiswal	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 Deborah A Kimbrell Washington J de Carvalho	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 Michael J McKay Carl N Sprung	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 Eva H Stukenbrock	Amitava Bhattacharyya Stephan Poppe Rachel B Brem	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 Rosario M. Piro	Stefan Wiesberg Gunnar Schramm Nico Rebel Marcus Oswald Gerhard Reinelt Rainer König	BMC Systems Biology
RNA sequencing analysis of the gametophyte transcriptome from the liverwort, Marchantia polymorpha.	2014-05-19	Mohan B. Singh Prem L. Bhalla	Niharika Sharma Chol-Hee Jung	PLoS ONE
A SUF Fe-S cluster biogenesis system in the mitochondrion-related organelles of the anaerobic protist Pygsuia.	2014-05-22	Laura Eme Matthew W. Brown Mark van der Giezen Courtney W Stairs Graham Dellaire	Cornelis Mutsaers Edward Susko Darren M Soanes Andrew J Roger	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 Lisete Sousa Mónica Sebastiana Rui Manuel Tavares Andreia Figueiredo	Teresa Lino-Neto Maria Salomé Pais	PLoS ONE
DUX4-induced gene expression is the major molecular signature in FSHD skeletal muscle	2014-05-26	Silvère M van der Maarel	Zizhen Yao Lauren Snider Judit Balog Richard J L F Lemmers Rabi Tawil Stephen J Tapscott	Human Molecular Genetics
Time-resolved gene expression profiling during reprogramming of C/EBPα-pulsed B cells into iPS cells	2014-05-27	Bruno Di Stefano	Samuel Collombet Thomas Graf	Scientific Data
Transcription of nuclear organellar DNA in a model plant system.	2014-05-27	David L. Adelson	Dong Wang Zhipeng Qu Jian-Kang Zhu 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 Wentian Yang Matthew L Warman	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 Jason Van Houten Ying Wang Biao Ding Zhangjun Fei Thomas H Clarke Esther van der Knaap	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 Zhi Chen Vincent Butty	Tarmo Äijö Verna Salo Subhash Tripathi Christopher B Burge Riitta Lahesmaa	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 Ai-Min Li Adeniyi C Adeola Yan-Hu Liu Hai-Bing Xie Ya-Ping Zhang	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 Elia Stupka Raquel Marco-Ferreres Ivan Conte Dejan Lazarevic Paola Bovolenta Sandro Banfi	Stefania Merella Jose Manuel Garcia-Manteiga Chiara Migliore Sabrina Carrella Raffaella Avellino Nathan Paul Davidson Warren Emmett Nicholas Bockett Germana Meroni	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 Christoph M Tang	BMC Genomics
Comparative transcriptional analysis of asexual and sexual morphs reveals possible mechanisms in reproductive polyphenism of the cotton aphid.	2014-06-10	Wei Guo	Li-Jun Liu Hong-Yuan Zheng Feng Jiang Shu-Tang Zhou	PLoS ONE
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 Nicola J Holden	Frontiers in Microbiology
Single-cell RNA-seq reveals dynamic paracrine control of cellular variation.	2014-06-11	Nir Friedman Aviv Regev Rahul Satija Nir Hacohen Schraga Schwartz Raktima Raychowdhury Alex K. Shalek	Joe Shuga John J Trombetta Dave Gennert Diana Lu Peilin Chen Rona S Gertner Jellert T Gaublomme Nir Yosef Brian Fowler Suzanne Weaver Jing Wang Xiaohui Wang Ruihua Ding Raktima Raychowdhury Hongkun Park Andrew P May	Nature
Comparison of REST cistromes across human cell types reveals common and context-specific functions	2014-06-12	Elaine Fuchs Deyou Zheng	Shira Rockowitz Wen-Hui Lien Erika Pedrosa Gang Wei Mingyan Lin Keji Zhao Herbert M Lachman	PLOS Computational Biology
A novel functional role for MMSET in RNA processing based on the link between the REIIBP isoform and its interaction with the SMN complex	2014-06-12	Fabio Mirabella Andrew Thompson C Pawlyn Christopher P Wardell Brian A. Walker	Alexander Murison Lauren I Aronson Sarah J Hanrahan Jacqueline H L Fok Martin F Kaiser Faith E Davies Gareth J Morgan	PLoS ONE
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 Ruoxi Hu Qiyu Wang Barbara Klanderman Reid M Whitaker Qingling Duan Christina Nikolos William Jester Martin Johnson Reynold A Panettieri Kelan G Tantisira Scott T Weiss Quan Lu	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 Cheng-Ting Yeh	Yanxiang Zhang Anja Paschold Caroline Marcon Sanzhen Liu Huanhuan Tai Josefine Nestler Christa Lanz Patrick S Schnable	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	Andrew W Foster Samantha J Dainty Carl J Patterson Hannah Blackburn Clare Wilson Corinna R Hess Julian C Rutherford Laura Quaranta Andy Corran	Molecular Microbiology
Transcriptomic landscape of prophase I sunflower male meiocytes.	2014-06-16	Octavio Martínez	Nathalia M V Flórez-Zapata M H Reyes-Valdés Fernando Hernandez-Godínez	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	Michael Regulski Marcelo Bertalan Adhemar Zerlotini Neto Renato Vicentini Laurent Farinelli Adriana Silva Hemerly Robert A Martienssen Paulo Cavalcanti Gomes Ferreira	The Plant Journal
The Chlamydomonas genome project: a decade on.	2014-06-17	David Goodstein Jane Grimwood Crysten E Blaby-Haas	Ian K Blaby Nicolas Tourasse Erik F Y Hom David Lopez Munevver Aksoy Arthur Grossman James Umen Susan Dutcher Mary Porter Stephen King George B Witman Mario Stanke Elizabeth H Harris Jane Grimwood Jeremy Schmutz Olivier Vallon Sabeeha S Merchant Simon Prochnik	Trends in Plant Science
Adolescent mouse takes on an active transcriptomic expression during postnatal cerebral development	2014-06-18	Songnian Hu	Wei Xu Chengqi Xin Qiang Lin Feng Ding Wei Gong Yuanyuan Zhou Jun Yu Peng Cui	Genomics Proteomics and Bioinformatics
Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing.	2014-06-19	Dominique Rocha Daniel Gautheret	Coline Billerey Mekki Boussaha Diane Esquerré Emmanuelle Rebours Anis Djari Cédric Meersseman Christophe Klopp	BMC Genomics
RNA-Seq for the identification of novel Mediator transcripts in endothelial progenitor cells.	2014-06-19	Valerio Costa Concetta Schiano Claudio Napoli Monica Rienzo	Margherita Scarpato Amelia Casamassimi Vincenzo Grimaldi Alfredo Ciccodicola	Gene
Epigenetic regulation by chromatin activation mark H3K4me3 in primate progenitor cells within adult neurogenic niche	2014-06-20	Richard Sandstrom Eric Haugen	Michael R Foret Douglas A Grow Christopher T Rhodes Astrid E Cardona Clyde F Phelix Yufeng Wang Mitchel S Berger Chin-Hsing Annie Lin	Scientific Reports
RNA-binding protein RBM20 represses splicing to orchestrate cardiac pre-mRNA processing.	2014-06-24	Markus Landthaler Nikolaus Rajewsky Marvin Jens Martin Liss Michael H Radke Matthias Heinig Michael Gotthardt	Henrike Maatz Sebastian Schafer Marieluise Kirchner Eleonora Adami Carola Rintisch Vita Dauksaite Matthias Selbach Paul J R Barton Stuart A Cook Norbert Hubner	Journal of Clinical Investigation
A comparison of transcriptional patterns and mycological phenotypes following infection of Fusarium graminearum by four mycoviruses	2014-06-25	Kyunghun Min	Kyung-Mi Lee Won Kyong Cho Jisuk Yu Moonil Son Hoseong Choi Yin-Won Lee Kook-Hyung Kim	PLoS ONE
A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package.	2014-06-27	Jia Meng	Zhiliang Lu Hui Liu Lin Zhang Shaowu Zhang Yidong Chen Manjeet K Rao Yufei Huang	Methods
Profile of whole blood gene expression following immune stimulation in a wild passerine	2014-06-27	Peeter Hõrak Reidar Andreson	Richard Meitern Peeter Hõrak	BMC Genomics
Response of the hepatic transcriptome to aflatoxin B1 in domestic turkey (Meleagris gallopavo).	2014-06-30	Melissa S Monson	Robert E Settlage Kevin W McMahon Kristelle M Mendoza Sumit Rawal Hani S El-Nezami Roger A Coulombe Kent M Reed	PLoS ONE
Building the sugarcane genome for biotechnology and identifying evolutionary trends.	2014-06-30	Hélène Bergès Monalisa Sampaio Carneiro Claudio Benicio Cardoso-Silva Carlos T Hotta Cushla Jane Metcalfe Glaucia Mendes Souza Changsoo Kim Alessandro Varani Marie-Anne Van Sluys Anete Pereira Souza	Nathalia de Setta Cláudia Barros Monteiro-Vitorello Guilherme Marcelo Queiroga Cruz Luiz Eduardo Del Bem Renato Vicentini Fábio Tebaldi Silveira Nogueira Roberta Alvares Campos Sideny Lima Nunes Paula Cristina Gasperazzo Turrini Andreia Prata Vieira Edgar Andrés Ochoa Cruz Tatiana Caroline Silveira Corrêa Sonia Vautrin Adilson Silva da Trindade Mariane de Mendonça Vilela Carolina Gimiliani Lembke Paloma Mieko Sato Rodrigo Fandino de Andrade Milton Yutaka Nishiyama Katia Castanho Scortecci Antônio Augusto Franco Garcia Andrew H Paterson Angélique D'Hont Michel Vincentz João Paulo Kitajima	BMC Genomics
The coding and noncoding architecture of the Caulobacter crescentus genome	2014-07	Bo Zhou Jared M Schrader Sean Crosson	Gene-Wei Li Keren Lasker W Seth Childers Brandon Williams Tao Long Harley H McAdams Jonathan S Weissman Lucy Shapiro	PLOS Genetics
Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing	2014-07-01	Aviv Regev Rahul Satija Alex K. Shalek	John J. Trombetta David Gennert Diana Lu	Current protocols in molecular biology
Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data.	2014-07-01	Jingyi Jessica Li Steven E. Brenner	Haiyan Huang Peter J Bickel	Genome Research
Comprehensive high-throughput RNA sequencing analysis reveals contamination of multiple nasopharyngeal carcinoma cell lines with HeLa cell genomes.	2014-07-02	Melody Baddoo Asuka Nanbo	Michael J Strong Melody Baddoo Miao Xu Adriane Puetter Zhen Lin	Journal of Virology
Novel bioinformatics method for identification of genome-wide non-canonical spliced regions using RNA-Seq data.	2014-07-03	Gil Omenn	Yongsheng Bai Justin Hassler Ahdad Ziyar Philip Li Zachary Wright Rajasree Menon James D Cavalcoli Randal J Kaufman Maureen A Sartor	PLoS ONE
Status of duckweed genomics and transcriptomics.	2014-07-04	Wenqin Wang	J Messing	Plant Biology
De novo transcriptome sequencing and sequence analysis of the malaria vector Anopheles sinensis (Diptera: Culicidae).	2014-07-07	Liang Qiao	Bin Chen Yu-Juan Zhang Zhengbo He Wanshun Li Fengling Si Yao Tang Qiyi He Zhentian Yan Wenbo Fu Yanfei Che	Parasites & Vectors
Comparative Analysis of Glycogene Expression in Different Mouse Tissues Using RNA-Seq Data	2014-07-09	Vivekanand Jha Ahmad Firoz Sanjay Kumar Singh	Adeel Malik Amjad Ali	International Journal of Genomics
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 Ludi Koning Robert Roomer Wilfred F J van IJcken Kim Kreefft Bi-Sheng Liu Harry L A Janssen Robert J de Knegt	Antiviral Research
Apomictic and sexual germline development differ with respect to cell cycle, transcriptional, hormonal and epigenetic regulation.	2014-07-10	Christian Sailer Ueli Grossniklaus	Anja Schmidt Marc W Schmid Ulrich C Klostermeier Weihong Qi Daniela Guthörl Manuel Waller Philip Rosenstiel Ueli Grossniklaus	PLOS Genetics
Expression pattern of immunoglobulin superfamily members in the silkworm, Bombyx mori.	2014-07-11	Moli Huang	Lei He Guangli Cao Renyu Xue Xiaolong Hu Chengliang Gong	Gene
Reference genes for RT-qPCR studies in Corynebacterium pseudotuberculosis identified through analysis of RNA-seq data.	2014-07-15	Bruno Bastos	Daiane M Carvalho Pablo H de Sá Thiago L P Castro Rodrigo D Carvalho Anne Pinto Danilo J P Gil Priscilla Bagano Lilia F M Costa Roberto Meyer Artur Silva Vasco Azevedo Rommel T J Ramos Luis G C Pacheco	Antonie van Leeuwenhoek
Roothairless5, which functions in maize (Zea mays L.) root hair initiation and elongation encodes a monocot-specific NADPH oxidase.	2014-07-15	Frank Hochholdinger	Josefine Nestler Sanzhen Liu Tsui-Jung Wen Anja Paschold Caroline Marcon Ho Man Tang Delin Li Li Li Robert B Meeley Hajime Sakai Wesley Bruce Patrick S Schnable	The Plant Journal
Whole transcriptome RNA-seq analysis: tumorigenesis and metastasis of melanoma.	2014-07-15	Songnian Hu	Hua Zhao Yongjun Li Shaobin Wang Yadong Yang Junyun Wang Xiuyan Ruan Yaran Yang Kan Cai Bing Zhang Peng Cui Jiangwei Yan Yongliang Zhao Edward K Wakeland Quanzhen Li Xiangdong Fang	Gene
SigFuge: single gene clustering of RNA-seq reveals differential isoform usage among cancer samples	2014-07-16	Charles M. Perou Liza Makowski Patrick K Kimes	Christopher R Cabanski Matthew D Wilkerson Ni Zhao Amy R Johnson Christopher A Maher Yufeng Liu J S Marron D Neil Hayes	Nucleic Acids Research
Differential gene expression in the respiratory tree of the sea cucumber Apostichopus japonicus during aestivation.	2014-07-16	Kenneth B. Storey	Ye Zhao Hongsheng Yang Kenneth B Storey Muyan Chen	Marine Genomics
Polyphosphate accumulation is driven by transcriptome alterations that lead to near-synchronous and near-equivalent uptake of inorganic cations in an arbuscular mycorrhizal fungus.	2014-07-16	Katsuharu Saito Tatsuhiro Ezawa	Yusuke Kikuchi Nowaki Hijikata Kaede Yokoyama Ryo Ohtomo Yoshihiro Handa Masayoshi Kawaguchi	New Phytologist
Bioinformatic exploration of RIO protein kinases of parasitic and free-living nematodes.	2014-07-17	Pasi K. Korhonen Neil D. Young Andreas Hofmann Robin B. Gasser	Bert Breugelmans Aaron R Jex Stefano Mangiola Paul W Sternberg 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 T Mauad S Chowdhury E H Bel R Lutter 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
Sequence, structural and expression divergence of duplicate genes in the bovine genome.	2014-07-23	Graham Plastow	Xiaoping Liao Hua Bao Yan Meng Stephen Moore Paul Stothard	PLoS ONE
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 Bram Van de Sande Gert Hulselmans	Rekin's Janky Annelien Verfaillie Hana Imrichová Laura Standaert Valerie Christiaens 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 Sarah Pohl Denitsa Eckweiler	Piotr Bielecki Uthayakumar Muthukumarasamy Agata Bielecka 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 Hans Lehrach	Marc Sultan Vyacheslav Amstislavskiy Thomas Risch Moritz Schuette Simon Dökel Meryem Ralser Daniela Balzereit 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
De novo transcriptome assembly and comparative analysis of differentially expressed genes in Prunus dulcis Mill. in response to freezing stress.	2014-08-14	Arghavan Alisoltani	Sadegh Mousavi Behrouz Shiran Hossein Fallahi Esameil Ebrahimie Ali Imani Saadollah Houshmand	PLoS ONE
Insights into the epigenomic landscape of the human malaria vector Anopheles gambiae	2014-08-15	Elena Gómez-Díaz Fabrice Chandre	Ana Rivero Victor G Corces	Frontiers in Genetics
Genetic and pharmacological reactivation of the mammalian inactive X chromosome.	2014-08-18	Sanchita Bhatnagar	Xiaochun Zhu Jianhong Ou Ling Lin Lynn Chamberlain Lihua J Zhu Narendra Wajapeyee Michael R Green	Proceedings of the National Academy of Sciences of the United States of America
H3S28 phosphorylation is a hallmark of the transcriptional response to cellular stress.	2014-08-18	Karl Mechtler	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
Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations	2014-08-22	Pratik D. Jagtap	Gloria M Sheynkman James E Johnson Michael R Shortreed Getiria Onsongo Brian L Frey Timothy J Griffin Lloyd M Smith	BMC Genomics
Normalization of RNA-seq data using factor analysis of control genes or samples	2014-08-24	Davide Risso	John Ngai Terence P Speed Sandrine Dudoit	Nature Biotechnology
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
Ionotropic GABA and glycine receptor subunit composition in human pluripotent stem cell-derived excitatory cortical neurones.	2014-08-28	Owen Dando Peter C Kind David J Wyllie Giles E. Hardingham	Owain T James Matthew R Livesey Jing Qiu Bilada Bilican Ghazal Haghi Rinku Rajan Karen Burr Siddharthan Chandran	The Journal of Physiology
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 Rasmus L Marvig	María Gómez-Lozano 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		Frontiers in cell and developmental biology
Optimization of extraction of circulating RNAs from plasma--enabling small RNA sequencing	2014-09-17	Bettina Haase Benedikt Kirchner Michael W Pfaffl	Melanie Spornraft Vladimir Benes Irmgard Riedmaier	PLoS ONE
SOX9 regulates multiple genes in chondrocytes, including genes encoding ECM proteins, ECM modification enzymes, receptors, and transporters.	2014-09-17	Yue Lu	Chun-do Oh Shoudan Liang Yuko Mori-Akiyama Di Chen Benoit de Crombrugghe Hideyo Yasuda	PLoS ONE
Clonal variation in interferon response determines the outcome of oncolytic virotherapy in mouse CT26 colon carcinoma model.	2014-09-18	Seppo Ylä-Herttuala Minna Niittykoski	J J Ruotsalainen M U Kaikkonen M W Martikainen C G Lemay J Cox N S De Silva A Kus T J Falls J-S Diallo F Le Boeuf J C Bell A E Hinkkanen M J Vähä-Koskela	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
Maize and millet transcription factors annotated using comparative genomic and transcriptomic data.	2014-09-27	Chun-Ping Yu Wen-Hsiung Li	Jinn-Jy Lin Yao-Ming Chang Sean Chun-Chang Chen	BMC Genomics
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
Tracking difference in gene expression in a time-course experiment using gene set enrichment analysis.	2014-09-30	Tsuyoshi Tanaka	Pui Shan Wong Michihiro Tanaka Yoshihiko Sunaga Masayoshi Tanaka Takeaki Taniguchi Tomoko Yoshino Wataru Fujibuchi Sachiyo Aburatani	PLoS ONE
Weak base pairing in both seed and 3' regions reduces RNAi off-targets and enhances si/shRNA designs.	2014-09-30	Martin Kampmann	Shuo Gu Yue Zhang Lan Jin Yong Huang Feijie Zhang Michael C Bassik Mark A Kay	Nucleic Acids Research
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 Triin Viltrop Maire Peters Q16408409	Tauno Metsalu Airi Tiirats Balaji Rajashekar Ganesh Acharya Purusotam Basnet 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 Reinhard Georg Lührmann	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 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 Marta Biagioli Christelle Golzio	Aarathi Sugathan 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
Differential expression of endogenous plant cell wall degrading enzyme genes in the stick insect (Phasmatodea) midgut.	2014-10-21	Lynn Kimsey	Matan Shelomi W Cameron Jasper Joel Atallah Brian R Johnson	BMC Genomics
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
Large-scale coding sequence change underlies the evolution of postdevelopmental novelty in honey bees.	2014-10-28	Timothy A Linksvayer	William Cameron Jasper Timothy A Linksvayer Joel Atallah Daniel Friedman Joanna C Chiu Brian R Johnson	Molecular Biology and Evolution
The multidrug resistance 1 gene Abcb1 in brain and placenta: comparative analysis in human and guinea pig	2014-10-29	Gustavo Turecki	Jane J Pappas Sophie Petropoulos Matthew Suderman Majid Iqbal Vasilis Moisiadis Stephen G Matthews Moshe Szyf	PLoS ONE
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
DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data.	2014-11-05	Shin Kawano	Ayako Suzuki Hiroyuki Wakaguri Riu Yamashita Katsuya Tsuchihara Sumio Sugano Yutaka Suzuki Kenta Nakai	Nucleic Acids Research
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
Nasonia vitripennis venom causes targeted gene expression changes in its fly host.	2014-11-10	Aisha L Siebert	Ellen O Martinson David Wheeler Jeremy Wright Mrinalini John H Werren	Molecular Ecology
Suppression of the FOXM1 transcriptional programme via novel small molecule inhibition	2014-11-12	Christopher Lowe Michael V Gormally Ajit Jadhav	Thomas S Dexheimer Giovanni Marsico Deborah A Sanders Dijana Matak-Vinković Sam Michael Ganesha Rai David J Maloney Anton Simeonov Shankar Balasubramanian	Nature Communications
The putative Leishmania telomerase RNA (LeishTER) undergoes trans-splicing and contains a conserved template sequence	2014-11-12	Marcelo Santos da Silva	Elton J R Vasconcelos Vinícius S Nunes Marcela Segatto Peter J Myler Maria Isabel N Cano	PLoS ONE
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
De-regulation of gene expression and alternative splicing affects distinct cellular pathways in the aging hippocampus.	2014-11-13	Stefan Bonn Roman Stilling	Eva Benito Michael Gertig Jonas Barth Vincenzo Capece Susanne Burkhardt Andre Fischer	Frontiers in Cellular Neuroscience
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
Detection theory in identification of RNA-DNA sequence differences using RNA-sequencing.	2014-11-14	Gregory R Grant	Jonathan M Toung Nicholas Lahens John B Hogenesch	PLoS ONE
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 Adriana R Carneiro Daniel M Santos Marta S P Carepo Vasco Azevedo Maria P C Schneider Artur Silva	BMC Genomics
IsoSCM: improved and alternative 3' UTR annotation using multiple change-point inference.	2014-11-18	Pedro Miura Piero Sanfilippo Eric C Lai	Sol Shenker	RNA
Expression of human skin-specific genes defined by transcriptomics and antibody-based profiling	2014-11-19	Mathias Uhlén Linn Fagerberg	Per-Henrik D Edqvist Björn M Hallström Angelika Danielsson Karolina Edlund Mathias Uhlén Fredrik Pontén	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 Marcin Jąkalski	Hiroyuki Wakaguri Yoshifumi Nishikawa Shin-ichiro Kawazu Makoto Matsubayashi Fumiya Kawahara Naotoshi Tsuji Shinuo Cao Fujiko Sunaga Xuenan Xuan Kazuhiro Okubo Ikuo Igarashi Josef Tuda Arthur E Mongan Yuki Eshita Ryuichiro Maeda Wojciech Makałowski Yutaka Suzuki Junya Yamagishi	Nucleic Acids Research
Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing.	2014-11-24	Sten Linnarsson Peter Lönnerberg Jens Hjerling-Leffler Patrik Ernfors	Dmitry Usoskin Alessandro Furlan Saiful Islam Hind Abdo Peter Lönnerberg Daohua Lou Jens Hjerling-Leffler Jesper Haeggström Olga Kharchenko Peter V Kharchenko Sten Linnarsson Patrik Ernfors	Nature Neuroscience
Promiscuous mRNA splicing under the control of AIRE in medullary thymic epithelial cells.	2014-11-25	Rhodri Ceredig	Peter Keane Cathal Seoighe	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 Francesc X. Marsellach Christopher T. Workman	Mathieu Clément-Ziza Sandra Codlin Manos A Papadakis Susanne Reinhardt Stuart Martin Samuel Marguerat Alexander Schmidt Eunhye Lee Jürg Bähler Andreas Beyer	Molecular Systems Biology
The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease	2014-12	Kerstin Lindblad-Toh Jessica Alföldi Federica Di Palma Marcia Lara Thibaut Hourlier Adam C. Siepel Christophe Dessimoz Jason Turner-Maier David Brawand Kevin Gori Bronwen Aken John F Engelhardt	Xinxia Peng Amie J Eisfeld Scott R Tyler Jennifer Tisoncik-Go G Lynn Law Nives Skunca Masato Hatta David J Gasper Sara M Kelly Jean Chang Matthew J Thomas Jeremy Johnson Aaron M Berlin Pamela Russell Ross Swofford Jason Turner-Maier Sarah Young Steve Searle Xingshen Sun Yaling Yi M Suresh Terrence M Tumpey Samantha M Wisely Yoshihiro Kawaoka Bruce W Birren Robert E Palermo Michael G Katze	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 Shawn W Polson	Abby L Manthey Anne M Terrell Salil A Lachke	Genomics Data
Transcriptome profiling of Set5 and Set1 methyltransferases: Tools for visualization of gene expression.	2014-12-01	Devin A King Ashby Morrison	Glòria Mas Martín Pablo E Garcia-Nieto	Genomics Data
Genotet: An Interactive Web-based Visual Exploration Framework to Support Validation of Gene Regulatory Networks.	2014-12-01	Christoph Hafemeister	Bowen Yu Harish Doraiswamy Xi Chen Emily Miraldi Mario Luis Arrieta-Ortiz Christoph Hafemeister Aviv Madar Richard Bonneau Cláudio T Silva	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 Stefano Campanaro	Alessandro Sardu	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 Chon-Kit Kenneth Chan Sophie Dove	Paulina Kaniewska Edmund Yew Siang Ling David Edwards Ove Hoegh-Guldberg	BMC Genomics
Impact of the genetic background on the composition of the chicken plasma MiRNome in response to a stress	2014-12-04	Marie-Laure Endale Ahanda	Tatiana Zerjal Sophie Dhorne-Pollet Andrea Rau Amanda Cooksey Elisabetta Giuffra	PLoS ONE
QuASAR: quantitative allele-specific analysis of reads.	2014-12-04	Xiaoquan Wen Francesca Luca Roger Pique-Regi	Chris T Harvey Gregory A Moyerbrailean Gordon O Davis	Bioinformatics
rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data	2014-12-05 2014-12-23	Zhi-xiang Lu Michael D. Henry	Shihao Shen Juw Won Park Lan Lin Ying Nian Wu Qing Zhou Yi Xing Michael D. Henry	Proceedings of the National Academy of Sciences of the United States of America
SNPlice: variants that modulate Intron retention from RNA-sequencing data.	2014-12-06	Kamran Kowsari	Prakriti Mudvari Mercedeh Movassagh Ali Seyfi Maria Kokkinaki Nathan J Edwards Nady Golestaneh Anelia Horvath	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 Sophie FouchÉCourt Frédéric Flamant	Molecular Reproduction and Development
Dynamic changes in the cardiac methylome during postnatal development.	2014-12-09	Mark Ziemann James E Hudson Enzo R Porrello Assam El-osta	Choon Boon Sim Antony Kaspi K N Harikrishnan Jenny Ooi Ishant Khurana Lisa Chang	FASEB Journal
An epigenomic roadmap to induced pluripotency reveals DNA methylation as a reprogramming modulator.	2014-12-10	Thomas Bleazard Thomas Preiss Nicole Cloonan Andras Nagy Sean M. Grimmond	Dong-Sung Lee Jong-Yeon Shin Peter D Tonge Mira C Puri Seungbok Lee Hansoo Park Won-Chul Lee Samer M I Hussein Ji-Young Yun Jihye Kim Mira Li David Wood Jennifer L Clancy Rowland Mosbergen Jae-Hyuk Yi Kap-Seok Yang Hyungtae Kim Hwanseok Rhee Christine A Wells Ian M Rogers Jeong-Sun Seo	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 Damarius Fleming Michael E Persia Chris M Ashwell Max F Rothschild Susan J Lamont	BMC Genomics
High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies	2014-12-11	Aviv Regev Nir Hacohen Raktima Raychowdhury Nir Friedman	Michal Rabani Raktima Raychowdhury Marko Jovanovic Michael Rooney Deborah J Stumpo Andrea Pauli Alexander F Schier Perry J Blackshear Ido Amit	Cell
Whole exome sequencing of a single osteosarcoma case--integrative analysis with whole transcriptome RNA-seq data.	2014-12-11	Q16408409	Ene Reimann Xuan Dung Ho Katre Maasalu Aare Märtson	Human genomics
The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data	2014-12-16	Richard Weinshilboum Kevin J Thompson Xiaojia Tang Krishna R Kalari	Saurabh Baheti Khader Shameer Quin Wills Nifang Niu Ilona N Holcomb Stephane C Boutet Ramesh Ramakrishnan Jennifer M Kachergus Jean-Pierre A Kocher Richard M Weinshilboum Liewei Wang E Aubrey Thompson	Nucleic Acids Research
Regulation of the KNOX-GA gene module induces heterophyllic alteration in North American lake cress.	2014-12-16	Hitoshi Sakakibara Seisuke Kimura	Hokuto Nakayama Naomi Nakayama Sumer Seiki Mikiko Kojima Neelima Sinha	The Plant Cell
Recurrent PRDM10 gene fusions in undifferentiated pleomorphic sarcoma.	2014-12-16	Fredrik Mertens	Jakob Hofvander Johnbosco Tayebwa Jenny Nilsson Linda Magnusson Otte Brosjö Olle Larsson Fredrik Vult von Steyern Nils Mandahl Christopher D M Fletcher	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 Giulia Bertolini Louise Carter Massimo Moro Crispin J. Miller Fiona Blackhall Caroline Dive	Dominic G Rothwell Yaoyong Li Mahmood Ayub Catriona Tate Gillian Newton Yvonne Hey Suzanne Faulkner Stuart Pepper Ged Brady	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 Andreas Heger Jacqueline Stockley Ian Sudbery Hing Y Leung	Prabhakar Rajan Janis T Fleming Ann Hedley Gabriela Kalna David Sims Craig N Robson Rhona M McMenemin Ian D Pedley	BMC Cancer
Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference.	2014-12-18	Delphine Potier Kristofer Davie Stein Aerts Gert Hulselmans	Marina Naval Sanchez Lotte Haagen Vân Anh Huynh-Thu Duygu Koldere Arzu Celik Pierre Geurts Valerie Christiaens	Cell Reports
RNA-seq analysis reveals significant transcriptome changes in turbot (Scophthalmus maximus) suffering severe enteromyxosis.	2014-12-19	Paolo Ronza Ana Paula Losada Peter W Harrison Belén G Pardo Ariadna Sitjà-Bobadilla Paulino Martínez	Diego Robledo Roberto Bermúdez María José Redondo María Isabel Quiroga	BMC Genomics
Genome-wide analysis of the human p53 transcriptional network unveils a lncRNA tumour suppressor signature.	2014-12-19	Maite Huarte Alejandro Athie Francesco P Marchese	Yolanda Sánchez Victor Segura Oskar Marín-Béjar Jovanna González Luis Bujanda Shuling Guo Ander Matheu	Nature Communications
plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants.	2014-12-23	Peter F. Stadler David Langenberger	Deblina Patra Mario Fasold Gerhard Steger Ivo Grosse	Frontiers in Plant Science
RNA-seq profiling of small numbers of Drosophila neurons.	2014-12-26	Michael Rosbash E Nagoshi	Katharine Abruzzi Xiao Chen Abby Zadina	Methods in Enzymology
Considerations for RNA-seq analysis of circadian rhythms.	2014-12-26	Gregory R Grant	Jiajia Li John B Hogenesch Michael E Hughes	Methods in Enzymology
Identification of RNA polymerase III-transcribed Alu loci by computational screening of RNA-Seq data.	2014-12-29	Silvia Fustinoni Giorgio Dieci Davide Carnevali Matteo Pellegrini	Anastasia Conti	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 Martin März Matthias C Vogg David Eccles Laura Grífol-Boldú Daniel Wehner Suthira Owlarn Teresa Adell Kerstin Bartscherer	Cell Reports
Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties	2015	Eshita Mutt Pritha Ghosh Oommen K Mathew	Atul K Upadhyay Anita R Chacko A Gandhimathi K Harini Agnel P Joseph Adwait G Joshi Snehal D Karpe Swati Kaushik Nagesh Kuravadi Chandana S Lingu J Mahita Ramya Malarini Sony Malhotra Manoharan Malini Mahantesha Naika Sathyanarayanan Nitish Shaik Naseer Pasha Upadhyayula S Raghavender Anantharamanan Rajamani S Shilpa Prashant N Shingate Heikham Russiachand Singh Anshul Sukhwal Margaret S Sunitha Manojkumar Sumathi S Ramaswamy Malali Gowda Ramanathan Sowdhamini	BMC Plant Biology
ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines	2015	Fabian Amman Florian Eggenhofer	Michael T Wolfinger Jörg Fallmann	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 John Fazakerley Mick Watson Hana Tykalová	Sabine Weisheit Marina Popara Julia Loecherbach Daniel Růžek Libor Grubhoffer Lesley Bell-Sakyi	Parasites & Vectors
Remodeling of the Nuclear Envelope and Lamina during Bovine Preimplantation Development and Its Functional Implications	2015	Valeri Zakhartchenko Eckhard Wolf Volker J Schmid	Jens Popken Alexander Graf Stefan Krebs Helmut Blum Axel Strauss Tuna Guengoer Thomas Cremer	PLoS ONE
Genes expressed in grapevine leaves reveal latent wood infection by the fungal pathogen Neofusicoccum parvum	2015	Andrew J McElrone	Stefan Czemmel Erin R Galarneau Renaud Travadon Grant R Cramer Kendra Baumgartner	PLoS ONE
Whole transcriptome analysis using next-generation sequencing of sterile-cultured Eisenia andrei for immune system research	2015	Tetsuya Sakurai	Yoshikazu Mikami Atsushi Fukushima Takao Kuwada-Kusunose Taiichi Kitano Yusuke Komiyama Takashi Iwase Kazuo Komiyama	PLoS ONE
Transcriptomic Characterization of Innate and Acquired Immune Responses in Red-Legged Partridges (Alectoris rufa): A Resource for Immunoecology and Robustness Selection	2015	Natalia Sevane	Javier Cañon Ignacio Gil Susana Dunner	PLoS ONE
Size of the Ovulatory Follicle Dictates Spatial Differences in the Oviductal Transcriptome in Cattle	2015	Fernando S Mesquita Luiz L Coutinho	Angela María Gonella-Diaza Sónia Cristina da Silva Andrade Mariana Sponchiado Guilherme Pugliesi Veerle Van Hoeck Ricardo de Francisco Strefezzi Gustavo R Gasparin Mario Binelli	PLoS ONE
Comparative Analysis of Muscle Transcriptome between Pig Genotypes Identifies Genes and Regulatory Mechanisms Associated to Growth, Fatness and Metabolism	2015	Rita Benítez Ana Isabel Rey C Ovilo	Miriam Ayuso Almudena Fernández Yolanda Núñez Beatriz Isabel Carmen Barragán Ana Isabel Fernández Juan F Medrano Ángela Cánovas Antonio González-Bulnes Clemente López-Bote	PLoS ONE
From Insect to Man: Photorhabdus Sheds Light on the Emergence of Human Pathogenicity	2015	Helge Bode Nicholas J Tobias Michael L. Beeton Richard ffrench-Constant	Geraldine Mulley Paul Wilkinson Isabella Vlisidou Nina Ockendon-Powell Alexia Hapeshi Friederike I Nollmann Jean van den Elsen Nicholas R Waterfield	PLoS ONE
A cell-based systems biology assessment of human blood to monitor immune responses after influenza vaccination	2015	Nripesh Prasad Parimal Samir Sebastian Joyce Shawn Levy	Kristen L Hoek Leigh M Howard Xinnan Niu Allison Galassie Qi Liu Tara M Allos Kyle A Floyd Yan Guo Yu Shyr Kathryn M Edwards Andrew J Link	PLoS ONE
Activin-A and Bmp4 levels modulate cell type specification during CHIR-induced cardiomyogenesis	2015	Karl Stamm	Min-Su Kim Audrey Horst Steven Blinka Donna Mahnke James Schuman Rebekah Gundry Aoy Tomita-Mitchell John Lough	PLoS ONE
mRNA profiling reveals determinants of trastuzumab efficiency in HER2-positive breast cancer	2015	Manuel Nietert	Silvia von der Heyde Steve Wagner Alexander Czerny Fabian Ludewig Gabriela Salinas-Riester Dorit Arlt Tim Beißbarth	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 Brian Steffenson Kanwarpal S Dhugga	Kelly Houston Beata Sznajder Antoni J Rafalski Jillian Taylor Robbie Waugh Geoffrey B Fincher	PLoS ONE
Differential Expression Analysis by RNA-Seq Reveals Perturbations in the Platelet mRNA Transcriptome Triggered by Pathogen Reduction Systems	2015	Abdimajid Osman Patrick Provost Adam Ameur	Walter E Hitzler	PLoS ONE
Asparagus Spears as a Model to Study Heteroxylan Biosynthesis during Secondary Wall Development	2015	Kelsey L. Picard Wei Zeng Edwin R. Lampugnani	Lili Song Aimin Wu Roshan Cheetamun Cherie Beahan Andrew Cassin Andrew Lonsdale Monika S Doblin Antony Bacic	PLoS ONE
Global Gene Expression Profiling through the Complete Life Cycle of Trypanosoma vivax	2015	Matthew Berriman Mandy Sanders Sophie Goyard Andrew P Jackson Dong Xia Paola Minoprio	Bernardo J Foth Jonathan M Wastling	PLOS Neglected Tropical Diseases
Towards Elucidating Carnosic Acid Biosynthesis in Lamiaceae: Functional Characterization of the Three First Steps of the Pathway in Salvia fruticosa and Rosmarinus officinalis	2015	Fani Chatzopoulou Angelos K Kanellis Alain Tissier Sotirios Kampranis Irini Pateraki Albert Ferrer	Dragana Božić Dimitra Papaefthimiou Kathleen Brückner Ric C H de Vos Constantinos A Tsoleridis Dimitra Katsarou Antigoni Papanikolaou Eleni Dimitriadou Stefanos Kostas David Manzano Ulschan Scheler Antonios M Makris	PLoS ONE
Gene Expression Ratios Lead to Accurate and Translatable Predictors of DR5 Agonism across Multiple Tumor Lineages	2015	John Monahan	Anupama Reddy Joseph D Growney Nick S Wilson Caroline M Emery Jennifer A Johnson Rebecca Ward Kelli A Monaco Joshua Korn Mark D Stump Felipa A Mapa Christopher J Wilson Janine Steiger Jebediah Ledell Richard J Rickles Vic E Myer Seth A Ettenberg Robert Schlegel William R Sellers Heather A Huet Joseph Lehár	PLoS ONE
RNA-Seq Analysis of Human Trigeminal and Dorsal Root Ganglia with a Focus on Chemoreceptors	2015	Janine Altmüller Hanns Hatt Günter Gisselmann	Caroline Flegel Nicole Schöbel Christian Becker Andrea Tannapfel Günter Gisselmann	PLoS ONE
Whole Body Melanoma Transcriptome Response in Medaka	2015	Manfred Schartl	Yingjia Shen Katja Maurus Ron Walter Chad Tomlinson Richard K Wilson John Postlethwait Wesley C Warren	PLoS ONE
OperomeDB: A Database of Condition-Specific Transcription Units in Prokaryotic Genomes	2015	Sarath Chandra Janga	Kashish Chetal Sarath Chandra Janga	BioMed Research International
Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli	2015-01-01	Thorsten Bischler Alexander Herbig Cynthia Sharma Konrad Förstner	Maureen K Thomason Sara K Eisenbart Aixia Zhang Kay Nieselt Gisela Storz	Journal of Bacteriology
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 Wei Shi Louise Y Cheng	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 Martin A Kohli Lubov Nathanson Patrice Whitehead Gary Beecham Eden Martin Deborah C Mash John Gilbert	Journal of Alzheimer's Disease
Nuclear transcriptome profiling of induced pluripotent stem cells and embryonic stem cells identify non-coding loci resistant to reprogramming	2015-01-01	Piero Carninci	Alexandre Fort Daisuke Yamada Kosuke Hashimoto Haruhiko Koseki	Cell Cycle
Characterization of the Olfactory Receptors Expressed in Human Spermatozoa	2015-01-01	Hanns Hatt Günter Gisselmann	Caroline Flegel Felix Vogel Adrian Hofreuter Benjamin S P Schreiner Sandra Osthold Sophie Veitinger Christian Becker Norbert H Brockmeyer Michael Muschol Gunther Wennemuth Janine Altmüller Günter Gisselmann	Frontiers in molecular biosciences
MicroRNA profiling of the bovine alveolar macrophage response to Mycobacterium bovis infection suggests pathogen survival is enhanced by microRNA regulation of endocytosis and lysosome trafficking.	2015-01-01	Kenneth Bryan Daniel G. Bradley David J. Lynn David E. MacHugh Stephen V. Gordon	Peter Vegh David A Magee Nicolas C Nalpas Matthew S McCabe John A Browne Kevin M Conlon	Tuberculosis
Noncoding regions of C. elegans mRNA undergo selective adenosine to inosine deamination and contain a small number of editing sites per transcript.	2015-01-01	Michael C Washburn	Emily C Wheeler Francois Major Douglas B Rusch Heather A Hundley	RNA Biology
Integrative genome-wide analysis of the determinants of RNA splicing in kidney renal clear cell carcinoma.	2015-01-01	Oliver Stegle	Kjong-Van Lehmann André Kahles Cyriac Kandoth William Lee Nikolaus Schultz Gunnar Rätsch	Pacific Symposium on Biocomputing
Analysis of alternative splicing events in custom gene datasets by AStalavista.	2015-01-01	Sylvain Foissac Michael Sammeth		Methods in Molecular Biology
First insights into the giant panda (Ailuropoda melanoleuca) blood transcriptome: a resource for novel gene loci and immunogenetics.	2015-01-02	Bisong Yue	Lianming Du Wujiao Li Zhenxin Fan Fujun Shen Mingyu Yang Zili Wang Zuoyi Jian Rong Hou Xiuyue Zhang	Molecular Ecology Resources
Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data.	2015-01-05	Åslaug Helland Lynnette Fernandez-Cuesta Joachim H Clement Martin Peifer Stefan Haas Gavin Wright Peter Nürnberg	Ruping Sun Roopika Menon Julie George Susanne Lorenz Leonardo A Meza-Zepeda Dennis Plenker Johannes M Heuckmann Frauke Leenders Thomas Zander Ilona Dahmen Mirjam Koker Jakob Schöttle Roland T Ullrich Christian Becker Henrik Seidel Diana Böhm Friederike Göke Sascha Ansén Prudence A Russell Zoe Wainer Benjamin Solomon Iver Petersen Jörg Sänger Odd-Terje Brustugun Steinar Solberg Marius Lund-Iversen Reinhard Buettner Jürgen Wolf Elisabeth Brambilla Martin Vingron Sven Perner Roman K Thomas	Genome Biology
Characterization of human cyclin-dependent kinase 12 (CDK12) and CDK13 complexes in C-terminal domain phosphorylation, gene transcription, and RNA processing	2015-01-05	Laurence Florens Michael P. Washburn	Kaiwei Liang Xin Gao Joshua M Gilmore Edwin Smith Ali Shilatifard	Molecular and Cellular Biology
iRNA-seq: computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data	2015-01-06	Susanne Mandrup Bjørk Ditlev Larsen Søren Fisker Schmidt	Jesper Grud Skat Madsen Anne Loft Ronni Nielsen	Nucleic Acids Research
Astrovirus VA1/HMO-C: an increasingly recognized neurotropic pathogen in immunocompromised patients	2015-01-07	Vincent Plagnol Divya Shah Sofia Morfopoulou Julianne R Brown Judith Breuer Waseem Qasim	Jonathan Hubb Warren A Emmett Winnie Ip Tony Brooks Simon M L Paine Glenn Anderson Alex Virasami C Y William Tong Duncan A Clark Thomas S Jacques Mike Hubank	Clinical Infectious Diseases
Systems biology with high-throughput sequencing reveals genetic mechanisms underlying the metabolic syndrome in the Lyon hypertensive rat.	2015-01-08	Man Chun John Ma Anne E Kwitek	Jinkai Wang Amanda K Mennie Janette M Pettus Yang Xu Lan Lin Matthew G Traxler Jessica Jakoubek Santosh S Atanur Timothy J Aitman Yi Xing	Circulation: Cardiovascular Genetics
Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli.	2015-01-12	Xiaoliang Sunney Xie	Huiyi Chen Katsuyuki Shiroguchi Hao Ge	Molecular Systems Biology
Deep sequencing of the murine olfactory receptor neuron transcriptome.	2015-01-15	Hanns Hatt Günter Gisselmann Christian H. Wetzel Eva M. Neuhaus	Ninthujah Kanageswaran Marilen Demond Maximilian Nagel Benjamin S P Schreiner Sabrina Baumgart Paul Scholz Janine Altmüller Christian Becker Julia F Doerner Heike Conrad Sonja Oberland Günter Gisselmann	PLoS ONE
Blocking miRNA Biogenesis in Adult Forebrain Neurons Enhances Seizure Susceptibility, Fear Memory, and Food Intake by Increasing Neuronal Responsiveness.	2015-01-16	Angel Barco	Anna Fiorenza Jose P Lopez-Atalaya Victor Rovira Marilyn Scandaglia Emilio Geijo-Barrientos	Cerebral Cortex
Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation in Caenorhabditis elegans intestine and muscles.	2015-01-20	Marco Mangone	Stephen M Blazie Cody Babb Henry Wilky Alan Rawls Jin G Park	BMC Biology
Combining RNA and protein profiling data with network interactions identifies genes associated with spermatogenesis in mouse and human.	2015-01-21	Bernard Jégou Fatima Smagulova Soazik P Jamin Fabrice G Petit Emmanuelle Becker Frédéric Chalmel Michael Primig	Christine Kervarrec Chunxiang Hao Bernard Jégou	Biology of Reproduction
RNA-Seq reveals a role for NFAT-signaling in human retinal microvascular endothelial cells treated with TNFα.	2015-01-24	Colin A Bretz	Sara R Savage John S Penn	PLoS ONE
The long intergenic noncoding RNA landscape of human lymphocytes highlights the regulation of T cell differentiation by linc-MAF-4.	2015-01-26	Sergio Abrignani Massimiliano Pagani	Valeria Ranzani Grazisa Rossetti Ilaria Panzeri Alberto Arrigoni Raoul Jp Bonnal Serena Curti Paola Gruarin Elena Provasi Elisa Sugliano Maurizio Marconi Raffaele De Francesco Jens Geginat Beatrice Bodega	Nature Immunology
Next-Generation Sequencing Reveals Low-Dose Effects of Cationic Dendrimers in Primary Human Bronchial Epithelial Cells	2015-01-27	Pekka Kohonen Hanna L. Karlsson Bengt Fadeel Neus Feliu Yuning Zhang	Neus Feliu Jie Ji Lena Palmberg Andreas Nyström	ACS Nano
Computational and analytical challenges in single-cell transcriptomics.	2015-01-28	Sarah Teichmann John C Marioni Oliver Stegle		Nature Reviews Genetics
The transcriptional stress response of Candida albicans to weak organic acids.	2015-01-29	Norman Pavelka Michael Poidinger	Fabien Cottier Alrina Shin Min Tan Jinmiao Chen Josephine Lum Francesca Zolezzi	G3
The avian transcriptome response to malaria infection	2015-01-29	Olof Hellgren Gediminas Valkiūnas Elin Videvall Vaidas Palinauskas	Charlie K Cornwallis Gediminas Valkiūnas	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 Behrouz Shiran Anousheh Alisoltani Esmaeil Ebrahimie	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 John R. Roche	P A McGettigan J A Browne S D Carrington M A Crowe B J Loftus A Lohan P Lonergan K Pluta S Mamo A Murphy S W Walsh C J Creevey B Earley S Keady D A Kenny D Matthews M McCabe D Morris A O'Loughlin S Waters M G Diskin A C O Evans	Reproduction, Fertility and Development
The role of TP53 in miRNA loading onto AGO2 and in remodelling the miRNA-mRNA interaction network.	2015-02-01	Teresa Colombo Valerio Fulci	Jonathan Krell Justin Stebbing Adam Enver Frampton Claudia Carissimi Victoria Harding Alexander De Giorgio Giuseppe Macino Leandro Castellano	The Lancet
Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers.	2015-02-02	Laura Clarke Paul Flicek Xabier Agirre Michael I Robson Marien Pascual Avik Datta Renée Beekman David Richardson Giancarlo Castellano Juan R Rodriguez-Madoz José I Martín-Subero Norma C. Gutiérrez José M García-Verdugo Elias Campo Simon Heath Felipe Prosper	Marta Kulis Victor Segura Anke Bergmann Anna Esteve Angelika Merkel Emanuele Raineri Lidia Agueda Julie Blanc Nuria Russiñol Ana C Queirós Edurne San José-Enériz Fang Fang Eric C Schirmer Elisabeth Guruceaga Joost H A Martens Marta Gut Maria J Calasanz Reiner Siebert Jesús F San Miguel Ari Melnick Hendrik G Stunnenberg Ivo G Gut	Genome Research
Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling.	2015-02-02	Jens Nielsen	Pouyan Ghaffari Adil Mardinoglu Anna Asplund Saeed Shoaie Caroline Kampf Mathias Uhlen	Scientific Reports
The genomic landscape of phaeochromocytoma.	2015-02-02	Stephen B. Fox Richard W. Tothill Rodney J. Hicks Aidan Flynn Jason Li Grant McArthur	Diana Benn Roderick Clifton-Bligh Bruce Robinson Alison H Trainer Paul James Annette Hogg Kelly Waldeck Joshy George Anthony J Gill	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 F Rob Jackson	G3
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 Jung-Woong Kim	Progress in Retinal and Eye Research
Regulatory small RNAs from the 3' regions of bacterial mRNAs.	2015-02-09	Jörg Vogel Masatoshi Miyakoshi Yanjie Chao		Current Opinion in Microbiology
Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome.	2015-02-10	Catherine Feuillet Etienne Paux Frédéric Choulet Adriana Alberti	Lise Pingault Natasha Glover Patrick Wincker	Genome Biology
Rapid changes in gene expression direct rapid shifts in intestinal form and function in the Burmese python after feeding.	2015-02-10	David D. Pollock	Audra L Andrew Daren C Card Robert P Ruggiero Drew R Schield Richard H Adams Stephen M Secor Todd A Castoe	Physiological Genomics
Distinct Transcriptomic Features are Associated with Transitional and Mature B-Cell Populations in the Mouse Spleen.	2015-02-11	Daria Salyakina Jean-Christophe Renauld	Eden Kleiman Magali De Heusch Kristen L Hoek Joan M Llanes Iris Castro Jacqueline A Wright Emily S Clark Derek M Dykxhoorn Enrico Capobianco Akiko Takeda Wasif N Khan	Frontiers in Immunology
Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues.	2015-02-12	Je Hyuk Lee George M Church	Evan R Daugharthy Jonathan Scheiman Reza Kalhor Thomas C Ferrante Richard Terry Brian M Turczyk Joyce L Yang Ho Suk Lee John Aach Kun Zhang	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
The evolutionary panorama of organ-specifically expressed or repressed orthologous genes in nine vertebrate species.	2015-02-13	Zhan Zhou	Libing Shen Gangbiao Liu Yangyun Zou Zhixi Su Xun Gu	PLoS ONE
Asexual expansion of Toxoplasma gondii merozoites is distinct from tachyzoites and entails expression of non-overlapping gene families to attach, invade, and replicate within feline enterocytes.	2015-02-13	Peter Deplazes	Adrian B Hehl Walter U Basso Christoph Lippuner Chandra Ramakrishnan Michal Okoniewski Robert A Walker Michael E Grigg Nicholas C Smith	BMC Genomics
Differential RNA-seq of Vibrio cholerae identifies the VqmR small RNA as a regulator of biofilm formation	2015-02-17	Cynthia Sharma Kai Papenfort	Konrad U Förstner Jian-Ping Cong Bonnie L Bassler	Proceedings of the National Academy of Sciences of the United States of America
DNA methylation-based subtype prediction for pediatric acute lymphoblastic leukemia.	2015-02-17	Ann-Christine Syvänen Christofer L Bäcklin Ann Nordgren Jonas Abrahamsson	Jessica Nordlund Vasilios Zachariadis Lucia Cavelier Johan Dahlberg Ingegerd Öfverholm Gisela Barbany Elin Övernäs Trond Flaegstad Mats M Heyman Ólafur G Jónsson Jukka Kanerva Rolf Larsson Josefine Palle Kjeld Schmiegelow Mats G Gustafsson Gudmar Lönnerholm Erik Forestier	Clinical epigenetics
Aging-like changes in the transcriptome of irradiated microglia	2015-02-17	Matthew D Li Steven A. Sloan	Terry C Burns Sunny Kumar Alexander A Morgan Theo D Palmer	Glia
Molecular characterization and transcriptome analysis of orange head Chinese cabbage (Brassica rapa L. ssp. pekinensis).	2015-02-17	Barry J Pogson	Junxiang Zhang Hui Yuan Zhangjun Fei Lugang Zhang Li Li	Planta
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads	2015-02-18	Steven Salzberg Mihaela Pertea	Geo M Pertea Corina M Antonescu Tsung-Cheng Chang Joshua T Mendell	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 Catherine M Miller Christoph Lippuner Michal Okoniewski Ramon M Eichenberger Chandra Ramakrishnan Fabien Brossier Adrian B Hehl Nicholas C Smith	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 Gioele La Manno Hermany Munguba C. Rolny Gonçalo Castelo-Branco	Amit Zeisel Ana B Muñoz-Manchado Simone Codeluppi Peter Lönnerberg Anna Juréus Sueli Marques Liqun He Christer Betsholtz Jens Hjerling-Leffler Sten Linnarsson	Science
The lncRNA DRAIC/PCAT29 Locus Constitutes a Tumor-Suppressive Nexus.	2015-02-20	Anindya Dutta Jordan Anaya	Kouhei Sakurai Brian J Reon	Molecular Cancer Research
A transcriptome derived female-specific marker from the invasive Western mosquitofish (Gambusia affinis).	2015-02-23	Manfred Schartl Shinichi Nakagawa	Dunja K Lamatsch Sofia Adolfsson Alistair M Senior Guntram Christiansen Maria Pichler Yuichi Ozaki Linnea Smeds	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 Peter M Clark Aristeidis G Telonis Yohei Kirino Michelle Lally Karen E Knudsen Isidore Rigoutsos	Eric Londin Phillipe Loher Kevin Quann Yi Jing Eleftheria Hatzimichael Shozo Honda Bharat Ramratnam Clay E S Comstock Leonard Gomella George L Spaeth Lisa Hark L Jay Katz Agnieszka Witkiewicz Abdolmohamad Rostami Sergio A Jimenez Michael A Hollingsworth Jen Jen Yeh Chad A Shaw Steven E McKenzie Paul Bray Peter T Nelson Simona Zupo Katrien Van Roosbroeck Michael J Keating George A Calin Charles Yeo Masaya Jimbo Joseph Cozzitorto Jonathan R Brody Kathleen Delgrosso Paolo Fortina	Proceedings of the National Academy of Sciences of the United States of America
Polyribosomal RNA-Seq reveals the decreased complexity and diversity of the Arabidopsis translatome.	2015-02-23	Vivek Krishnakumar	Xingtan Zhang Benjamin D Rosen Haibao Tang Christopher D Town	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 Katja Dierking Daniela Esser Matthias Leippe Philip Rosenstiel Hinrich Schulenburg	Developmental and Comparative Immunology
RNA-Seq: Improving Our Understanding of Retinal Biology and Disease.	2015-02-26	Eric A Pierce	Michael H Farkas Elizabeth D Au Maria E Sousa	Cold Spring Harbor Perspectives in Medicine
Exon Skipping Is Correlated with Exon Circularization.	2015-02-26	Steven Kelly Argyris Papantonis	Chris Greenman Peter R Cook	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 Udit Singhal Anirban Sahu Yasuyuki Hosono Terrence R Barrette Joseph R Evans Shuang Zhao Anton Poliakov Xuhong Cao Saravana M Dhanasekaran Yi-Mi Wu Dan R Robinson David G Beer Felix Y Feng Hariharan K Iyer Arul M Chinnaiyan	Nature Genetics
Open pipelines for integrated tumor genome profiles reveal differences between pancreatic cancer tumors and cell lines	2015-03	James Taylor	Jeremy Goecks Bassel F El-Rayes Shishir K Maithel H Jean Khoury Michael R Rossi	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 Sebastien M Weyn-Vanhentenryck Jie Wu Ye Zhang Kenian Chen Jia Qian Wu Ben A Barres Chaolin Zhang	Proceedings of the National Academy of Sciences of the United States of America
Discovery of putative small non-coding RNAs from the obligate intracellular bacterium Wolbachia pipientis.	2015-03-04	Jean Popovici Jonathan M Keith	Megan Woolfit Manjula Algama Elizabeth A McGraw	PLoS ONE
Activation of an endogenous retrovirus-associated long non-coding RNA in human adenocarcinoma.	2015-03-05	Gregg B Morin	Ewan A Gibb René L Warren Gavin W Wilson Scott D Brown Gordon A Robertson Robert A Holt	Genome Medicine
PATZ1 Is a DNA Damage-Responsive Transcription Factor That Inhibits p53 Function.	2015-03-09	Wilfried Ellmeier	Nazli Keskin Emre Deniz Jitka Eryilmaz Manolya Un Tugce Batur Tulin Ersahin Rengul Cetin Atalay Shinya Sakaguchi Batu Erman	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 Marcel E. Dinger Kim-Anh Lê Cao Tommaso Leonardi Giovanni Bussotti Michael B. Clark Joanna Crawford Gethin Thomas	Tim R Mercer Katelin R Haynes Marion E Brunck Kim-Anh Lê Cao Wendy Y Chen Ryan J Taft	Nature Methods
Conditional-ready mouse embryonic stem cell derived macrophages enable the study of essential genes in macrophage function	2015-03-10	Oliver Billker	A T Y Yeung C Hale J Xia P H Tate D Goulding J A Keane S Mukhopadhyay L Forrester W C Skarnes R E W Hancock G Dougan	Scientific Reports
DNA methylation dynamics at imprinted genes during bovine pre-implantation embryo development.	2015-03-10	Niamh Forde Alan M O'Doherty Trudee Fair	David A Magee Lynee C O'Shea Marijke E Beltman Solomon Mamo	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 Michael Baldwin Michael Macarulay Ashley M Vaughan Stefan H I Kappe	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 Beatriz Sánchez-Calvo Francisco Luque Jaime Jiménez-Ruiz María N Padilla Jesús Fierro-Risco Raquel Valderrama Ana Fernández-Ocaña Juan B Barroso	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 Céline Keime Frédéric Parmentier François-Xavier Lejeune Anne-Laurence Boutillier Christian Néri Karine Merienne	Human Molecular Genetics
Goodness-of-fit tests and model diagnostics for negative binomial regression of RNA sequencing data	2015-03-18	Gu Mi	Yanming Di Daniel W Schafer	PLoS ONE
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 Weiqiang Zhao Susan Long Joseph Flynn Ian Flinn Jeffrey Jones Kami Maddocks Leslie Andritsos Emanuela M Ghia Laura Z Rassenti Thomas J Kipps John C Byrd	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 Manfred Schartl	I Matos M P Machado	PLoS ONE
The transcriptome of equine peripheral blood mononuclear cells.	2015-03-19	Alicja Pacholewska	Michaela Drögemüller Jolanta Klukowska-Rötzler Simone Lanz Eman Hamza Emmanouil T Dermitzakis Eliane Marti Vincent Gerber Tosso Leeb Vidhya Jagannathan	PLoS ONE
GLI2 inhibition abrogates human leukemia stem cell dormancy.	2015-03-21	John McPherson	Anil Sadarangani Gabriel Pineda Kathleen M Lennon Hye-Jung Chun Alice Shih Annelie E Schairer Angela C Court Daniel J Goff Sacha L Prashad Ifat Geron Russell Wall Richard A Moore Minya Pu Lei Bao Amy Jackson-Fisher Michael Munchhof Todd VanArsdale Tannishtha Reya Sheldon R Morris Mark D Minden Karen Messer Hanna K A Mikkola Marco A Marra Thomas J Hudson Catriona H M Jamieson	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 Anamaria Aranha Camargo	Pedro A F Galante Elisabeth Limbeck Patrick Möhnle Raphael B Parmigiani Lucila Ohno-Machado Simone Kreth	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 Isabella Gazzoli Peter A C 't Hoen Nisha Verwey Johan T den Dunnen Jeroen F J Laros	Nucleic Acids Research
The RNAi machinery controls distinct responses to environmental signals in the basal fungus Mucor circinelloides.	2015-03-25	V Garre Simon Moxon	Francisco E Nicolás Ana Vila María D Cascales Santiago Torres-Martínez Rosa M Ruiz-Vázquez	BMC Genomics
Discovery of molecular markers to discriminate corneal endothelial cells in the human body.	2015-03-25	Masahito Yoshihara Hideya Kawaji Masayoshi Itoh Kohji Nishida	Hiroko Ohmiya Susumu Hara Satoshi Kawasaki FANTOM consortium Yoshihide Hayashizaki Motokazu Tsujikawa	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 Daria V. Zhernakova Kristin Abbott Patrick Deelen Jingyuan Fu Marc J Bonder	Mark de Haan Marijke van der Sijde Juha Karjalainen K Joeri van der Velde Richard J Sinke Morris A Swertz Lude Franke	Genome Medicine
Folate receptor-α (FOLR1) expression and function in triple negative tumors	2015-03-27	Krishna R Kalari Karla V Ballman Zhifu Sun	Brian M Necela Jennifer A Crozier Cathy A Andorfer Laura Lewis-Tuffin Jennifer M Kachergus Xochiquetzal J Geiger Daniel J Serie Alvaro Moreno-Aspitia Daniel J O'Shannessy Julia D Maltzman Ann E McCullough Barbara A Pockaj Heather E Cunliffe E Aubrey Thompson Edith A Perez	PLoS ONE
Functional characterization of BC039389-GATM and KLK4-KRSP1 chimeric read-through transcripts which are up-regulated in renal cell cancer	2015-03-27	Mark Rubin	Dorothee Pflueger Christiane Mittmann Silvia Dehler Holger Moch Peter Schraml	BMC Genomics
The Listeria monocytogenes strain 10403S BioCyc database.	2015-03-28	Teresa M Bergholz Kathryn J Boor Martin Wiedmann	Renato H Orsi	Database
UV irradiation responses in Giardia intestinalis.	2015-03-28	Karin Troell Staffan G Svärd	Elin Einarsson	Experimental Parasitology
Long intervening non-coding RNA 00320 is human brain-specific and highly expressed in the cortical white matter.	2015-03-29	Glenda Halliday	James D Mills Jieqiong Chen Woojin S Kim Paul D Waters Avanita S Prabowo Eleonora Aronica Michael Janitz	Neurogenetics
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 Filippo Tatino Luciano Xumerle Alessandra Dal Molin Carla Avanzato Alberto Ferrarini Massimo Delledonne Luigi Frusciante Domenico Carputo	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 Stephen D Turner Steffen Jung	James C Cronk Noël C Derecki Emily Ji Yang Xu Aaron E Lampano Igor Smirnov Wendy Baker Geoffrey T Norris Ioana Marin Nathan Coddington Yochai Wolf Alan Aderem Alexander L Klibanov Vladimir Litvak	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 Marilyn Li Thomas Carroll Leif Oxburgh Yumei Feng Zubaida Saifudeen	Development
A pooled shRNA screen for regulators of primary mammary stem and progenitor cells identifies roles for Asap1 and Prox1.	2015-04-03	Ross A. Dickins Matthew E Ritchie Geoffrey J. Lindeman	Julie M Sheridan Sarah A Best Kun Jiang Tamara J Beck François Vaillant Kevin Liu Gordon K Smyth Jane E Visvader	BMC Cancer
EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments.	2015-04-05	Christina Kendziorski	Ning Leng Yuan Li Brian E McIntosh Bao Kim Nguyen Bret Duffin Shulan Tian James A Thomson Colin N Dewey Ron Stewart	Bioinformatics
Regulation of early T-lineage gene expression and developmental progression by the progenitor cell transcription factor PU.1.	2015-04-06	Stephen L. Nutt Ellen V. Rothenberg	Ameya Champhekar Sagar S Damle George Freedman Sebastian Carotta	Genes & Development
The level of residual dispersion variation and the power of differential expression tests for RNA-Seq data	2015-04-07	Gu Mi	Yanming Di	PLoS ONE
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	Tiantian Cai Hsin-I Jen Hyojin Kang Tiemo J Klisch	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 Jiwen Yu Hengling Wei Qifeng Ma Libei Li Chi Zhang Shuxun Yu	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 Josephine Bowles Kathryn S McClelland Vincent R Harley Peter Koopman	Katrina Bell Christian Larney Andrew H Sinclair	Biology of Reproduction
New basal cell carcinoma susceptibility loci.	2015-04-09	Laufey Tryggvadottir Unnur Þorsteinsdóttir Hrefna Johannsdottir Anne Tjønneland Gudmar Thorleifsson Thorunn Rafnar Y Gilaberte Hreinn Stefansson Eduardo Nagore Rajiv Kumar Ulla Vogel	Simon N Stacey Hannes Helgason Sigurjon A Gudjonsson Gudmar Thorleifsson Florian Zink Asgeir Sigurdsson Birte Kehr Julius Gudmundsson Patrick Sulem Bardur Sigurgeirsson Kristrun R Benediktsdottir Kristin Thorisdottir Rafn Ragnarsson Victoria Fuentelsaz Cristina Corredera Matilde Grasa Dolores Planelles Onofre Sanmartin Peter Rudnai Eugene Gurzau Kvetoslava Koppova Bjørn A Nexø Kim Overvad Jon G Jonasson Anna M Kristinsdottir Gisli Masson Olafur T Magnusson Bjarni V Halldorsson Augustine Kong Thorunn Rafnar José I Mayordomo Daniel F Gudbjartsson Jon H Olafsson Kari Stefansson	Nature Communications
New signaling pathways govern the host response to C. albicans infection in various niches.	2015-04-09	Jacques Ravel Jennifer Schwartz Amol C Shetty	Yaoping Liu L Latey Bradford Wenjie Xu Qyunh T Phan Priti Kumari Anup Mahurkar Aaron P Mitchell Claire M Fraser Scott G Filler Vincent M Bruno	Genome Research
Allelic Imbalance Is a Prevalent and Tissue-Specific Feature of the Mouse Transcriptome.	2015-04-09	Bernhard Payer David Colognori Ruslan I Sadreyev	Stefan F Pinter Brian J Beliveau Eda Yildirim Chao-Ting Wu Jeannie T Lee	Genetics
High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin.	2015-04-13	Kaia Achim Daria Gavriouchkina Luis R. Saraiva John C Marioni	Jean-Baptiste Pettit Tomas Larsson Detlev Arendt	Nature Biotechnology
Spatial reconstruction of single-cell gene expression data.	2015-04-13	Aviv Regev Rahul Satija Jeffrey A Farrell	David Gennert Alexander F Schier	Nature Biotechnology
Identification of non-coding RNAs associated with telomeres using a combination of enChIP and RNA sequencing	2015-04-13	Hodaka Fujii Daisuke Okuzaki	Toshitsugu Fujita Miyuki Yuno Rieko Ohki	PLoS ONE
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 Adam D Werts Jason D Lieb	PLOS Genetics
Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum.	2015-04-13	Gad Shaulsky	Rafael David Rosengarten Balaji Santhanam Danny Fuller Mariko Katoh-Kurasawa William F Loomis Blaz Zupan	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	Audrey Laurent Manuela Calabrese Marie-Laure Yaspo Vsevolod Tkachuk Francesco Blasi Dmitry Penkov	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 Leiming You Anlong Xu Shengfeng Huang	PLoS ONE
NMD3 regulates both mRNA and rRNA nuclear export in African trypanosomes via an XPOI-linked pathway.	2015-04-14	Paul Capewell Isabel Roditi Alasdair Ivens	Melanie Bühlmann Pegine Walrad Eva Rico Arunasalam Naguleswaran Keith R Matthews	Nucleic Acids Research
Identification of candidate mimicry proteins involved in parasite-driven phenotypic changes	2015-04-15	Nadia Aubin-Horth Mahesh Panchal Iain Barber	Francois Olivier Hebert Luke Phelps Irene Samonte Stephan Grambauer Martin Kalbe Christian R Landry	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 Graeme C Smith David A Ellis Yuan Y C Chen Michal Malecki Sandra Codlin Jean-François Lemay Cristina Cotobal François Bachand Samuel Marguerat Juan Mata Jürg Bähler	Genome Research
SF3B1 association with chromatin determines splicing outcomes.	2015-04-16	Arnab Datta	Nir Kfir Galit Lev-Maor Ohad Glaich Adi Alajem Siu K Sze Eran Meshorer Gil Ast	Cell Reports
First description of small proteins encoded by spRNAs in Methanosarcina mazei strain Gö1.	2015-04-16	Ruth Schmitz-Streit Dörte Becher	Daniela Prasse Jens Thomsen Rebecca De Santis Jan Muntel	Biochimie
PGTools: A Software Suite for Proteogenomic Data Analysis and Visualization.	2015-04-17	Sean M. Grimmond	Shivashankar H Nagaraj Nicola Waddell Anil K Madugundu Scott Wood Alun Jones Ramya A Mandyam Katia Nones John V Pearson	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 Ganesan Vadamalai James Rookes Neda Naderali	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	Emmanuel Dimont Jiantao Shi	Bioinformatics
From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data.	2015-04-22	Thomas P Mawhinney	Jilong Li Jie Hou Lin Sun Jordan Maximillian Wilkins Yuan Lu Chad E Niederhuth Benjamin Ryan Merideth Valeri V Mossine C Michael Greenlief John C Walker William R Folk Mark Hannink Dennis B Lubahn James A Birchler Jianlin Cheng	PLoS ONE
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 Bo Peng Huan Yan Yonghe Qi Yinyan Sun Ju-Tao Guo Fengchao Wang	PLOS Pathogens
Functional analysis and transcriptomic profiling of iPSC-derived macrophages and their application in modeling Mendelian disease.	2015-04-22	Muredach P. Reilly	Hanrui Zhang Chenyi Xue Rhia Shah Kate Bermingham Christine C Hinkle Wenjun Li Amrith Rodrigues Jennifer Tabita-Martinez John S Millar Marina Cuchel Evanthia E Pashos Ying Liu Ruilan Yan Wenli Yang Sager J Gosai Daniel VanDorn Stella T Chou Brian D Gregory Edward E Morrisey Mingyao Li Daniel J Rader	Circulation Research
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	S Tsygankova N Zhigalova A Mazur E Prokhortchouk	Gene
ZNF804A Transcriptional Networks in Differentiating Neurons Derived from Induced Pluripotent Stem Cells of Human Origin	2015-04-23	Deyou Zheng	Jian Chen Mingyan Lin Anastasia Hrabovsky Erika Pedrosa Jason Dean Swati Jain Herbert M Lachman	PLoS ONE
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 M Rita T Casari Philipp M Guenzl Daniel Wenzel Daniel Andergassen Anastasiya Hladik Paul Datlinger Matthias Farlik H-Christian Theussl Denise P Barlow Quanah J Hudson	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 Jean-Charles Leplé Rebecca Van Acker Annegret Kohler Julie Candiracci Laure Twyffels Antanas V Spokevicius Gerd Bossinger Françoise Laurans Nicole Brunel Marjorie Vermeersch Mondher El Jaziri Marie Baucher	The Plant Journal
Tet3 regulates synaptic transmission and homeostatic plasticity via DNA oxidation and repair	2015-04-27	Guo-Li Ming Hongjun Song Daniel Geschwind	Huimei Yu Yijing Su Jaehoon Shin Chun Zhong Junjie U Guo Yi-Lan Weng Fuying Gao Giovanni Coppola	Nature Neuroscience
High-performance probes for light and electron microscopy	2015-04-27	Gerald M. Rubin Megan E Williams Erik B. Bloss Brian P. English	Sarada Viswanathan Timothy J Stasevich Colenso M Speer Aljoscha Nern Barret D Pfeiffer Bryan M Hooks Wei-Ping Li Teresa Tian Gilbert L Henry John J Macklin Ronak Patel Charles R Gerfen Xiaowei Zhuang Yalin Wang Loren L Looger	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 Michael J Strong Tina O'Grady	Subing Cao Walter Moss Monica Concha Xia Wang Yi Yu Melody Baddoo Kun Zhang Claire Fewell Zhen Lin 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 V Maillo Peadar Ó Gaora D Rizos	Urban Besenfelder Vitezslav Havlicek Patrick Lonergan	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 Yiqin Xiong Nikhil Tellakula Vivek Nanda Nikitha Murthy William A Boisvert Ljubica Perisic Silvia Aldi Milos Pjanic Gary K Owens	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 Brian S White Sanghyun Kim Justin Tibbitts Jin Shao Matthew Ndonwi Brian Wadugu Eric J Duncavage Theresa Okeyo-Owuor Tuoen Liu Vincent Magrini Robert S Fulton Catrina Fronick Michelle O'Laughlin Matthew J Walter	Cancer Cell
Integrative Analysis of Normal Long Intergenic Non-Coding RNAs in Prostate Cancer.	2015-05-01	Saurabh Gupta	Pushpinder Bawa Sajna Zackaria Mohit Verma R Srivatsan Bibha Chaudhary Subhashini Srinivasan	PLoS ONE
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 Martina Del Lungo Flavio Ronzoni Rostyslav Kuziakiv Virpi Tohonen Marco Zucchelli Federico Santoni Michel Guipponi Biljana Dumevska Outi Hovatta Marisa E Jaconi	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 Hagop Kantarjian	Derrick Sek Tong Ong Yamini Ogoti Nipun A Mistry Karen Clise-Dwyer Sonny A Ang Andrea Viale Kathryn Ruisaard Irene Ganan Gomez Christopher A Bristow David C Weksberg Yan Wing Ho Baoli Hu Giannicola Genovese Piergiorgio Pettazzoni Asha S Multani Shan Jiang Sujun Hua Michael C Ryan Alessandro Carugo Luigi Nezi Yue Wei Hui Yang Li Zhang Sarah Gaddis Ting Gong James W Horner Timothy P Heffernan Philip Jones Laurence J N Cooper Han Liang Y Alan Wang Lynda Chin Carlos Bueso-Ramos Guillermo Garcia-Manero Ronald A DePinho	Cancer Cell
Bariatric Surgery Induces Disruption in Inflammatory Signaling Pathways Mediated by Immune Cells in Adipose Tissue: A RNA-Seq Study	2015-05-04	Yuna Blum	Christine Poitou Claire Perret François Mathieu Vinh Truong Hervé Durand Rohia Alili Nadjim Chelghoum Véronique Pelloux Judith Aron-Wisnewsky Adriana Torcivia Jean-Luc Bouillot Brian W Parks Ewa Ninio Karine Clément Laurence Tiret	PLoS ONE
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 Julio Benavides Gwenola Tosser-Klopp Juan J Arranz Valentín Pérez	Aroa Suárez-Vega Beatriz Gutiérrez-Gil Christophe Klopp Stephen J Keennel	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 Hiten D. Madhani James J. Becnel	Christopher A Desjardins Neil D Sanscrainte Jonathan M Goldberg David Heiman Sarah Young Qiandong Zeng	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
Ratios of Four STAT3 Splice Variants in Human Eosinophils and Diffuse Large B Cell Lymphoma Cells	2015-05-18	Stephane Esnault	Keren B Turton Douglas S Annis Lixin Rui Deane F Mosher	PLoS ONE
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
Diffusion maps for high-dimensional single-cell analysis of differentiation data.	2015-05-21	Florian Buettner Fabian J. Theis	Laleh Haghverdi	Bioinformatics
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 Philippe Bouloc	Elisabeth Sauvage Odile Sismeiro Adrien Villain Violette Da Cunha Marie-Elise Caliot Marie-Agnès Dillies Marie-Frédérique Lartigue Philippe Glaser	BMC Genomics
Functionally defined therapeutic targets in diffuse intrinsic pontine glioma	2015-06	Wenchao Sun Jacques Grill	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 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
RNA-Seq analysis of isolated satellite cells in Prmt5 deficient mice.	2015-06-03	Carsten T Kuenne Mario Looso Thomas Braun	Stefan Guenther Ting Zhang Marcus Krueger Yonggang Zhou Johnny Kim	Genomics Data
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 M Ramsdale	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 Tom Maniatis Junqiang Ye Lindsey J. Macpherson	Nadine Beetz Sean O'Keeffe Juan Carlos Tapia Weisheng V. Chen Eric N. Olson	Proceedings of the National Academy of Sciences of the United States of America
From Glacier to Sauna: RNA-Seq of the Human Pathogen Black Fungus Exophiala dermatitidis under Varying Temperature Conditions Exhibits Common and Novel Fungal Response	2015-06-10	Barbara Blasi Hakim Tafer	Donatella Tesei Katja Sterflinger	PLoS ONE
Molecular characterization of two novel molecular chaperones in bacterial-challenged Apostichopus japonicus.	2015-06-10	Chenghua Li	Haihong Wang Yina Shao Weiwei Zhang Zhimeng Lv Chunhua Jin	Gene
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 Nirali M Patel Vonn Walter	Xiaobei Zhao Anyou Wang David A Eberhard Michele C Hayward Ashley H Salazar Heejoon Jo Matthew G Soloway Matthew D Wilkerson Joel S Parker Xiaoying Yin Guosheng Zhang Marni B Siegel Gary B Rosson H Shelton Earp Margaret L Gulley Karen E Weck D Neil Hayes Stergios J Moschos	PLoS ONE
Suppressing Sorbitol Synthesis Substantially Alters the Global Expression Profile of Stress Response Genes in Apple (Malus domestica) Leaves.	2015-06-15	Yi Zheng Abhaya Dandekar	Ting Wu Yi Wang Zhangjun Fei Kenong Xu Zhenhai Han Lailiang Cheng	Plant and Cell Physiology
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 Dan Nettleton	Fengwei Jiang Chunxia An Yinli Bao Xuefeng Zhao Robert L Jernigan Andrew Lithio Ling Li Lisa K Nolan Chengping Lu Ganwu Li	Infection and Immunity
RNA Seq profiling reveals a novel expression pattern of TGF-β target genes in human blood eosinophils.	2015-06-22	Stephane Esnault	Zhong-Jian Shen Jie Hu Igor Dozmorov James S Malter	Immunology Letters
RNA-seq Reveals Complicated Transcriptomic Responses to Drought Stress in a Nonmodel Tropic Plant, Bombax ceiba L.	2015-06-23	Yuan Chen Liuyang Wang	Zhili Zhou Huancheng Ma Kevin Lin Youjie Zhao Zhi Xiong Bin Tian	Evolutionary Bioinformatics
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 Esko Kankuri	H Annika Siitonen Kristo Nuutila Mari H Tervaniemi Jyrki Vuola Anna Johnsson Peter Lönnerberg Sten Linnarsson Outi Elomaa	BMC Genomics
Comparison of RNA-seq and microarray-based models for clinical endpoint prediction.	2015-06-25	Benedikt Brors Danielle Thierry-Mieg Falk Hertwig Weihong Xu Marco Chierici Lee Lancashire Richard G Grundy Heng Luo Davide Albanese Martin Peifer Jean Thierry-Mieg Jun Wang	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
Age-Related Gene Expression Differences in Monocytes from Human Neonates, Young Adults, and Older Adults.	2015-07-06	Tobias Kollmann	Michelle M Lissner Brandon J Thomas Kathleen Wee Ann-Jay Tong Stephen T Smale	PLoS ONE
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 Massimiliano Peana	Freda Laulicht Jason Brocato Laura Cartularo Joshua Vaughan Feng Wu Thomas Kluz Hong Sun Betul Akgol Oksuz 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
Evolutionary Divergence of Gene and Protein Expression in the Brains of Humans and Chimpanzees.	2015-07-10	Chet C. Sherwood	Amy L Bauernfeind Erik J Soderblom Meredith E Turner M Arthur Moseley John J Ely Patrick R Hof Gregory A Wray Courtney C Babbitt	Genome Biology and Evolution
Differential and coherent processing patterns from small RNAs	2015-07-13	Jan Gorodkin Sachin Pundhir		Scientific Reports
Microbes & neurodevelopment--Absence of microbiota during early life increases activity-related transcriptional pathways in the amygdala.	2015-07-13	Roman Stilling Feargal J Ryan Marcus J Claesson Gerard Clarke Timothy G. Dinan	Alan E Hoban Fergus Shanahan 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 Surendra Kumar	Sunniva Stordal Bjørklund Vessela N Kristensen Michael Seiler Grethe I Grenaker Alnæs Yao Ming John Kerrigan Bjørn Naume Ravi Sachidanandam Gyan Bhanot Shridar Ganesan	BMC Cancer
A nonlethal sampling method to obtain, generate and assemble whole blood transcriptomes from small, wild mammals.	2015-07-17	Emma C. Teeling Sébastien Puechmaille Michaël Bekaert	Zixia Huang Aurore Gallot Nga T Lao Nicole M Foley David Jebb	Molecular Ecology Resources
Genome-wide association analysis on normal hearing function identifies PCDH20 and SLC28A3 as candidates for hearing function and loss.	2015-07-17	Dragana Vuckovic Sally J. Dawson Giorgia Girotto Anne Viljanen Taina Rantanen Marina Ciullo Diego Vozzi Teresa Nutile Ginevra Biino	Deborah I Scheffer Anna Morgan Mariateresa Di Stazio Maria P Concas 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 Foivos Gypas	Alexander Kanitz Georges Martin	Genome Biology
Identifying new sex-linked genes through BAC sequencing in the dioecious plant Silene latifolia.	2015-07-25	Alex Widmer Nicolas Blavet Niklaus Zemp Jos Käfer	H Blavet A Muyle R Cegan C Deschamps S Mousset S Aubourg R Bergero D Charlesworth R Hobza G A B Marais	BMC Genomics
Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17 Human Proteome Project.	2015-07-28	Gil Omenn	Hong-Dong Li Rajasree Menon Brandon Govindarajoo Bharat Panwar Yang Zhang Yuanfang Guan	Journal of Proteome Research
Transcriptional profiling of macrophages derived from monocytes and iPS cells identifies a conserved response to LPS and novel alternative transcription	2015-07-30	Siamon Gordon	Kaur Alasoo Fernando O Martinez Christine Hale Fiona Powrie Gordon Dougan Subhankar Mukhopadhyay Daniel J Gaffney	Scientific Reports
Transcriptome Dynamics of Developing Photoreceptors in Three-Dimensional Retina Cultures Recapitulates Temporal Sequence of Human Cone and Rod Differentiation Revealing Cell Surface Markers and Gene Networks	2015-07-31	Anand Swaroop	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 Linn Fagerberg William M Gallagher	Gillian O'Hurley Christer Busch Björn M Hallström Charlotte Stadler Anna Tolf Emma Lundberg Jochen M Schwenk Karin Jirström Anders Bjartell 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 K Vijay-Shanker 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 Yamile Marquez Maria Kalyna Geoffrey Michael Gadd	John W S Brown Craig G Simpson	The Plant Cell
The mRNA expression of soluble urokinase plasminogen activator surface receptor in human adipose tissue is positively correlated with body mass index.	2015-08-18	Kok Gan Chan	Hien Fuh Ng Kin Fah Chin Yun Fong Ngeow	Genome
Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis.	2015-08-19	Guo-Li Ming Hongjun Song Daniel A Berg David Nauen	Jaehoon Shin Yunhua Zhu Joseph Y Shin Juan Song Michael A Bonaguidi Grigori Enikolopov Kimberly M Christian	Cell Stem Cell
Assembly and Analysis of Differential Transcriptome Responses of Hevea brasiliensis on Interaction with Microcyclus ulei.	2015-08-19	Ibonne Aydee García Romero Dolly Montoya Castaño Silvia Restrepo	Uriel Alonso Hurtado Páez Fabio Ancizar Aristizábal Gutiérrez	PLoS ONE
Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development.	2015-08-19	Dmitry A Ovchinnikov Deanne M. Taylor Ernst J. Wolvetang	Yu Hasegawa Laurence de Torrenté Jessica C Mar	PLOS Genetics
Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms	2015-08-19	Mihaela Pertea	Tsung-Cheng Chang Sungyul Lee Steven L Salzberg Joshua T Mendell	Genome Research
Regulation of alternative splicing in Drosophila by 56 RNA binding proteins.	2015-08-20	Steven E. Brenner	Angela N Brooks Michael O Duff Gemma May Li Yang Mohan Bolisetty Jane Landolin Ken Wan Jeremy Sandler Benjamin W Booth Susan E Celniker Brenton R Graveley	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
Concordance between RNA-sequencing data and DNA microarray data in transcriptome analysis of proliferative and quiescent fibroblasts	2015-09	Brett Trost	Catherine A Moir Zoe E Gillespie Anthony Kusalik Jennifer A Mitchell Christopher H Eskiw	Royal Society Open Science
Cullin4 Is Pro-Viral during West Nile Virus Infection of Culex Mosquitoes.	2015-09-01	Peter Walker Julio Rodriguez-Andres Jean-bernard Duchemin	Prasad N Paradkar Lee Trinidad	PLOS Pathogens
RNA-Seq analysis identifies key genes associated with haustorial development in the root hemiparasite Santalum album.	2015-09-01	Oliver Berkowitz James Whelan	Xinhua Zhang Jaime A Teixeira da Silva Muhan Zhang Guohua Ma Jun Duan	Frontiers in Plant Science
Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses	2015-09-02	Aviv Regev Rahul Satija Roi Avraham Alex K. Shalek	Nathan Haseley Douglas Brown Cristina Penaranda Humberto B Jijon John J Trombetta Ramnik J Xavier Deborah T Hung	Cell
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 Chadi A El Farran Yinghui Li Matthew C. Lorincz	Bin Xia Yang Hong Chao Guo Tao Yu Hai Tong Fang Hao Fei Wang Sharon Schlesinger Yu Fen Samantha Seah Germaine Yen Lin Goh Suat Peng Neo Vinay Tergaonkar Tit-Meng Lim Lingyi Chen Jayantha Gunaratne James J Collins Stephen P Goff Hu Li Frederic A Bard Yuin-Han Loh	Cell
Molecular analyses of juvenile granulosa cell tumors bearing AKT1 mutations provide insights into tumor biology and therapeutic leads.	2015-09-11	Aurélie Auguste S Caburet Sabine Sarnacki	Laurianne Bessière Anne-Laure Todeschini Jaime Prat Emanuela D'angelo Pierre De La Grange Olivier Ariste Fréderic Lemoine Bérangère Legois Charles Sultan Alain Zider Louise Galmiche Nicolas Kalfa Reiner A Veitia	Human Molecular Genetics
Genome-wide RNA sequencing analysis of quorum sensing-controlled regulons in the plant-associated Burkholderia glumae PG1 strain.	2015-09-11	Andreas Knapp Rolf Daniel	Rong Gao Dagmar Krysciak Katrin Petersen Christian Utpatel Christel Schmeisser Sonja Voget Karl-Erich Jaeger Wolfgang R Streit	Applied and Environmental Microbiology
The role of antigen presenting cells in the induction of HIV-1 latency in resting CD4(+) T-cells.	2015-09-11	Vanessa A Evans David Powell Sharon R. Lewin	Nitasha A Kumar Karey Cheong Candida da Fonseca Pereira Jenny Anderson Paul U Cameron	Retrovirology
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 SungSoo Kim	Eugene Fletcher Amir Feizi	Microbial Cell Factories
A novel workflow correlating RNA-seq data to Phythophthora infestans resistance levels in wild Solanum species and potato clones.	2015-09-17	Estelle Proux-Wéra Erik Andreasson	Itziar Frades Kibrom B Abreha Åsa Lankinen Erik Alexandersson	Frontiers in Plant Science
Tools and best practices for data processing in allelic expression analysis.	2015-09-17	Tuuli Lappalainen Pejman Mohammadi	Stephane E Castel Ami Levy-Moonshine Eric Banks	Genome Biology
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 Ilaria Panzeri	Raoul J P Bonnal Valeria Ranzani Alberto Arrigoni Serena Curti Paola Gruarin	Scientific Data
Transcriptome Characteristics and X-Chromosome Inactivation Status in Cultured Rat Pluripotent Stem Cells.	2015-09-29	Irina S. Zakharova Sergey P Medvedev Fedor Kolpakov Suren M Zakian Alexander Karaskov	Evgeniya A Vaskova Anastasiya E Sorokina Artem A Nemudryy Evgeniy A Elisaphenko Alexander I Shevchenko Elena A Kizilova Antonina I Zhelezova Ivan S Evshin Ruslan N Sharipov Julia M Minina Natalia S Zhdanova Igor I Khegay Gennadiy T Sukhikh Evgeniy A Pokushalov Valentin V Vlasov Ludmila N Ivanova	Stem Cells and Development
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 Julie Hanotel Ian Quigley Aurore Thelie Alessandra Pierani Michael Schubert	Simon Desiderio Benoit Van Driessche Anthony Rodari Mark D Borromeo Sadia Kricha François Lahaye Jenifer Croce Gustavo Cerda-Moya Jesús Ordoño Fernandez Barbara Bolle Katharine E Lewis Maike Sander Jane E Johnson Christopher R Kintner Tomas Pieler Kristine A Henningfeld Eric J Bellefroid Claude Van Campenhout	Development
Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells.	2015-10-01	Aviv Regev Itay Tirosh	Monika S Kowalczyk Itay Tirosh Dirk Heckl Tata Nageswara Rao Atray Dixit Brian J Haas Rebekka K Schneider Amy J Wagers Benjamin L Ebert	Genome Research
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 Hans-Peter Piepho	Nina Opitz Caroline Marcon Anja Paschold Andrew Lithio Ronny Brandt Frank Hochholdinger	Journal of Experimental Botany
Computational analysis of stochastic heterogeneity in PCR amplification efficiency revealed by single molecule barcoding.	2015-10-13	James M Heather Benny Chain	Katharine Best Theres Oakes John Shawe-Taylor	Scientific Reports
Dynamic association rules for gene expression data analysis	2015-10-14	Wen-Hsiung Li	Shu-Chuan Chen Tsung-Hsien Tsai Cheng-Han Chung	BMC Genomics
Insights into the role of immunosenescence during varicella zoster virus infection (shingles) in the aging cell model	2015-10-14	Mukesh Kumar	Ji-Ae Kim Seul-Ki Park Chan-Hee Lee Ok Sarah Shin	Oncotarget
Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies.	2015-10-14	Jörg Vogel Lars Barquist		Annual Review of Genetics
Decay-Initiating Endoribonucleolytic Cleavage by RNase Y Is Kept under Tight Control via Sequence Preference and Sub-cellular Localisation.	2015-10-16	Peter Redder Julien Prados	Vanessa Khemici Patrick Linder	PLOS Genetics
Effect of heparin on the biological properties and molecular signature of human mesenchymal stem cells	2015-10-17	Rebekah M Samsonraj Drew M Titmarsh Emily T Camilleri	Ling Ling Torben Helledie Ren Jie Chua Oliver Dreesen Christian Dombrowski David A Rider Mario Galindo Ian Lee Wanjin Hong James H Hui Victor Nurcombe Andre J van Wijnen Simon M Cool	Gene
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 Rory Kirchner Yasunobu Murata Sung-Yon Kim	Andrew D Bolton Andrew Young Tru Dang Yuchio Yanagawa	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
Identification of Genes Related to Growth and Lipid Deposition from Transcriptome Profiles of Pig Muscle Tissue.	2015-10-27	Hao Zhang	Zhixiu Wang Qinggang Li Yangzom Chamba Bo Zhang Peng Shang Changxin Wu	PLoS ONE
A Database of microRNA Expression Patterns in Xenopus laevis	2015-10-27	Sara Lopez-Gomollon Simon Moxon Tamas Dalmay	Ayisha Ahmed Nicole J Ward Camille Viaut Matthew L Tomlinson Ilya Patrushev Michael J Gilchrist Dario Dotlic Andrea E Münsterberg Grant N Wheeler	PLoS ONE
RNA-Seq of Tumor-Educated Platelets Enables Blood-Based Pan-Cancer, Multiclass, and Molecular Pathway Cancer Diagnostics.	2015-10-27	Bauke Ylstra Pieter Wesseling Jan Koster	Myron G Best Nik Sol Irsan Kooi Jihane Tannous Bart A Westerman François Rustenburg Pepijn Schellen Heleen Verschueren Edward Post Najim Ameziane Josephine Dorsman Egbert F Smit Henk M Verheul David P Noske Jaap C Reijneveld R Jonas A Nilsson Bakhos A Tannous Thomas Wurdinger	Cancer Cell
Transcriptomic Changes in Coral Holobionts Provide Insights into Physiological Challenges of Future Climate and Ocean Change.	2015-10-28	Nedeljka N. Rosic David I Kline Chon-Kit Kenneth Chan Sophie Dove	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 Roger Pique-Regi	G A Moyerbrailean G O Davis C T Harvey D Watza	Scientific Reports
RNA Editing in Chloroplasts of Spirodela polyrhiza, an Aquatic Monocotelydonous Species	2015-10-30	Wenqin Wang Joachim Messing	Wei Zhang Yongrui Wu Pal Maliga	PLoS ONE
ccmGDB: a database for cancer cell metabolism genes	2015-10-30	Feixiong Cheng	Pora Kim Junfei Zhao Zhongming Zhao	Nucleic Acids Research
The vitamin D-dependent transcriptome of human monocytes.	2015-10-30	Veijo Nurminen Antonio Neme Carsten Carlberg	Sabine Seuter	The Journal of Steroid Biochemistry and Molecular Biology
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
A resource of ribosomal RNA-depleted RNA-Seq data from different normal adult and fetal human tissues.	2015-11-10	Nicolas Bertin	Jocelyn Y H Choy Priscilla L S Boon Melissa J Fullwood	Scientific Data
Cancer genetics: RNA-seq for blood-based pan-cancer diagnostics.	2015-11-10	Liesbet Lieben		Nature Reviews Genetics
REST-Governed Gene Expression Profiling in a Neuronal Cell Model Reveals Novel Direct and Indirect Processes of Repression and Up-Regulation.	2015-11-10	Davide Cittaro	Jose M Garcia-Manteiga Silvia Bonfiglio Lucrezia Folladori Maria L Malosio Dejan Lazarevic Elia Stupka Jacopo Meldolesi	Frontiers in Cellular Neuroscience
Saccular Transcriptome Profiles of the Seasonal Breeding Plainfin Midshipman Fish (Porichthys notatus), a Teleost with Divergent Sexual Phenotypes.	2015-11-11	Joseph A. Sisneros	Joshua Faber-Hammond Manoj P Samanta Elizabeth A Whitchurch Dustin Manning Allison B Coffin	PLoS ONE
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
miRge - A Multiplexed Method of Processing Small RNA-Seq Data to Determine MicroRNA Entropy	2015-11-16	Marc K. Halushka	Alexander S Baras Christopher J Mitchell Jason R Myers Simone Gupta Lien-Chun Weng John M Ashton Toby C Cornish Akhilesh Pandey	PLoS ONE
Interaction of Arabidopsis Trihelix-Domain Transcription Factors VFP3 and VFP5 with Agrobacterium Virulence Protein VirF.	2015-11-16	Vitaly Citovsky	Elena García-Cano Shimpei Magori Qi Sun Zehong Ding Sondra G Lazarowitz	PLoS ONE
Dual RNA-seq of Nontypeable Haemophilus influenzae and Host Cell Transcriptomes Reveals Novel Insights into Host-Pathogen Cross Talk	2015-11-17	Buket Baddal Raffaele A. Calogero	Alessandro Muzzi Stefano Censini Giulia Torricelli Silvia Guidotti Anna R Taddei Antonello Covacci Mariagrazia Pizza Rino Rappuoli Marco Soriani Alfredo Pezzicoli	mBio
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 Chuan Wu Gerd Meyer zu Horste	Chao Wang Nir Yosef Jellert Gaublomme Youjin Lee Clary B Clish Jim Kaminski Sheng Xiao Mathias Pawlak Yasuhiro Kishi Nicole Joller Katarzyna Karwacz Chen Zhu Maria Ordovas-Montanes Asaf Madi Ivo Wortman Toru Miyazaki Raymond A Sobel Hongkun Park Vijay K Kuchroo	Cell
Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity.	2015-11-18	Pier Paolo Pandolfi Aviv Regev Rahul Satija Chuan Wu Alex K. Shalek Li V. Yang	Jellert T Gaublomme Nir Yosef Youjin Lee Rona S Gertner Tak Mak Vijay K Kuchroo Hongkun Park	Cell
Deciphering the molecular adaptation of the king scallop (Pecten maximus) to heat stress using transcriptomics and proteomics.	2015-11-23	Romain Lavaud Jonathan Flye-Sainte-Marie Fred Jean Vianney Pichereau Melody S Clark	Sébastien Artigaud Joëlle Richard Michael A S Thorne Lloyd S Peck	BMC Genomics
RNA-Seq and Mass-Spectrometry-Based Lipidomics Reveal Extensive Changes of Glycerolipid Pathways in Brown Adipose Tissue in Response to Cold.	2015-11-24	Susanne Mandrup	Ann-Britt Marcher Anne Loft Ronni Nielsen Terhi Vihervaara Jesper Grud Skat Madsen Marko Sysi-Aho Kim Ekroos	Cell Reports
Analysis of nucleosome positioning landscapes enables gene discovery in the human malaria parasite Plasmodium falciparum.	2015-11-25	Evelien M. Bunnik	Xueqing Maggie Lu Neeti Pokhriyal Sara Nasseri Stefano Lonardi Karine G Le Roch	BMC Genomics
Different mechanisms of resistance modulate sulfite tolerance in wine yeasts.	2015-11-28	Chiara Nadai Alessio Giacomini Viviana Corich Laura Treu Stefano Campanaro		Applied Microbiology and Biotechnology
Bromodomain Proteins Contribute to Maintenance of Bloodstream Form Stage Identity in the African Trypanosome	2015-12	Nina Papavasiliou Monica Mugnier Erik W. Debler	Danae Schulz Eda-Margaret Paulsen Hee-Sook Kim Chun-wa W Chung David F Tough Inmaculada Rioja Rab K Prinjha F Nina Papavasiliou	PLOS Biology
mRNA-seq reveals skeletal muscle atrophy in response to handling stress in a marine teleost, the red cusk-eel (Genypterus chilensis)	2015-12-01	Herman Silva	Jorge E Aedo Jonathan Maldonado Víctor Aballai Juan M Estrada Macarena Bastias-Molina Claudio Meneses Cristian Gallardo-Escarate Alfredo Molina Juan A Valdés	BMC Genomics
Exposure to sixty minutes of hyperoxia upregulates myocardial humanins in patients with coronary artery disease - a pilot study.	2015-12-01	Joel Starkopf	I Karu P Tahepold A Ruusalepp E Reimann S Koks	Journal of Physiology and Pharmacology
Nitro-Fatty Acids in Plant Signaling: Nitro-Linolenic Acid Induces the Molecular Chaperone Network in Arabidopsis.	2015-12-01	Francisco J. Corpas	Capilla Mata-Pérez Beatriz Sánchez-Calvo María N Padilla Juan C Begara-Morales Francisco Luque Manuel Melguizo Jaime Jiménez-Ruiz Jesús Fierro-Risco Antonio Peñas-Sanjuán Raquel Valderrama Juan B Barroso	Plant Physiology
Phenotypic Heterogeneity Affects Stenotrophomonas maltophilia K279a Colony Morphotypes and β-Lactamase Expression	2015-12-02	Konrad Förstner Thomas A Kohl	Ebrahim M. Abda Dagmar Krysciak Ines Krohn-Molt Uwe Mamat Christel Schmeisser Ulrich E. Schaible Stefan Nieman Wolfgang R. Streit	Frontiers in Microbiology
Transcriptome profiling of two Iberian freshwater fish exposed to thermal stress.	2015-12-04	Maria Manuela Coelho Ana R. Grosso	Tiago Filipe Jesus Vera Maria Fonseca Almeida-Val	Journal of Thermal Biology
Topographical mapping of α- and β-keratins on developing chicken skin integuments: Functional interaction and evolutionary perspectives	2015-12-08	Wen-Hsiung Li	Ping Wu Chen Siang Ng Jie Yan Yung-Chih Lai Chih-Kuan Chen Yu-Ting Lai Siao-Man Wu Jiun-Jie Chen Weiqi Luo Randall B Widelitz Cheng-Ming Chuong	Proceedings of the National Academy of Sciences of the United States of America
Reproducible features of small RNAs in C. elegans reveal NU RNAs and provide insights into 22G RNAs and 26G RNAs	2015-12-08	Antony M Jose	Andrew L Blumenfeld	RNA
Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation	2015-12-08	Shaun Jackman	René L Warren Ewan A Gibb Benjamin P Vandervalk Hamid Mohamadi Justin Chu Anthony Raymond Stephen Pleasance Robin Coope Mark R Wildung Carol E Ritland Jean Bousquet Steven J M Jones Joerg Bohlmann Inanç Birol	Genome Biology and Evolution
High-throughput transcriptomics reveals common and strain-specific responses of human macrophages to infection with Mycobacterium abscessus Smooth and Rough variants.	2015-12-09	Aleksandra A Miranda-CasoLuengo Kévin Rue-Albrecht Brendan Loftus David E. MacHugh	Anna Aulicino Adam M Dinan John A Browne	BMC Genomics
RNA-seq reveals post-transcriptional regulation of Drosophila insulin-like peptide dilp8 and the neuropeptide-like precursor Nplp2 by the exoribonuclease Pacman/XRN1.	2015-12-09	Christopher Jones	Amy L Pashler Benjamin P Towler Sophie R Robinson Sarah F Newbury	Nucleic Acids Research
Investigating the Influence of Ribavirin on Human Respiratory Syncytial Virus RNA Synthesis by Using a High-Resolution Transcriptome Sequencing Approach.	2015-12-09	Christiane Hertz-Fowler David A. Matthews Julian Hiscox John Barr	Waleed Aljabr Olivier Touzelet Georgios Pollakis Weining Wu Diane C Munday Margaret Hughes John Kenny Rachel Fearns	Journal of Virology
Transcriptome profiling of human FoxP3+ regulatory T cells	2015-12-10	Cuong K. Nguyen	Ravikiran Bhairavabhotla Yong C Kim Deborah D Glass Thelma M Escobar Mira C Patel Rami Zahr Gokhul K Kilaru Stefan A Muljo Ethan M Shevach	Human Immunology
Comparative transcriptome analysis reveals molecular strategies of oriental river prawn Macrobrachium nipponense in response to acute and chronic nitrite stress.	2015-12-11	Jian G. Qin	Zhixin Xu Tongyu Li Erchao Li Ke Chen Zhili Ding Liqiao Chen Jinyun Ye	Fish and Shellfish Immunology
Fine-mapping cellular QTLs with RASQUAL and ATAC-seq.	2015-12-14	Daniel J Gaffney	Natsuhiko Kumasaka Andrew J Knights	Nature Genetics
Comparative Transcriptome Analysis in the Hepatopancreas Tissue of Pacific White Shrimp Litopenaeus vannamei Fed Different Lipid Sources at Low Salinity.	2015-12-15	Jian G. Qin	Ke Chen Erchao Li Zhixin Xu Tongyu Li Chang Xu Liqiao Chen	PLoS ONE
Transcriptional, post-transcriptional and chromatin-associated regulation of pri-miRNAs, pre-miRNAs and moRNAs.	2015-12-15	Laure Bally-Cuif Chirag Nepal Yavor Hadzhiev Marion Coolen Jesper B. Andersen Boris Lenhard Piero Carninci	Delphine Cussigh Piotr Mydel Vidar M Steen Ferenc Müller	Nucleic Acids Research
Adeno-associated virus gene therapy vector scAAVIGF-I for transduction of equine articular chondrocytes and RNA-seq analysis.	2015-12-16	Richard Slayden	D D Hemphill C W McIlwraith R J Samulski L R Goodrich	Osteoarthritis and Cartilage
Lin28A Binds Active Promoters and Recruits Tet1 to Regulate Gene Expression	2015-12-16	Guo-Li Ming Hongjun Song Jun Wan	Yaxue Zeng Bing Yao Jaehoon Shin Li Lin Namshik Kim Qifeng Song Shuang Liu Yijing Su Junjie U Guo Luoxiu Huang Hao Wu Jiang Qian Xiaodong Cheng Heng Zhu Peng Jin	Molecular Cell
Characterization and Comparative Analysis of the Milk Transcriptome in Two Dairy Sheep Breeds using RNA Sequencing	2015-12-18	Gwenola Tosser-Klopp Beatriz Gutierrez-Gil Gwenola Tosser-Klopp Juan J Arranz	Aroa Suárez-Vega Christophe Klopp Christèle Robert-Granie	Scientific Reports
Integration of electrophysiological recordings with single-cell RNA-seq data identifies neuronal subtypes	2015-12-21	Sten Linnarsson	János Fuzik Amit Zeisel Zoltán Máté Daniela Calvigioni Yuchio Yanagawa Gábor Szabó Sten Linnarsson Tibor Harkany	Nature Biotechnology
Single-cell transcriptomes reveal characteristic features of human pancreatic islet cell types	2015-12-21	Christoph Bock Johanna Klughammer Ekaterine Berishvili Andreas Spittler	Jin Li Matthias Farlik Thomas Penz Charlotte Barbieux Stefan Kubicek	EMBO Reports
Human cerebral organoids recapitulate gene expression programs of fetal neocortex development	2015-12-22	Svante Pääbo Farhath Badsha Barbara Treutlein Madeline Lancaster Juergen A Knoblich Marta Florio	J Gray Camp Sabina Kanton Tobias Gerber Michaela Wilsch-Bräuninger Eric Lewitus Alex Sykes Wulf Hevers Robert Lachmann Wieland B Huttner	Proceedings of the National Academy of Sciences of the United States of America
RNA Sequencing Analysis of the msl2msl3, crl, and ggps1 Mutants Indicates that Diverse Sources of Plastid Dysfunction Do Not Alter Leaf Morphology Through a Common Signaling Pathway.	2015-12-22	Elizabeth S. Haswell	Darron R Luesse Margaret E Wilson	Frontiers in Plant Science
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	Dimitar Kenanov Hao Han Wai Har Ng Sze Sing Lee Jeyakumar Masilamani Toan Thang Phan Oi Lian Kon	Molecular Therapy
Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis.	2015-12-23	Jeremy Chien Wei Zhang Baolin Wu	Jae-Woong Chang Lilong Lin Kay Minn Jeongsik Yong Hui Zheng Rui Kuang	PLOS Computational Biology
Late Embryogenesis Abundant (LEA) Constitutes a Large and Diverse Family of Proteins Involved in Development and Abiotic Stress Responses in Sweet Orange (Citrus sinensis L. Osb.).	2015-12-23	Marcio Gilberto Cardoso Costa	Andresa Muniz Pedrosa Cristina de Paula Santos Martins Luana Pereira Gonçalves	PLoS ONE
Elimination of Chromosomal Island SpyCIM1 from Streptococcus pyogenes Strain SF370 Reverses the Mutator Phenotype and Alters Global Transcription	2015-12-23	Scott V Nguyen	Christina Hendrickson Chad W Euler Maliha Rahman Kimberly A McCullor Catherine J King Vincent A Fischetti W Michael McShan	PLoS ONE
Chromatin and RNA Maps Reveal Regulatory Long Noncoding RNAs in Mouse.	2015-12-28	Miguel Beato del Rosal Marc A. Martí‐Renom	Gireesh K Bogu Pedro Vizán Lawrence W Stanton Luciano Di Croce	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	Laura A L Dillon Rahul Suresh Kwame Okrah David M Mosser	BMC Genomics
Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences.	2015-12-30	Mark D. Robinson Michael I Love	Charlotte Soneson	F1000Research
Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq	2015-12-31	Ricardo DeMarco Joao Carlos Setubal Sergio Verjovski-Almeida	Letícia Anderson Murilo S Amaral Felipe Beckedorff Lucas F Silva Bianca Dazzani Katia C Oliveira Giulliana T Almeida Monete R Gomes David S Pires	PLOS Neglected Tropical Diseases
Single-Cell Genomics for Virology	2016	Amalio Telenti	Angela Ciuffi Sylvie Rato	Viruses
Comparative Transcriptomic Analysis of Rectal Tissue from Beef Steers Revealed Reduced Host Immunity in Escherichia coli O157:H7 Super-Shedders	2016	Graham Plastow Tim A. McAllister	Ou Wang Guanxiang Liang Kim Stanford Brent Selinger Le Luo Guan	PLoS ONE
Sphingomonas wittichii Strain RW1 Genome-Wide Gene Expression Shifts in Response to Dioxins and Clay	2016	Syed A. Hashsham Hui Li	Benli Chai Tamara V Tsoi Shoko Iwai Cun Liu Jordan A Fish Cheng Gu Timothy A Johnson Gerben Zylstra Brian J Teppen Stephen A Boyd James R Cole James M Tiedje	PLoS ONE
Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla	2016	Samuel O Purvine	Peter H Waltman Jian Guo Emily Nahas Reistetter Charles K Ansong Marijke J van Baren Chee-Hong Wong Chia-Lin Wei Richard D Smith Stephen J Callister Joshua M Stuart Alexandra Z Worden	PLoS ONE
Contrasting Potato Foliage and Tuber Defense Mechanisms against the Late Blight Pathogen Phytophthora infestans	2016	Liangliang Gao James M Bradeen		PLoS ONE
5'-Hydroxymethylcytosine Precedes Loss of CpG Methylation in Enhancers and Genes Undergoing Activation in Cardiomyocyte Maturation	2016	Rolf Backofen Ralf Gilsbach Björn A Grüning	David K Kranzhöfer Thomas G Nührenberg Lutz Hein	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 Ying-Hsuan Sun Miwa Ohnishi Tetsuro Mimura Hungchen E Yen	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 Guillermo Ortí Keith A. Crandall	Ying Sun Xiaofeng Li Carole C Baldwin Zhuocheng Zhou Zhixiang Yan Yong Zhang Xiaomeng Zhao Min Wang Alex Wong Chao Fang Xinhui Zhang Hai Huang Kirk Kilfoyle Qiong Shi	GigaScience
Identifying stably expressed genes from multiple RNA-Seq data sets	2016	Jeff H. Chang	Bin Zhuo Sarah Emerson Yanming Di	PeerJ
Forkhead Box C1 Regulates Human Primary Keratinocyte Terminal Differentiation	2016-01-01	Lianghua Bin	Liehua Deng Hengwen Yang Leqing Zhu Xiao Wang Michael G. Edwards Brittany Richers Donald Y. M. Leung	PLoS ONE
Loss of neurogenesis in Hydra leads to compensatory regulation of neurogenic and neurotransmission genes in epithelial cells.	2016-01-01	Brigitte Galliot Y Wenger	W Buzgariu	Philosophical Transactions of the Royal Society B
Utility of next-generation RNA-sequencing in identifying chimeric transcription involving human endogenous retroviruses.	2016-01-01	Finn Skou Pedersen	Martin Sokol Karen Margrethe Jessen Finn Skou Pedersen	Acta Pathologica et Microbiologica Scandinavica
Using RNA-seq for Analysis of Differential Gene Expression in Fungal Species.	2016-01-01	Geraldine Butler	Can Wang Markus S Schröder Stephen Hammel	Methods in Molecular Biology
Genome-Wide Identification of Alternative Polyadenylation Events Using 3'T-Fill.	2016-01-01	Vicent Pelechano	Stefan Wilkening Lars M Steinmetz	Methods in Molecular Biology
Comparison of normalization and differential expression analyses using RNA-Seq data from 726 individual Drosophila melanogaster.	2016-01-05	Zhen-Xia Chen	Yanzhu Lin Kseniya Golovnina Hang Noh Lee Yazmin L Serrano Negron Hina Sultana Brian Oliver Susan T Harbison	BMC Genomics
A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages.	2016-01-06	Paul C. Blainey Gregory Szeto Alex K. Shalek	Robert J Kimmerling Jennifer W Li Alex S Genshaft Samuel W Kazer Kristofor R Payer Jacob de Riba Borrajo Darrell J Irvine Scott R Manalis	Nature Communications
Tunable protein synthesis by transcript isoforms in human cells	2016-01-06	Jennifer Doudna Stephen N Floor		eLife
OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data	2016-01-06	Christina Kendziorski	Ning Leng Jeea Choi Li-Fang Chu James A Thomson Ron Stewart	Bioinformatics
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	Keiko Yasuma Jun-ichirou Yasunaga Keiko Takemoto Kenji Sugata Norihiro Takenouchi Masanori Nakagawa Yutaka Suzuki	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 Shikai Liu Luyang Sun Lisui Bao Chen Jiang Chao Li Yun Li Qifan Zeng Zhanjiang Liu	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 Stephen W Holman Philip Brownridge Karin Lanthaler Victoria M Harman Rachel Watkins Dean E Hammond Rebecca L Miller Paul F G Sims Christopher M Grant Claire E Eyers Simon J Hubbard	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 Phillip A Richmond	PLOS Genetics
Mitochondrial iron chelation ameliorates cigarette smoke-induced bronchitis and emphysema in mice.	2016-01-11	John Quackenbush Kristen T Rooney Monica P Goldklang Francesca Polverino	Suzanne M Cloonan Kimberly Glass Maria E Laucho-Contreras Abhiram R Bhashyam Morgan Cervo Maria A Pabón Csaba Konrad Ilias I Siempos Elizabeth Perez Kenji Mizumura Manik C Ghosh Harikrishnan Parameswaran Niamh C Williams Zhi-Hua Chen Guo-Cheng Yuan Stephen C Moore Dawn L Demeo Tracey A Rouault Jeanine M D'Armiento Eric A Schon Giovanni Manfredi Ashfaq Mahmood Edwin K Silverman Caroline A Owen Augustine M K Choi	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 Tomislav Ilicic Sarah A Teichmann	Nature Communications
RNA-Seq identifies SPGs as a ventral skeletal patterning cue in sea urchins.	2016-01-11	Evan S Bardot Jonas Ibn-Salem Michael L Piacentino	Daniel T Zuch Julie Fishman Sviatlana Rose Emily E Speranza Christy Li Jia Yu Oliver Chung Janani Ramachandran Patrick Ferrell Vijeta Patel Arlene Reyna Hajerah Hameeduddin James Chaves Finnegan B Hewitt David Lee Amanda B Core John D Hogan Jessica L Keenan Lingqi Luo Jasmin Coulombe-Huntington Todd A Blute Ekaterina Oleinik Albert J Poustka Cynthia A Bradham	Development
The power and promise of RNA-seq in ecology and evolution.	2016-01-12	Michael A. Black Neil J. Gemmell Erica V Todd		Molecular Ecology
Choline Kinase Alpha (CHKα) as a Therapeutic Target in Pancreatic Ductal Adenocarcinoma: Expression, Predictive Value, and Sensitivity to Inhibitors.	2016-01-14	Miriam Marqués Eithne Costello Juan C. Lacal Francisco X Real	José M Mazarico Victor J Sánchez-Arévalo Lobo Rosy Favicchio William Greenhalf Enrique Carrillo-de Santa Pau Eric Aboagye	Molecular Cancer Therapeutics
Genome-wide transcriptome analysis of soybean primary root under varying water-deficit conditions.	2016-01-15	Trupti Joshi Babu Valliyodan	Li Song Silvas Prince Joao V Maldonado dos Santos Jiaojiao Wang Li Lin Jinrong Wan Yongqin Wang Dong Xu Henry T Nguyen	BMC Genomics
Dosage Compensation in the African Malaria Mosquito Anopheles gambiae.	2016-01-18	Graham Rose Luca Ferretti	Elzbieta Krzywinska Jan Kim Loic Revuelta Jaroslaw Krzywinski	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 Ingo Backert Axel Hueber Georg Schett Michael Vieth Hans Christian Probst Tobias Bopp Markus F Neurath Clemens Neufert	Gut
Dual RNA-seq unveils noncoding RNA functions in host–pathogen interactions	2016-01-20	Konrad Förstner Jörg Vogel Alexander Westermann Fabian Amman Lars Barquist Peter F. Stadler Yanjie Chao	Leon N. Schulte Lydia Müller Richard Reinhardt	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 Nickolas Papadopoulos	Scientific Reports
Cross-platform normalization of microarray and RNA-seq data for machine learning applications	2016-01-21	Casey S. Greene	Jeffrey A Thompson Jie Tan	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 S Adam Fuller Chao Li Bartholomew W Green Honggang Zhao Steven D Rawles Carl D Webster	Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics
Identification of Putative Biomarkers for the Early Stage of Porcine Spermatogonial Stem Cells Using Next-Generation Sequencing	2016-01-22	Kyung-Woon Kim	Won-Young Lee Jeong Tae Do Chankyu Park Jin Hoi Kim Hak-Jae Chung Chang-Hyun Gil Nam-Hyung Kim Hyuk Song	PLoS ONE
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 F Piscitelli V Gil J A Del Río T P Moore H Agbemenyah G Salinas-Riester C Pommerenke S Lorenzen T Beißbarth S Hoyer-Fender U Havemann-Reinecke	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 Kenshiro Oshima Tomokazu Yamazaki Sangwan Kim Zhe Yu Mai Yoshihara Kohei Takeda Tsuyoshi Takeshita Aiko Hirata Kateřina Bišová Vilém Zachleder Shigeyuki Kawano Masahira Hattori	Biotechnology for Biofuels
De novo transcriptome assembly of Perkinsus olseni trophozoite stimulated in vitro with Manila clam (Ruditapes philippinarum) plasma.	2016-01-25	Peter W Harrison Paulino Martínez	Abul Farah Md Hasanuzzaman Diego Robledo Antonio Gómez-Tato Jose A Alvarez-Dios Asunción Cao Sergio Fernández-Boo Antonio Villalba Belén G Pardo	Journal of Invertebrate Pathology
A survey of best practices for RNA-seq data analysis	2016-01-26	Ana Conesa Michał Wojciech Szcześniak Pedro Madrigal David Gomez-Cabrero	Sonia Tarazona Alejandra Cervera Andrew McPherson Daniel J. Gaffney Laura L. Elo Xuegong Zhang Ali Mortazavi	Genome Biology
The Phenazine 2-Hydroxy-Phenazine-1-Carboxylic Acid Promotes Extracellular DNA Release and Has Broad Transcriptomic Consequences in Pseudomonas chlororaphis 30-84.	2016-01-26	Jun Myoung Yu	Dongping Wang Robert J Dorosky Leland S Pierson Elizabeth A Pierson	PLoS ONE
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 Brennan G Olson	Journal of Visualized Experiments
Gene expression under thermal stress varies across a geographical range expansion front.	2016-01-28	Rachael Y. Dudaniec Maren Wellenreuther Erik I Svensson	Lesley T Lancaster Pallavi Chauhan Bengt Hansson	Molecular Ecology
RiboGalaxy: A browser based platform for the alignment, analysis and visualization of ribosome profiling data.	2016-01-29	Vimalkumar Velayudhan Audrey M Michel	James P A Mullan Patrick B F O'Connor Claire A Donohue Pavel V Baranov	RNA Biology
Reduced CYFIP1 in Human Neural Progenitors Results in Dysregulation of Schizophrenia and Epilepsy Gene Networks.	2016-01-29	Deyou Zheng	Rebecca A Nebel Dejian Zhao Erika Pedrosa Jill Kirschen Herbert M Lachman Brett S Abrahams	PLoS ONE
Expression of mRNA Encoding Mcu and Other Mitochondrial Calcium Regulatory Genes Depends on Cell Type, Neuronal Subtype, and Ca2+ Signaling	2016-02-01	Owen Dando Peter C Kind Giles E. Hardingham	Nóra M Márkus Philip Hasel Jing Qiu Karen F S Bell Samuel Heron T Ian Simpson	PLoS ONE
Proteomic and Genomic Analyses of the Rvb1 and Rvb2 Interaction Network upon Deletion of R2TP Complex Components	2016-02-01	Laurence Florens Gaye L Hattem Michael P. Washburn	Mahadevan Lakshminarasimhan Gina Boanca Charles A S Banks Ana E Gabriel Brad D Groppe Christine Smoyer Kate E Malanowski Allison Peak	Molecular & Cellular Proteomics
Transcriptome Analysis of Murine Olfactory Sensory Neurons during Development Using Single Cell RNA-Seq.	2016-02-02	Hanns Hatt Günter Gisselmann	Paul Scholz Benjamin Kalbe Fabian Jansen Janine Altmueller Christian Becker Julia Mohrhardt Benjamin Schreiner Guenter Gisselmann Sabrina Osterloh	Chemical Senses
Cancer-associated SF3B1 mutations affect alternative splicing by promoting alternative branchpoint usage.	2016-02-04	Sophie Piperno-Neumann Sergio Roman-Roman Franck Tirode Marc-Henri Stern Martin Dutertre	Samar Alsafadi Alexandre Houy Aude Battistella Tatiana Popova Michel Wassef Emilie Henry Angelos Constantinou	Nature Communications
Comparative transcriptomic profiling of hydrogen peroxide signaling networks in zebrafish and human keratinocytes: Implications toward conservation, migration and wound healing	2016-02-05	Benjamin King	Thomas S Lisse Sandra Rieger	Scientific Reports
Erratum to: Dynamics of gene silencing during X inactivation using allele-specific RNA-seq.	2016-02-05	Hendrik Marks	Hindrik H D Kerstens Tahsin Stefan Barakat Erik Splinter René A M Dirks Guido van Mierlo Onkar Joshi Shuang-Yin Wang Tomas Babak Cornelis A Albers Tüzer Kalkan Austin Smith Alice Jouneau Wouter de Laat Joost Gribnau Hendrik G Stunnenberg	Genome Biology
Comprehensive transcriptomic and proteomic characterization of human mesenchymal stem cells reveals source specific cellular markers	2016-02-09	Anja M Billing Johannes Graumann Karsten Suhre	Hisham Ben Hamidane Shaima S Dib Richard J Cotton Aditya M Bhagwat Pankaj Kumar Shahina Hayat Noha A Yousri Neha Goswami Arash Rafii	Scientific Reports
New insights into the Plasmodium vivax transcriptome using RNA-Seq.	2016-02-09	Bruce Russell Zbynek Bozdech François H Nosten Nicholas P J Day Nicholas John White Mallika Imwong	Lei Zhu Sachel Mok Anchalee Jaidee Peter R Preiser	Scientific Reports
Linking the T cell receptor to the single cell transcriptome in antigen-specific human T cells.	2016-02-10	Auda A. Eltahla Simone Rizzetto Rowena A Bull Katherine Kedzierska Andrew R. Lloyd	Mehdi R Pirozyan Brigid D Betz-Stablein Vanessa Venturi Fabio Luciani	Immunology & Cell Biology
A genome-wide search for epigenetically [corrected] regulated genes in zebra finch using MethylCap-seq and RNA-seq	2016-02-11	Annemie Van der Linden	Sandra Steyaert Jolien Diddens Jeroen Galle Ellen De Meester Sarah De Keulenaer Antje Bakker Nina Sohnius-Wilhelmi Carolina Frankl-Vilches Wim Van Criekinge Wim Vanden Berghe Tim De Meyer	Scientific Reports
Selective amplification and sequencing of cyclic phosphate-containing RNAs by the cP-RNA-seq method.	2016-02-11	Yohei Kirino	Shozo Honda Keisuke Morichika	Nature Protocols
Expression Profiling of Macrophages Reveals Multiple Populations with Distinct Biological Roles in an Immunocompetent Orthotopic Model of Lung Cancer	2016-02-12	Vinod Yadav Howard Li Teresa T Nguyen	Joanna M Poczobutt Subhajyoti De Trisha R Sippel Mary C M Weiser-Evans Raphael A Nemenoff	Journal of Immunology
Single-cell transcriptome analysis of endometrial tissue.	2016-02-13	Juha Kere M Vera-Rodriguez Triin Laisk-Podar Shintaro Katayama Andres Salumets	K Krjutškov M Saare D Lubenets K Samuel H Teder E Einarsdottir	Human Reproduction
Identification of novel long non-coding RNAs deregulated in hepatocellular carcinoma using RNA-sequencing.	2016-02-13	Nora Fernandez-Jimenez	Davide Degli Esposti Hector Hernandez-Vargas Catherine Voegele Nora Fernandez-Jimenez Nathalie Forey Brigitte Bancel Florence Le Calvez-Kelm James McKay Philippe Merle Zdenko Herceg	Oncotarget
Molecular signatures of age-associated chronic degeneration of shoulder muscles.	2016-02-14	Wibowo Arindrarto Yotam Raz	Jan Ferdinand Henseler Arjen Kolk Zuotian Tatum Niels Kuipers Groosjohan Nisha E Verwey Szymon M Kielbasa Jochem Nagels Peter A C 't Hoen Rob G H H Nelissen Vered Raz	Oncotarget
Extreme Hypoxic Conditions Induce Selective Molecular Responses and Metabolic Reset in Detached Apple Fruit.	2016-02-16	Leonardo Tenori	Dubravka Cukrov Monica Zermiani Stefano Brizzolara Alessandro Cestaro Francesco Licausi Claudio Luchinat Claudio Santucci Hans Van Veen Andrea Zuccolo Benedetto Ruperti Pietro Tonutti	Frontiers in Plant Science
Classification of low quality cells from single-cell RNA-seq data	2016-02-17	Aleksandra A Kolodziejczyk Davis J McCarthy Frederik Otzen Bagger John C Marioni	Tomislav Ilicic Jong Kyoung Kim Sarah A Teichmann	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 Tao Chen Tao Qin Zhenyu Wang Hao Chen Liming Xiong	The Plant Cell
Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons	2016-02-18	Jennifer Erwin	Suguna Rani Krishnaswami Rashel V Grindberg Mark Novotny Pratap Venepally Benjamin Lacar Kunal Bhutani Sara B Linker Son Pham Jeremy A Miller Rebecca Hodge James K McCarthy Martin Kelder Jamison McCorrison Brian D Aevermann Francisco Diez Fuertes Richard H Scheuermann Jun Lee Ed S Lein Nicholas Schork Michael J McConnell Fred H Gage Roger S Lasken	Nature Protocols
The Nuclear Receptor, RORγ, Regulates Pathways Necessary for Breast Cancer Metastasis.	2016-02-18	Tae Gyu Oh Bipul R. Acharya Shu-Ching Mary Wang Christine Clarke Alpha S. Yap	Joel M Goode J Dinny Graham George E O Muscat	EBioMedicine
Hemocytome: deep sequencing analysis of mosquito blood cells in Indian malarial vector Anopheles stephensi.	2016-02-22	Rajnikant Dixit	Tina Thomas Tanwee Das De Punita Sharma Suman Lata Priyanka Saraswat Kailash C Pandey	Gene
RNA-seq analysis of clinical-grade osteochondral allografts reveals activation of early response genes.	2016-02-22	A. Noelle Larson	Yang Lin Eric A Lewallen Emily T Camilleri Carolina A Bonin Dakota L Jones Amel Dudakovic Catalina Galeano-Garces Wei Wang Marcel J Karperien Diane L Dahm Michael J Stuart Bruce A Levy Jay Smith Daniel B Ryssman Jennifer J Westendorf Hee-Jeong Im Andre J van Wijnen Scott M Riester Aaron J Krych	Journal of Orthopaedic Research
The MazF-regulon: a toolbox for the post-transcriptional stress response in Escherichia coli.	2016-02-22	Michael T. Wolfinger	Martina Sauert Oliver Vesper Christian Müller Konstantin Byrgazov Isabella Moll	Nucleic Acids Research
Enhancer methylation dynamics contribute to cancer plasticity and patient mortality.	2016-02-23	Yankel Gabet	Rachel E Bell Tamar Golan Danna Sheinboim Hagar Malcov David Amar Avi Salamon Tamar Liron Sahar Gelfman Ron Shamir Carmit Levy	Genome Research
Nitric oxide release from nitro-fatty acids in Arabidopsis roots.	2016-02-24	Francisco J. Corpas	Capilla Mata-Pérez Beatriz Sánchez-Calvo Juan C Begara-Morales María N Padilla Raquel Valderrama Juan B Barroso	Plant Signaling and Behavior
Isolation of the protein and RNA content of active sites of transcription from mammalian cells.	2016-02-25	Argyris Papantonis Karsten Rippe Ian M. Carr Maïwen Caudron-Herger	Svitlana Melnik Lilija Brant Peter R Cook	Nature Protocols
Transcriptional signature induced by a metastasis-promoting c-Src mutant in a human breast cell line.	2016-02-26	Mathias Heikenwalder Hans Lehrach	Felix Broecker Christopher Hardt Ralf Herwig Bernd Timmermann Martin Kerick Andrea Wunderlich Michal R Schweiger Lubor Borsig Karin Moelling	FEBS Journal
TRX-1 Regulates SKN-1 Nuclear Localization Cell Non-autonomously in Caenorhabditis elegans.	2016-02-26	Peter Swoboda Katie C McCallum Juan Carlos Fierro-González Bin Liu Antonio Miranda-Vizuete	Swathi Arur Danielle A Garsin	Genetics
Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis.	2016-02-27	Nicolas Terrapon Christopher J Fields Evelyne Forano Bernard Henrissat	Jordane Despres Pascale Lepercq Sophie Comtet-Marre Grégory Jubelin Carl J Yeoman Margret E Berg Miller Carine Le Bourvellec Catherine M G C Renard Bryan A White Pascale Mosoni	BMC Genomics
Overlapping cell population expression profiling and regulatory inference in C. elegans.	2016-02-29	Arjun Raj	Joshua Burdick Travis Walton Elicia Preston Amanda Zacharias John Isaac Murray	BMC Genomics
Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations.	2016-02-29	Jason A. Hackney Florian Gnad	Raphael Bueno Eric W Stawiski Leonard D Goldstein Steffen Durinck Assunta De Rienzo Zora Modrusan Thong T Nguyen Bijay S Jaiswal Lucian R Chirieac Daniele Sciaranghella Nhien Dao Corinne E Gustafson Kiara J Munir Amitabha Chaudhuri Ravi Gupta Joseph Guillory Karen Toy Connie Ha Ying-Jiun Chen Jeremy Stinson Subhra Chaudhuri Na Zhang Thomas D Wu David J Sugarbaker Frederic J de Sauvage William G Richards Somasekar Seshagiri	Nature Genetics
Expression Analysis Highlights AXL as a Candidate Zika Virus Entry Receptor in Neural Stem Cells	2016-03	Carmen Sandoval-Espinosa	Tomasz J. Nowakowski Alex A. Pollen Elizabeth Di Lullo Marina Bershteyn Arnold R. Kriegstein	Cell Stem Cell
Human MicroRNA miR-532-5p Exhibits Antiviral Activity against West Nile Virus via Suppression of Host Genes SESTD1 and TAB3 Required for Virus Replication	2016-03	A Slonchak Alexander A. Khromykh	Rory P Shannon Gabor Pali	Journal of Virology
Genome-Wide Profiles of Extra-cranial Malignant Rhabdoid Tumors Reveal Heterogeneity and Dysregulated Developmental Pathways.	2016-03-01	Andrew Mungall	Hye-Jung E Chun Emilia L Lim Alireza Heravi-Moussavi Saeed Saberi Karen L Mungall Mikhail Bilenky Annaick Carles Kane Tse Inna Shlafman Kelsey Zhu Jenny Q Qian Diana L Palmquist An He William Long Rodrigo Goya Michelle Ng Veronique G LeBlanc Erin Pleasance Nina Thiessen Tina Wong Eric Chuah Yong-Jun Zhao Jacquie E Schein Daniela S Gerhard Michael D Taylor Richard A Moore Yussanne Ma Steven J M Jones Elizabeth J Perlman Martin Hirst Marco A Marra	Cancer Cell
Transcriptional profiling of subcutaneous adipose tissue in Italian Large White pigs divergent for backfat thickness.	2016-03-01	Paolo Zambonelli	E Gaffo M Zappaterra S Bortoluzzi R Davoli	Animal Genetics
Tolerant and Susceptible Sesame Genotypes Reveal Waterlogging Stress Response Patterns.	2016-03-02	Xin Wei Linhai Wang	Donghua Li Yanxin Zhang Yuan Gao Jingyin Yu Xiurong Zhang	PLoS ONE
FgSsn3 kinase, a component of the mediator complex, is important for sexual reproduction and pathogenesis in Fusarium graminearum	2016-03-02	Huiquan Liu	Shulin Cao Shijie Zhang Chaofeng Hao Jin-Rong Xu Qiaojun Jin	Scientific Reports
De novo assembly and comparative transcriptome analysis of Euglena gracilis in response to anaerobic conditions	2016-03-03	Takanori Maruta Kazuharu Arakawa	Yuta Yoshida Takuya Tomiyama Masaru Tomita Takahiro Ishikawa	BMC Genomics
Developmental Progression in the Coral Acropora digitifera Is Controlled by Differential Expression of Distinct Regulatory Gene Networks	2016-03-03	Alejandro Villar-Briones	Alejandro Reyes-Bermudez Catalina Ramirez-Portilla Michio Hidaka Alexander S Mikheyev	Genome Biology and Evolution
Early alterations on photosynthesis-related parameters in Chlamydomonas reinhardtii cells exposed to atrazine: A multiple approach study.	2016-03-04	Marta Seoane Marta Esperanza Concepción Herrero Carmen Rioboo Ángeles Cid		Science of the Total Environment
Genomic and transcriptomic analysis of the streptomycin-dependent Mycobacterium tuberculosis strain 18b.	2016-03-05	Jérémie Piton	Andrej Benjak Swapna Uplekar Ming Zhang Stewart T Cole Claudia Sala Jérémie Piton	BMC Genomics
Spermatogenesis Drives Rapid Gene Creation and Masculinization of the X Chromosome in Stalk-Eyed Flies (Diopsidae).	2016-03-06	Josephine A Reinhardt Gerald Wilkinson	Richard H Baker Apurva Narechania Rob DeSalle Philip M Johns	Genome Biology and Evolution
Comparative Validation of Conventional and RNA-Seq Data-Derived Reference Genes for qPCR Expression Studies of Colletotrichum kahawae.	2016-03-07	Octávio S. Paulo Ana Cabral Ana Vieira Ana Sofia Pires Vitor Varzea Andreia Loureiro Helena Azinheira Helena Oliveira Dora Batista Maria do Céu Silva	Joana Fino Pedro Talhinhas Pilar Moncada	PLoS ONE
Comparative analysis of human and mouse transcriptomes of Th17 cell priming.	2016-03-07	Brigitta Stockinger Sini Rautio Ubaid Ullah Zhi Chen	Soile Tuomela Helena Ahlfors Viveka Öling Verna Salo Saara Hämälistö Subhash K Tripathi Tarmo Äijö Omid Rasool Hayssam Soueidan Lodewyk Wessels Harri Lähdesmäki Riitta Lahesmaa	Oncotarget
Striatal mRNA expression patterns underlying peak dose L-DOPA-induced dyskinesia in the 6-OHDA hemiparkinsonian rat.	2016-03-08	Michael A. Black	L M Smith L C Parr-Brownlie E J Duncan N J Gemmell P K Dearden J N J Reynolds	Neuroscience
Microglia Transcriptome Changes in a Model of Depressive Behavior after Immune Challenge.	2016-03-09	Robert Dantzer	Dianelys Gonzalez-Pena Scott E Nixon Jason C O'Connor Bruce R Southey Marcus A Lawson Robert H McCusker Tania Borras Debbie Machuca Alvaro G Hernandez Keith W Kelley Sandra L Rodriguez-Zas	PLoS ONE
Engineering EMT using 3D micro-scaffold to promote hepatic functions for drug hepatotoxicity evaluation.	2016-03-09	Chenyu Huang	Jingyu Wang Fengling Chen Longwei Liu Chunxiao Qi Bingjie Wang Xiaojun Yan Wei Hou Michael Q Zhang Yang Chen Yanan Du	Biomaterials
Changes in the miRNA-mRNA Regulatory Network Precede Motor Symptoms in a Mouse Model of Multiple System Atrophy: Clinical Implications	2016-03-10	Michaela Willi Hubert Hackl Gregor K Wenning	Simon Schafferer Rimpi Khurana Violetta Refolo Serena Venezia Edith Sturm Paolo Piatti Clara Hechenberger Roman Kessler Ronald Gstir Anne Krogsdam Alexandra Lusser Werner Poewe Alexander Hüttenhofer Nadia Stefanova	PLoS ONE
Gene expression changes in damaged osteoarthritic cartilage identify a signature of non-chondrogenic and mechanical responses	2016-03-10	Jean-Marc Schwartz	S L Dunn J Soul S Anand R P Boot-Handford T E Hardingham	Osteoarthritis and Cartilage
GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data	2016-03-11	David E. MacHugh Kévin Rue-Albrecht Stephen V. Gordon	Paul A McGettigan Belinda Hernández Nicolas C Nalpas David A Magee Andrew C Parnell	BMC Bioinformatics
Integrating RNA-seq and ChIP-seq data to characterize long non-coding RNAs in Drosophila melanogaster	2016-03-11	Fang-Hua Chu Wen-Hsiung Li	Mei-Ju May Chen Li-Kai Chen Yu-Shing Lai Yu-Yu Lin Dung-Chi Wu Yi-An Tung Kwei-Yan Liu Hsueh-Tzu Shih Yi-Jyun Chen Yan-Liang Lin Li-Ting Ma Jian-Long Huang Po-Chun Wu Ming-Yi Hong June-Tai Wu Chien-Yu Chen	BMC Genomics
The Ess/Type VII secretion system of Staphylococcus aureus shows unexpected genetic diversity.	2016-03-11	Catriona P Harkins	Ben Warne Simon R Harris Alexandra Vatsiou Nicola Stanley-Wall Julian Parkhill Sharon J Peacock Tracy Palmer Matthew T G Holden	BMC Genomics
Comprehensive profiling of EBV gene expression in nasopharyngeal carcinoma through paired-end transcriptome sequencing.	2016-03-11	Elliott D. Kieff	Lijuan Hu Zhirui Lin Yanheng Wu Juqin Dong Bo Zhao Yanbing Cheng Peiyu Huang Lihua Xu Tianliang Xia Dan Xiong Hongbo Wang Manzhi Li Ling Guo Yixin Zeng Qian Zhong Musheng Zeng	Frontiers of medicine
miR2118-triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species.	2016-03-12	Francois Sabot Yves Vigouroux	K N Ta H Adam S De Mita A Ghesquière N V Do P Gantet S Jouannic	Rice
Transcriptional profiling of Klebsiella pneumoniae defines signatures for planktonic, sessile and biofilm-dispersed cells	2016-03-15	Damien Balestrino	Cyril Guilhen Nicolas Charbonnel Nicolas Parisot Nathalie Gueguen Agnès Iltis Christiane Forestier	BMC Genomics
Exploring the surfaceome of Ewing sarcoma identifies a new and unique therapeutic target	2016-03-15	Lucy F Stead Terence Rabbitts	Jennifer Town Helio Pais Sally Harrison Carole Bataille Wilawan Bunjobpol Jing Zhang	Proceedings of the National Academy of Sciences of the United States of America
Differential regulation of meristem size, morphology and organization by the ERECTA, CLAVATA and class III HD-ZIP pathways.	2016-03-17	Héctor Candela	Tali Mandel Udi Landau Lior Asis Einat Zelinger Cristel C Carles Leor Eshed Williams	Development
Systems Biology of Metabolic Regulation by Estrogen Receptor Signaling in Breast Cancer.	2016-03-17	Zeynep Madak-Erdogan	Yiru Chen Zhao	Journal of Visualized Experiments
Integrative Single-Cell Transcriptomics Reveals Molecular Networks Defining Neuronal Maturation During Postnatal Neurogenesis.	2016-03-17	Yu Gao	Feifei Wang Brian E Eisinger Laurel E Kelnhofer Emily M Jobe Xinyu Zhao	Cerebral Cortex
Identification by FFPE RNA-Seq of a new recurrent inversion leading to RBM10-TFE3 fusion in renal cell carcinoma with subtle TFE3 break-apart FISH pattern.	2016-03-21	Eric Pasmant	Pierre-Alexandre Just Franck Letourneur Christelle Pouliquen Florence Dome Anne Audebourg Philippe Biquet Michel Vidaud Benoit Terris Mathilde Sibony	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 Gabriele Colozza Kelvin Zhang Yuki Moriyama Diego Ploper Eric A Sosa Maria D J Benitez	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 Thomas Preiss	R Soetanto C J Hynes H R Patel D T Humphreys M Evers G Duan B J Parker S K Archer J L Clancy R M Graham N J Smith	Biochimica et Biophysica Acta
Transcriptomic and epigenomic characterization of the developing bat wing.	2016-03-28	Nicola Illing Zoe Gill Nadav Ahituv	Walter L Eckalbar Stephen A Schlebusch Mandy K Mason Ash V Parker Betty M Booker Sierra Nishizaki Christiane Muswamba-Nday Elizabeth Terhune Kimberly A Nevonen Nadja Makki Tara Friedrich Julia E VanderMeer Katherine S Pollard Lucia Carbone Jeff D Wall Nicola Illing	Nature Genetics
Prognostic and Functional Significance of MAP4K5 in Pancreatic Cancer.	2016-03-29	Nancy Azizian	Oliver H Wang Ming Guo Michela Capello Defeng Deng Fenglin Zang Jason Fry Matthew H Katz Jason B Fleming Jeffrey E Lee Robert A Wolff Samir Hanash Huamin Wang Anirban Maitra	PLoS ONE
Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes.	2016-03-29	Roberto Galizi Omar S Akbari Sergey Koren Changde Cheng Tony Nolan Adam Phillippy	Andrew Brantley Hall Philippos-Aris Papathanos Atashi Sharma Lauren Assour Nicholas H Bergman Alessia Cagnetti Andrea Crisanti Tania Dottorini Elisa Fiorentini Jonathan Hnath Xiaofang Jiang Diane Radune Maria V Sharakhova Aaron Steele Vladimir A Timoshevskiy Nikolai Windbichler Simo Zhang Matthew W Hahn Scott J Emrich Igor V Sharakhov Zhijian Jake Tu Nora J Besansky	Proceedings of the National Academy of Sciences of the United States of America
Quaking promotes monocyte differentiation into pro-atherogenic macrophages by controlling pre-mRNA splicing and gene expression.	2016-03-31	Hilde Van Esch Janine M van Gils Anton Jan van Zonneveld Ton J Rabelink	Ruben G de Bruin Lily Shiue Jurriën Prins Hetty C de Boer Anjana Singh W Samuel Fagg Jacques M G J Duijs Sol Katzman Adriaan O Kraaijeveld Stefan Böhringer Wai Y Leung Szymon M Kielbasa John P Donahue Patrick H J van der Zande Rick Sijbom Carla M A van Alem Ilze Bot Cees van Kooten J Wouter Jukema Hilal Kazan Erik A L Biessen Manuel Ares Eric P van der Veer	Nature Communications
Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants.	2016-03-31	Igor V Grigoriev Jane Grimwood Hang Yu Charles Bachy Samuel O Purvine	Marijke J van Baren Emily Nahas Reistetter Jane Grimwood Sebastian Sudek Camille Poirier Thomas J Deerinck Alan Kuo Chee-Hong Wong Richard D Smith Stephen J Callister Chia-Lin Wei Jeremy Schmutz Alexandra Z Worden	BMC Genomics
Transcriptome Analysis of Differentially Expressed Genes Provides Insight into Stolon Formation in Tulipa edulis	2016-03-31	Qiaosheng Guo	Yuanyuan Miao Zaibiao Zhu Yunhao Zhu Xiaohua Yang Yuan Sun	Frontiers in Plant Science
Wheat miRNA ancestors: evident by transcriptome analysis of A, B, and D genome donors.	2016-03-31	Hikmet Budak Burcu Alptekin		Functional and Integrative Genomics
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq	2016-04-01	Aviv Regev Itay Tirosh Alex K. Shalek Peter K. Sorger Orit Rozenblatt-Rosen	Itay Tirosh Benjamin Izar Sanjay M Prakadan Marc H Wadsworth Daniel Treacy John J Trombetta Asaf Rotem Christopher Rodman Christine Lian George Murphy Mohammad Fallahi-Sichani Ken Dutton-Regester Jia-Ren Lin Ofir Cohen Parin Shah Diana Lu Alex S Genshaft Travis K Hughes Carly G K Ziegler Samuel W Kazer Aleth Gaillard Kellie E Kolb Alexandra-Chloé Villani Cory M Johannessen Aleksandr Y Andreev Eliezer M Van Allen Monica Bertagnolli Ryan J Sullivan Keith T Flaherty Dennie T Frederick Judit Jané-Valbuena Charles H Yoon Levi A Garraway	Science
Near-optimal probabilistic RNA-seq quantification.	2016-04-04	Lior Pachter Harold Pimentel Páll Melsted	Nicolas L Bray	Nature Biotechnology
Comparison of syncytiotrophoblast generated from human embryonic stem cells and from term placentas	2016-04-05	Yoel Sadovsky	Shinichiro Yabe Andrei P Alexenko Mitsuyoshi Amita Ying Yang Danny J Schust Toshihiko Ezashi R Michael Roberts	Proceedings of the National Academy of Sciences of the United States of America
Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos.	2016-04-05	Sten Linnarsson Alvaro Plaza Reyes Björn Reinius Qiaolin Deng	Sophie Petropoulos Daniel Edsgärd Sarita Pauliina Panula Simone Codeluppi Sten Linnarsson Rickard Sandberg Fredrik Lanner	Cell
Combined Inhibition of DNMT and HDAC Blocks the Tumorigenicity of Cancer Stem-like Cells and Attenuates Mammary Tumor Growth	2016-04-05	Vadivel Ganapathy	Rajneesh Pathania Sabarish Ramachandran Gurusamy Mariappan Priyanka Thakur Huidong Shi Jeong-Hyeon Choi Santhakumar Manicassamy Ravindra Kolhe Puttur D Prasad Suash Sharma Bal L Lokeshwar Muthusamy Thangaraju	Cancer Research
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 Eduardo de Paiva Alves Stefan Hoppler	Development
Refined Pichia pastoris reference genome sequence.	2016-04-12	Ruth Birner-Gruenberger Kasey J Day Anton Glieder	Lukas Sturmberger Thomas Chappell Martina Geier Florian Krainer Ursa Vide Sara Trstenjak Anja Schiefer Toby Richardson Leah Soriaga Barbara Darnhofer Benjamin S Glick Ilya Tolstorukov James Cregg Knut Madden	Journal of Biotechnology
Erratum for Baddal et al., Dual RNA-seq of Nontypeable Haemophilus influenzae and Host Cell Transcriptomes Reveals Novel Insights into Host-Pathogen Cross Talk.	2016-04-12	Buket Baddal	Alessandro Muzzi Stefano Censini Raffaele A Calogero Giulia Torricelli Silvia Guidotti Anna R Taddei Antonello Covacci Mariagrazia Pizza Rino Rappuoli Marco Soriani Alfredo Pezzicoli	mBio
Beyond comparisons of means: understanding changes in gene expression at the single-cell level.	2016-04-15	John C Marioni	Catalina A Vallejos Sylvia Richardson	Genome Biology
A Class of Diacylglycerol Acyltransferase 1 Inhibitors Identified by a Combination of Phenotypic High-throughput Screening, Genomics, and Genetics	2016-04-16	Herbert Waldmann Mathias Beller Thomas O Eichmann	Kirsten Tschapalda Ya-Qin Zhang Li Liu Kseniya Golovnina Thomas Schlemper Madhu Lal-Nag Urmila Sreenivasan John McLenithan Slava Ziegler Carole Sztalryd Achim Lass Douglas Auld Brian Oliver Zhuyin Li Min Shen Matthew B Boxer	EBioMedicine
Burkholderia pseudomallei Capsule Exacerbates Respiratory Melioidosis but Does Not Afford Protection against Antimicrobial Signaling or Bacterial Killing in Human Olfactory Ensheathing Cells.	2016-04-18	Glen C Ulett	Samantha J Dando Deepak S Ipe Michael Batzloff Matthew J Sullivan David K Crossman Michael Crowley Emily Strong Stephanie Kyan Sophie Y Leclercq Jenny A K Ekberg James St John Ifor R Beacham	Infection and Immunity
Nuclear RNA-seq of single neurons reveals molecular signatures of activation	2016-04-19	Carolyn O'Connor Jerika Barron Baptiste N Jaeger Jennifer Erwin	Benjamin Lacar Sara B Linker Suguna Krishnaswami Martijn Kelder Sarah Parylak Apuã Paquola Pratap Venepally Mark Novotny Conor Fitzpatrick Jonathan Y Hsu David Husband Michael J McConnell Roger Lasken Fred H Gage	Nature Communications
Beta-Poisson model for single-cell RNA-seq data analyses.	2016-04-19	Trung N. Vu Krishna R Kalari	Quin F Wills Nifang Niu Liewei Wang Mattias Rantalainen Yudi Pawitan	Bioinformatics
Transcriptional Profiling of Ileocecal Valve of Holstein Dairy Cows Infected with Mycobacterium avium subsp. Paratuberculosis.	2016-04-19	John P. Bannantine	Randy J Hempel Judith R Stabel	PLoS ONE
The transcriptomic response of the coral Acropora digitifera to a competent Symbiodinium strain: the symbiosome as an arrested early phagosome.	2016-04-20	Cheong Xin Chan Mark A. Ragan	A R Mohamed V Cumbo S Harii C Shinzato D G Bourne B L Willis E E Ball N Satoh D J Miller	Molecular Ecology
Trisomy 21 Alters DNA Methylation in Parent-of-Origin-Dependent and -Independent Manners.	2016-04-21	Bruna Lancia Zampieri Enrique Medina-Acosta	Antônio Francisco Alves da Silva Filipe Brum Machado Érika Cristina Pavarino Joice Matos Biselli-Périco Ronaldo da Silva Francisco Junior Pedro Thyago Mozer Rodrigues Douglas Terra Machado Cíntia Barros Santos-Rebouças Maria Gomes Fernandes Susana Marina Chuva de Sousa Lopes Álvaro Fabricio Lopes Rios	PLoS ONE
Dysregulation of miRNA-9 in a Subset of Schizophrenia Patient-Derived Neural Progenitor Cells	2016-04-21	Manuel Mattheisen Jessica Johnson Gerard Cagney Kristen J. Brennand Douglas Ruderfer	Aaron Topol Shijia Zhu Brigham J Hartley Jane English Mads E Hauberg Ben Readhead Ngoc Tran Chelsea Ann Rittenhouse Anthony Simone Yoav Hadas Peter A Gochman Ying-Chih Wang Hardik Shah Judith Rapoport Fred H Gage Joel T Dudley Pamela Sklar David Cotter Gang Fang	Cell Reports
RNA-seq analysis of early enteromyxosis in turbot (Scophthalmus maximus): new insights into parasite invasion and immune evasion strategies.	2016-04-21	Ariadna Sitjà-Bobadilla Paolo Ronza Ana Paula Losada Belén G Pardo Paulino Martínez	Diego Robledo Roberto Bermúdez María Isabel Quiroga	International Journal for Parasitology
Abnormal Osmotic Avoidance Behavior in C. elegans Is Associated with Increased Hypertonic Stress Resistance and Improved Proteostasis	2016-04-25	Benjamin King	Elaine C Lee Heejung Kim Jennifer Ditano Dacie Manion Kevin Strange	PLoS ONE
Survey of cryptic unstable transcripts in yeast.	2016-04-26	Robin Dowell	Jessica M Vera	BMC Genomics
A spectrum of CodY activities drives metabolic reorganization and virulence gene expression in Staphylococcus aureus.	2016-04-26	Nicholas R Waters	David J Samuels Ranjan K Behera Jonathan Livny Kyu Y Rhee Marat R Sadykov Shaun R Brinsmade	Molecular Microbiology
Pooling across cells to normalize single-cell RNA sequencing data with many zero counts.	2016-04-27	John C Marioni	Aaron T L Lun Karsten Bach	Genome Biology
CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq.	2016-04-28	Aviv Regev Yaron de Leeuw Leon Anavy Itai Yanai Orit Rozenblatt-Rosen	Tamar Hashimshony Naftalie Senderovich Gal Avital Agnes Klochendler Dave Gennert Shuqiang Li Kenneth J Livak Yuval Dor	Genome Biology
Recurrent DUX4 fusions in B cell acute lymphoblastic leukemia of adolescents and young adults.	2016-05	Toshiaki Yujiri Masahito Kawazu Eisei Kondo	Takahiko Yasuda Shinobu Tsuzuki Fumihiko Hayakawa Shinya Kojima Toshihide Ueno Naoto Imoto Shinji Kohsaka Akiko Kunita Koichiro Doi Toru Sakura Katsumichi Fujimaki Yasunori Ueda Yasutaka Aoyama Shigeki Ohtake Junko Takita Eirin Sai Masafumi Taniwaki Mineo Kurokawa Shinichi Morishita Masashi Fukayama Hitoshi Kiyoi Yasushi Miyazaki Tomoki Naoe Hiroyuki Mano	Nature Genetics
The Staphylococcus aureus Global Regulator MgrA Modulates Clumping and Virulence by Controlling Surface Protein Expression	2016-05	Heidi A Crosby Wilmara Salgado-Pabón Patrick M. Schlievert	Joseph A Merriman Jessica M King Alexander R Horswill	PLOS Pathogens
RNA-sequencing study of peripheral blood monocytes in chronic periodontitis	2016-05-01	Melody Baddoo Hong-Wen Deng	Yao-Zhong Liu Pooja Maney Jyoti Puri Yu Zhou Melody Baddoo Michael Strong Yu-Ping Wang Erik Flemington	Gene
Wishbone identifies bifurcating developmental trajectories from single-cell data.	2016-05-02	Dana Pe'er	Manu Setty Michelle D Tadmor Shlomit Reich-Zeliger Omer Angel Tomer Meir Salame Pooja Kathail Kristy Choi Sean Bendall Nir Friedman Dana Pe'er	Nature Biotechnology
Transcriptomic Analysis Reveals Adaptive Responses of an Enterobacteriaceae Strain LSJC7 to Arsenic Exposure.	2016-05-02	Yong-Guan Zhu	Yingjiao Zhang Songcan Chen Xiuli Hao Jian-Qiang Su Ximei Xue Yu Yan Jun Ye	Frontiers in Microbiology
Conserved Senescence Associated Genes and Pathways in Primary Human Fibroblasts Detected by RNA-Seq.	2016-05-03	Alessandro Cellerino	S Marthandan M Baumgart S Priebe M Groth J Schaer C Kaether R Guthke M Platzer S Diekmann P Hemmerich	PLoS ONE
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 Arsène Burny Nicolas Rosewick	Keith Durkin Maria Artesi Vincent Hahaut Philip Griebel Natasa Arsic Michel Georges Anne Van den Broeke	Retrovirology
Xylan degradation by the human gut Bacteroides xylanisolvens XB1A(T) involves two distinct gene clusters that are linked at the transcriptional level.	2016-05-04	Nicolas Terrapon Christopher J Fields Evelyne Forano Bernard Henrissat	Jordane Despres Pascale Lepercq Sophie Comtet-Marre Gregory Jubelin Christophe Chambon Carl J Yeoman Margaret E Berg Miller Eric Martens Bryan A White Pascale Mosoni	BMC Genomics
NUDT2 Disruption Elevates Diadenosine Tetraphosphate (Ap4A) and Down-Regulates Immune Response and Cancer Promotion Genes.	2016-05-04	Nikki A. Copeland	Andrew S Marriott Olga Vasieva Yongxiang Fang Alexander G McLennan Nigel J Jones	PLoS ONE
Exploiting single-cell expression to characterize co-expression replicability	2016-05-06	Jesse Gillis	Megan Crow Anirban Paul Sara Ballouz Z Josh Huang	Genome Biology
Candidate gene networks and blood biomarkers of methamphetamine-associated psychosis: an integrative RNA-sequencing report.	2016-05-10	Dan J. Stein Anne Uhlmann	M S Breen C M Nday S J Glatt M Mitt A Metsalpu N Illing	Translational Psychiatry
Targeting super-enhancer-associated oncogenes in oesophageal squamous cell carcinoma.	2016-05-10	Ling-Wen Ding Anand Mayakonda Liang Xu	Yan-Yi Jiang De-Chen Lin Masaharu Hazawa Wen-Wen Chien Ye Chen Jin-Fen Xiao William Senapedis Erkan Baloglu Deepika Kanojia Li Shang Xin Xu Henry Yang Jeffrey W Tyner Ming-Rong Wang H Phillip Koeffler	Gut
Persistent Alterations in Microglial Enhancers in a Model of Chronic Pain.	2016-05-11	Douglas M. Lopes Athanasios Didangelos Franziska Denk	Megan Crow Stephen B McMahon	Cell Reports
RNA-Seq Analysis Reveals Genes Underlying Different Disease Responses to Porcine Circovirus Type 2 in Pigs.	2016-05-12	Shijin Jiang	Yanping Li Hao Liu Pengfei Wang Liyuan Wang Yi Sun Gen Liu Ping Zhang Li Kang Yunliang Jiang	PLoS ONE
Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation	2016-05-12	Tapio Lönnberg Valentina Proserpio Giacomo Donati Kedar N Natarajan Oliver Billker Mario Nicodemi	Andrea Piccolo Liora Haim-Vilmovsky Gozde Kar Valentine Svensson Jhuma Pramanik Weichao Zhai Xiuwei Zhang Melis Kayikci Jurij Kotar Andrew N J McKenzie Ruddy Montandon Steven Woodhouse Pietro Cicuta Sarah A Teichmann	Genome Biology
An updated human snoRNAome.	2016-05-12	Mihaela Zavolan Jana Hertel Stephanie Kehr	Hadi Jorjani Dominik J Jedlinski Rafal Gumienny Peter F Stadler Andreas R Gruber	Nucleic Acids Research
The transcriptome of mouse central nervous system myelin.	2016-05-13	Sudhir Thakurela Hauke Werner	Angela Garding Ramona B Jung Christina Müller Sandra Goebbels Robin White Vijay K Tiwari	Scientific Reports
Polycomb repressive complex 1 controls uterine decidualization.	2016-05-16	Artem Barski Anil G. Jegga	Fenghua Bian Fei Gao Andrey V Kartashov Sanjoy K Das	Scientific Reports
Molecular Mechanisms of Malignant Transformation by Low Dose Cadmium in Normal Human Bronchial Epithelial Cells.	2016-05-17	Steven Shen	Laura Cartularo Thomas Kluz Lisa Cohen Max Costa	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 Yuan Liang Yue-Ting Dai Chen-Tao Yang Ming-Zheng Duan Zhuo Zhang Zhi-Wu Zhang Yu Li	Molecules
Altered RNA metabolism due to a homozygous RBM7 mutation in a patient with spinal motor neuropathy.	2016-05-18	Yaobo Xu Aurora Gomez-Duran Rita Horvath	Michele Giunta Shimon Edvardson Markus Schuelke Veronika Boczonadi Orly Elpeleg Juliane S Müller	Human Molecular Genetics
The Proteasome Stress Regulon Is Controlled by a Pair of NAC Transcription Factors in Arabidopsis.	2016-05-18	Richard D Vierstra	Nicholas P Gladman Richard S Marshall Kwang-Hee Lee	The Plant Cell
Identification of new regulators of embryonic patterning and morphogenesis in Xenopus gastrulae by RNA sequencing.	2016-05-18	David K. Crossman	Ivan K Popov Taejoon Kwon Michael R Crowley John B Wallingford Chenbei Chang	Developmental Biology
Hair-Cell Mechanotransduction Persists in TRP Channel Knockout Mice.	2016-05-19	Artur A Indzhykulian	Xudong Wu Paul D Niksch Roxanna M Webber Miguel Garcia-Gonzalez Terry Watnick Jing Zhou Melissa A Vollrath David P Corey	PLoS ONE
Group II mGluRs suppress hyperexcitability in mouse and human nociceptors.	2016-05-21	Pradipta R Ray Theodore J. Price	Steve Davidson Judith P Golden Bryan A Copits Sherri K Vogt Manouela V Valtcheva Robert E Schmidt Andrea Ghetti Robert W Gereau	Pain
Identification of host genes leading to West Nile virus encephalitis in mice brain using RNA-seq analysis.	2016-05-23	Mukesh Kumar	Mahdi Belcaid Vivek R Nerurkar	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 Jenny K Rieger Anika Witten Monika Stoll Martin Kalbe Alexander Schmidt-Drewello Jörn P Scharsack Thorsten B H Reusch	Zoology
CTCF and CohesinSA-1 Mark Active Promoters and Boundaries of Repressive Chromatin Domains in Primary Human Erythroid Cells	2016-05-24	Vincent Schulz	Laurie A Steiner Yelena Makismova Kimberly Lezon-Geyda Patrick G Gallagher	PLoS ONE
Comprehensive RNA-Seq Analysis on the Regulation of Tomato Ripening by Exogenous Auxin.	2016-05-26	Jiayin Li	Xiaoya Tao Li Li Linchun Mao Zisheng Luo Zia Ullah Khan Tiejin Ying	PLoS ONE
Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts	2016-05-26	Lior Pachter	Vasilis Ntranos Govinda M Kamath Jesse M Zhang David N Tse	Genome Biology
RNA sequencing of pancreatic adenocarcinoma tumors yields novel expression patterns associated with long-term survival and reveals a role for ANGPTL4	2016-05-26	Jason Gertz Donald J Buchsbaum	Marie K Kirby Ryne C Ramaker Nicholas S Davis Bobbi E Johnston Patsy G Oliver Katherine C Sexton Edward W Greeno John D Christein Martin J Heslin James A Posey William E Grizzle Selwyn M Vickers Sara J Cooper Richard M Myers	Molecular Oncology
Hsf1 and Hsp90 orchestrate temperature-dependent global transcriptional remodelling and chromatin architecture in Candida albicans.	2016-05-26	Christina A Cuomo Robert T Wheeler Michelle D Leach Rhys A Farrer	Kaeling Tan Zhengqiang Miao Louise A Walker Alistair J P Brown Koon Ho Wong Leah E Cowen	Nature Communications
An atlas of gene expression and gene co-regulation in the human retina.	2016-05-27	Luisa Cutillo Sandro Banfi Diego di Bernardo	Michele Pinelli Annamaria Carissimo Ching-Hung Lai Margherita Mutarelli Maria Nicoletta Moretti Marwah Veer Singh Marianthi Karali Diego Carrella Mariateresa Pizzo Francesco Russo Stefano Ferrari Diego Ponzin Claudia Angelini	Nucleic Acids Research
Landscape of tumor-infiltrating T cell repertoire of human cancers	2016-05-30	Nir Hacohen	Bo Li Taiwen Li Jean-Christophe Pignon Binbin Wang Jinzeng Wang Sachet A Shukla Ruoxu Dou Qianming Chen F Stephen Hodi Toni K Choueiri Catherine Wu Sabina Signoretti Jun S Liu X Shirley Liu	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 S D Castellarin	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
Bluetongue Virus NS4 Protein Is an Interferon Antagonist and a Determinant of Virus Virulence	2016-06-01	Anna Janowicz Marco Caporale Massimo Palmarini	Maxime Ratinier Andrew E Shaw Gerald Barry Quan Gu Luigina Di Gialleonardo Mariana Varela Richard E Randall	Journal of Virology
The contribution of cell cycle to heterogeneity in single-cell RNA-seq data.	2016-06-01	Andrew McDavid	Greg Finak Raphael Gottardo	Nature Biotechnology
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 Robert Feil	Vincenzo Riso Harpreet Kukreja Zahra Anvar Angela Sparago Basilia Acurzio Shraddha Lad Enza Lonardo 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
RNA-seq Analysis of δ9-Tetrahydrocannabinol-treated T Cells Reveals Altered Gene Expression Profiles That Regulate Immune Response and Cell Proliferation.	2016-06-06	Mitzi Nagarkatti	Xiaoming Yang Marpe Bam Prakash S Nagarkatti	Journal of Biological Chemistry
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 Jude Fitzgibbon	Joshua B N Dawkins Eleni Maniati James A Heward Lola Koniali Hemant M Kocher Sarah A Martin 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
A unique stylopod patterning mechanism by Shox2-controlled osteogenesis.	2016-06-10	Marco Osterwalder Axel Visel	Wenduo Ye Yingnan Song Zhen Huang Anja Ljubojevic Jue Xu Brent Bobick Samuel Abassah-Oppong Ningsheng Ruan Ross Shamby Diankun Yu Lu Zhang Chen-Leng Cai Yanding Zhang John Cobb YiPing Chen	Development
RTFBSDB: an integrated framework for transcription factor binding site analysis.	2016-06-10	Charles G Danko	Zhong Wang André L Martins	Bioinformatics
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
Characterization of RON protein isoforms in pancreatic cancer: implications for biology and therapeutics.	2016-06-14	Carsten Schultz-Fademrecht	Jeffery Chakedis Randall French Michele Babicky Dawn Jaquish Evangeline Mose Peter Cheng Patrick Holman Haleigh Howard Jaclyn Miyamoto Paula Porras Zakk Walterscheid Christina Esdar Oliver Schadt Jan Eickhoff Andrew M Lowy	Oncotarget
Comparing the functions of equine and canine influenza H3N8 virus PA-X proteins: Suppression of reporter gene expression and modulation of global host gene expression.	2016-06-14	Edward C. Holmes	Kurtis H Feng Miao Sun Sho Iketani Colin R Parrish	Virology
Genome-wide analysis of pentatricopeptide-repeat proteins of an aquatic plant.	2016-06-15	Wenqin Wang Joachim Messing	Yongrui Wu	Planta
Different Endosymbiotic Interactions in Two Hydra Species Reflect the Evolutionary History of Endosymbiosis	2016-06-19	Takashi Gojobori	Masakazu Ishikawa Ikuko Yuyama Hiroshi Shimizu Masafumi Nozawa Kazuho Ikeo	Genome Biology and Evolution
Transcriptional Profiling of Mycobacterium tuberculosis Exposed to In Vitro Lysosomal Stress.	2016-06-20	Martin L Hibberd	Wenwei Lin Paola Florez de Sessions Garrett Hor Keong Teoh Ahmad Naim Nazri Mohamed Yuan O Zhu Vanessa Hui Qi Koh Michelle Lay Teng Ang Peter C Dedon Sylvie Alonso	Infection and Immunity
From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline	2016-06-20	Gordon K Smyth	Yunshun Chen Aaron T L Lun	F1000Research
GATA6 regulates EMT and tumour dissemination, and is a marker of response to adjuvant chemotherapy in pancreatic cancer.	2016-06-20	Marina Pajic Andrew V. Biankin John P Neoptolemos Paola Martinelli Nelson Dusetti Francisco X Real Eithne Costello	Enrique Carrillo-de Santa Pau Trevor Cox Bruno Sainz William Greenhalf Lorenzo Rinaldi Paula Ghaneh Núria Malats Markus Büchler Juan Iovanna	Gut
Hypoxia-related microRNA-210 is a diagnostic marker for discriminating osteoblastoma and osteosarcoma.	2016-06-21	Anne-Marie Cleton-Jansen Emily T Camilleri A. Noelle Larson	Scott M Riester Jorge Torres-Mora Amel Dudakovic Wei Wang Fuhua Xu Roman R Thaler Jared M Evans René Zwartbol Inge H Briaire-de Bruijn Avudaiappan Maran Andrew L Folpe Carrie Y Inwards Peter S Rose Thomas C Shives Michael J Yaszemski Franklin H Sim David R Deyle Mario A Galindo Arjen G H Cleven Andre M Oliveira Anne-Marie Cleton-Jansen Judith V M G Bovée Andre J van Wijnen	Journal of Orthopaedic Research
The activation of OR51E1 causes growth suppression of human prostate cancer cells.	2016-06-21	Hanns Hatt Günter Gisselmann Désirée Maßberg	Désirée Maßberg Nikolina Jovancevic Anne Offermann Annika Simon Aria Baniahmad Sven Perner Thanakorn Pungsrinont Katarina Luko Stathis Philippou Burkhard Ubrig Markus Heiland Lea Weber Janine Altmüller Christian Becker Günter Gisselmann Lian Gelis	Oncotarget
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 Francesco Neri	Mara Maldotti Danny Incarnato 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 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 Avinash Ramu	Malachi Griffith Obi L Griffith Matthew J Christopher Jeffery M Klco Tamara L Lamprecht Alex H Wagner Robert Lesurf Jasreet Hundal Jin Zhang Nicholas C Spies David E Larson Sharon E Heath 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 Samina Naseeb	Katarzyna B Hooks 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 David R. Westhead	Helene Thygesen Walter Gregory 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 Gwenola Tosser-Klopp	Aroa Suárez-Vega Beatriz Gutiérrez-Gil Christophe Klopp Juan-José Arranz	Scientific Data
Pho4 mediates phosphate acquisition in Candida albicans and is vital for stress resistance and metal homeostasis	2016-07-06	Janet Quinn Elizabeth A. Veal Donna M MacCallum	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 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
Transcriptomic Profiling Discloses Molecular and Cellular Events Related to Neuronal Differentiation in SH-SY5Y Neuroblastoma Cells.	2016-07-15	Alessandro Simonati Maciej Lalowski	Francesco Pezzini Laura Bettinetti Francesca Di Leva Marzia Bianchi Elisa Zoratti Rosalba Carrozzo Filippo M Santorelli Massimo Delledonne	Cellular and Molecular Neurobiology
RNA editing generates cellular subsets with diverse sequence within populations.	2016-07-15	Theodore Papamarkou Violeta Rayon-Estrada	Dewi Harjanto Chris J Oates Violeta Rayon-Estrada F Nina Papavasiliou Anastasia Papavasiliou	Nature Communications
Increase of Alternatively Activated Antigen Presenting Cells in Active Experimental Autoimmune Encephalomyelitis.	2016-07-16	Frauke Zipp	Beatrice Wasser Gautam Pramanik Moritz Hess Matthias Klein Felix Luessi Klaus Dornmair Tobias Bopp Esther Witsch	Journal of Neuroimmune Pharmacology
Sympatric speciation of spiny mice, Acomys, unfolded transcriptomically at Evolution Canyon, Israel	2016-07-19	Eviatar Nevo	Kexin Li Huihua Wang Zhenyuan Cai Liuyang Wang Qinqin Xu Matěj Lövy Zhenlong Wang	Proceedings of the National Academy of Sciences of the United States of America
Identification and Comparative Analysis of Differential Gene Expression in Soybean Leaf Tissue under Drought and Flooding Stress Revealed by RNA-Seq.	2016-07-19	Babu Valliyodan Rupesh K. Deshmukh Rajeev 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 I Klöting M Kern P Kovacs M Stumvoll M Blüher N Klöting	International Journal of Obesity
End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data.	2016-07-28	Jeremy Luban	Alan Derr Chaoxing Yang Rapolas Zilionis Alexey Sergushichev David M Blodgett Sambra Redick Rita Bortell David M Harlan Sebastian Kadener Dale L Greiner Allon Klein Maxim N Artyomov Manuel Garber	Genome Research
FAR-RED ELONGATED HYPOCOTYL3 activates SEPALLATA2 but inhibits CLAVATA3 to regulate meristem determinacy and maintenance in Arabidopsis.	2016-07-28	Xuemei Chen	Dongming Li Xing Fu Lin Guo Zhigang Huang Yongpeng Li Yang Liu Zishan He Xiuwei Cao Xiaohan Ma Meicheng Zhao Guohui Zhu Langtao Xiao Haiyang Wang Renyi Liu Xigang Liu	Proceedings of the National Academy of Sciences of the United States of America
Characterization of circular RNAs in human, mouse and rat hearts.	2016-07-28	Thomas Meitinger Stephan Nothjunge Stefan Engelhardt	Stanislas Werfel Thomas Schwarzmayr Tim-Matthias Strom	Journal of Molecular and Cellular Cardiology
Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons.	2016-07-28	Aviv Regev	Naomi Habib Yinqing Li Matthias Heidenreich Lukasz Swiech Inbal Avraham-Davidi John J Trombetta Cynthia Hession Feng Zhang	Science
Zika Virus Disrupts Phospho-TBK1 Localization and Mitosis in Human Neuroepithelial Stem Cells and Radial Glia	2016-08	Nenad Sestan Jernej Mlakar Marco Onorati	Zhen Li Fuchen Liu André M.M. Sousa Naoki Nakagawa Mingfeng Li Maria Teresa Dell’Anno Forrest O. Gulden Sirisha Pochareddy Andrew T.N. Tebbenkamp Wenqi Han Mihovil Pletikos Tianliuyun Gao Ying Zhu Candace Bichsel Luis Varela Klara Szigeti-Buck Steven Lisgo Yalan Zhang Anze Testen Xiao-Bing Gao Mara Popovic Marie Flamand Stephen M. Strittmatter Leonard K. Kaczmarek E.S. Anton Tamas L. Horvath Brett D. Lindenbach	Cell Reports
Atad2 is a generalist facilitator of chromatin dynamics in embryonic stem cells	2016-08	François-Loïc Cosset Saadi Khochbin Apirat Chaikuad Stefan Knapp Matthieu Gérard	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 Brian V. Nahed	Andrew Sean Venteicher Itay Tirosh Christine Hebert Leah Escalante Robert L Martuza William T Curry Daniel P Cahill Bradley Bernstein David N Louis Mario Suva	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 Mikael Jumppanen Sari Mäkelä Teemu D Laajala Tero Aittokallio	Riikka Huhtaniemi Vidal Fey Amanpreet Kaur Matias Knuuttila Eija Aho Riikka Oksala Matti Poutanen	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 Francesca Cicchetti	Scientific Reports
Modulatory Effects of Sex Steroids Progesterone and Estradiol on Odorant Evoked Responses in Olfactory Receptor Neurons.	2016-08-05	Hanns Hatt Günter Gisselmann	Ninthujah Kanageswaran Maximilian Nagel Paul Scholz Julia Mohrhardt Günter Gisselmann	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 Rebecca C Robey Natalie G Skinner Christopher D Tomlinson Stephen Goodbourn	Veterinary Research
scphaser: haplotype inference using single-cell RNA-seq data	2016-08-06	Björn Reinius	Daniel Edsgärd Rickard Sandberg	Bioinformatics
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 Elham Rahimy Hao Zheng Selena Z Kuo Elizabeth Kim Weg M Ongkeko	Oncology Letters
Spliced synthetic genes as internal controls in RNA sequencing experiments.	2016-08-08	Lars K. Nielsen John Mattick Simon A Hardwick Ira Deveson	Wendy Y Chen Ted Wong James Blackburn Stacey B Andersen Tim R Mercer	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 Cynthia R Clark Danos C Christodoulou Christine E Seidman H Scott Baldwin J G Seidman Joey V Barnett	PLoS ONE
Ordered chromatin changes and human X chromosome reactivation by cell fusion-mediated pluripotent reprogramming.	2016-08-10	Tatyana B Nesterova Claire Rougeulle Irene Cantone Matthias Merkenschlager	Hakan Bagci Dirk Dormann Gopuraja Dharmalingam Neil Brockdorff Claire Rougeulle Celine Vallot Edith Heard Ronan Chaligne Amanda G Fisher	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 Marie Jordan	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 Luigi Orru' Greice Amaral Carneiro Ilenia Siciliano Giampiero Valé Maria Lodovica Gullino	BMC Genomics
Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta.	2016-08-11	Robert M. Waterhouse Thorsten Burmester Ioannis Michalopoulos Julio Rozas Ramesh T Gunaratna Suyog S Kuwar Xiaolong Cao Tom K Walsh Seung-Joon Ahn Adriana D Briscoe Yannick Pauchet Alexie Papanicolaou Ewald Grosse-Wilde Guillaume Tetreau R Feyereisen John G Oakeshott Gary W. Blissard	Michael R Kanost Estela L Arrese Yun-Ru Chen Sanjay Chellapilla Marian R Goldsmith David G Heckel Nicolae Herndon Haobo Jiang Jiaxin Qu Jose L Soulages Heiko Vogel James Walters Francisca C Almeida Chunju An Peshtewani Aqrawi Anne Bretschneider William B Bryant Sascha Bucks Hsu Chao Germain Chevignon Jayne M Christen David F Clarke Neal T Dittmer Laura C F Ferguson Spyridoula Garavelou Karl H J Gordon Yi Han Frank Hauser Yan He Hanna Heidel-Fischer Ariana Hirsh Yingxia Hu Hongbo Jiang Divya Kalra Christian Klinner Christopher König Christie Kovar Ashley R Kroll Sandy L Lee Rüdiger Lehman Kai Li Zhaofei Li Hanquan Liang Shanna Lovelace Zhiqiang Lu Jennifer H Mansfield Kyle J McCulloch Tittu Mathew Brian Morton Donna M Muzny David Neunemann Fiona Ongeri Ling-Ling Pu Ioannis Pyrousis Xiang-Jun Rao Amanda Redding Charles Roesel Alejandro Sanchez-Gracia Sarah Schaack Aditi Shukla Yang Wang Guang-Hua Xiong Walther Traut Kim C Worley Di Wu Wenbi Wu Yuan-Qing Wu Xiufeng Zhang Zhen Zou Hannah Zucker Rollie J Clem Cornelis J P Grimmelikhuijzen Stavros J Hamodrakas Bill S Hansson Elisabeth Huguet Lars S Jermiin Que Lan Herman K Lehman Marce Lorenzen Hans Merzendorfer David B Morton Subbaratnam Muthukrishnan Will Palmer Yoonseong Park A Lorena Passarelli Lawrence M Schwartz Wendy Smith Agnes Southgate Andreas Vilcinskas Richard Vogt Ping Wang John Werren Xiao-Qiang Yu Jing-Jiang Zhou Susan J Brown Steven E Scherer Stephen Richards	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 Melanie Boerries Hauke Busch Thomas Reinheckel	Larissa E Hillebrand Fee Bengsch Jochen Hochrein Jan Hülsdünker Julia Bender	Oncotarget
Critical re-evaluation of neuroglobin expression reveals conserved patterns among mammals.	2016-08-16	Thorsten Burmester	Andrej Fabrizius Daniel Andre Tilmann Laufs Anne Bicker Stefan Reuss Elena Porto Thomas Hankeln	Neuroscience
REST is a hypoxia-responsive transcriptional repressor	2016-08-17	Miguel Cavadas Carsten C Scholz Zsolt Fabian Alex Cheong Murtaza M Tambuwala	Marion Mesnieres Bianca Crifo Mario C Manresa Andrew C Selfridge Ciara E Keogh Karen A Nolan Liliane M A Rocha Stuart Brown Anita Wdowicz Danielle Corbett Keith J Murphy Catherine Godson Eoin P Cummins Cormac T Taylor	Scientific Reports
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 Nicolas Serafini Deborah R Winter Amir Giladi David Lara-Astiaso Maayan Levy Tomer Meir Salame Assaf Weiner Eyal David Hagit Shapiro Mally Dori-Bachash Meirav Pevsner-Fischer Erika Lorenzo-Vivas Hadas Keren-Shaul Franziska Paul Alon Harmelin Gérard Eberl Shalev Itzkovitz Amos Tanay James P Di Santo Eran Elinav Ido Amit	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 Ning Leng Jue Zhang Zhonggang Hou Daniel Mamott David T Vereide Jeea Choi Ron Stewart James A Thomson	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 Susanne Mandrup Bjørk Ditlev Larsen Louise T Dalgaard Pierre Maechler	Søren Fisker Schmidt Jesper Grud Skat Madsen Kari Østerli Frafjord Lars la Cour Poulsen Sofia Salö Michael Boergesen Anne Loft Maria Stahl Madsen	Cell Reports
C. elegans Stress-Induced Sleep Emerges from the Collective Action of Multiple Neuropeptides.	2016-08-17	Han Wang Erich M Schwarz	Ravi D Nath Elly S Chow Paul W Sternberg	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 Johanna Klughammer Felix Albert Offner Felix Krueger Sébastien Smallwood Silke Szymczak Arthur Kaser Andre Franke	Scientific Reports
Determining Physical Mechanisms of Gene Expression Regulation from Single Cell Gene Expression Data	2016-08-23	Daphne Ezer	Victoria Moignard Berthold Göttgens Boris Adryan	PLOS Computational Biology
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 Yimin Hua Henriette Skovgaard Andersen Sabrina Brøner Ying Hsiu Liu Anna Wieckowska Maja Dembic Gitte Hoffmann Bruun Adrian R Krainer	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 Parham Solaimani Kathy Knezevic Alexia Eliades Rahima Patel Roshana Thambyrajah Ashwin Unnikrishnan Julie Thoms Dominik Beck Chris S Vink Aileen Smith Mairi Shepherd David Kent Fabian Paul Julia Klippert Annette Hammes Thomas Willnow Bertie Göttgens Elaine Dzierzak Leonard I Zon George Lacaud Valerie Kouskoff John E Pimanda	Blood
Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V'DJer.	2016-08-24	Jonathan S. Serody	Lisle E Mose Sara R Selitsky Lisa M Bixby David L Marron Michael D Iglesia Charles M Perou Benjamin G Vincent Joel S Parker	Bioinformatics
An integrative transcriptomic atlas of organogenesis in human embryos.	2016-08-24	Dave Gerrard	Andrew A Berry Rachel E Jennings Karen Piper Hanley Nicoletta Bobola Neil A Hanley	eLife
Genomewide Association Study of African Children Identifies Association of SCHIP1 and PDE8A with Facial Size and Shape.	2016-08-25	Washington Mio Benedikt Hallgrímsson	Joanne B Cole Mange Manyama Emmanuel Kimwaga Joshua Mathayo Jacinda R Larson Denise K Liberton Ken Lukowiak Tracey M Ferrara Sheri L Riccardi Mao Li Washington Mio Michaela Prochazkova Trevor Williams Hong Li Kenneth L Jones Ophir D Klein Stephanie A Santorico Benedikt Hallgrimsson Richard A Spritz	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 Samuel G. Jacobson	Ricky S Joshi Paras Garg Noah Zaitlen Tuuli Lappalainen Corey T Watson Nidha Azam Daniel Ho Xin Li Stylianos E Antonarakis Han G Brunner Sau Wai Cheung Bradford Coffee Thomas Eggermann David Francis Joep P Geraedts Giorgio Gimelli Cedric Le Caignec Nicole de Leeuw Thomas Liehr Deborah J Mackay Stephen B Montgomery Alistair T Pagnamenta Peter Papenhausen David O Robinson Claudia Ruivenkamp Charles Schwartz Bernhard Steiner David A Stevenson Urvashi Surti Thomas Wassink Andrew J Sharp	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 Lu Cheng Jian Chen Zhuqiang Zhang Ting Shen Min Wang Ting Ni Chunsheng Han	RNA Biology
Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach	2016-08-26	Feixiong Cheng Bairong Shen	Chuang Liu Zhongming Zhao	BMC Systems Biology
Inferring expressed genes by whole-genome sequencing of plasma DNA.	2016-08-29	Peter Ulz Gerhard G Thallinger Michael R. Speicher	Martina Auer Ricarda Graf Karl Kashofer Stephan W Jahn Luca Abete Gunda Pristauz Edgar Petru Jochen B Geigl Ellen Heitzer	Nature Genetics
Characterization of non-olfactory GPCRs in human sperm with a focus on GPR18	2016-08-30	Janine Altmüller Hanns Hatt Günter Gisselmann Christa E Müller	Caroline Flegel Felix Vogel Adrian Hofreuter Sebastian Wojcik Clara Schoeder Katarzyna Kieć-Kononowicz Norbert H Brockmeyer Christian Becker Günter Gisselmann	Scientific Reports
Chromatin recruitment of activated AMPK drives fasting response genes co-controlled by GR and PPARα.	2016-08-30	Bart Staels Réjane Paumelle Karolien De Bosscher Lode De Cauwer Michal Pawlak Nathalie Hennuyer	Dariusz Ratman Viacheslav Mylka Nadia Bougarne Sandrine Caron Jonathan Thommis Mark H Rider Claude Libert Sam Lievens Jan Tavernier Karolien De Bosscher	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 Davis J McCarthy	Aaron T L Lun	F1000Research
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 Nima Niknejad David J Stewart Harmanjatinder S Sekhon Patrick J Villeneuve Jim Dimitroulakos	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 Miriam S Moraes David C Martins Ronaldo F Hashimoto Pedro A F Galante Célia R S Garcia	Genes & Cancer
ANGIOGENES: knowledge database for protein-coding and noncoding RNA genes in endothelial cells.	2016-09-01	Stefanie Dimmeler Tyler Weirick Shizuka Uchida	Raphael Müller David John Giuseppe Militello Wei Chen	Scientific Reports
Mammary Tumor-Associated RNAs Impact Tumor Cell Proliferation, Invasion, and Migration.	2016-09-01	Sarah Diermeier	Kung-Chi Chang Susan M Freier Junyan Song Osama El Demerdash Alexander Krasnitz Frank Rigo C Frank Bennett David L Spector	Cell Reports
Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos.	2016-09-01	Sten Linnarsson Björn Reinius Fredrik Lanner	Sophie Petropoulos Daniel Edsgärd Qiaolin Deng Sarita Pauliina Panula Simone Codeluppi Alvaro Plaza Reyes Sten Linnarsson Rickard Sandberg	Cell
A full-body transcriptome and proteome resource for the European common carp.	2016-09-02	Hans J Jansen Christiaan V. Henkel	I C R M Kolder S J van der Plas-Duivesteijn G Tan G F Wiegertjes M Forlenza A T Guler D Y Travin M Nakao T Moritomo I Irnazarow J T den Dunnen S Y Anvar R P Dirks M Palmblad B Lenhard H P Spaink	BMC Genomics
Complementarity of SOMAscan to LC-MS/MS and RNA-seq for quantitative profiling of human embryonic and mesenchymal stem cells.	2016-09-06	Anja M Billing Johannes Graumann Karsten Suhre	Hisham Ben Hamidane Aditya M Bhagwat Richard J Cotton Shaima S Dib Pankaj Kumar Shahina Hayat Neha Goswami Arash Rafii	Journal of Proteomics
Pro-invasive Effect of Proto-oncogene PBF Is Modulated by an Interaction with Cortactin.	2016-09-07	Vicki E Smith Erica Gentilin Martin L. Read H Mehanna	Rachel J Watkins Waraporn Imruetaicharoenchoke Neil Sharma Vikki L Poole Sukhchain Bansal Emy Bosseboeuf Rachel Fletcher Hannah R Nieto Ujjal Mallick Allan Hackshaw Kristien Boelaert Christopher J McCabe	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	Charles A S Banks Gina Boanca Zachary T Lee Cassandra G Eubanks Allison Peak Lauren E Weems Juliana J Conkright	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 Rosa Figueroa-Balderas Daniel P Lawrence Kendra Baumgartner	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 Tuuli Lappalainen	Scientific Reports
Localizing gene regulation reveals a staggered wood decay mechanism for the brown rot fungus Postia placenta	2016-09-12	Dehong Hu	Jiwei Zhang Gerald N Presley Kenneth E Hammel Jae-San Ryu Jon R Menke Melania Figueroa Galya Orr Jonathan S Schilling	Proceedings of the National Academy of Sciences of the United States of America
Gene expression profiling of granule cells and Purkinje cells in the zebrafish cerebellum.	2016-09-12	Shigehiro Kuraku Masahiko Hibi	Miki Takeuchi Shingo Yamaguchi Yoshimasa Sakakibara Takuto Hayashi Koji Matsuda Yuichiro Hara Chiharu Tanegashima Takashi Shimizu	The Journal of Comparative Neurology
CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data.	2016-09-13	Sohiya Yotsukura	David A duVerle Seitaro Nomura Hiroyuki Aburatani Koji Tsuda	BMC Bioinformatics
Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes	2016-09-13	Aldons Jake Lusis	Yehudit Hasin-Brumshtein Arshad H Khan Farhad Hormozdiari Calvin Pan Brian W Parks Vladislav A Petyuk Paul D Piehowski Anneke Brümmer Matteo Pellegrini Xinshu Xiao Eleazar Eskin Richard D Smith Desmond J Smith	eLife
Zinc finger protein 407 overexpression upregulates PPAR target gene expression and improves glucose homeostasis in mice.	2016-09-13	Dave Bridges David A. Buchner	Alyssa Charrier Li Wang Erin J Stephenson Siddharth V Ghanta Chih-Wei Ko Colleen M Croniger	American Journal of Physiology - Endocrinology and Metabolism
MdMyb93 is a regulator of suberin deposition in russeted apple fruit skins.	2016-09-15	Marc Boutry	Sylvain Legay Gea Guerriero Christelle André Cédric Guignard Emmanuelle Cocco Sophie Charton Owen Rowland Jean-Francois Hausman	New Phytologist
Alternative Splicing May Not Be the Key to Proteome Complexity	2016-09-16	Alfonso Valencia	Michael L. Tress Federico Abascal	Trends in Biochemical Sciences
Regulation of X-linked gene expression during early mouse development by Rlim	2016-09-19	Aviv Regev Alex K. Shalek Oliver J Rando	Feng Wang JongDae Shin Jeremy M Shea Jun Yu Ana Bošković Meg Byron Xiaochun Zhu Jeanne B Lawrence Eduardo M Torres Lihua J Zhu Ingolf Bach	eLife
Transcriptomic profiles of the upper olfactory rosette in cultured and wild Senegalese sole (Solea senegalensis) males.	2016-09-20	Elvira Fatsini Manuel Manchado	R Bautista N J Duncan	Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics
Single-Cell Transcriptomics Bioinformatics and Computational Challenges	2016-09-21	Lana Garmire	Olivier B. Poirion Xun Zhu Travers Ching Lana Garmire	Frontiers in Genetics
The tubulin repertoire of C. elegans sensory neurons and its context-dependent role in process outgrowth.	2016-09-21	Erich M Schwarz Michael Krieg Robert O'Hagan	Dean Lockhead Sebastian Bellotti Maureen M Barr Alexander R Dunn Paul W Sternberg Miriam B Goodman	Molecular Biology of the Cell
Long non-coding RNAs in human early embryonic development and their potential in ART.	2016-09-21	John De Vos	Julien Bouckenheimer Said Assou Sébastien Riquier Cyrielle Hou Nicolas Philippe Caroline Sansac Thierry Lavabre-Bertrand Thérèse Commes Jean-Marc Lemaître Anthony Boureux	Human Reproduction Update
Probiotic Enterococcus faecalis Symbioflor® down regulates virulence genes of EHEC in vitro and decrease pathogenicity in a Caenorhabditis elegans model.	2016-09-21	Klaus Neuhaus	Marina C Lamparter Benjamin Zölch Richard Landstorfer Svenja Simon Britta Spanier Matthias A Ehrmann Rudi F Vogel	Archives of Microbiology
A Global Analysis of the Polygalacturonase Gene Family in Soybean (Glycine max).	2016-09-22	Fanjiang Kong	Feifei Wang Xia Sun Xinyi Shi Hong Zhai Changen Tian Baohui Liu Xiaohui Yuan	PLoS ONE
C14orf132 gene is possibly related to extremely low birth weight	2016-09-22	Triin Viltrop Andres Salumets Q16408409 Ene Reimann	Airi Tiirats Margit Nõukas	BMC Genetics
Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms.	2016-09-22	Cornelia M. van Duijn André Uitterlinden Cisca Wijmenga Jenny van Dongen Rick Jansen Eco De Geus	Roderick C Slieker Maarten van Iterson René Luijk Marian Beekman Daria V Zhernakova Matthijs H Moed Hailiang Mei Michiel van Galen Patrick Deelen Marc Jan Bonder Alexandra Zhernakova Ettje F Tigchelaar Coen D A Stehouwer Casper G Schalkwijk Carla J H van der Kallen Albert Hofman Diana van Heemst Joris Deelen Leonard H van den Berg Joyce van Meurs Peter A C 't Hoen Lude Franke Jan H Veldink Morris A Swertz Marleen M J van Greevenbroek Dorret I Boomsma BIOS consortium P Eline Slagboom Bastiaan T Heijmans	Genome Biology
A perspective on single cell behavior during infection	2016-09-22	Roi Avraham	Deborah T Hung	Gut microbes
Pre-mRNA splicing repression triggers abiotic stress signaling in plants.	2016-09-24	Stefan T Arold Sahar Alshareef Yu Ling Hiroaki Fujii Jorge Lozano-Juste Paula Duque Ahmed Moustafa Magdy M. Mahfouz	Haroon Butt Lixin Li Aya A Galal Afaque A Momin Manal Tashkandi Dale N Richardson Pedro L Rodriguez	The Plant Journal
Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development	2016-09-26	Svante Pääbo Farhath Badsha Barbara Treutlein Zhisong He	Felipe Mora-Bermúdez Sabina Kanton J Gray Camp Benjamin Vernot Kathrin Köhler Birger Voigt Keisuke Okita Tomislav Maricic Robert Lachmann Wieland B Huttner	eLife
Protein C receptor (PROCR) is a negative regulator of Th17 pathogenicity.	2016-09-26	Aviv Regev Chuan Wu Norio Chihara	Yasuhiro Kishi Takaaki Kondo Sheng Xiao Nir Yosef Jellert Gaublomme Chao Wang Nicole Joller Vijay K Kuchroo	Journal of Experimental Medicine
Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq.	2016-09-26	Rickard Sandberg Daniel Ramsköld Björn Reinius Qiaolin Deng	Jeff E Mold Per Johnsson Jakob Michaëlsson Jonas Frisén	Nature Genetics
Time-resolved dual RNA-seq reveals extensive rewiring of lung epithelial and pneumococcal transcriptomes during early infection.	2016-09-27	Jan-Willem Veening Jelle Slager	Rieza Aprianto Siger Holsappel	Genome Biology
Consensus Analysis of Whole Transcriptome Profiles from Two Breast Cancer Patient Cohorts Reveals Long Non-Coding RNAs Associated with Intrinsic Subtype and the Tumour Microenvironment.	2016-09-29	James R. Bradford	Angela Cox Philip Bernard Nicola J Camp	PLoS ONE
Mammalian Period represses and de-represses transcription by displacing CLOCK-BMAL1 from promoters in a Cryptochrome-dependent manner.	2016-09-29	Aziz Sancar	Yi-Ying Chiou Yanyan Yang Naim Rashid Rui Ye Christopher P Selby	Proceedings of the National Academy of Sciences of the United States of America
Developing a Novel Two-Dimensional Culture System to Enrich Human Prostate Luminal Progenitors that Can Function as a Cell of Origin for Prostate Cancer.	2016-09-29	Hsueh-Ping Chao Dingxiao Zhang Yue Lu	Kevin Lin Kiera Rycaj Yi Zhong Tammy Calhoun-Davis Jianjun Shen Dean G Tang	Stem Cells Translational Medicine
Downregulation of sphingosine kinase-1 induces protective tumor immunity by promoting M1 macrophage response in melanoma.	2016-09-30	Nathalie Andrieu-Abadie Bruno Ségui Jean-Christophe Marine	Marguerite Mrad Caroline Imbert Virginie Garcia Florian Rambow Nicole Therville Stéphane Carpentier Thierry Levade Rania Azar Mona Diab-Assaf Céline Colacios	Oncotarget
Identification of Aedes aegypti Long Intergenic Non-coding RNAs and Their Association with Wolbachia and Dengue Virus Infection	2016-10	Sassan Asgari	Kayvan Etebari Sultan Asad Guangmei Zhang	PLOS Neglected Tropical Diseases
Profiling of adhesive-related genes in the freshwater cnidarian Hydra magnipapillata by transcriptomics and proteomics.	2016-10-01	Peter Ladurner	Marcelo Rodrigues Thomas Ostermann Leopold Kremeser Herbert Lindner Christian Beisel Eugene Berezikov Bert Hobmayer	Biofouling
Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells.	2016-10-01	Sten Linnarsson Peter Lönnerberg	Gioele La Manno Daniel Gyllborg Simone Codeluppi Kaneyasu Nishimura Carmen Salto Amit Zeisel Lars E Borm Simon R W Stott Enrique M Toledo J Carlos Villaescusa Peter Lönnerberg Jesper Ryge Roger A Barker Ernest Arenas Sten Linnarsson	Cell
Model systems of DUX4 expression recapitulate the transcriptional profile of FSHD cells.	2016-10-01	Rebecca Resnick Sujatha Jagannathan Silvère M van der Maarel	Sean C Shadle Lauren Snider Rabi N Tawil Robert K Bradley Stephen J Tapscott	Human Molecular Genetics
Correlation of an epigenetic mitotic clock with cancer risk	2016-10-03	Diana Kuh Andrew Wong	Zhen Yang Dirk S Paul Vardhman K Rakyan R David Leslie Shijie C Zheng Martin Widschwendter Stephan Beck Andrew E Teschendorff	Genome Biology
Predicting the functional states of human iPSC-derived neurons with single-cell RNA-seq and electrophysiology	2016-10-04	Cedric Bardy	M van den Hurk B Kakaradov J A Erwin B N Jaeger R V Hernandez T Eames A A Paucar M Gorris C Marchand R Jappelli J Barron A K Bryant M Kellogg R S Lasken B P F Rutten H W M Steinbusch G W Yeo F H Gage	Molecular Psychiatry
Ethylene responsive transcription factor ERF109 retards PCD and improves salt tolerance in plant	2016-10-06	Sherif Edris	Ahmed Bahieldin Ahmed Atef Nour O Gadalla Hani M Ali Sabah M Hassan Magdy A Al-Kordy Ahmed M Ramadan Rania M Makki Abdulrahman S M Al-Hajar Fotouh M El-Domyati	BMC Plant Biology
Discovering Single Nucleotide Polymorphisms Regulating Human Gene Expression Using Allele Specific Expression from RNA-seq Data.	2016-10-07	Sagiv Shifman Eyal Ben-David Aldons Jake Lusis	Eun Yong Kang Lisa J Martin Serghei Mangul Warin Isvilanonda Jennifer Zou Buhm Han Eleazar Eskin	Genetics
The Molecular Circuit Regulating Tooth Development in Crocodilians.	2016-10-07	A Abdelhamid	S Tsai M K Khan A Elkarargy R B Widelitz C M Chuong P Wu	Journal of Dental Research
Optimization of techniques for multiple platform testing in small, precious samples such as human chorionic villus sampling.	2016-10-08	Charles R. Farber Jerome I Rotter	Margareta D Pisarska Marzieh Akhlaghpour Bora Lee Gillian M Barlow Ning Xu Erica T Wang Aaron J Mackey Stephen S Rich Yii-der I Chen Mark O Goodarzi Seth Guller John Williams	Prenatal Diagnosis
Transcriptomic alterations in Sitophilus zeamais in response to allyl isothiocyanate fumigation.	2016-10-11	Xing Zhang	Chao Zhang Zhiqing Ma Hua Wu	Pesticide Biochemistry and Physiology
Alternative genetic mechanisms of BRAF activation in Langerhans cell histiocytosis.	2016-10-11	Kenneth L McClain	Rikhia Chakraborty Thomas M Burke Oliver A Hampton Daniel J Zinn Karen Phaik Har Lim Harshal Abhyankar Brooks Scull Vijetha Kumar Nipun Kakkar David A Wheeler Angshumoy Roy Poulikos I Poulikakos Miriam Merad D Williams Parsons Carl E Allen	Blood
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 Steven Goossens Leo A van Grunsven Danny Huylebroeck Wilfred F J van IJcken	Agata Stryjewska Ruben Dries Tim Pieters Griet Verstappen Andrea Conidi Kathleen Coddens Annick Francis Lieve Umans Geert Berx Frank G Grosveld Jody J Haigh	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 Joy Lincoln	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 A Maxwell Burroughs Shohei Noma Harukazu Suzuki Yumi Kawamura Yoshihide Hayashizaki Akila Mayeda 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 Thomas F Gajewski Francesco M Marincola Craig L Slingluff	OncoImmunology
The Ser82 RAGE Variant Affects Lung Function and Serum RAGE in Smokers and sRAGE Production In Vitro.	2016-10-18	Tracy L Rimington Amanda P Henry Andrew Wardlaw Ian P. Hall Suzanne Miller Stuart G. Parker Charlotte E Bolton	Emily Hodge Alexander K Kheirallah Charlotte K Billington Sangita K Bhaker Ma'en Obeidat Erik Melén Simon K Merid Caroline Swan Catherine Gowland Carl P Nelson Ceri E Stewart Iain Kilty Anders Malarstig Miriam F Moffatt Ian Sayers	PLoS ONE
High-resolution analysis of multi-copy variant surface glycoprotein gene expression sites in African trypanosomes.	2016-10-18	Horn DA	Sebastian Hutchinson Lucy Glover	BMC Genomics
Expression and prognostic significance of the autoimmune regulator gene in breast cancer cells.	2016-10-18	Francesca Bianchi Lucia Sfondrini Michele Sommariva Tiziana Triulzi Loris De Cecco Andrea Balsari	Sandra Romero-Cordoba Elda Tagliabue	Cell Cycle
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
A Multifaceted Role for Myd88-Dependent Signaling in Progression of Murine Mammary Carcinoma.	2016-10-27	Maureen A Carey	Mary J Higgins Antonio Serrano Kofi Y Boateng Victoria A Parsons Tiffany Phuong Alyssa Seifert Jacob M Ricca Kyle C Tucker Alec S Eidelman Robert A Kurt	Breast cancer : basic and clinical research
Cells Respond to Distinct Nanoparticle Properties with Multiple Strategies As Revealed by Single-Cell RNA-Seq.	2016-10-27	Dehong Hu Ronald Taylor	Hugh D Mitchell Lye Meng Markillie William B Chrisler Matthew J Gaffrey Craig J Szymanski Yumei Xie Eric S Melby Alice Dohnalkova Eva K Grate Scott K Cooley Jason E McDermott Alejandro Heredia-Langner Galya Orr	ACS Nano
Single-Cell Analysis Reveals a Close Relationship between Differentiating Dopamine and Subthalamic Nucleus Neuronal Lineages.	2016-10-27	Malin Parmar Sara Nolbrant Agnete Kirkeby	Nigel Kee Nikolaos Volakakis Lina Dahl Helena Storvall 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 Aviv Regev Orit Rozenblatt-Rosen Aanand A Patel Christopher W Mount Brian V. Nahed	Andrew S Venteicher Christine Hebert Leah E Escalante Anoop P Patel Keren Yizhak Jonathan M Fisher Christopher Rodman Mariella G Filbin Cyril Neftel Niyati Desai Jackson Nyman Benjamin Izar Christina C Luo Joshua M Francis Maristela L Onozato Nicolo Riggi Kenneth J Livak Dave Gennert William T Curry Robert L Martuza Ravindra Mylvaganam A John Iafrate Matthew P Frosch Todd R Golub Miguel N Rivera Gad Getz Michelle Monje Bradley E Bernstein David N Louis Mario L Suvà	Nature
The founder-cell transcriptome in the Arabidopsis apetala1 cauliflower inflorescence meristem.	2016-11-03	Peter Frommolt	Anneke Frerichs Rahere Thoma Ali Taleb Abdallah Wolfgang Werr John William Chandler	BMC Genomics
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 Bingshu E Chen	Sinead Cuffe Shermi Liang Lu Cheng Yonathan Brhane Xin Qiu David W Cescon Jeffrey Bruce Zhuo Chen Dangxiao Cheng Devalben Patel Brandon C Tse Scott A Laurie Glenwood Goss Natasha B Leighl Rayjean Hung Penelope A Bradbury Lesley Seymour Frances A Shepherd Wei Xu David N Reisman	Clinical Cancer Research
Single-Cell Resolution of Temporal Gene Expression during Heart Development.	2016-11-09	Daniel M DeLaughter	Daniel M DeLaughter Alexander G Bick Hiroko Wakimoto David McKean Joshua M Gorham Irfan S Kathiriya John T Hinson Jason Homsy Jesse Gray William Pu Benoit G Bruneau J G Seidman Christine E Seidman	Developmental Cell
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 Leon N Schulte Lei Li Silke Appenzeller	Antoine-Emmanuel Saliba Alexander J Westermann Daphne A C Stapels 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 I King Jordan	Frontiers in molecular biosciences
Aging is associated with impaired angiogenesis, but normal microvascular network structure, in the rat mesentery.	2016-11-18	Melody Baddoo	Richard S Sweat David C Sloas Scott A Stewart Malwina Czarny-Ratajczak James R Eastwood Ariana D Suarez-Martinez Mohammad S Azimi Hope E Burks Lee O Chedister Leann Myers Walter L Murfee	American Journal of Physiology - Heart and Circulatory Physiology
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 Charles F. Burant	Akhil Upneja Andrzej Galecki Yi-Miau Tsai Sasha Raskind Quanwei Zhang Zhengdong D Zhang Andrei Seluanov Clary B Clish Richard A Miller Vadim N Gladyshev	eLife
5'-Terminal nucleotide variations in human cytoplasmic tRNAHisGUG and its 5'-halves.	2016-11-22	Yohei Kirino	Megumi Shigematsu	RNA
Cancer somatic mutations cluster in a subset of regulatory sites predicted from the ENCODE data	2016-11-25	David R. Westhead	Nisar A Shar M S Vijayabaskar	Molecular Cancer
Tsetse fly tolerance to T. brucei infection: transcriptome analysis of trypanosome-associated changes in the tsetse fly salivary gland	2016-11-25	Jan Van Den Abbeele Guy Caljon	Irina Matetovici	BMC Genomics
RNA-Sequencing for profiling goat milk transcriptome in colostrum and mature milk.	2016-11-25	Alessandra Crisà Bianca Moioli Giovanni Chillemi	Fabrizio Ferrè	BMC Veterinary Research
Mapping heterogeneity in patient-derived melanoma cultures by single-cell RNA-seq.	2016-11-26	Manfred Schartl Barbara Treutlein	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 Yoseph Barash	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 Mark O Cunningham	Cell Reports
The Lair: a resource for exploratory analysis of published RNA-Seq data.	2016-12-01	Lior Pachter Harold Pimentel Páll Melsted	Pascal Sturmfels Nicolas Bray	BMC Bioinformatics
Transcriptome and Multivariable Data Analysis of Corynebacterium glutamicum under Different Dissolved Oxygen Conditions in Bioreactors.	2016-12-01	Yankun Yang	Yang Sun Wenwen Guo Fen Wang Feng Peng Xiaofeng Dai Xiuxia Liu Zhonghu Bai	PLoS ONE
InFusion: Advancing Discovery of Fusion Genes and Chimeric Transcripts from Deep RNA-Sequencing Data.	2016-12-01	Thomas F. Meyer Lukas Rajkowitsch	Konstantin Okonechnikov Aki Imai-Matsushima Alexander Seitz Fernando Garcia-Alcalde	PLoS ONE
QSEA-modelling of genome-wide DNA methylation from sequencing enrichment experiments.	2016-12-01	Ralf Herwig	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 Marco Y. Hein	Britt Adamson Thomas M Norman Marco Jost Min Y Cho James K Nuñez Yuwen Chen Jacqueline E Villalta Luke A Gilbert Max A Horlbeck Ryan A Pak Andrew N Gray Carol A Gross Atray Dixit Oren Parnas Jonathan S Weissman	Cell
Global Deletion of TSPO Does Not Affect the Viability and Gene Expression Profile.	2016-12-01	Weiqing Wang	Huaishan Wang Kangle Zhai Yingchao Xue Jia Yang Qi Yang Yi Fu Yu Hu Fang Liu Lianxian Cui Hui Chen Jianmin Zhang Wei He	PLoS ONE
Epigenomics-Based Identification of Major Cell Identity Regulators within Heterogeneous Cell Populations.	2016-12-01	Peter Frommolt Alvaro Rada-Iglesias	Rizwan Rehimi Milos Nikolic Sara Cruz-Molina Christina Tebartz Esther Mahabir Mathieu Clément-Ziza	Cell Reports
Notch Pathway Is Activated via Genetic and Epigenetic Alterations and Is a Therapeutic Target in Clear Cell Renal Cancer.	2016-12-01	John Greally Katalin Susztak Shizheng Huang Niraj Shenoy	Tushar D Bhagat Yiyu Zou Jihwan Park Matthew B Palmer Caroline Hu Weijuan Li Orsolya Giricz Gaurav Choudhary Yiting Yu Yi-An Ko María C Izquierdo Ae Seo Deok Park Nishanth Vallumsetla Remi Laurence Robert Lopez Masako Suzuki James Pullman Justin Kaner Benjamin Gartrell A Ari Hakimi Bharvin Patel Karim Benhadji Kith Pradhan Amit Verma	Journal of Biological Chemistry
LncPRESS1 Is a p53-Regulated LncRNA that Safeguards Pluripotency by Disrupting SIRT6-Mediated De-acetylation of Histone H3K56.	2016-12-01	Michelle Craig Barton Abhinav K Jain Lalit Patel	Yuanxin Xi Ryan McCarthy Kendra Allton Kadir C Akdemir Bruce Aronow Chunru Lin Wei Li Liuqing Yang	Molecular Cell
Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq.	2016-12-01	Alexander van Oudenaarden Hadas Keren-Shaul	Diego Adhemar Jaitin Assaf Weiner Ido Yofe David Lara-Astiaso Hadas Keren-Shaul Eyal David Tomer Meir Salame Amos Tanay Ido Amit	Cell
MS23, a master basic helix-loop-helix factor, regulates the specification and development of the tapetum in maize.	2016-12-02	Blake Meyers	Guo-Ling Nan Jixian Zhai Siwaret Arikit Darren Morrow John Fernandes Lan Mai Nhi Nguyen Virginia Walbot	Development
Transcriptomic Analysis of Mouse Cochlear Supporting Cell Maturation Reveals Large-Scale Changes in Notch Responsiveness Prior to the Onset of Hearing.	2016-12-05	Andrew K. Groves Zhandong Liu	Juan C Maass Rende Gu Tiantian Cai Ying-Wooi Wan Silvia C Cantellano Joanna S T Asprer Hongyuan Zhang Hsin-I Jen Renée K Edlund	PLoS ONE
Transcriptome and long noncoding RNA sequencing of three extracellular vesicle subtypes released from the human colon cancer LIM1863 cell line.	2016-12-05	Richard Simpson	Maoshan Chen Rong Xu Hong Ji David W Greening Alin Rai Keiichi Izumikawa Hideaki Ishikawa Nobuhiro Takahashi	Scientific Reports
Identification of context-dependent expression quantitative trait loci in whole blood.	2016-12-05	Lude Franke Harm-Jan Westra André Uitterlinden Cornelia M. van Duijn Cisca Wijmenga Wibowo Arindrarto Patrick Deelen Marc 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 V Bharti D G Simmons A Adam S S J Hur G J Maghzal E Whitelaw R Stocker C M Suter R P Harvey S K Harten	Differentiation
Macrophage Colony Stimulating Factor Derived from CD4+ T Cells Contributes to Control of a Blood-Borne Infection	2016-12-06	Mary F Fontana Chioma Anidi Charles C. Kim	Gabrielly L de Melo Rebecca Hamburger Chris Y Kim So Youn Lee Jennifer Pham	PLOS Pathogens
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
Sugarcane transcriptome analysis in response to infection caused by Acidovorax avenae subsp. avenae.	2016-12-09	Clícia Grativol	Ailton B Santa Brigida Cristian A Rojas Elvismary M de Armas Júlio O P Entenza Flávia Thiebaut Marcelo de F Lima Laurent Farrinelli Adriana S Hemerly Sérgio Lifschitz Paulo C G Ferreira	PLoS ONE
Developmental Stage, Muscle and Genetic Type Modify Muscle Transcriptome in Pigs: Effects on Gene Expression and Regulatory Factors Involved in Growth and Metabolism.	2016-12-09	Rita Benítez	Miriam Ayuso Almudena Fernández Yolanda Núñez Beatriz Isabel Ana I Fernández Ana I Rey Antonio González-Bulnes Juan F Medrano Ángela Cánovas Clemente J López-Bote Cristina Óvilo	PLoS ONE
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 Eric C Lai	Ching-Jung Lin Fernando Bejarano Fuqu Hu Diane Bortolamiol-Becet Lijuan Kan Piero Sanfilippo	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
An atlas of transcriptional, chromatin accessibility, and surface marker changes in human mesoderm development.	2016-12-20	Lay Teng Ang Anshul Kundaje	Pang Wei Koh Rahul Sinha Amira A Barkal Rachel M Morganti Angela Chen Irving L Weissman Kyle M Loh	Scientific Data
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 Kelly N Roeszler Claire Hirst David M Lambert	EvoDevo
Transcriptome Profiling of Trypanosoma brucei Development in the Tsetse Fly Vector Glossina morsitans	2016-12-21	Aurélien Vigneron	Amy F Savage Nikolay G Kolev Joseph B Franklin Serap Aksoy Christian Tschudi	PLoS ONE
A Rapid Spin Column-Based Method to Enrich Pathogen Transcripts from Eukaryotic Host Cells Prior to Sequencing.	2016-12-21	Robert J. Meagher	Zachary W Bent Kunal Poorey Annette E LaBauve Rachelle Hamblin Kelly P Williams	PLoS ONE
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 Claudia Döring	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 Gos Micklem 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 Lisa Müller Johannes Ptok Wolfgang Kaisers Gereon Poschmann Kai Stühler Stephan Theiss Heiner Schaal	Nucleic Acids Research
Correlated 5-Hydroxymethylcytosine (5hmC) and Gene Expression Profiles Underpin Gene and Organ-Specific Epigenetic Regulation in Adult Mouse Brain and Liver	2017	I-Hsuan Lin	Yi-Fan Chen Ming-Ta Hsu	PLoS ONE
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
Coupled Proliferation and Apoptosis Maintain the Rapid Turnover of Microglia in the Adult Brain	2017-01-01	Olga Garaschuk Amanda Sierra Yajie Liang Diego Gómez-Nicola Zoltán Molnár Mark S Cragg	Katharine Askew Kaizhen Li Adrian Olmos-Alonso Fernando Garcia-Moreno Philippa Richardson Tom Tipton Mark A Chapman Kristoffer Riecken Sol Beccari V Hugh Perry	Cell Reports
Some Thoughts on Experimental Design.	2017-01-01	Claudio Daniel Stern		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 Christopher E Ramsden Michael J Iadarola Andrew J Mannes	Cephalalgia
Bioinformatics Pipeline for Transcriptome Sequencing Analysis.	2017-01-01	Thomas Derrien	Sarah Djebali Valentin Wucher Sylvain Foissac Christophe Hitte Evan Corre	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	Melody Baddoo 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 Alberto Arrigoni Grazisa Rossetti Ilaria Panzeri Raoul J P Bonnal Massimiliano Pagani	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 Danielle Tenen Manju Kumari Evan D Rosen	Cell Reports
RNA-Seq Data Analysis Protocol: Combining In-House and Publicly Available Data.	2017-01-01	Marc W Schmid		Methods in Molecular Biology
Optimized Whole Transcriptome Profiling of Motor Axons.	2017-01-01	Michael Sendtner	Lena Saal-Bauernschubert Michael Briese	Methods in Molecular Biology
ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data.	2017-01-03	Roderic Guigó i Serra Emilio Palumbo A Rastrojo	Bernardo Rodríguez-Martín Santiago Marco-Sola Thasso Griebel Paolo Ribeca Graciela Alonso Begoña Aguado Sarah Djebali	BMC Genomics
JACUSA: site-specific identification of RNA editing events from replicate sequencing data.	2017-01-03	Markus Landthaler	Michael Piechotta Emanuel Wyler Uwe Ohler 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 Agostino Steffan M. Dominici	S Rubina Baglio Tonny Lagerweij Maria Pérez-Lanzón Xuan Dung Ho Nicolas Léveillé Anne-Marie Cleton-Jansen Ekaterina S Jordanova Laura Roncuzzi Michelina Greco Monique A J van Eijndhoven Giulia Grisendi Sinead M Lougheed Tanja D de Gruijl Nicoletta Zini Silvia Cervo Vincenzo Canzonieri Aare Martson Katre Maasalu Sulev Köks Tom Wurdinger Nicola Baldini D Michiel Pegtel	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 Lei Li Kai Papenfort Hans-Joachim Wieden	Yanjie Chao Dylan Girodat Nelly Said Colin Corcoran Michał Śmiga Richard Reinhardt Ben F Luisi	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 Fanny Kortüm Anju Shukla Malik Alawi Ashwin Dalal Lauren Brady Mark Tarnopolsky Lynne M. Bird Sophia Ceulemans Martina Bebin Kevin M. Bowling Susan M. Hiatt Edward J. Lose Michelle Primiano Wendy K. Chung Jane Juusola Zeynep C. Akdemir Matthew Bainbridge Wu-Lin Charng Margaret Drummond-Borg Mohammad K. Eldomery Ayman W. El-Hattab Mohammed A. M. Saleh Stéphane Bézieau Benjamin Cogné Bertrand Isidor Sébastien Küry James R. Lupski Richard M. Myers Gregory M. Cooper	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 Andrea Cortini Lingyan Chen Alfonso Buil Emmanouil T Dermitzakis David L Morris Timothy J Vyse Deborah S Cunninghame Graham	Human Molecular Genetics
SBDS-Deficient Cells Have an Altered Homeostatic Equilibrium due to Translational Inefficiency Which Explains their Reduced Fitness and Provides a Logical Framework for Intervention.	2017-01-05	Elisa Pesce Sara Ricciardi Stefano Biffo Diego Luis Medina Massimiliano Pagani	Piera Calamita Annarita Miluzio Arianna Russo Farhat Khanim Cristina Cheroni Roberta Alfieri Marilena Mancino Chiara Gorrini Grazisa Rossetti Ivana Peluso Johanna Rommens	PLOS Genetics
Single-cell transcriptomics of small microbial eukaryotes: limitations and potential.	2017-01-06	Karla B Heidelberg	Zhenfeng Liu Sarah K Hu Victoria Campbell Avery O Tatters David A Caron	The ISME Journal
The nature and nurture of cell heterogeneity: accounting for macrophage gene-environment interactions with single-cell RNA-Seq	2017-01-07	Sergi Padilla-Parra William James	Quin F Wills Esther Mellado-Gomez Rory Nolan Damien Warner Eshita Sharma John Broxholme Benjamin Wright Helen Lockstone Mark Lynch Michael Gonzales Jay West Anne Leyrat Sarah Filippi Chris Holmes Michael D Moore Rory Bowden	BMC Genomics
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 Steven R Head Diane J Nugent	Cancer Genetics
Whole-Genome Sequencing of Invasion-Resistant Cells Identifies Laminin α2 as a Host Factor for Bacterial Invasion	2017-01-10	Victor Nizet Bjørn Voldborg Nathan E. Lewis	Xander M van Wijk Simon Döhrmann Björn M Hallström Shangzhong Li Brandon X Meng Karen K McKee Toin H van Kuppevelt Peter D Yurchenco Bernhard O Palsson Jeffrey D Esko	mBio
A Hypothesis Testing Based Method for Normalization and Differential Expression Analysis of RNA-Seq Data.	2017-01-10	Jun Zhang	Yan Zhou Guochang Wang Han Li	PLoS ONE
Long noncoding RNA repertoire in chicken liver and adipose tissue	2017-01-10	Hervé Acloque Fabrice Legeai Kévin Muret Thomas Derrien Sandrine Lagarrigue	Christophe Klopp Valentin Wucher Diane Esquerré Frédéric Lecerf Colette Désert Morgane Boutin Frédéric Jehl 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 Juan C Begara-Morales	Capilla Mata-Pérez Beatriz Sánchez-Calvo María N Padilla Raquel Valderrama Juan B Barroso	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
Global Gene Expression Analysis of Cross-Protected Phenotype of Pectobacterium atrosepticum.	2017-01-12	Stanford Kwenda Elena Osipova Lucy Moleleki	Vladimir Gorshkov Olga Petrova Yuri Gogolev	PLoS ONE
Transcriptome and network analyses in Saccharomyces cerevisiae reveal that amphotericin B and lactoferrin synergy disrupt metal homeostasis and stress response.	2017-01-12	Chi Nam Ignatius Pang Dee A Carter	Yu-Wen Lai Leona T Campbell Sharon C-A Chen Marc R Wilkins	Scientific Reports
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
Effective detection of variation in single-cell transcriptomes using MATQ-seq.	2017-01-16	Chenghang Zong	Kuanwei Sheng Wenjian Cao Yichi Niu Qing Deng	Nature Methods
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 Kaustuv Sanyal	Yafeng Zhu Christian Tellgren-Roth Charles D Baudo John C Kennell Sheng Sun R Blake Billmyre Markus S Schröder Anna Andersson Tina Holm Benjamin Sigurgeirsson Guangxi Wu Sundar Ram Sankaranarayanan Rahul Siddharthan Joakim Lundeberg Björn Nystedt Teun Boekhout Thomas L Dawson Joseph Heitman Annika Scheynius	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 Frank C Schroeder	Matthew R Gronquist Ravi David Nath Ching-Han Lee Shalha Gharib Paul W Sternberg	eLife
UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy	2017-01-18	Andreas Heger Tom Smith Ian Sudbery		Genome Research
Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization	2017-01-19	Lana Garmire	Xun Zhu Travers Ching Xinghua Pan Sherman M Weissman Lana Garmire	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
RNA-Sequencing Reveals Biological Networks during Table Grapevine ('Fujiminori') Fruit Development.	2017-01-24	Jinggui Fang	Lingfei Shangguan Qian Mu Xiang Fang Kekun Zhang Haifeng Jia Xiaoying Li Yiqun Bao	PLoS ONE
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 Ching-Ling Lien Brendan H Grubbs Tracy C Grikscheit	BMC Genomics
A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples.	2017-01-25	Marc Dabad Nuria de la Iglesia Avelina Tortosa Carmen Balaña	Anna Esteve-Codina Oriol Arpi Maria Martinez-García Estela Pineda Mar Mallo Marta Gut Cristina Carrato Anna Rovira Raquel Lopez Sonia Del Barco Simon Heath Silvia Bagué Teresa Ribalta Francesc Alameda GLIOCAT Group	PLoS ONE
Two-Way Chemical Communication between Artificial and Natural Cells.	2017-01-25	Luca Belmonte Sheref S. Mansy	Roberta Lentini Noël Yeh Martín Michele Forlin Jason Fontana Michele Cornella Laura Martini Sabrina Tamburini William E Bentley Olivier Jousson	ACS Central Science
Guanylate-binding protein 1 (GBP1) contributes to the immunity of human mesenchymal stromal cells against Toxoplasma gondii.	2017-01-25	Geoff Hide De-Hua Lai Francisco J. Ayala	Aiping Qin Qifa Liu Weijun Huang Ya-Ping Wu Xiaoyong Chen Sunxing Yan Huimin Xia Zhao-Rong Lun Andy Peng Xiang	Proceedings of the National Academy of Sciences of the United States of America
Stably Expressed Genes Involved in Basic Cellular Functions.	2017-01-26	Vikrant Vijay	Kejian Wang James C Fuscoe	PLoS ONE
Epigenetic Alterations Affecting Transcription Factors and Signaling Pathways in Stromal Cells of Endometriosis	2017-01-26	Lukas Kenner	Iveta Yotova Emily Hsu Catherine Do Aulona Gaba Matthias Sczabolcs Sabine Dekan Rene Wenzl Benjamin Tycko	PLoS ONE
Molecular phenotyping of multiple mouse strains under metabolic challenge uncovers a role for Elovl2 in glucose-induced insulin secretion.	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 Mark Ibberson	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 Halil Dudakovic Farzaneh Khani Roman Thaler Farah S Ahmed Xiaodong Li Gary S Stein Martin A Montecino David R Deyle Jennifer J Westendorf Andre J van Wijnen	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 Joshua Napier Eric C Rouchka Carolyn M Klinge	Molecular and Cellular Endocrinology
MicroRNA and mRNA Transcriptome Profiling in Primary Human Astrocytes Infected with Borrelia burgdorferi	2017-01-30	Timothy Casselli Ata Abbas	Humaira Qureshi Elizabeth Peterson Danielle Perley Emily Blake Bradley Jokinen Sergei Nechaev John A Watt Archana Dhasarathy Catherine A Brissette	PLoS ONE
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 Abdul Halim Quazi Md Mosaddeque Hossen Md Zakir Hossain Rasel Ahmed Md Sabbir Hossain Shah Md Tamim Kabir Md Sarwar Alam Khan Md Mursalin Khan Rajnee Hasan Nasima Aktar Ummay Honi Rahin Islam Md Mamunur Rashid Shaobin Hou Taslima Haque Muhammad Shafiul Azam Mahdi Muhammad Moosa Sabrina M Elias A M Mahedi Hasan Niaz Mahmood Md Shafiuddin Saima Shahid Nusrat Sharmeen Shommu Sharmin Jahan Saroj Roy Amlan Chowdhury Ashikul Islam Akhand Golam Morshad Nisho Khaled Salah Uddin Taposhi Rabeya S M Ekramul Hoque Afsana Rahman Snigdha Sarowar Mortoza Syed Abdul Matin Md Kamrul Islam M Z H Lashkar Mahboob Zaman Anton Yuryev Md Kamal Uddin Md Sharifur Rahman Md Samiul Haque Md Monjurul Alam Haseena Khan Maqsudul Alam	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 Joel H Graber Luanne L Peters James J Bieker 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 Xia Zhao Jie Yang Ziwei Zhang 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
Comparative Analysis of Single-Cell RNA Sequencing Methods.	2017-02-01	Swati Parekh Beate Vieth Björn Reinius	Christoph Ziegenhain Amy Guillaumet-Adkins Martha Smets Heinrich Leonhardt Holger Heyn Ines Hellmann Wolfgang Enard	Molecular Cell
RNA-Seq Analysis of Gene Expression, Viral Pathogen, and B-Cell/T-Cell Receptor Signatures in Complex Chronic Disease.	2017-02-01	Jerome Bouquet Theodore S Steiner Charles Y. Chiu	Jennifer L Gardy Scott Brown Jacob Pfeil Ruth R Miller Muhammad Morshed Antonio Avina-Zubieta Kam Shojania Mark McCabe Shoshana Parker Miguel Uyaguari Scot Federman Patrick Tang Michael Otterstater Rob Holt Richard Moore David M Patrick Complex Chronic Disease Study Group	Clinical Infectious Diseases
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 Liang Lin Siqi Liu Elizabeth Montague Imre Janko John Choiniere Natali Kolker William S Hancock Susan Fanayan	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 Nelly Fontaine Amina Ababsa Simonetta Bandiera Tom Croonenborghs Nathalie Pochet Vito De Blasi Patrick Pessaux Tullio Piardi Daniele Sommacale Atsushi Ono Kazuaki Chayama Masashi Fujita Hidewaki Nakagawa Yujin Hoshida Mirjam B Zeisel Thomas F Baumert Joachim Lupberger	Gut
RNA-seq in kinetoplastids: A powerful tool for the understanding of the biology and host-pathogen interactions.	2017-02-04	Juan D Ramírez	Luz Helena Patino	Infection, Genetics and Evolution
A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma	2017-02-06	Gregory P Way Robert J Allaway Casey S. Greene	Stephanie J Bouley Camilo E Fadul Yolanda Sanchez	BMC Genomics
Expression map of a complete set of gustatory receptor genes in chemosensory organs of Bombyx mori.	2017-02-06	Qingyou Xia Tingcai Cheng Emmanuelle Jacquin-Joly	Huizhen Guo Zhiwei Chen Liang Jiang Youbing Guo Jianqiu Liu Shenglong Li Kiyoko Taniai Kiyoshi Asaoka Keiko Kadono-Okuda Kallare P Arunkumar Jiaqi Wu Hirohisa Kishino Huijie Zhang Rakesh K Seth Karumathil P Gopinathan Nicolas Montagné Marian R Goldsmith Kazuei Mita	Insect Biochemistry and Molecular Biology
Transcriptional regulation of male-sterility in 7B-1 male-sterile tomato mutant.	2017-02-08	Irina Mohorianu Tamas Dalmay	Vahid Omidvar Yi Zheng Zhangjun Fei Anna Pucci Andrea Mazzucato Vendula Večeřová Michaela Sedlářova Martin Fellner	PLoS ONE
RNA-seq analysis of Drosophila clock and non-clock neurons reveals neuron-specific cycling and novel candidate neuropeptides	2017-02-09	Michael Rosbash Katharine C Abruzzi	Abigail Zadina Weifei Luo Evelyn Wiyanto Reazur Rahman Fang Guo Orie Shafer	PLOS Genetics
Reduced mitochondrial activity in colonocytes facilitates AMPKα2-dependent inflammation.	2017-02-09	Melody Baddoo Harrison M Penrose	Sandra Heller 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 J Christopher Love	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
A reference gene set construction using RNA-seq of multiple tissues of Chinese giant salamander, Andrias davidianus	2017-02-15	Xiaodong Fang	Xiaofang Geng Wanshun Li Haitao Shang Qiang Gou Fuchun Zhang Xiayan Zang Benhua Zeng Jiang Li Ying Wang Ji Ma Jianlin Guo Jianbo Jian Bing Chen Zhigang Qiao Minghui Zhou Hong Wei Cunshuan Xu	GigaScience
Endometrial factors similarly induced by IFNT2 and IFNTc1 through transcription factor FOXS1	2017-02-15	Kazuya Kusama	Rulan Bai Keigo Nakamura Sayaka Okada Jiro Yasuda Kazuhiko Imakawa	PLoS ONE
Variant discovery in the sheep milk transcriptome using RNA sequencing	2017-02-15	Gwenola Tosser-Klopp Gwenola Tosser-Klopp Juan J Arranz	Aroa Suárez-Vega Beatriz Gutiérrez-Gil Christophe Klopp	BMC Genomics
RNA-Seq analysis of chikungunya virus infection and identification of granzyme A as a major promoter of arthritic inflammation	2017-02-16	Francesca Di Giallonardo Pierre Roques Andreas Suhrbier	Natalie A. Prow Wayne A. Schroder Jonathan J. Ellis Helen E. Cumming Linden J. Gearing Yee Suan Poo Adam Taylor Paul J. Hertzog Linda Hueston Roger Le Grand Bing Tang Thuy T. Le Joy Gardner Suresh Mahalingam Phillip I. Bird	PLOS Pathogens
Resolving host-pathogen interactions by dual RNA-seq.	2017-02-16	Jörg Vogel Lars Barquist	Alexander J Westermann	PLOS Pathogens
RNA-seq and metabolomic analyses of Akt1-mediated muscle growth reveals regulation of regenerative pathways and changes in the muscle secretome.	2017-02-16	Kenneth Walsh	Chia-Ling Wu Yoshinori Satomi	BMC Genomics
Transcriptional analysis of defense mechanisms in upland tetraploid switchgrass to greenbugs	2017-02-16	Scott E. Sattler	Teresa Donze-Reiner Nathan A Palmer Erin D Scully Travis J Prochaska Kyle G Koch Tiffany Heng-Moss Jeffrey D Bradshaw Paul Twigg Keenan Amundsen Gautam Sarath	BMC Plant Biology
Epigenomics of human CD8 T cell differentiation and aging.	2017-02-17	Sabine Le Saux Bin Hu David Moskowitz	David W Zhang Rolando E Yanes Zhongde Ye Jason D Buenrostro Cornelia M Weyand William J Greenleaf Jörg J Goronzy	Science immunology
Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research.	2017-02-20	Eric Peatman Geoff Waldbieser Terrence Tiersch Acacia Alcivar-Warren Wilawan Thongda Brian P Bosworth	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
Pentose sugars inhibit metabolism and increase expression of an AgrD-type cyclic pentapeptide in Clostridium thermocellum.	2017-02-23	Thomas Rydzak James G. Elkins Adam Guss Nancy Engle Timothy Tschaplinski	Tobin J Verbeke Richard J Giannone Dawn M Klingeman Steven D Brown Robert L Hettich	Scientific Reports
CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor.	2017-02-23	D Yap	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
Can milk cell or skim milk miRNAs be used as biomarkers for early pregnancy detection in cattle?	2017-02-24	Benedikt Kirchner Michael W Pfaffl	Corina I Schanzenbach Susanne E Ulbrich	PLoS ONE
MINT: a multivariate integrative method to identify reproducible molecular signatures across independent experiments and platforms	2017-02-27	Kim-Anh Lê Cao	Florian Rohart Aida Eslami Nicholas Matigian Stéphanie Bougeard Kim-Anh Lê Cao	BMC Bioinformatics
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 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 Tina Kyndt Diana Fernandez	Anne-Sophie Petitot Rana Haidar Alexis Dereeper Myriam Collin Godelieve Gheysen	Annals of Botany
Hypomorphic Pathogenic Variants in TAF13 Are Associated with Autosomal-Recessive Intellectual Disability and Microcephaly.	2017-03-01	Heinrich Sticht Igor Martianov Fulvia Ferrazzi Irwin Davidson André Reis	Hasan Tawamie Natalie Wohlfahrt Rebecca Buchert Gabrielle Mengus Steffen Uebe Luigi Janiri Franz Wolfgang Hirsch Johannes Schumacher Roberto Colombo Rami Abou Jamra	American Journal of Human Genetics
Dissecting common and divergent molecular pathways elicited by CdSe/ZnS quantum dots in freshwater and marine sentinel invertebrates.	2017-03-01	Beatriz Pelaz Abuelmagd M. Abdelmonem Angela Tino Claudia Tortiglione	Alfredo Ambrosone Modi Roopin Lisa-Maria Ackermann Lucia Mattera Mariateresa Allocca Markus Klapper Wolfgang J Parak Oren Levy	Nanotoxicology
Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq.	2017-03-01	Daniel P Cahill Itay Tirosh Orit Rozenblatt-Rosen Aviv Regev Shawn M. Gillespie Christopher W Mount Brian V. Nahed	Andrew S Venteicher Christine Hebert Keren Yizhak Cyril Neftel Mariella G Filbin Volker Hovestadt Leah E Escalante McKenzie L Shaw Christopher Rodman Danielle Dionne Christina C Luo Hiranmayi Ravichandran Ravindra Mylvaganam Maristela L Onozato Hiroaki Wakimoto William T Curry A John Iafrate Miguel N Rivera Matthew P Frosch Todd R Golub Priscilla K Brastianos Gad Getz Anoop P Patel Michelle Monje David N Louis Bradley E Bernstein 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
Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning.	2017-03-06	Daniele Ramazzotti	Bo Wang Junjie Zhu Emma Pierson Serafim Batzoglou	Nature Methods
Total RNA-seq to identify pharmacological effects on specific stages of mRNA synthesis.	2017-03-06	Sarah A Boswell Andrew Snavely	Heather M Landry L Stirling Churchman Jesse M Gray Michael Springer	Nature Chemical Biology
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 S Hahn	Lea Weber Klaudia Al-Refae Juliane Ebbert Peter Jägers Janine Altmüller Christian Becker Günter Gisselmann	PLoS ONE
Quantifying circular RNA expression from RNA-seq data using model-based framework.	2017-03-08	Tong Zhou	Musheng Li Xueying Xie Jing Zhou Mengying Sheng Xiaofeng Yin Eun-A Ko Wanjun Gu	Bioinformatics
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 Kamel Djaout Hubert F Becker Hannu Myllykallio	Alice Héliou Mireille Regnier	RNA Biology
Smooth muscle cell-specific deletion of Col15a1 unexpectedly leads to impaired development of advanced atherosclerotic lesions.	2017-03-10	Joshua T Butcher Delphine Gomez	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
Heterarchy of transcription factors driving basal and luminal cell phenotypes in human urothelium.	2017-03-10	Simon Moxon Jennifer Southgate	Carl Fishwick Janet Higgins Lawrence Percival-Alwyn Arianna Hustler Joanna Pearson Sarah Bastkowski David Swarbreck Chris D Greenman	Cell Death & Differentiation
Model-based unsupervised learning informs metformin-induced cell-migration inhibition through an AMPK-independent mechanism in breast cancer	2017-03-10	Richard Weinshilboum	Arjun P Athreya Krishna R Kalari Junmei Cairns Alan J Gaglio Quin F Wills Nifang Niu 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 Ian G Mills	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
The duplication mutation of Quebec platelet disorder dysregulates PLAU, but not C10orf55, selectively increasing production of normal PLAU transcripts by megakaryocytes but not granulocytes.	2017-03-16	Andrew D. Paterson	Catherine P M Hayward Minggao Liang Subia Tasneem Asim Soomro John S Waye Georges E Rivard Michael D Wilson	PLoS ONE
Correspondence of D. melanogaster and C. elegans developmental stages revealed by alternative splicing characteristics of conserved exons.	2017-03-16	Jingyi Jessica Li	Ruiqi Gao	BMC Genomics
Assessing the miRNA sponge potential of RUNX1T1 in t(8;21) acute myeloid leukemia.	2017-03-16	Jan Gorodkin Alexander Junge	Roza Zandi Jakob Hull Havgaard Jack Bernard Cowland	Gene
Lentinula edodes Genome Survey and Postharvest Transcriptome Analysis.	2017-03-17	Yuichi Sakamoto	Keiko Nakade Shiho Sato Kentaro Yoshida Kazuhiro Miyazaki Satoshi Natsume Naotake Konno	Applied and Environmental Microbiology
Transcriptomics Indicates Active and Passive Metronidazole Resistance Mechanisms in Three Seminal Giardia Lines.	2017-03-17	Staffan G Svärd Robin B. Gasser	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
Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors.	2017-03-20	Elise T Courtois Paul Robson	Huipeng Li Debarka Sengupta Yuliana Tan Kok Hao Chen Jolene Jie Lin Goh Say Li Kong Clarinda Chua Lim Kiat Hon Wah Siew Tan Mark Wong Paul Jongjoon Choi Lawrence J K Wee Axel M Hillmer Iain Beehuat Tan Shyam Prabhakar	Nature Genetics
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 Tallulah Andrews Kedar N Natarajan Kristina Kirschner Anthony R Green	Vladimir Yu Kiselev Michael T Schaub Andrew Yiu Tamir Chandra Wolf Reik 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 Lynn Schriml	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
RNA-sequence analysis of gene expression from honeybees (Apis mellifera) infected with Nosema ceranae.	2017-03-28	John L. Williams	Bouabid Badaoui André Fougeroux Fabien Petit Anna Anselmo Chiara Gorni Marco Cucurachi Antonella Cersini Anna Granato Giusy Cardeti Giovanni Formato Franco Mutinelli Elisabetta Giuffra Sara Botti	PLoS ONE
Top2b is involved in the formation of outer segment and synapse during late-stage photoreceptor differentiation by controlling key genes of photoreceptor transcriptional regulatory network.	2017-03-30	Ronald P Hart	Ying Li Hailing Hao Mavis R Swerdel Hyeon-Yeol Cho Ki-Bum Lee Yi Lisa Lyu Li Cai	Journal of Neuroscience Research
Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors.	2017-04-01	Aviv Regev Rahul Satija Nir Hacohen Gary Reynolds Andrew Butler Shiwei Zheng Orit Rozenblatt-Rosen	Alexandra-Chloé Villani Siranush Sarkizova Karthik Shekhar James Fletcher Morgane Griesbeck Suzan Lazo Laura Jardine David Dixon Emily Stephenson Emil Nilsson Ida Grundberg David McDonald Andrew Filby Weibo Li Philip L De Jager Andrew A Lane Muzlifah Haniffa	Science
Differentially expressed genes during spontaneous lytic switch of Marek's disease virus in lymphoblastoid cell lines determined by global gene expression profiling.	2017-04-01	Mick Watson Venugopal Nair	William N Mwangi Deepali Vasoya Lydia B Kgosana	Journal of General Virology
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 Xuan Zhang	Chenyi Xue Hanrui Zhang Jane F Ferguson Ying Wang Christine C Hinkle Mingyao Li	Physiological Genomics
Novel insights into systemic autoimmune rheumatic diseases using shared molecular signatures and an integrative analysis.	2017-04-07	Celia Greenwood	Marie Hudson Sasha Bernatsky Ines Colmegna Maximilien Lora Tomi Pastinen Kathleen Klein Oros	Epigenetics
Expression and functional assessment of candidate type 2 diabetes susceptibility genes identify four new genes contributing to human insulin secretion.	2017-04-08	Philippe Froguel Mickaël Canouil Odile Poulain-Godefroy Lorella Marselli Amar Abderrahmani Amélie Bonnefond	Fatou K Ndiaye Ana Ortalli Marlène Huyvaert Clara Salazar-Cardozo Cécile Lecoeur Marie Verbanck Valérie Pawlowski Raphaël Boutry Emmanuelle Durand Iandry Rabearivelo Olivier Sand Julie Kerr-Conte Vikash Chandra Raphaël Scharfmann Piero Marchetti François Pattou	Molecular Metabolism
CRISPR/Cas9-mediated targeted gene correction in amyotrophic lateral sclerosis patient iPSCs.	2017-04-11	Juan Carlos Izpisúa Belmonte	Lixia Wang Fei Yi Lina Fu Jiping Yang Si Wang Zhaoxia Wang Keiichiro Suzuki Liang Sun Xiuling Xu Yang Yu Jie Qiao Ze Yang Yun Yuan Jing Qu Guang-Hui Liu	Protein & cell
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
Epithelial-Mesenchymal Micro-niches Govern Stem Cell Lineage Choices.	2017-04-13	Elaine Fuchs	Hanseul Yang Rene C Adam Yejing Ge Zhong L Hua	Cell
Single-Cell RNA-Seq Analysis Maps Development of Human Germline Cells and Gonadal Niche Interactions.	2017-04-13	Fan Guo Jie Qiao	Li Li Ji Dong Liying Yan Jun Yong Xixi Liu Yuqiong Hu Xiaoying Fan Xinglong Wu Hongshan Guo Xiaoye Wang Xiaohui Zhu Rong Li Jie Yan Yuan Wei Yangyu Zhao Wei Wang Yixin Ren Peng Yuan Zhiqiang Yan Boqiang Hu Lu Wen Fuchou Tang	Cell Stem Cell
Omics and cytokine discovery in fish: Presenting the Yellowtail kingfish (Seriola lalandi) as a case study.	2017-04-14	Steve Bird Maria Forlenza	Gregory Jacobson Simon Muncaster Koen Mensink Nick Elliot Grant Broomfield Beth Signal	Developmental and Comparative Immunology
Enhanced offspring predisposition to steatohepatitis with maternal high-fat diet is associated with epigenetic and microbiome alterations	2017-04-17	Umesh Wankhade Kartik Shankar	Ying Zhong Ping Kang Maria Alfaro Sree V Chintapalli Keshari M Thakali	PLoS ONE
A Kinase-Independent Role for Cyclin-Dependent Kinase 19 in p53 Response.	2017-04-17	Robin Dowell	K Audrey Audetat Matthew D Galbraith Aaron T Odell Thomas Lee Ahwan Pandey Joaquin M Espinosa Dylan J Taatjes	Molecular and Cellular Biology
SCnorm: robust normalization of single-cell RNA-seq data.	2017-04-17	Christina Kendziorski Michael Newton Rhonda Bacher	Li-Fang Chu Ning Leng Audrey P Gasch James A Thomson Ron M Stewart	Nature Methods
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 G Duggal L Tilleman E Sutherland J Taelman M Popovic S Lierman S Chuva De Sousa Lopes A Van Soom L Peelman F Van Nieuwerburgh D I M De Coninck B Menten P Mestdagh J Van de Sompele P De Sutter B Heindryckx	Nature Communications
Genome-Wide Investigation of Biofilm Formation in Bacillus cereus.	2017-04-21	Yun Chen	Fang Yan Yiyang Yu Kevin Gozzi Jian-Hua Guo Yunrong Chai	Applied and Environmental Microbiology
Whole transcriptome profiling of the human hippocampus suggests an involvement of the KIBRA rs17070145 polymorphism in differential activation of the MAPK signaling pathway.	2017-04-22	Isabelle Schrauwen Ignazio Stefano Piras	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 Andriy Yabluchanskiy	Mira Jung Yonggang Ma Rugmani Padmanabhan Iyer Kristine Y DeLeon-Pennell Michael R Garrett	Basic Research in Cardiology
Next-Generation Sequencing Analysis and Algorithms for PDX and CDX Models.	2017-04-25	Crispin J. Miller Caroline Dive	Garima Khandelwal María Romina Girotti Christopher Smowton Sam Taylor Christopher Wirth Marek Dynowski Kristopher K Frese Ged Brady Richard Marais	Molecular Cancer Research
Effects of RNA integrity on transcript quantification by total RNA sequencing of clinically collected human placental samples.	2017-04-26	Maris Laan Kristiina Rull Siim Sõber	Mario Reiman	FASEB Journal
Poly(A)-ClickSeq: click-chemistry for next-generation 3΄-end sequencing without RNA enrichment or fragmentation.	2017-04-26	Andrew Routh	Ping Ji Elizabeth Jaworski Zheng Xia Wei Li Eric J Wagner	Nucleic Acids Research
Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways	2017-04-27	Lior Pachter Harold Pimentel Lynn Yi		PLoS ONE
miRNA-mRNA network involved in folliculogenesis interactome: systems biology approach.	2017-04-27	Ali Najafi	Abolfazl Bahrami Seyed Reza Miraie-Ashtiani Mostafa Sadeghi	Reproduction
Assessment of engineered cells using CellNet and RNA-seq.	2017-04-27	Patrick Cahan	Arthur H Radley Remy M Schwab Yuqi Tan Jeesoo Kim Emily K W Lo	Nature Protocols
Signal Transductions of BEAS-2B Cells in Response to Carcinogenic PM2.5 Exposure Based on a Microfluidic System.	2017-04-27	Jian Xu	Lulu Zheng Sixiu Liu Guoshun Zhuang Qi Liu Xinlian Zhang Congrui Deng Zhigang Guo Wang Zhao Tingna Liu Yiqi Wang Yuxiao Zhang Jing Lin Qiongzhen Wang Guodong Sui	Analytical Chemistry
Altered nucleocytoplasmic proteome and transcriptome distributions in an in vitro model of amyotrophic lateral sclerosis	2017-04-28	Jong-Il Kim	Jee-Eun Kim Yoon Ho Hong Jin Young Kim Gye Sun Jeon Jung Hee Jung Byung-Nam Yoon Sung-Yeon Son Kwang-Woo Lee Jung-Joon Sung	PLoS ONE
The Distinct Transcriptional Response of the Midgut of Amblyomma sculptum and Amblyomma aureolatum Ticks to Rickettsia rickettsii Correlates to Their Differences in Susceptibility to Infection	2017-04-28	Andréa C Fogaça Sirlei Daffre	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 Simone Lubrano Giovanni Signore Monica Evangelista Giorgio Cozza Laura Poliseno	Andrea Marranci Zhijie Jiang Marianna Vitiello Elena Guzzolino Laura Comelli Samanta Sarti Cinzia Franchin Ileabett Echevarría-Vargas Andrea Tuccoli Paolo Sportoletti Ettore Luzi Enrico Capobianco Jessie Villanueva Giorgio Arrigoni Silvia Rocchiccioli Nicholas Tsinoremas	Molecular Cancer
Gene length and detection bias in single cell RNA sequencing protocols.	2017-04-28	Alicia Oshlack Luke Zappia Belinda Phipson		F1000Research
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
Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development.	2017-05-01	Tom Maniatis Raul Rabadan	Abbas H Rizvi Pablo G Camara Elena K Kandror Thomas J Roberts Ira Schieren	Nature Biotechnology
Conditional knockin of Dnmt3a R878H initiates acute myeloid leukemia with mTOR pathway involvement.	2017-05-01	Yue-Ying Wang	Yu-Jun Dai Jin-Yan Huang Li Xia Xiao-Dong Shi Jie Xu Jing Lu Xian-Bin Su Ying Yang Wei-Na Zhang Pan-Pan Wang Song-Fang Wu Ting Huang Jian-Qing Mi Ze-Guang Han Zhu Chen Sai-Juan Chen	Proceedings of the National Academy of Sciences of the United States of America
Genomic Characterization of Murine Monocytes Reveals C/EBPβ Transcription Factor Dependence of Ly6C- Cells.	2017-05-01	Achim Leutz Franziska Paul Alexander Mildner Steffen Jung	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 Marco Osterwalder Aimée Zuniga Rolf Zeller	Frédéric Laurent Ausra Girdziusaite Julie Gamart Iros Barozzi Jennifer A Akiyama Joy Lincoln	Cell Reports
Neurons and neuronal activity control gene expression in astrocytes to regulate their development and metabolism.	2017-05-02	Alison C Todd Owen Dando Roser Masgrau Elena Galea David J Wyllie Giles E. Hardingham	Philip Hasel Zoeb Jiwaji Paul Baxter Samuel Heron Nóra M Márkus Jamie McQueen David W Hampton Megan Torvell Sachin S Tiwari Sean McKay Abel Eraso-Pichot Antonio Zorzano Siddharthan Chandran T Ian Simpson	Nature Communications
Vitamin A-Retinoic Acid Signaling Regulates Hematopoietic Stem Cell Dormancy.	2017-05-03	Michael A Rieger Oliver Stegle Timm Schroeder Andreas Trumpp	Nina Cabezas-Wallscheid Florian Buettner Pia Sommerkamp Daniel Klimmeck Luisa Ladel Frederic B Thalheimer Daniel Pastor-Flores Leticia P Roma Simon Renders Petra Zeisberger Adriana Przybylla Katharina Schönberger Roberta Scognamiglio Sandro Altamura Carolina M Florian Malak Fawaz Dominik Vonficht Melania Tesio Paul Collier Dinko Pavlinic Hartmut Geiger Vladimir Benes Tobias P Dick	Cell
Gene expression profiling in Pekin duck embryonic breast muscle.	2017-05-04	Kyle Schachtschneider	Tie-Shan Xu Li-Hong Gu Wei Huang Wan-Liang Xia Yun-Sheng Zhang Ya-Ge Zhang Guang Rong Shui-Sheng Hou	PLoS ONE
Age, gender and UV-exposition related effects on gene expression in in vivo aged short term cultivated human dermal fibroblasts	2017-05-05	Wolfgang Kaisers	Petra Boukamp Hans-Jürgen Stark Holger Schwender Julia Tigges Jean Krutmann Heiner Schaal	PLoS ONE
Connective Tissue Growth Factor Promotes Efficient Generation of Human Induced Pluripotent Stem Cell-Derived Choroidal Endothelium.	2017-05-05	Budd A. Tucker Kristan S Worthington Robert F. Mullins Edwin M. Stone	Allison E Songstad Kathleen R Chirco Joseph C Giacalone S Scott Whitmore Kristin R Anfinson Dalyz Ochoa Cathryn M Cranston Megan J Riker Maurine Neiman	Stem Cells Translational Medicine
Characterization of joining sites of a viral histone H4 on host insect chromosomes	2017-05-09	Yonggyun Kim	Sunil Kumar Jin-Kyo Jung	PLoS ONE
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
The core transcriptome of mammalian placentas and the divergence of expression with placental shape.	2017-05-12	Eviatar Nevo	Don L Armstrong Michael R McGowen Amy Weckle Priyadarshini Pantham Jason Caravas Dalen Agnew Kurt Benirschke Sue Savage-Rumbaugh Chong J Kim Günter P Wagner Roberto Romero Derek E Wildman	Placenta
RNA-seq analyses reveal that cervical spinal cords and anterior motor neurons from amyotrophic lateral sclerosis subjects show reduced expression of mitochondrial DNA-encoded respiratory genes, and rhTFAM may correct this respiratory deficiency.	2017-05-13	Nicholas J Tustison	Amy C Ladd David G Brohawn Ravindar R Thomas Paula M Keeney Stuart S Berr Shaharyar M Khan Francisco R Portell Meiram Zh Shakenov Patrick F Antkowiak Bijoy Kundu James P Bennett	Brain Research
Sexual Dimorphism and Retinal Mosaic Diversification Following the Evolution of a Violet Receptor in Butterflies.	2017-05-15	Adriana D Briscoe Peter Andolfatto	Kyle J McCulloch Furong Yuan Ying Zhen Matthew L Aardema Gilbert Smith Jorge Llorente-Bousquets	Molecular Biology and Evolution
Elevated PTTG and PBF predicts poor patient outcome and modulates DNA damage response genes in thyroid cancer.	2017-05-15	Martin L. Read	J C Fong B Modasia A Fletcher W Imruetaicharoenchoke R J Thompson H Nieto J J Reynolds A Bacon U Mallick A Hackshaw J C Watkinson K Boelaert A S Turnell C J McCabe	Oncogene
Isolation of tissues and preservation of RNA from intact, germinated barley grain. </