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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
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome	2008-07-03	Stefan Haas	Marc Sultan Marcel H Schulz Hugues Richard Alon Magen Andreas Klingenhoff Matthias Scherf Martin Seifert Tatjana Borodina Aleksey Soldatov Dmitri Parkhomchuk Dominic Schmidt Sean O'Keeffe Martin Vingron Hans Lehrach Marie-Laure Yaspo	Science
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays	2008-09	Yoav Gilad John C Marioni	Christopher E Mason Shrikant M Mane Matthew Stephens	Genome Research
Transcript length bias in RNA-seq data confounds systems biology	2009	Alicia Oshlack Matthew Wakefield		Biology Direct
RNA-Seq: a revolutionary tool for transcriptomics	2009-01	Mark Bender Gerstein	Zhong Wang Michael Snyder	Nature Reviews Genetics
Estimating accuracy of RNA-Seq and microarrays with proteomics	2009-04-16	Wei Chen	Xing Fu Ning Fu Song Guo Zheng Yan Ying Xu Hao Hu Corinna Menzel Yixue Li Rong Zeng Philipp Khaitovich	BMC Genomics
TopHat: discovering splice junctions with RNA-Seq	2009-05-01	Steven Salzberg Lior Pachter	Cole Trapnell	Bioinformatics
A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi.	2009-07-17	Julian Parkhill Paul P. Gardner Jyoti Choudhary Nicholas Thomson	Timothy T Perkins Robert A Kingsley Maria C Fookes Keith D James Lu Yu Samuel A Assefa Miao He Nicholas J Croucher Derek J Pickard Duncan J Maskell Gordon Dougan	PLOS Genetics
A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos.	2009-09-01	Simon J van Heeringen Gert Jan C Veenstra	Robert C Akkers Ulrike G Jacobi Eva M Janssen-Megens Kees-Jan Françoijs Hendrik G Stunnenberg	Developmental Cell
Identifiability of isoform deconvolution from junction arrays and RNA-Seq.	2009-09-16	Hui Jiang	David Hiller Weihong Xu Wing Hung Wong	Bioinformatics
Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts.	2009-10-16	Chad Nusbaum	Joshua Z Levin Michael F Berger Xian Adiconis Peter Rogov Alexandre Melnikov Timothy Fennell Levi A Garraway Andreas Gnirke	Genome Biology
Transcript quantification with RNA-Seq data.	2009-10-19	Gunnar Rätsch	Regina Bohnert Jonas Behr	BMC Bioinformatics
DEGseq: an R package for identifying differentially expressed genes from RNA-seq data.	2009-10-24	Likun Wang Xi Wang	Zhixing Feng Xiaowo Wang Xuegong Zhang	Bioinformatics
RNA-seq: from technology to biology.	2009-10-27 2010-02-01	Jürg Bähler	Samuel Marguerat Jürg Bähler	Cellular and Molecular Life Sciences
GenomeRNAi: a database for cell-based RNAi phenotypes. 2009 update.	2009-11-12	M Boutros	Moritz Gilsdorf Thomas Horn Zeynep Arziman Oliver Pelz Evgeny Kiner	Nucleic Acids Research
Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome.	2009-11-18	Cynthia Sharma Jörg Vogel Richard Reinhardt	Marco Albrecht 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 Uri Keich	Haley F Oliver Renato H Orsi Lalit Ponnala 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
From RNA-seq reads to differential expression results	2010 2010-12-22	Alicia Oshlack Mark D. Robinson	Matthew D Young	Genome Biology
A scaling normalization method for differential expression analysis of RNA-seq data	2010	Alicia Oshlack Mark D. Robinson		Genome Biology
Global and unbiased detection of splice junctions from RNA-seq data	2010	Ulf Gyllensten Adam Ameur	Anna Wetterbom Lars Feuk	Genome Biology
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
Next-generation sequencing	2010-01-01	Jonathan Arnold	Momiao Xiong Zhongming Zhao Fuli Yu	Journal of Biomedicine and Biotechnology
Defining transcribed regions using RNA-seq.	2010-01-21	Jürg Bähler	Brian T Wilhelm Samuel Marguerat Ian Goodhead Jürg Bähler	Nature Protocols
Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life	2010-01-26	Mark Johnston Antonis Rokas	Chris Todd Hittinger John T Tossberg	Proceedings of the National Academy of Sciences of the United States of America
Characterization of transcriptional complexity during berry development in Vitis vinifera using RNA-Seq.	2010-01-29	Luciano Xumerle Giovanni Malerba Diana Bellin	Sara Zenoni Alberto Ferrarini Enrico Giacomelli Marianna Fasoli Mario Pezzotti Massimo Delledonne	Plant Physiology
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 Jacob Lemieux Bart Barrell 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
Close association of RNA polymerase II and many transcription factors with Pol III genes	2010-02-05	Mark Bender Gerstein	Debasish Raha Zhong Wang Zarmik Moqtaderi Linfeng Wu Guoneng Zhong Kevin Struhl Michael Snyder	Proceedings of the National Academy of Sciences of the United States of America
Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments.	2010-02-11	Marie-Laure Yaspo Stefan Haas Hans Lehrach Martin Vingron	Hugues Richard Marcel H Schulz Marc Sultan Asja Nürnberger Sabine Schrinner Daniela Balzereit Emilie Dagand Axel Rasche 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 Richard Reinhardt	Steve Hoffmann Jérémy Reignier Sven Findeiss Alexandra Sittka Sandrine Chabas	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 Karsten Kristiansen Huanming Yang Jian Wang Xiuqing Zhang	Guangwu Guo Xueda Hu Yong Zhang Ruiqiang Li Ruhong Zhuang Zhike Lu Zengquan He Xiaodong Fang Li Chen Wei Tian Yong Tao Songgang Li	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 Matthew Meyerson Stacey Gabriel	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 David B Jaffe 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
Detection of splice junctions from paired-end RNA-seq data by SpliceMap.	2010-04-05	Hui Jiang	Kin Fai Au Lan Lin Yi Xing Wing Hung Wong	Nucleic Acids Research
Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites	2010-04-12	Tim Nicolai Siegel	Doeke R Hekstra Xuning Wang Scott Dewell George A M Cross	Nucleic Acids Research
Supersplat--spliced RNA-seq alignment.	2010-04-21	Weng-Keen Wong	Douglas W Bryant Rongkun Shen Henry D Priest Todd C Mockler	Bioinformatics
Bacillus anthracis genome organization in light of whole transcriptome sequencing	2010-04-29	Karla D Passalacqua	Jeffrey Martin Wenhan Zhu Nicholas Bergman Mark Borodovsky	BMC Bioinformatics
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation	2010-05	Steven Salzberg Lior Pachter	Cole Trapnell Brian A Williams Geo Pertea Ali Mortazavi Gordon Kwan Marijke J van Baren Barbara J Wold	Nature Biotechnology
Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis.	2010-05-01	Azim Surani	Fuchou Tang Catalin Barbacioru Siqin Bao Caroline Lee Ellen Nordman Xiaohui Wang Kaiqin Lao	Cell Stem Cell
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs	2010-05-02	J Z Levin Magdalena J Koziol John L. Rinn	Mitchell Guttman Manuel Garber Julie Donaghey James Robinson Xian Adiconis Lin Fan Andreas Gnirke Chad Nusbaum Eric S Lander Aviv Regev	Nature Biotechnology
A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling	2010-05-05	James R. Bradford Crispin J. Miller	Yvonne Hey Tim Yates Yaoyong Li Stuart D Pepper	BMC Genomics
Modeling non-uniformity in short-read rates in RNA-Seq data	2010-05-11	Jun Li	Hui Jiang Wing Hung Wong	Genome Biology
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
rQuant.web: a tool for RNA-Seq-based transcript quantitation	2010-06-15	Gunnar Rätsch	Regina Bohnert	Nucleic Acids Research
Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays.	2010-06-17	Andrea Sboner Joel Rozowsky Mark Bender Gerstein Valerie Reinke	Ashish Agarwal David Koppstein Lukas Habegger Ladeana W Hillier Rajkumar Sasidharan Robert H Waterston	BMC Genomics
A probabilistic framework for aligning paired-end RNA-seq data	2010-06-23	Derek Y Chiang	Yin Hu Kai Wang Xiaping He Jan F Prins Jinze Liu	Bioinformatics
Uncovering the complexity of transcriptomes with RNA-Seq.	2010-06-27	Valerio Costa Claudia Angelini Italia DeFeis	Alfredo Ciccodicola	Journal of Biomedicine and Biotechnology
Transcriptome and targetome analysis in MIR155 expressing cells using RNA-seq	2010-06-28	Dale Hedges Erik K Flemington	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	RNA
RNA-seq analysis of sulfur-deprived Chlamydomonas cells reveals aspects of acclimation critical for cell survival.	2010-06-29	David Casero Sabeeha Merchant Matteo Pellegrini	David González-Ballester Shawn Cokus Arthur R Grossman	The Plant Cell
Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq.	2010-07-01	Mehmet Somel Wei Chen Augix Guohua Xu Svante Pääbo	Liu He Zhongshan Li Ying Xu Mingfeng Li Xing Fu Zheng Yan Yuan Yuan Corinna Menzel Na Li Hao Hu Philipp Khaitovich	PLOS Computational Biology
Adaptive Changes in Mycobacterium avium Gene Expression Profile Following Infection of Genetically Susceptible and Resistant Mice.	2010-07-01	Timofey Skvortsov	D V Ignatov K B Majorov A S Apt T L Azhikina	Acta naturae
Next-generation sequencing techniques for eukaryotic microorganisms: sequencing-based solutions to biological problems.	2010-07-02	Minou Nowrousian	Minou Nowrousian	Eukaryotic Cell
Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq.	2010-07-13	Guojun Lu Bin Han	Tingting Lu Danlin Fan Chuanrang Zhu Wei Li Qiang Zhao Qi Feng Yan Zhao Yunli Guo Wenjun Li Xuehui Huang	Genome Research
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
Transcriptome sequencing, microarray, and proteomic analyses reveal cellular and metabolic impact of hepatitis C virus infection in vitro.	2010-08-01	Paul Klenerman	Stephen D Woodhouse Ramamurthy Narayan Sally Latham Sheena Lee Robin Antrobus Bevin Gangadharan Shujun Luo Gary P Schroth Nicole Zitzmann	Hepatology
RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome	2010-08-05	Michelle Graham Gary J Muehlbauer	Andrew J Severin Jenna L Woody Yung-Tsi Bolon Bindu Joseph Brian W Diers Andrew D Farmer Rex T Nelson David Grant James E Specht Steven B Cannon Gregory D May Carroll P Vance Randy C Shoemaker	BMC Plant Biology
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
MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.	2010-08-27	Charles M. Perou Piotr A Mieczkowski Derek Y Chiang	Kai Wang Darshan Singh Zheng Zeng Stephen J Coleman Yan Huang Gleb L Savich Xiaping He Sara A Grimm James N MacLeod Jan F Prins Jinze Liu	Nucleic Acids Research
Comparison between NuGEN's WT-Ovation Pico and one-direct amplification systems.	2010-09-01	Lauren McIntyre	Alison M Morse Valentina Carballo Donald A Baldwin Christopher G Taylor	Journal of Biomolecular Techniques
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 Alexander Meissner	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 Marco A Marra Martin Hirst Aleksandar Milosavljevic Joseph F Costello	Nature Biotechnology
Statistical Issues in the Analysis of ChIP-Seq and RNA-Seq Data.	2010-09-27	Zhaohui Steve Qin	Debashis Ghosh	Genes
Studying bacterial transcriptomes using RNA-seq.	2010-09-29 2010-10-01	Nicholas Thomson	Nicholas J Croucher	Current Opinion in Microbiology
Single molecule sequencing with a HeliScope genetic analysis system	2010-10-01	John F Thompson	Kathleen E Steinmann	Current protocols in molecular biology
De novo assembly and analysis of RNA-seq data.	2010-10-10	Shaun Jackman Malachi Griffith Timothee Cezard Steven Jones Pamela A. Hoodless Inanc Birol	Gordon Robertson Jacqueline Schein Readman Chiu Richard Corbett Matthew Field Karen Mungall Sam Lee Hisanaga Mark Okada Jenny Q Qian Anthony Raymond Nina Thiessen Yaron S Butterfield Richard Newsome Simon K Chan Rong She Richard Varhol Baljit Kamoh Anna-Liisa Prabhu Angela Tam YongJun Zhao Richard A Moore Martin Hirst Marco A Marra	Nature Methods
Quantitative and qualitative RNA-Seq-based evaluation of Epstein-Barr virus transcription in type I latency Burkitt's lymphoma cells.	2010-10-13	Erik K Flemington	Zhen Lin Guorong Xu Nan Deng Christopher Taylor Dongxiao Zhu	Journal of Virology
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
The RNA-Seq approach to studying the expression of mosquito mitochondrial genes.	2010-10-19	Gareth J Lycett	M Neira-Oviedo A Tsyganov-Bodounov V Kokoza A S Raikhel J Krzywinski	Insect Molecular Biology
RNA-seq analysis of 2 closely related leukemia clones that differ in their self-renewal capacity.	2010-10-27	Geneviève Boucher	Brian T Wilhelm Mathieu Briau Pamela Austin Amélie Faubert Pierre Chagnon Kristin Hope Simon Girard Nadine Mayotte Josette-Renee Landry Josée Hébert Guy Sauvageau	Blood
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 Mark Bender Gerstein	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	Genome Research
SNP discovery in the bovine milk transcriptome using RNA-Seq technology	2010-11-06	Alma Islas-Trejo	Angela Cánovas Gonzalo Rincon Saumya Wickramasinghe Juan F Medrano	Mammalian Genome
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
Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads	2010-11-24	Gavin Sherlock Matthew Blow	Jeffrey Martin Vincent M Bruno Zhide Fang Xiandong Meng Tao Zhang Michael Snyder Zhong Wang	BMC Genomics
Scaffolding a Caenorhabditis nematode genome with RNA-seq	2010-12	Erich M Schwarz Paul W. Sternberg	Ali Mortazavi Brian Williams Lorian Schaeffer Igor Antoshechkin Barbara J Wold	Genome Research
RNA-Seq Read Alignments with PALMapper	2010-12	Gunnar Rätsch	Géraldine Jean André Kahles Vipin T. Sreedharan Fabio De Bona
Defining the transcriptome and proteome in three functionally different human cell lines.	2010-12-01	Cajsa Algenäs Daniel Klevebring Linn Fagerberg Ivan Matic Mathias Uhlén	Emma Lundberg Tamar Geiger Juergen Cox Cajsa Algenäs Joakim Lundeberg Matthias Mann	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
Isoform abundance inference provides a more accurate estimation of gene expression levels in RNA-seq.	2010-12-01	Xi Wang	Zhengpeng Wu Xuegong Zhang	Journal of Bioinformatics and Computational Biology
De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-seq technology	2010-12-02	Jacob E. Crawford	Wamdaogo M Guelbeogo Antoine Sanou Alphonse Traoré Kenneth D Vernick N'Fale Sagnon Brian P Lazzaro	PLOS ONE
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 Joakim Lundeberg	BMC Genomics
RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries.	2010-12-05	Andrea Sboner Joel Rozowsky Mark Bender Gerstein	Lukas Habegger Tara A Gianoulis Ashish Agarwal Michael Snyder	Bioinformatics
The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment.	2010-12-14	Alexey I Nesvizhskii	Kang Ning	BMC Bioinformatics
A dual platform approach to transcript discovery for the planarian Schmidtea mediterranea to establish RNAseq for stem cell and regeneration biology	2010-12-14	Aziz A. Aboobaker	Martin J Blythe Damian Kao Sunir Malla Joanna Rowsell Ray Wilson Deborah Evans Jamie Jowett Amy Hall Virginie Lemay Sabrina Lam	PLOS ONE
H2A.Z demarcates intergenic regions of the plasmodium falciparum epigenome that are dynamically marked by H3K9ac and H3K4me3	2010-12-16	Richard Bartfai Arne H Smits Moritz Treeck	Wieteke A M Hoeijmakers Adriana M Salcedo-Amaya Eva Janssen-Megens Anita Kaan Tim-Wolf Gilberger Kees-Jan Françoijs Hendrik G Stunnenberg	PLOS Pathogens
Comparison of transcriptomic landscapes of bovine embryos using RNA-Seq	2010-12-17	Wen Huang	Hasan Khatib	BMC Genomics
Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq.	2010-12-17	Xi Wang	Zhengpeng Wu Xuegong Zhang	Bioinformatics
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
Polycomb preferentially targets stalled promoters of coding and noncoding transcripts	2010-12-22	Moritz Gerstung	Daniel Enderle Christian Beisel Michael B Stadler Prashanth Athri Renato Paro	Genome Research
miR-191 regulates mouse erythroblast enucleation by down-regulating Riok3 and Mxi1.	2010-12-31	Johan Flygare Harvey Lodish	Lingbo Zhang Piu Wong Bing Lim	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
RNA-seq analyses of blood-induced changes in gene expression in the mosquito vector species, Aedes aegypti	2011	Mariangela Bonnizoni Osvaldo Marinotti	W Augustine Dunn Corey L Campbell Ken E Olson Michelle T Dimon Anthony A James	BMC Genomics
Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans	2011	Matthew Berriman Karen Mungall Gary Saunders Anna V Protasio Martin Hunt Roz Laing Michael Andrew Quail	Steven Laing Frank Jackson Robin Beech John S Gilleard	PLOS ONE
The post-apoptotic fate of RNAs identified through high-throughput sequencing of human hair	2011	Benjamin Yu	Gloria K Lefkowitz Anandaroop Mukhopadhyay Christopher Cowing-Zitron	PLOS ONE
A low-cost library construction protocol and data analysis pipeline for Illumina-based strand-specific multiplex RNA-seq	2011	Thomas Brutnell	Lin Wang Yaqing Si Lauren K Dedow Ying Shao Peng Liu	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 Hiram Clawson Ann S Zweig	Brian J Raney Melissa S Cline Kate R Rosenbloom Timothy R Dreszer Katrina Learned Galt P Barber Laurence R Meyer Cricket A Sloan Krishna M Roskin Bernard B Suh Vanessa Kirkup Pauline A Fujita Brooke Rhead Kayla E Smith Andy Pohl Robert M Kuhn W James Kent	Nucleic Acids Research
Insights into global mechanisms and disease by gene expression profiling.	2011-01-01	Hubert Hackl Johannes Rainer Ana Dopazo	Fátima Sánchez-Cabo Zlatko Trajanoski	Methods in Molecular Biology
Identifying mRNA editing deaminase targets by RNA-Seq.	2011-01-01	Nina Papavasiliou	Brad R Rosenberg Scott Dewell F Nina Papavasiliou	Methods in Molecular Biology
The NBP Negative Binomial Model for Assessing Differential Gene Expression from RNA-Seq	2011-01-12	Jeff H. Chang	Yanming Di Daniel W Schafer Jason S Cumbie	Statistical Applications in Genetics and Molecular Biology
A pipeline for RNA-seq data processing and quality assessment	2011-01-13	Alvis Brazma Angela Goncalves	Andrew Tikhonov Misha Kapushesky	Bioinformatics
RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts	2011-01-17	Katherine Lontok	Michelle T Dimon Joseph L DeRisi	Nucleic Acids Research
Length bias correction for RNA-seq data in gene set analyses	2011-01-19	Xiangqin Cui	Liyan Gao Zhide Fang Kui Zhang Degui Zhi	Bioinformatics
Identification of fusion genes in breast cancer by paired-end RNA-sequencing.	2011-01-19	Olli-Pekka Kallioniemi Anne-Lise Børresen-Dale Sara Kangaspeska Vesa Hongisto Kristine Kleivi	Henrik Edgren Astrid Murumagi Sara Kangaspeska Daniel Nicorici Vesa Hongisto Inga H Rye Sandra Nyberg Maija Wolf	Genome Biology
Understanding the pathogenesis of Alzheimer's disease: will RNA-Seq realize the promise of transcriptomics?	2011-01-19	Greg T. Sutherland Jillian J. Kril	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 Zhanjiang Liu	Zunchun Zhou Jianguo Lu Fanyue Sun Hong Liu Yanliang Jiang	BMC Genomics
Augmented annotation of the Schizosaccharomyces pombe genome reveals additional genes required for growth and viability.	2011-01-26	Agnes Grallert Valerie Wood Iain M. Hagan Crispin J. Miller	Danny A Bitton Paul J Scutt Tim Yates Duncan L Smith	Genetics
In vitro culture and characterization of putative porcine embryonic germ cells derived from domestic breeds and Yucatan mini pig embryos at Days 20-24 of gestation.	2011-01-31	Hendrik Marks Yu Gao Poul Hyttel	Stoyan G Petkov Tino Klein Rodrigo S Garcia Henk Stunnenberg	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	Jochen Wolf Jarosław Bryk	Jochen Bw Wolf	BMC Genomics
The next generation: using new sequencing technologies to analyse gene regulation.	2011-02-01	Olivia Alder Pamela A. Hoodless	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 S E Lott	Jacqueline E Villalta Gary P Schroth Shujun Luo Leath A Tonkin	PLOS Biology
Identification and optimization of small molecules that restore E-cadherin expression and reduce invasion in colorectal carcinoma cells.	2011-02-09	Robert Daniel Beauchamp Craig W Lindsley	Sydney L Stoops A Scott Pearson Connie Weaver Alex G Waterson Emily Days Chris Farmer Suzanne Brady C David Weaver	ACS Chemical Biology
Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads.	2011-02-10	Ernest Turro Angela Goncalves Lachlan Coin Sylvia Richardson Alexandra M. Lewin	Shu-Yi Su	Genome Biology
Isoform-level microRNA-155 target prediction using RNA-seq	2011-02-11	Erik K Flemington	Nan Deng Adriane Puetter Kun Zhang Kristen Johnson Zhiyu Zhao Christopher Taylor Dongxiao Zhu	Nucleic Acids Research
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 Olivier Harismendy	Marcus Kinsella Masakazu Nakano Kelly A Frazer	Bioinformatics
Targeted disruption of py235ebp-1: invasion of erythrocytes by Plasmodium yoelii using an alternative Py235 erythrocyte binding protein.	2011-02-17	Thomas D Otto Arnab Pain Anthony A Holder Rita Tewari	Solabomi A Ogun Steven A Howell Ellen Knuepfer Deirdre A Cunningham Zhengyao Xu	PLOS Pathogens
RNA-seq reveals cooperative metabolic interactions between two termite-gut spirochete species in co-culture	2011-02-17	Avigdor Eldar	Adam Z Rosenthal Eric G Matson Jared R Leadbetter	The ISME Journal
ACT: aggregation and correlation toolbox for analyses of genome tracks.	2011-02-23	Joel Rozowsky Kevin Y Yip Lucas Lochovsky	Justin Jee Robert Bjornson Guoneng Zhong Zhengdong Zhang Yutao Fu Jie Wang Zhiping Weng Mark Gerstein	Bioinformatics
Method for improved Illumina sequencing library preparation using NuGEN Ovation RNA-Seq System.	2011-03-01	Traver Hart	Steven R Head H Kiyomi Komori John Shimashita Lana Schaffer Daniel R Salomon Phillip T Ordoukhanian	BioTechniques
Accurate estimation of expression levels of homologous genes in RNA-seq experiments.	2011-03-01	Bogdan Pasaniuc Noah Zaitlen	Eran Halperin	Journal of Computational Biology
The carbonic anhydrase isoforms of Chlamydomonas reinhardtii: intracellular location, expression, and physiological roles.	2011-03-02	Bratati Mukherjee	James V Moroney Yunbing Ma Wesley D Frey Katelyn A Fusilier Trang T Pham Tiffany A Simms Robert J DiMario Jing Yang	Photosynthesis Research
Improving RNA-Seq expression estimates by correcting for fragment bias.	2011-03-16	Lior Pachter John L. Rinn	Adam Roberts Cole Trapnell Julie Donaghey	Genome Biology
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
A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii.	2011-03-21	Sabeeha Merchant Matteo Pellegrini David Casero	Janette Kropat Anne Hong-Hermesdorf Petr Ent Madeli Castruita Davin Malasarn	The Plant Journal
ExpEdit: a webserver to explore human RNA editing in RNA-Seq experiments.	2011-03-22	Graziano Pesole Ernesto Picardi	Mattia D'Antonio Danilo Carrabino Tiziana Castrignanò	Bioinformatics
Composite transcriptome assembly of RNA-seq data in a sheep model for delayed bone healing	2011-03-24	Peter Robinson Stefan Mundlos	Marten Jäger Claus-Eric Ott Johannes Grünhagen Jochen Hecht Hanna Schell Stefan Mundlos Georg N Duda Jasmin Lienau	BMC Genomics
Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays	2011-03-24	Nicole A Walter Jessica Ezzell Hunter Michael A Mooney Shannon K McWeeney	Daniel Bottomly Priscila Darakjian Sunita Kawane Kari J Buck Robert P Searles Robert Hitzemann	PLOS ONE
Effects of nickel treatment on H3K4 trimethylation and gene expression.	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
Genome-wide analysis of the 5' and 3' ends of vaccinia virus early mRNAs delineates regulatory sequences of annotated and anomalous transcripts.	2011-04-13	Bernard Moss	Zhilong Yang Daniel P Bruno Craig A Martens Stephen F Porcella	Journal of Virology
A multiplex RNA-seq strategy to profile poly(A+) RNA: application to analysis of transcription response and 3' end formation.	2011-04-15	Jeremy Davis-Turak Yu Zhou	Kristi Fox-Walsh Hairi Li Xiang-Dong Fu	Genomics
Design and validation issues in RNA-seq experiments.	2011-04-15	Xiangqin Cui	Zhide Fang	Briefings in Bioinformatics
Systems biology approach in Chlamydomonas reveals connections between copper nutrition and multiple metabolic steps.	2011-04-15	David Casero Sabeeha Merchant Matteo Pellegrini Astrid Vieler Christoph Benning	Madeli Castruita Steven J Karpowicz Janette Kropat Scott I Hsieh Weihong Yan Shawn Cokus Joseph A Loo	The Plant Cell
Estimation of alternative splicing isoform frequencies from RNA-Seq data	2011-04-19	Ion I. Mandoiu Alexander Zelikovsky	Marius Nicolae Serghei Mangul	Algorithms for Molecular Biology
Massive-scale RNA-Seq analysis of non ribosomal transcriptome in human trisomy 21.	2011-04-20	Luciana D'Apice Aldo Donizetti Monica Rienzo Paola Salvatore Stefania Crispi Valerio Costa Piergiuseppe De Berardinis Teresa Infante Claudia Angelini Marco Picardi Berardo Sarubbi Raffaele Calabrò Claudio Napoli Amelia Casamassimi	Margherita Mutarelli Linda Sommese Maria Assunta Gallo Marianna Aprile Roberta Esposito Luigi Leone Alfredo Ciccodicola	PLOS ONE
BM-map: Bayesian mapping of multireads for next-generation sequencing data.	2011-04-22	Yuan Yuan Han Liang	Yuan Ji Yanxun Xu Qiong Zhang Kam-Wah Tsui Clift Norris Shoudan Liang	Biometrics
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
FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq.	2011-05-05	Jeremy Chien Jian Ma	Yang Li David I Smith	Bioinformatics
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
Detecting copy number status and uncovering subclonal markers in heterogeneous tumor biopsies.	2011-05-11	Antonella Bacchiocchi	Fabio Parisi Stephan Ariyan Deepak Narayan Kathleen Hoyt Elaine Cheng Fang Xu Peining Li Ruth Halaban Yuval Kluger	BMC Genomics
The sensitivity of massively parallel sequencing for detecting candidate infectious agents associated with human tissue	2011-05-13	Curtis A. Suttle Julia A Gustavsen Jan M Friedman Robert A Holt	Richard A Moore René L Warren J Douglas Freeman Caroline Chénard Yongjun Zhao	PLOS ONE
NSMAP: a method for spliced isoforms identification and quantification from RNA-Seq.	2011-05-16	Zheng Xia	Jianguo Wen Chung-Che Chang Xiaobo Zhou	BMC Bioinformatics
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
Genome-wide RNA-seq analysis of human and mouse platelet transcriptomes.	2011-05-19	A S Weyrich	Jesse W Rowley Andrew J Oler Neal D Tolley Benjamin N Hunter Elizabeth N Low David A Nix Christian C Yost Guy A Zimmerman	Blood
The zebrafish transcriptome during early development.	2011-05-24	Juha Kere Outi Hovatta Liselotte Vesterlund	Hong Jiao Per Unneberg Outi Hovatta	BMC Developmental Biology
Transcriptome profiling of chemosensory appendages in the malaria vector Anopheles gambiae reveals tissue- and sex-specific signatures of odor coding	2011-05-27	Antonis Rokas Laurence J. Zwiebel	R Jason Pitts David C Rinker Patrick L Jones	BMC Genomics
Pyrosequencing-based expression profiling and identification of differentially regulated genes from Manduca sexta, a lepidopteran model insect.	2011-05-27	Haobo Jiang	Shuguang Zhang Ramesh T Gunaratna Xiufeng Zhang Fares Najar Yang Wang Bruce Roe	Insect Biochemistry and Molecular Biology
Megakaryocytes differentially sort mRNAs for matrix metalloproteinases and their inhibitors into platelets: a mechanism for regulating synthetic events.	2011-05-31	Loredana Bury A S Weyrich Paolo Gresele	Luca Cecchetti Neal D Tolley Noemi Michetti	Blood
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
RNA-seq: technical variability and sampling.	2011-06-06	Lauren McIntyre	Kenneth K Lopiano Alison M Morse Victor Amin Ann L Oberg Linda J Young Sergey V Nuzhdin	BMC Genomics
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 Renata Pasqualini	Elisa Napolitano Ferreira Gustavo de Campos Molina Renato David Puga Eduardo Fernandes Abrantes Adriana Priscila Trapé Bedrich L Eckhardt Diana Noronha Nunes Maria Mitzi Brentani Wadih Arap Ricardo Renzo Brentani	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
Transcription factor TEAD4 regulates expression of myogenin and the unfolded protein response genes during C2C12 cell differentiation	2011-06-24	Gabrielle Mengus Irwin Davidson	A Benhaddou C Keime T Ye A Morlon I Michel B Jost	Cell Death & Differentiation
Directional RNA deep sequencing sheds new light on the transcriptional response of Anabaena sp. strain PCC 7120 to combined-nitrogen deprivation.	2011-06-28	Filip Van Nieuwerburgh James W Golden	Britt L Flaherty Steven R Head	BMC Genomics
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	Genome Research
Full-length transcriptome assembly from RNA-Seq data without a reference genome	2011-07	Kerstin Lindblad-Toh Aviv Regev Chad Nusbaum Andreas Gnirke Evan Mauceli Nir Friedman Nicholas Rhind Nir Hacohen Raktima Raychowdhury	Manfred G Grabherr Brian J Haas Moran Yassour Joshua Z Levin Dawn A Thompson Ido Amit Xian Adiconis Lin Fan Raktima Raychowdhury Qiandong Zeng Zehua Chen Federica di Palma Bruce W Birren	Nature Biotechnology
Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling.	2011-07-01	Paweł P Łabaj Steven Wiley D Kreil	Germán G Leparc Bryan E Linggi Lye Meng Markillie	Bioinformatics
Global transcriptome changes underlying colony growth in the opportunistic human pathogen Aspergillus fumigatus.	2011-07-01	Antonis Rokas	John G Gibbons Anne Beauvais Remi Beau Kriston L McGary Jean-Paul Latgé	Eukaryotic Cell
Exploring the Schistosoma mansoni adult male transcriptome using RNA-seq.	2011-07-02	Ricardo DeMarco Sergio Verjovski-Almeida	Giulliana Tessarin Almeida Murilo Sena Amaral Felipe Cesar Ferrarezi Beckedorff João Paulo Kitajima	Experimental Parasitology
An efficient approach to finding Siraitia grosvenorii triterpene biosynthetic genes by RNA-seq and digital gene expression analysis.	2011-07-05	Iain W Wilson	Qi Tang Xiaojun Ma Changming Mo Cai Song Huan Zhao Yanfang Yang Wei Fu Deyou Qiu	BMC Genomics
A comparative analysis of DNA methylation across human embryonic stem cell lines.	2011-07-06	Matteo Pellegrini	Pao-Yang Chen Suhua Feng Jong Wha Joanne Joo Steve E Jacobsen	Genome Biology
SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data	2011-07-07	Tak-Wah Lam	Songbo Huang Jinbo Zhang Ruiqiang Li Wenqian Zhang Zengquan He Zhiyu Peng Siu-Ming Yiu	Frontiers in Genetics
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 Sabeeha Merchant	David Lopez Shawn J Cokus	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
Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM).	2011-07-19	Angel Pizarro Gregory R Grant Eric A Pierce	Michael H Farkas Nicholas F Lahens Jonathan Schug Brian P Brunk Christian J Stoeckert John B Hogenesch	Bioinformatics
RseqFlow: workflows for RNA-Seq data analysis.	2011-07-27	Ewa Deelman	Ying Wang Gaurang Mehta Rajiv Mayani Jingxi Lu Tade Souaiaia Yangho Chen Andrew Clark Hee Jae Yoon Lin Wan Oleg V Evgrafov James A Knowles Ting Chen	Bioinformatics
Detection of splicing events and multiread locations from RNA-seq data based on a geometric-tail (GT) distribution of intron length	2011-07-27	Jing Woei Li Stephen Kwok-Wing Tsui T F Chan	Shao-Ke Lou Hao Qin Aldrin Kay-Yuen Yim Leung-Yau Lo Bing Ni Kwong-Sak Leung	BMC Bioinformatics
ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data.	2011-07-28	Tom Maniatis Brad Friedman		Genome Biology
Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure.	2011-07-29	Mikhail Matz	E Meyer G V Aglyamova	Molecular Ecology
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
RNA-Seq-based monitoring of infection-linked changes in Vibrio cholerae gene expression.	2011-08-01	Jennifer M Ritchie	Anjali Mandlik Jonathan Livny William P Robins John J Mekalanos Matthew K Waldor	Cell Host & Microbe
AlleleSeq: analysis of allele-specific expression and binding in a network framework.	2011-08-02	Yong Kong Alexej Abyzov Joel Rozowsky Mark Rubin Mark Bender Gerstein	Jing Wang Pedro Alves Debasish Raha Arif Harmanci Jing Leng Robert Bjornson Naoki Kitabayashi Nitin Bhardwaj Michael Snyder	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
Quantitative RNA-seq analysis of the Campylobacter jejuni transcriptome	2011-08-04	Paul P. Gardner Roy R Chaudhuri Jyoti Choudhary	Lu Yu Alpa Kanji Timothy T Perkins Duncan J Maskell Andrew J Grant	Microbiology
RNA-seq discovery, functional characterization, and comparison of sesquiterpene synthases from Solanum lycopersicum and Solanum habrochaites trichomes	2011-08-05	Eran Pichersky	Petra M Bleeker Eleni A Spyropoulou Paul J Diergaarde Hanne Volpin Michiel T J De Both Philipp Zerbe Joerg Bohlmann Vasiliki Falara Yuki Matsuba Eran Pichersky Michel A Haring Robert C Schuurink	Plant Molecular Biology
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
Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation.	2011-08-11	Jason Gertz Katherine E Varley Timothy E Reddy	Kevin M Bowling Florencia Pauli Stephanie L Parker Katerina S Kucera Huntington F Willard Richard M Myers	PLOS Genetics
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
Local and global factors affecting RNA sequencing analysis.	2011-08-16	Graham D Johnson	Edward Sendler Stephen A Krawetz	Analytical Biochemistry
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
An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype	2011-08-18	Michele Balsamo	Irina M Shapiro Albert W Cheng Nicholas C Flytzanis John S Condeelis Maja H Oktay Christopher B Burge Frank B Gertler	PLOS Genetics
Transcriptional profiling of psoriasis using RNA-seq reveals previously unidentified differentially expressed genes.	2011-08-18	Ali Jabbari	Mayte Suárez-Fariñas Scott Dewell James G Krueger	Journal of Investigative Dermatology
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
Lignin metabolism has a central role in the resistance of cotton to the wilt fungus Verticillium dahliae as revealed by RNA-Seq-dependent transcriptional analysis and histochemistry.	2011-08-23	Daojun Yuan Xianlong Zhang	Li Xu Longfu Zhu Lili Tu Linlin Liu Li Jin Lu Long	Journal of Experimental Botany
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
A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data.	2011-08-26	Daniel A Skelly	Marnie Johansson Jennifer Madeoy Jon Wakefield Joshua M Akey	Genome Research
Preservation of the Y transcriptome in a 10-million-year-old plant sex chromosome system.	2011-09-01	Deborah Charlesworth	Roberta Bergero	Current Biology
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses	2011-09-02	Loyal Goff Magdalena J Koziol John L. Rinn	Moran N Cabili Cole Trapnell Barbara Tazon-Vega Aviv Regev	Genes & Development
Wnt gene loss in flatworms.	2011-09-03	Nick Riddiford	Peter D Olson	Development Genes and Evolution
SpliceTrap: a method to quantify alternative splicing under single cellular conditions.	2011-09-06	W. Richard McCombie Adrian Robert Krainer	Jie Wu Martin Akerman Shuying Sun Michael Q Zhang	Bioinformatics
Genome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factor erythroid Kruppel-like factor during erythrocyte differentiation.	2011-09-06	Ross C Hardison James C Mullikin	Andre M Pilon Subramanian S Ajay Swathi Ashok Kumar Laurie A Steiner Praveen F Cherukuri Stephen Wincovitch Stacie M Anderson NISC Comparative Sequencing Center Patrick G Gallagher Elliott H Margulies David M Bodine	Blood
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
RNA-Seq of human neurons derived from iPS cells reveals candidate long non-coding RNAs involved in neurogenesis and neuropsychiatric disorders.	2011-09-07	Deyou Zheng	Mingyan Lin Erika Pedrosa Abhishek Shah Anastasia Hrabovsky Shahina Maqbool Herbert M Lachman	PLOS ONE
Differential expression in RNA-seq: a matter of depth.	2011-09-08	Joaquín Dopazo Ana Conesa Sonia Tarazona Alberto Ferrer	Fernando García-Alcalde	Genome Research
Proteomic and phosphoproteomic comparison of human ES and iPS cells.	2011-09-11	Justin Brumbaugh	Douglas H Phanstiel Craig D Wenger Shulan Tian Mitchell D Probasco Derek J Bailey Danielle L Swaney Mark A Tervo Jennifer M Bolin Victor Ruotti Ron Stewart James A Thomson Joshua J Coon	Nature Methods
Identification of common carp innate immune genes with whole-genome sequencing and RNA-Seq data.	2011-09-12	Elia Stupka Christiaan V. Henkel Herman P Spaink	Yanju Zhang Hans J Jansen Fons J Verbeek	Journal of integrative bioinformatics
Integrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes.	2011-09-13	Jurian Schuijers Michal Mokry	Pantelis Hatzis Nico Lansu Frans-Paul Ruzius Hans Clevers Edwin Cuppen	Nucleic Acids Research
Integrative approach involving RNA-Seq, foliar traits and growth measurements revealed genotype-specific plasticity on Eucalyptus subjected to seasonal water shortage.	2011-09-13	Christophe Plomion	Emilie Villar Jean-Marc Gion	BMC Proceedings
Pronounced and extensive microtubule defects in a Saccharomyces cerevisiae DIS3 mutant.	2011-09-15	Daniel L Kiss	Sarah B Smith Edward Turk Alan M Tartakoff Erik D Andrulis	Yeast
RNA-Seq methods for imperfect samples: development, evaluation and applications	2011-09-19 2011	Aviv Regev Chad Nusbaum Gad Getz	Xian Adiconis Lin Fan David DeLuca Andrey Sivachenko Nathalie Pochet Aaron Berlin Sarah Young Andreas Gnirke Joshua Z Levin	Genome Biology
Differential Expression for RNA Sequencing (RNA-Seq) Data: Mapping, Summarization, Statistical Analysis, and Experimental Design	2011-09-22	Davis J McCarthy Alicia Oshlack Gordon K Smyth	Matthew D. Young Matthew J. Wakefield Mark D. Robinson
Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals.	2011-09-25	Vincent Lynch Gunter P Wagner	Robert D Leclerc Gemma May	Nature Genetics
From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.).	2011-09-28	Thomas Schmutzer Martin Mascher Uwe Scholz Nils Stein Klaus Mayer Eva Bauer	Grit Haseneyer Michael Seidel Ruonan Zhou Chris-Carolin Schön Stefan Taudien	BMC Plant Biology
Accurate identification of A-to-I RNA editing in human by transcriptome sequencing.	2011-09-29	Jae-Hyung Lee Guangdun Peng Xinshu Xiao	Jae Hoon Bahn Gang Li Christopher Greer	Genome Research
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
RNA-Seq analysis in MeV.	2011-10-05	John Quackenbush	Eleanor A Howe Raktim Sinha Daniel Schlauch	Bioinformatics
RNA-seq analysis of small RNPs in Trypanosoma brucei reveals a rich repertoire of non-coding RNAs	2011-10-05	Tirza Doniger	Shulamit Michaeli Sachin Kumar Gupta Omri Wurtzel Mali Romano Damian Visnovezky Rotem Sorek Ron Unger Elisabetta Ullu	Nucleic Acids Research
GENE-counter: a computational pipeline for the analysis of RNA-Seq data for gene expression differences.	2011-10-06	Jeff H. Chang Jeffrey A Kimbrel James C. Carrington	Jason S Cumbie Yanming Di Daniel W Schafer Larry J Wilhelm Samuel E Fox Christopher M Sullivan Aron D Curzon Todd C Mockler	PLOS ONE
S-MART, a software toolbox to aid RNA-Seq data analysis	2011-10-06	Hadi Quesneville	Matthias Zytnicki	PLOS ONE
Nonrandom gene loss from the Drosophila miranda neo-Y chromosome.	2011-10-10	Doris Bachtrog	Vera B Kaiser Qi Zhou	Genome Biology and Evolution
The role of CYP3A4 mRNA transcript with shortened 3'-untranslated region in hepatocyte differentiation, liver development, and response to drug induction.	2011-10-13	Gaedigk R Steven N. Hart	Dan Li J Steven Leeder Xiao-bo Zhong	Molecular Pharmacology
RNA-Seq for Plant Pathogenic Bacteria.	2011-10-13	Jeffrey A Kimbrel Jeff H. Chang	Yanming Di Jason S Cumbie	Genes
Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens.	2011-10-18	Charles D. Johnson Ulisses Braga Neto	Ying Wang Noushin Ghaffari Hui Wang Rui Chen Huaijun Zhou	BMC Bioinformatics
The crystal structure of necrosis- and ethylene-inducing protein 2 from the causal agent of cacao's Witches' Broom disease reveals key elements for its activity	2011-10-21	Paulo José Pereira Lima Teixeira Joan Barau Antonio Costa-filho	Gustavo Zaparoli Mario Ramos de Oliveira Barsottini Juliana Ferreira de Oliveira Fabio Dyszy Odalys Garcia Andre Luis Berteli Ambrosio Gonçalo Amarante Guimarães Pereira Sandra Martha Gomes Dias	Biochemistry
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 Jorge Reis-Filho Rachael Natrajan Alan Ashworth	Kevin C H Ha Emilie Lalonde Lili Li Luca Cavallone Maryou B Lambros Costas Mitsopoulos Jarle Hakas Iwanka Kozarewa Kerry Fenwick Chris J Lord Mark Basik Jacek Majewski	BMC Medical Genomics
RNA-Seq reveals an integrated immune response in nucleated erythrocytes.	2011-10-27	Nerea Roher Laia Ribas Joan C Balasch Sebastian Boltana Steven B. Roberts Simon Mackenzie	Davinia Morera Carmen Doñate Agnes Callol 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
RNA-Seq improves annotation of protein-coding genes in the cucumber genome.	2011-11-02	Zhen Li Sanwen Huang	Zhonghua Zhang Pengcheng Yan Zhangjun Fei Kui Lin	BMC Genomics
deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns.	2011-11-03	Peter F. Stadler Jan Gorodkin David Langenberger Claus T. Ekstrøm Sachin Pundhir	Steve Hoffmann	Bioinformatics
Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain.	2011-11-06	Adam Ameur Ulf Gyllensten	Ammar Zaghlool Jonatan Halvardson Anna Wetterbom Lucia Cavelier Lars Feuk	Nature Structural & Molecular Biology
Exploring the gonad transcriptome of two extreme male pigs with RNA-seq	2011-11-08	Giovanni Bussotti Robert Kofler Cedric Notredame Miguel Perez-Enciso Anna Esteve-Codina	Nicola Palmieri	BMC Genomics
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
Non-laser capture microscopy approach for the microdissection of discrete mouse brain regions for total RNA isolation and downstream next-generation sequencing and gene expression profiling.	2011-11-13	Norman Atkins	Charlie M Miller Joseph R Owens Fred W Turek	Journal of Visualized Experiments
ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets.	2011-11-16	Jeffrey T. Leek Ben Langmead	Alyssa C Frazee	BMC Bioinformatics
Identification of new viral genes and transcript isoforms during Epstein-Barr virus reactivation using RNA-Seq.	2011-11-16	Melody Baddoo Dale Hedges Erik K Flemington	Monica Concha Xia Wang Subing Cao Melody Baddoo Claire Fewell Zhen Lin William Hulme Dale Hedges Jane McBride	Journal of Virology
Genetic variation of pre-mRNA alternative splicing in human populations	2011-11-17	Zhi-xiang Lu	Peng Jiang Yi Xing	Wiley interdisciplinary reviews. RNA
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
RNA-Seq reveals infection-related global gene changes in Phytophthora phaseoli, the causal agent of lima bean downy mildew.	2011-11-24	Blake Meyers	Sridhara G Kunjeti Thomas A Evans Adam G Marsh Nancy F Gregory Saritha Kunjeti Venugopal S Kalavacharla Nicole M Donofrio	Molecular Plant Pathology
Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data.	2011-11-28	Robert Tibshirani	Jun Li	Statistical Methods in Medical Research
Cell walls of developing wheat starchy endosperm: comparison of composition and RNA-Seq transcriptome.	2011-11-28	Paola Tosi J Paul Knox Jackie Freeman	Till K Pellny Alison Lovegrove Christopher G Love Peter R Shewry Rowan A C Mitchell	Plant Physiology
Transposase mediated construction of RNA-seq libraries.	2011-11-29	Jason Gertz Katherine E Varley	Nicholas S Davis Bradley J Baas Igor Y Goryshin Ramesh Vaidyanathan Scott Kuersten Richard M Myers	Genome Research
Comparative analysis of human protein-coding and noncoding RNAs between brain and 10 mixed cell lines by RNA-Seq.	2011-11-30	Jian Luo Mingyao Liu	Geng Chen Kangping Yin Leming Shi Yuanzhang Fang Ya Qi Peng Li Bing He Tieliu Shi	PLOS ONE
Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in Anabaena sp. PCC7120	2011-11-30	Agustín Vioque Fabian Haas Wolfgang R Hess Alicia María Muro-Pastor	Jan Mitschke	Proceedings of the National Academy of Sciences of the United States of America
Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation.	2011-12-01	Jingyi Jessica Li	Ci-Ren Jiang James B Brown Haiyan Huang Peter J Bickel	Proceedings of the National Academy of Sciences of the United States of America
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
Isoform diversity and its importance for axon regeneration.	2011-12-13	John L. Bixby Vance P. Lemmon	Jessica K Lerch	Neuropathology
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
Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study.	2011-12-14	Qiong-Yi Zhao	Yi Wang Yi-Meng Kong Da Luo Xuan Li Pei Hao	BMC Bioinformatics
GC-content normalization for RNA-Seq data	2011-12-17	Gavin Sherlock Davide Risso	Katja Schwartz Sandrine Dudoit	BMC Bioinformatics
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 Matthew Berriman	Alessandro Guida Claudia Lindstädt Chen Ding Nicola J Corton	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
Statistical methods on detecting differentially expressed genes for RNA-seq data.	2011-12-23	Saralees Nadarajah	Zhongxue Chen Jianzhong Liu Hon Keung Tony Ng Saralees Nadarajah Howard L Kaufman Jack Y Yang Youping Deng	BMC Systems Biology
Modulation of NF-κB-dependent gene transcription using programmable DNA minor groove binders	2011-12-27	Jordan L Meier Peter Dervan	Jevgenij A Raskatov James W Puckett Fei Yang Parameswaran Ramakrishnan	Proceedings of the National Academy of Sciences of the United States of America
Detection, annotation and visualization of alternative splicing from RNA-Seq data with SplicingViewer.	2011-12-28	Fangqing Zhao	Qi Liu Chong Chen Enjian Shen Zhongsheng Sun Jinyu Wu	Genomics
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 Giorgio Valle	Fabio De Pascale Riccardo Schiavon Douglas H Bartlett	BMC Genomics
Computational analysis of noncoding RNAs	2012	Manolis Kellis Stefan Washietl Bonnie Berger John L. Rinn	Sebastian Will David A. Hendrix Loyal A. Goff	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 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
Comparing Bowtie and BWA to Align Short Reads from a RNA-Seq Experiment	2012	Honghuang Lin	N. Medina-Medina A. Broka S. Lacey E. S. Klings C. T. Baldwin M. H. Steinberg P. Sebastiani	Advances in Intelligent and Soft Computing
DBTSS: DataBase of Transcriptional Start Sites progress report in 2012	2012-01	Sumio Sugano	Riu Yamashita Yutaka Suzuki Kenta Nakai	Nucleic Acids Research
Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes	2012-01-01	Andreas Gnirke Georgia Giannoukos Ashlee Earl Chad Nusbaum Dirk Gevers	Dawn M Ciulla Katherine Huang Brian J Haas Jacques Izard Joshua Z Levin Jonathan Livny Doyle V Ward Bruce W Birren	Genome Biology
How to analyze gene expression using RNA-sequencing data.	2012-01-01	Daniel Ramsköld Rickard Sandberg	Ersen Kavak	Methods in Molecular Biology
Detection and quantification of alternative splicing variants using RNA-seq.	2012-01-01	Henry D Priest	Douglas W Bryant Todd C Mockler	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
Sex-biased transcriptome evolution in Drosophila.	2012-01-01	Doris Bachtrog	Raquel Assis Qi Zhou	Genome Biology and Evolution
Defining the molecular profile of planarian pluripotent stem cells using a combinatorial RNAseq, RNA interference and irradiation approach.	2012-01-01	Jordi Solana Aziz A. Aboobaker	Damian Kao Yuliana Mihaylova Farah Jaber-Hijazi Sunir Malla Ray Wilson	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
Computational analysis of RNA-seq.	2012-01-01	Scott A. Givan	Christopher A Bottoms William G Spollen	Methods in Molecular Biology
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
Sequencing and de novo analysis of the Chinese Sika deer antler-tip transcriptome during the ossification stage using Illumina RNA-Seq technology.	2012-01-03	Baojin Yao	Yu Zhao Haishan Zhang Mei Zhang Meichen Liu Hailong Liu Juan Li	Biotechnology Letters
PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data.	2012-01-04	Zemin Ning Peter A.C. 't Hoen Pieternella E Slagboom	Yanju Zhang Eric-Wubbo Lameijer Kai Ye	Bioinformatics
IQSeq: integrated isoform quantification analysis based on next-generation sequencing.	2012-01-06	Andrea Sboner Mark Bender Gerstein	Jiang Du Jing Leng Lukas Habegger Drew McDermott	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 Erik K Flemington	Zhen Lin Adriane Puetter Joseph Coco Guorong Xu Michael J Strong Xia Wang Claire Fewell Melody Baddoo Christopher Taylor	Journal of Virology
Transcriptomic analysis of Chinese bayberry (Myrica rubra) fruit development and ripening using RNA-Seq.	2012-01-13	Andrew C. Allan Xue-ren Yin	Chao Feng Ming Chen Chang-jie Xu Lin Bai Xian Li Ian B Ferguson Kun-song Chen	BMC Genomics
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
FX: an RNA-Seq analysis tool on the cloud.	2012-01-17	Young Seok Ju Thomas Bleazard	Dongwan Hong Arang Rhie Sung-Soo Park Jongkeun Lee Sujung Kim Saet-Byeol Yu Hyun-Seok Park Hwanseok Rhee Hyonyong Chong Kap-Seok Yang Yeon-Su Lee In-Hoo Kim Jin Soo Lee Jong-Il Kim Jeong-Sun Seo	Bioinformatics
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
Comparison between Normalised and Unnormalised 454-Sequencing Libraries for Small-Scale RNA-Seq Studies.	2012-01-26	Robert Ekblom Jon Slate Terry Burke	Gavin J Horsburgh Tim Birkhead	Comparative and Functional Genomics
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
Removing technical variability in RNA-seq data using conditional quantile normalization.	2012-01-27	Kasper D. Hansen Zhijin Wu	Rafael A Irizarry	Biostatistics
The Transcriptome Analysis and Comparison Explorer--T-ACE: a platform-independent, graphical tool to process large RNAseq datasets of non-model organisms.	2012-01-27	Lars Kraemer Philip Rosenstiel	E E R Philipp D Mountfort M Schilhabel S Schreiber	Bioinformatics
A new approach to bias correction in RNA-Seq	2012-01-28	Walter L. Ruzzo	Daniel C Jones Xinxia Peng Michael G Katze	Bioinformatics
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
SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data.	2012-01-31	Asa Ben-Hur	Mark F Rogers Julie Thomas Anireddy Sn Reddy	Genome Biology
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 Mark W. Chase	Michael R McKain Yeting Zhang Saravanaraj Ayyampalayam 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	Jie Huang Yu Zhou Changwei Shao Yi Zhang	Rui Xiao Peng Tang Bo Yang 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 Michael B Thompson Gunter P Wagner	Matthew C Brandley Rebecca L Young	Genome Biology and Evolution
RNA-Seq Atlas--a reference database for gene expression profiling in normal tissue by next-generation sequencing.	2012-02-17	Jens U Marquardt Ugur Sahin	Markus Krupp Peter R Galle John Castle Andreas Teufel	Bioinformatics
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 the functional compartments within the rat placentation site.	2012-02-21	Kartik Shankar	Ying Zhong Ping Kang Michael L Blackburn Michael J Soares Thomas M Badger Horacio Gomez-Acevedo	Endocrinology
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 Huanming Yang	Shancheng Ren Zhiyu Peng Yongwei Yu Changjun Yin Xin Gao Zilian Cui Jibin Zhang Kang Yi Weidong Xu Chao Chen Fubo Wang Xinwu Guo Ji Lu Jun Yang Min Wei Zhijian Tian Yinghui Guan Liang Tang Chuanliang Xu Linhui Wang Xu Gao Wei Tian Jian Wang Yinghao Sun	Cell Research
Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data.	2012-02-29	Alexey I Nesvizhskii	Kang Ning Damian Fermin	Journal of Proteome Research
RNA-Seq quantification of the human small airway epithelium transcriptome	2012-02-29	Juan L Rodriguez-Flores	Neil R Hackett Marcus W Butler Renat Shaykhiev Jacqueline Salit Larsson Omberg Jason G Mezey Yael Strulovici-Barel Guoqing Wang Lukas Didon Ronald G Crystal	BMC Genomics
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
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks	2012-03	Loyal Goff Steven Salzberg Lior Pachter Harold Pimentel John L. Rinn	Cole Trapnell Adam Roberts Geo Pertea Daehwan Kim David R Kelley	Nature Protocols
Characterization and differential expression analysis of complete coding sequences of Vitis vinifera L. sirtuin genes.	2012-03-03	Giacomo Morreale Matteo Busconi Luigi Bavaresco	M Cucurachi A Zanetti 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 Fernanda Ortis Mark McCarthy	Décio L Eizirik Thomas Bouckenooghe Guy Bottu Giorgia Sisino Mariana Igoillo-Esteve Maikel L Colli Jenny Barthson Luc Bouwens Linda Hughes Lorna Gregory	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 Alberto Ferrarini Luciano Xumerle Anna Ferrari Cristina Papayannidis Simona Soverini	I Iacobucci M Sazzini E Giacomelli D Luiselli A Boattini P Garagnani A Vitale 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 Reinhard Guthke	Lanay Tierney Jörg Linde Sebastian Müller Juan Camilo Molina Bernhard Hube Ulrike Schöck	Frontiers in Microbiology
A new RNASeq-based reference transcriptome for sugar beet and its application in transcriptome-scale analysis of vernalization and gibberellin responses.	2012-03-19	Effie Mutasa-Göttgens Berthold Gottgens	Anagha Joshi Helen F Holmes Peter Hedden	BMC Genomics
Transcriptome landscape of the human placenta	2012-03-27	Zhi-xiang Lu Jin-kai Wang	Jinsil Kim Keyan Zhao Peng Jiang 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
Alternative splicing networks regulated by signaling in human T cells.	2012-03-27	Nicole M Martinez	Qun Pan Brian S Cole Christopher A Yarosh Grace A Babcock Florian Heyd William Zhu Sandya Ajith Benjamin J Blencowe Kristen W Lynch	RNA
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
A genome-wide identification analysis of small regulatory RNAs in Mycobacterium tuberculosis by RNA-Seq and conservation analysis	2012-03-28	Paolo Miotto Alessandro Ambrosi	Danilo Pellin Daniela Maria Cirillo Clelia Di Serio	PLOS ONE
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
Improving RNA-Seq Precision with MapAl.	2012-04-02	D Kreil	Paweł P Labaj Bryan E Linggi H Steven Wiley	Frontiers in Genetics
RNA-Seq analysis of developing nasturtium seeds (Tropaeolum majus): identification and characterization of an additional galactosyltransferase involved in xyloglucan biosynthesis	2012-04-02	Alex Schultink Jacob K Jensen Markus Pauly	Kenneth Keegstra Curtis G Wilkerson	Plant Physiology Journal
Deep sequencing the circadian and diurnal transcriptome of Drosophila brain	2012-04-03	Gregory R Grant	Michael E Hughes Christina Paquin Jack Qian Michael N Nitabach	Genome Research
The clonal and mutational evolution spectrum of primary triple-negative breast cancers	2012-04-04	Gavin Ha D Yap Daniel Lai Inanc Birol Malachi Griffith Gregg B Morin Suet-feung Chin Christina Curtis Mackey JR Wyeth W Wasserman Steven Jones	Sohrab P Shah Andrew Roth Rodrigo Goya Arusha Oloumi Yongjun Zhao Gulisa Turashvili Jiarui Ding Kane Tse Gholamreza Haffari Ali Bashashati Leah M Prentice Jaswinder Khattra Angela Burleigh Virginie Bernard Andrew McPherson Karey Shumansky Anamaria Crisan Ryan Giuliany Alireza Heravi-Moussavi Jamie Rosner Richard Varhol Angela Tam Noreen Dhalla Thomas Zeng Kevin Ma Simon K Chan Annie Moradian S-W Grace Cheng Peter Watson Karen Gelmon Stephen Chia Oscar M Rueda Paul D Pharoah Sambasivarao Damaraju Kelly Hoon Timothy Harkins Vasisht Tadigotla Mahvash Sigaroudinia Philippe Gascard Thea Tlsty Joseph F Costello Irmtraud M Meyer Connie J Eaves David Huntsman Martin Hirst Carlos Caldas Marco A Marra Samuel Aparicio	Nature
Spatial proximity and similarity of the epigenetic state of genome domains.	2012-04-04	Ekaterina E Khrameeva Gennady G Fedonin Mikhail S Gelfand	Andrey A Mironov Philipp Khaitovich	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
Rapid de novo evolution of X chromosome dosage compensation in Silene latifolia, a plant with young sex chromosomes.	2012-04-17	Niklaus Zemp	Aline Muyle Clothilde Deschamps Sylvain Mousset Alex Widmer Gabriel A B Marais	PLOS Biology
KISSPLICE: de-novo calling alternative splicing events from RNA-seq data	2012-04-19	Pierre Peterlongo Marie-France Sagot	Gustavo A T Sacomoto Janice Kielbassa Rayan Chikhi Raluca Uricaru Pavlos Antoniou Vincent Lacroix	BMC Bioinformatics
A context-based approach to identify the most likely mapping for RNA-seq experiments.	2012-04-19	Ralf Zimmer	Thomas Bonfert Gergely Csaba Caroline C Friedel	BMC Bioinformatics
A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy	2012-04-24	Daniel S. Rokhsar Kranthi Varala	Kankshita Swaminathan Won Byoung Chae Therese Mitros Liang Xie Adam Barling Katarzyna Glowacka Megan Hall Stanislaw Jezowski Ray Ming Matthew Hudson John A Juvik Stephen P Moose	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 Jeffrey A Fabrick Juan Luis Jurat-Fuentes	Brenda Oppert Scot E Dowd Pascal Bouffard Lewyn Li Marcé D Lorenzen Michelle Toutges Jeremy Marshall Cris Oppert	PLOS ONE
Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution.	2012-04-26	Ralf Zimmer	Lukas Windhager Thomas Bonfert Kaspar Burger Zsolt Ruzsics Stefan Krebs Stefanie Kaufmann Georg Malterer Anne L'Hernault Markus Schilhabel Stefan Schreiber Philip Rosenstiel Dirk Eick Caroline C Friedel Lars Dölken	Genome Research
Transcriptome sequencing revealed significant alteration of cortical promoter usage and splicing in schizophrenia.	2012-04-27	Jingqin Wu Xi Wang Murray J Cairns	Natalie J Beveridge Paul A Tooney Rodney J Scott Vaughan J Carr	PLOS ONE
Comprehensive Genomic Profiling Of The Lung Transcriptome In Emphysema And IPF Using RNA-Seq	2012-05	John Quackenbush Naftali Kaminski	Rebecca L. Kusko John Brothers II Gang Liu Lingqi Luo Brenda J. Guardela John R. Tedrow Yuriy Aleksyev Ivana V. Yang Mick Correll Mark Geraci Frank C. Sciurba Marc Lenburg David A. Schwartz Jennifer Beane Avrum Spira
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
Utilizing RNA-Seq data for de novo coexpression network inference	2012-05-03	Shannon K McWeeney	Ovidiu D Iancu Sunita Kawane Daniel Bottomly Robert Searles Robert Hitzemann	Bioinformatics
Identifying differentially expressed transcripts from RNA-seq data with biological variation.	2012-05-03	Magnus Rattray Antti Honkela	Peter Glaus Antti Honkela	Bioinformatics
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
Gene mapping via bulked segregant RNA-Seq (BSR-Seq).	2012-05-07	Cheng-Ting Yeh Dan Nettleton Patrick S Schnable	Sanzhen Liu Ho Man Tang	PLOS ONE
A simple strand-specific RNA-Seq library preparation protocol combining the Illumina TruSeq RNA and the dUTP methods.	2012-05-15	Marie-Laure Yaspo Hans Lehrach	Marc Sultan Simon Dökel Vyacheslav Amstislavskiy Daniela Wuttig Holger Sültmann Marie-Laure Yaspo	Biochemical and Biophysical Research Communications
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
RNA-seq analysis of differential gene expression in liver from lactating dairy cows divergent in negative energy balance.	2012-05-20	David J. Lynn Christopher J. Creevey David A Kenny	Matthew McCabe Sinéad Waters Dermot Morris	BMC Genomics
Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns	2012-05-24	Anders Krogh Jun Wang Johannes Waage Joachim Weischenfeldt Bo Torben Porse Janus Schou Jakobsen Karsten Kristiansen	Geng Tian Jing Zhao Inge Damgaard	Genome Biology
Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer	2012-05-25	Gavin Ha Daniel Lai Suet-feung Chin	Andrew Roth Ali Bashashati Jiarui Ding Rodrigo Goya Ryan Giuliany Jamie Rosner Arusha Oloumi Karey Shumansky Gulisa Turashvili Martin Hirst Marco A Marra Samuel Aparicio Sohrab P Shah Carlos Caldas	Genome Research
Dissect: detection and characterization of novel structural alterations in transcribed sequences	2012-06-01	Inanc Birol	Deniz Yorukoglu Faraz Hach Lucas Swanson Colin C Collins S Cenk Sahinalp	Bioinformatics
Trehalose-enhanced isolation of neuronal sub-types from adult mouse brain.	2012-06-01	Piero Carninci Yukihiko Noro	Alka Saxena Akiko Wagatsuma Takenobu Kuji Atsuko Asaka-Oba Akira Watahiki Cecile Gurnot Michela Fagiolini Takao K Hensch	BioTechniques
Transcriptomic signatures of attachment, NF-κB suppression and IFN stimulation in the catfish gill following columnaris bacterial infection.	2012-06-02	Eric Peatman Shikai Liu	Fanyue Sun Chao Li Yanliang Jiang Zunchun Zhou Zhanjiang Liu	Developmental and Comparative Immunology
RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics	2012-06-08	John E. Lunn Björn Usadel Alisdair R Fernie Mark Stitt	Marc Lohse Anthony M Bolger Axel Nagel	Nucleic Acids Research
Integrated genome analysis suggests that most conserved non-coding sequences are regulatory factor binding sites	2012-06-08	Gabriel Kreiman Nicole Cloonan Sean M. Grimmond	Martin Hemberg Jesse M Gray Scott Kuersten Michael E Greenberg	Nucleic Acids Research
Expression Profiling of a Heterogeneous Population of ncRNAs Employing a Mixed DNA/LNA Microarray.	2012-06-10	Marek Żywicki Marcel Scheideler Mathieu Rederstorff	Konstantinia Skreka Michael Karbiener Alexander Hüttenhofer	Journal of Nucleic Acids
Modeling gene expression using chromatin features in various cellular contexts	2012-06-13	Roderic Guigó i Serra Mark Bender Gerstein Ewan Birney Sarah Djebali Xianjun Dong Anshul Kundaje Thomas R. Gingeras	Melissa C Greven James B Brown Chao Cheng Zhiping Weng	Genome Biology
Identification of PTK6, via RNA sequencing analysis, as a suppressor of esophageal squamous cell carcinoma.	2012-06-13	Stephanie Ma Li Fu Xin-Yuan Guan Xin-Yuan Guan	Jessie Y J Bao Pak Shing Kwan Yuen Piu Chan Carol M Tong Na Zhang Amy H Y Tong Yan-Ru Qin Sai Wah Tsao Kwok Wah Chan Si Lok	Gastroenterology
Alternative splicing regulated by butyrate in bovine epithelial cells.	2012-06-14	Wen Huang Weizhong Li	Sitao Wu Congjun Li Robert W Li	PLOS ONE
Bellerophontes: an RNA-Seq data analysis framework for chimeric transcripts discovery based on accurate fusion model.	2012-06-17	Alberto Ferrarini Elisa Ficarra Simona Soverini Giovanni Martinelli Ilaria Iacobucci	Francesco Abate Andrea Acquaviva Giulia Paciello Carmelo Foti Massimo Delledonne Enrico Macii	Bioinformatics
Transcriptomic analysis of the stress response to weaning at housing in bovine leukocytes using RNA-seq technology.	2012-06-18	Sean Doyle David J. Lynn Bernadette Earley	Aran O'Loughlin Mark McGee Matthew McCabe	BMC Genomics
Detecting differential usage of exons from RNA-seq data	2012-06-21	Alejandro Reyes Simon Anders Wolfgang Huber		Genome Research
PM-Seq: Using Finite Poisson Mixture Models for RNA-Seq Data Analysis and Transcript Expression Level Quantification	2012-06-21	Zhaohui Steve Qin	Han Wu Yu Zhu	Statistics in biosciences
Expressed pseudogenes in the transcriptional landscape of human cancers	2012-06-22	John R. Prensner Shanker Kalyana-Sundaram Chandan Kumar-Sinha Irfan Asangani Nallasivam Palanisamy	Sunita Shankar Dan R Robinson Yi-Mi Wu Xuhong Cao Vishal Kothari Robert J Lonigro Matthew K Iyer Terrence Barrette Achiraman Shanmugam Saravana M Dhanasekaran Arul M Chinnaiyan	Cell
RNA-Seq and human complex diseases: recent accomplishments and future perspectives.	2012-06-27	Valerio Costa	Marianna Aprile Roberta Esposito Alfredo Ciccodicola	European Journal of Human Genetics
FusionFinder: a software tool to identify expressed gene fusion candidates from RNA-Seq data.	2012-06-27	Richard W Francis Kim Carter Denise Anderson Alex H. Beesley	Katherine Thompson-Wicking Ursula R Kees	PLOS ONE
A systematic comparison and evaluation of high density exon arrays and RNA-seq technology used to unravel the peripheral blood transcriptome of sickle cell disease.	2012-06-29	Gregory J. Kato	Nalini Raghavachari Jennifer Barb Yanqin Yang Poching Liu Kimberly Woodhouse Daniel Levy Christopher J O'Donnell Peter J Munson	BMC Medical Genomics
SAVoR: a server for sequencing annotation and visualization of RNA structures	2012-07	Otto Valladares Fan Li	Paul Ryvkin Daniel M Childress Brian D Gregory Li-San Wang	Nucleic Acids Research
Digging in the RNA-seq Garbage: Evaluating the Characteristics of Unmapped RNA-seq Reads in Normal Tissues	2012-07	Federica Cavallo	Matteo Carrara Maddalena Arigoni Raffaele A. Calogero
Molecular and developmental contributions to divergent pigment patterns in marine and freshwater sticklebacks	2012-07-01	Catherine L Peichel	Anna K Greenwood Jennifer N Cech	Evolution & Development
Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions	2012-07-01	Iros Barozzi Gioacchino Natoli	Dev M Bhatt Amy Pandya-Jones Ann-Jay Tong Michelle M Lissner Douglas L Black Stephen T Smale	Cell
RNA-seq analysis of the C. briggsae transcriptome.	2012-07-06	Bora Uyar	Jeffrey S C Chu Ismael A Vergara Shu Yi Chua Martin R Jones Tammy Wong David L Baillie Nansheng Chen	Genome Research
Incorporating RNA-seq data into the zebrafish Ensembl genebuild	2012-07-12	Simon White	John E Collins Stephen M J Searle Derek L Stemple	Genome Research
Paired-end sequencing of Fosmid libraries by Illumina.	2012-07-16	Gad Getz Chad Nusbaum Yotam Drier	Louise J S Williams Diana G Tabbaa Na Li Aaron M Berlin Terrance P Shea Iain Maccallum Michael S Lawrence Sarah K Young David B Jaffe Andreas Gnirke	Genome Research
Inflammatory priming predisposes mice to age-related retinal degeneration.	2012-07-17	Krzysztof Palczewski	Debarshi Mustafi Tadao Maeda Hideo Kohno Joseph H Nadeau	Journal of Clinical Investigation
RNA processing in the minimal organism Nanoarchaeum equitans	2012-07-18	L Randau	Lennart Randau	Genome Biology
Transcript profiling reveals complex auxin signalling pathway and transcription regulation involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton	2012-07-20	Daojun Yuan	Xiyan Yang Xianlong Zhang Fangyan Jin Yunchao Zhang Jiao Xu	BMC Plant Biology
Genomic imprinting absent in Drosophila melanogaster adult females.	2012-07-20	C Joel McManus Brenton R. Graveley	Joseph D Coolon Kraig R Stevenson Patricia J Wittkopp	Cell Reports
Differential gene expression in tamoxifen-resistant breast cancer cells revealed by a new analytical model of RNA-Seq data	2012-07-23	Willard M. Freeman Kent Vrana	Kathryn J Huber-Keener Xiuping Liu Zhong Wang Yaqun Wang Song Wu Maricarmen D Planas-Silva Xingcong Ren Yan Cheng Yi Zhang Chang-Gong Liu Jin-Ming Yang Rongling Wu	PLOS ONE
Metabolic Regulation of "Ca. Methylacidiphilum Fumariolicum" SolV Cells Grown Under Different Nitrogen and Oxygen Limitations.	2012-07-25	Huub J.M. Op den Camp	Ahmad F Khadem Arjan Pol Adam S Wieczorek Mike S M Jetten	Frontiers in Microbiology
Effects of drought on gene expression in maize reproductive and leaf meristem tissue revealed by RNA-Seq.	2012-07-26	Akshay Kakumanu Andy Pereira	Madana M R Ambavaram Curtis Klumas Arjun Krishnan Utlwang Batlang Elijah Myers Ruth Grene	Plant Physiology
Identification of miRNA signatures during the differentiation of hESCs into retinal pigment epithelial cells.	2012-07-27	Guoping Fan	Ganlu Hu Kevin Huang Juehua Yu Sailesh Gopalakrishna-Pillai Jun Kong He Xu Zhenshan Liu Kunshan Zhang Jun Xu Yuping Luo Siguang Li Yi E Sun Linda E Iverson Zhigang Xue	PLOS ONE
Identification of novel transcripts deregulated in buccal cancer by RNA-seq.	2012-07-27	Ajai K. Tripathi Subhash J Jakhesara Chaitanya G. Joshi	Manisha R Sajnani Amrutlal K Patel Vaibhav D Bhatt Viral B Ahir Vangipuram Shankar Siddharth Shah Tejas M Shah Prakash G Koringa	Gene
Mili and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis	2012-07-29	Anastassios Vourekas Panagiotis Alexiou Manolis Maragkakis Yohei Kirino Zissimos Mourelatos	Qi Zheng Brian D Gregory	Nature Structural & Molecular Biology
A mutation in the PP2C phosphatase gene in a Staphylococcus aureus USA300 clinical isolate with reduced susceptibility to vancomycin and daptomycin.	2012-07-30	Karla D Passalacqua	Sarah W Satola Emily K Crispell Timothy D Read	Antimicrobial Agents and Chemotherapy
easyRNASeq: a bioconductor package for processing RNA-Seq data	2012-07-30	Eileen E. M. Furlong Lars M Steinmetz	Nicolas Delhomme Ismaël Padioleau	Bioinformatics
RNASeq profiling of UTR expression during neuronal plasticity.	2012-07-31	Robert M. Flight Jeffrey C. Petruska	Benjamin J Harrison Abdallah Eteleeb Eric C Rouchka	BMC Bioinformatics
Recurrent R-spondin fusions in colon cancer.	2012-08-01	Robert Gentleman	Somasekar Seshagiri Eric W Stawiski Steffen Durinck Zora Modrusan Elaine E Storm Caitlin B Conboy Subhra Chaudhuri Yinghui Guan Vasantharajan Janakiraman Bijay S Jaiswal Joseph Guillory Connie Ha Gerrit J P Dijkgraaf Jeremy Stinson Florian Gnad Melanie A Huntley Jeremiah D Degenhardt Peter M Haverty Richard Bourgon Weiru Wang Hartmut Koeppen Timothy K Starr Zemin Zhang David A Largaespada Thomas D Wu Frederic J de Sauvage	Nature
Discovery and characterization of new transcripts from RNA-seq data in mouse CD4(+) T cells.	2012-08-04	Stéphane Poulain Andrew Paul Hutchins Hodaka Fujii	Diego Miranda-Saavedra	Genomics
Transcriptome profiling of resistant and susceptible Cavendish banana roots following inoculation with Fusarium oxysporum f. sp. cubense tropical race 4.	2012-08-05	Altus Viljoen	Chun-Yu Li Gui-Ming Deng Jing Yang Yan Jin Rui-Bin Kuang Cun-Wu Zuo Zhi-Cheng Lv Qiao-Song Yang Ou Sheng Yue-Rong Wei Chun-Hua Hu Tao Dong Gan-Jun Yi	BMC Genomics
Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples.	2012-08-08	Vincent Lynch	Günter P Wagner Koryu Kin	Theory in Biosciences
RNA-Seq provides new insights in the transcriptome responses induced by the carcinogen benzo[a]pyrene.	2012-08-13	Stan Gaj Hans Lehrach Ralf Herwig Jos Kleinjans	Joost van Delft Stan Gaj Matthias Lienhard Marcus W Albrecht Alexander Kirpiy Karen Brauers Sandra Claessen Daneida Lizarraga	Toxicological Sciences
Temperature during embryonic development has persistent effects on thermal acclimation capacity in zebrafish.	2012-08-13	Ian A Johnston	Graham R Scott	Proceedings of the National Academy of Sciences of the United States of America
Proteogenomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins.	2012-08-16	Peter A. DiMaggio Barry M Zee	Gary LeRoy Iouri Chepelev Mario A Blanco Keji Zhao Benjamin A Garcia	Genome Biology
Proteomics and deep sequencing comparison of seasonally active venom glands in the platypus reveals novel venom peptides and distinct expression profiles.	2012-08-16	Marilyn Renfree Anthony T. Papenfuss Emily S Wong Camilla M Whittington Glenn F King	David Morgenstern Ehtesham Mofiz Sara Gombert Katrina M Morris Peter Temple-Smith Wesley C Warren Katherine Belov	Molecular & Cellular Proteomics
RNA-seq transcriptome analysis of male and female zebra finch cell lines	2012-08-21	Christopher N. Balakrishnan Ya-Chi Lin Sarah E London David F. Clayton	Christopher N Balakrishnan Ya-Chi Lin Sarah E London David F Clayton	Genomics
Detecting transcription of ribosomal protein pseudogenes in diverse human tissues from RNA-seq data	2012-08-21	Shaojie Zhang	Peter Tonner Vinodh Srinivasasainagendra Degui Zhi	BMC Genomics
Research resource: RNA-Seq reveals unique features of the pancreatic β-cell transcriptome.	2012-08-21	Michael McManus Hail Kim	Gregory M Ku Ian W Vaughn Matthew J Hangauer Chang Myung Oh Michael S German	Molecular Endocrinology
shortran: a pipeline for small RNA-seq data analysis.	2012-08-22	Stig Uggerhøj Andersen Jens Stougaard	Vikas Gupta Katharina Markmann Christian N S Pedersen	Bioinformatics
Strand-specific RNA-seq reveals ordered patterns of sense and antisense transcription in Bacillus anthracis	2012-08-22	Karla D Passalacqua	Anjana Varadarajan Charlotte Weist Brian D Ondov Benjamin Byrd Timothy D Read Nicholas H Bergman	PLOS ONE
GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data.	2012-08-24	Yong Zhang	Jianxing Feng Clifford A Meyer Qian Wang Jun S Liu X Shirley Liu	Bioinformatics
An injury-response mechanism conserved across kingdoms determines entry of the fungus Trichoderma atroviride into development.	2012-08-27	Miguel Hernández-Oñate Alfredo Herrera-Estrella	Edgardo U Esquivel-Naranjo Artemio Mendoza-Mendoza Alison Stewart	Proceedings of the National Academy of Sciences of the United States of America
A simple and novel method for RNA-seq library preparation of single cell cDNA analysis by hyperactive Tn5 transposase.	2012-08-28	Anna Terry Niall G. Campbell Charles Mein	Scott Brouilette Scott Kuersten Monika Bozek Kerith-Rae Dias Leena Bhaw-Rosun Yasunori Shintani Steven Coppen Chiho Ikebe Vinit Sawhney Masahiro Kaneko Nobuko Tano Hidekazu Ishida Ken Suzuki Kenta Yashiro	Developmental Dynamics
A putative role for amino acid permeases in sink-source communication of barley tissues uncovered by RNA-seq.	2012-08-30	Winfriede Weschke	Stefan Kohl Julien Hollmann Frank R Blattner Volodymyr Radchuk Franka Andersch Burkhard Steuernagel Thomas Schmutzer Uwe Scholz Karin Krupinska Hans Weber	BMC Plant Biology
Allele-biased expression in differentiating human neurons: implications for neuropsychiatric disorders	2012-08-30	Deyou Zheng	Mingyan Lin Anastasia Hrabovsky Erika Pedrosa Tao Wang Herbert M Lachman	PLOS ONE
RNA-Seq of early-infected poplar leaves by the rust pathogen Melampsora larici-populina uncovers PtSultr3;5, a fungal-induced host sulfate transporter	2012-08-30	Nicolas Rouhier Julie Poulain Benjamin Petre Sébastien Duplessis Corinne Da Silva Francis Martin Emmanuelle Morin Annegret Kohler	Emilie Tisserant Stéphane Hacquard Christine Delaruelle	PLOS ONE
Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs	2012-09	Roderic Guigó i Serra Sarah Djebali Rory Johnson Thomas R. Gingeras	Hagen Tilgner David G Knowles Carrie A Davis Sudipto Chakrabortty João Curado Michael Snyder	Genome Research
Dual RNA-seq of pathogen and host.	2012-09-01	Alexander Westermann Jörg Vogel	Stanislaw A Gorski	Nature Reviews Microbiology
Long noncoding RNAs are rarely translated in two human cell lines	2012-09-01	Yanbao Yu Anshul Kundaje Brian D Strahl Krzysztof Krajewski	Balázs Bánfai Hui Jia Jainab Khatun Emily Wood Brian Risk William E Gundling Harsha P Gunawardena Ling Xie Xian Chen Peter Bickel Morgan C Giddings James B Brown Leonard Lipovich	Genome Research
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.	2012-09-01	Andrea Tanzer Jose M Gonzalez Bronwen Aken Tim Hubbard Jennifer Harrow Felix Kokocinski Roderic Guigó i Serra Cédric Howald Thibaut Hourlier Thomas Derrien Alexandre Reymond Simon White Adam Frankish	Jacqueline Chrast Nathalie Walters Jan-Hinnerk Vogel Stephen Searle	Genome Research
Initial characterization of shade avoidance response suggests functional diversity between Populus phytochrome B genes.	2012-09-03	Xiaohan Yang Gerald A Tuskan Sara S Jawdy Lee Gunter Stan D Wullschleger	Abhijit A Karve Sara M Allen David J Weston	New Phytologist
The grapevine expression atlas reveals a deep transcriptome shift driving the entire plant into a maturation program.	2012-09-04	Silvia Dal Santo Giovanni Battista Tornielli Vittorio Murino Luca Venturini Lorenzo Farina	Marianna Fasoli Sara Zenoni Anita Zamboni Andrea Porceddu Manuele Bicego Alberto Ferrarini Massimo Delledonne Mario Pezzotti	The Plant Cell
A novel computational strategy to identify A-to-I RNA editing sites by RNA-Seq data: de novo detection in human spinal cord tissue	2012-09-05	Graziano Pesole Angela Gallo Ernesto Picardi	Federica Galeano Sara Tomaselli	PLOS ONE
Modelling and simulating generic RNA-Seq experiments with the flux simulator.	2012-09-07	Roderic Guigó i Serra Michael Sammeth	Thasso Griebel Benedikt Zacher Paolo Ribeca Emanuele Raineri Vincent Lacroix	Nucleic Acids Research
Comparative transcriptome analyses of deltamethrin-resistant and -susceptible Anopheles gambiae mosquitoes from Kenya by RNA-Seq	2012-09-07	Mariangela Bonnizoni Guiyun Yan	Yaw Afrane William Augustine Dunn Francis K Atieli Goufa Zhou Daibin Zhong Jun Li Andrew Githeko	PLOS ONE
Id2a functions to limit Notch pathway activity and thereby influence the transition from proliferation to differentiation of retinoblasts during zebrafish retinogenesis.	2012-09-08	Taejoon Kwon Rosa A Uribe Jeffrey M Gross		Developmental Biology
A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae.	2012-09-10	Jens Nielsen Natapol Pornputtapong Linn Fagerberg Intawat Nookaew	Marta Papini Gionata Scalcinati Matthias Uhlén	Nucleic Acids Research
Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production.	2012-09-11	Todd P Michael	Chongyuan Luo David J Sidote Yi Zhang Randall A Kerstetter Eric Lam	The Plant Journal
The bench scientist's guide to statistical analysis of RNA-Seq data.	2012-09-14	Craig R Yendrek	Elizabeth A Ainsworth Jyothi Thimmapuram	BMC Research Notes
Gene expression changes in a tumor xenograft by a pyrrole-imidazole polyamide.	2012-09-17	Georgi K Marinov Peter Dervan	Jevgenij A Raskatov Nicholas G Nickols Amanda E Hargrove Barbara Wold	Proceedings of the National Academy of Sciences of the United States of America
Heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma cells	2012-09-18	Harri Lähdesmäki Vivek Anantharaman Lakshminarayanan Aravind Tarmo Aijö John Gagnon Xing Chang	Micah J Benson Tarmo Aijö Utz J Pape Juha-Pekka Pursiheimo Shalini Oberdoerffer X Shirley Liu Riitta Lahesmaa Anjana Rao	Proceedings of the National Academy of Sciences of the United States of America
Functional transcriptomics of a migrating cell in Caenorhabditis elegans.	2012-09-18	Erich M Schwarz Paul W. Sternberg	Mihoko Kato	Proceedings of the National Academy of Sciences of the United States of America
Differential Expression Analysis for RNA-Seq Data.	2012-09-20	Alok Bhattacharya	Rashi Gupta Isha Dewan Richa Bharti	ISRN bioinformatics
A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters	2012-09-20	Yi Zheng	Yun-Ru Chen Bao Liu Silin Zhong Jim Giovannoni Zhangjun Fei	Plant Methods
High-resolution transcriptome of human macrophages.	2012-09-21	Joachim Schultze Andrea Nino-Castro	Marc Beyer Michael R Mallmann Jia Xue Andrea Staratschek-Jox Daniela Vorholt Wolfgang Krebs Daniel Sommer Jil Sander Christina Mertens Susanne V Schmidt	PLOS ONE
A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data.	2012-09-22	Hao Wu Zhijin Wu	Chi Wang	Biostatistics
Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments.	2012-09-24	Axel Künstner	Nagarjun Vijay Jelmer W Poelstra Jochen B W Wolf	Molecular Ecology
RNA-Seq Assembly - Are We There Yet?	2012-09-25	Andrea Bräutigam	Simon Schliesky Udo Gowik Andreas P M Weber	Frontiers in Plant Science
Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3.	2012-09-26	Peggy Farnham	Seth Frietze Rui Wang Lijing Yao Yu Gyoung Tak Zhenqing Ye Malaina Gaddis Heather Witt Victor X Jin	Genome Biology
A next-generation sequencing approach to study the transcriptomic changes during the differentiation of physarum at the single-cell level.	2012-10-01	Israel Barrantes Jeremy Leipzig	Wolfgang Marwan	Gene Regulation and Systems Biology
The Snail family member Worniu is continuously required in neuroblasts to prevent Elav-induced premature differentiation	2012-10-01	Sen-Lin Lai	Michael R Miller Kristin J Robinson Chris Q Doe	Developmental Cell
Dual lineage-specific expression of Sox17 during mouse embryogenesis.	2012-10-01	Momoko Yoshimoto Mark A. Magnuson Elisabetta Manduchi Anne Grapin-Botton	Eunyoung Choi Marine R C Kraus Laurence A Lemaire Sasidhar Vemula Leah A Potter Christian J Stoeckert	Stem Cells
Comprehensive genomic profiling of the lung transcriptome in emphysema and idiopathic pulmonary fibrosis using RNA-Seq.	2012-10-01	Jennifer Beane John Quackenbush Naftali Kaminski	Rebecca L Kusko John Brothers Gang Liu Lingqi Luo Brenda Juan Guardela John Tedrow Yuriy Aleksyev Ivana V Yang Mick Correll Mark Geraci Frank Sciurba Marc Lenburg David A Schwartz Avrum Spira	BMC Proceedings
SERE: single-parameter quality control and sample comparison for RNA-Seq.	2012-10-03	Rahul Kanwar	Stefan K Schulze Meike Gölzenleuchter Terry M Therneau Andreas S Beutler	BMC Genomics
Evaluation of different reference based annotation strategies using RNA-Seq - a case study in Drososphila pseudoobscura.	2012-10-03	Anton Suvorov	Nicola Palmieri Viola Nolte Carolin Kosiol Christian Schlötterer	PLOS ONE
Systems and trans-system level analysis identifies conserved iron deficiency responses in the plant lineage.	2012-10-05	David Casero Eugen Urzica Crysten E Blaby-Haas Matteo Pellegrini Sabeeha Merchant	Hiroaki Yamasaki Scott I Hsieh Lital N Adler Steven J Karpowicz Steven G Clarke Joseph A Loo	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
Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads.	2012-10-11	Wei Li	Tao Jiang	Bioinformatics
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 Sabeeha Merchant	Scott I Hsieh Madeli Castruita Davin Malasarn Jonathan Erde M Dudley Page Hiroaki Yamasaki Joseph A Loo	Molecular & Cellular Proteomics
High levels of gene expression explain the strong evolutionary constraint of mitochondrial protein-coding genes.	2012-10-15	Hans Ellegren	Benoit Nabholz Jochen B W Wolf	Molecular Biology and Evolution
The biology of nematode- and IL4Rα-dependent murine macrophage polarization in vivo as defined by RNA-Seq and targeted lipidomics.	2012-10-16	Graham D Thomas Dominik Ruckerl Phillip D. Whitfield Mark Blaxter Judith Allen	Benjamin H Maskrey	Blood
A bioinformatics approach for integrated transcriptomic and proteomic comparative analyses of model and non-sequenced anopheline vectors of human malaria parasites.	2012-10-17	David R. Colquhoun Jürgen Hartler Gerhard G Thallinger Jesus Martinez-Barnetche Antonis Rokas Rhoel Dinglasan	Ceereena Ubaida Mohien Derrick K Mathias John G Gibbons Jennifer S Armistead Maria C Rodriguez Mario Henry Rodriguez Nathan J Edwards David R Graham	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
Transcriptomic profiling of the oyster pathogen Vibrio splendidus opens a window on the evolutionary dynamics of the small RNA repertoire in the Vibrio genus	2012-10-24	Daniel Gautheret Philippe Bouloc Annick Jacq	Claire Toffano-Nioche An N Nguyen Claire Kuchly Alban Ott	RNA
STAR: ultrafast universal RNA-seq aligner	2012-10-25	Philippe Batut Thomas R. Gingeras	Alexander Dobin Carrie A Davis Felix Schlesinger Jorg Drenkow Chris Zaleski Sonali Jha Mark Chaisson	Bioinformatics
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
RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.	2012-10-25	Matthew Berriman	Jonathan D Stoltzfus Samuel Minot Thomas J Nolan James B Lok	PLOS Neglected Tropical Diseases
The Population Genomics of Sunflowers and Genomic Determinants of Protein Evolution Revealed by RNAseq.	2012-10-25	Nolan Kane Brook T Moyers Sébastien Renaut Loren H. Rieseberg	Christopher J Grassa	Biology
Identification of cold-responsive genes in a New Zealand alpine stick insect using RNA-Seq.	2012-10-27	Richard D Newcomb Thomas R. Buckley Duckchul Park Brent J Sinclair Alice B Dennis Luke T Dunning		Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics
Identification of PADI2 as a potential breast cancer biomarker and therapeutic target.	2012-10-30	Obi Griffith Venkataraman Subramanian John L. McElwee Brian D Cherrington Louise R Howe	Sunish Mohanan Heike C Breuer Lynne J Anguish Ashley M Palmer 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
Resolving candidate genes of mouse skeletal muscle QTL via RNA-Seq and expression network analyses	2012-11-05	Andrew M Carroll Caroline Meharg David J Vandenbergh	Arimantas Lionikas Jonathan Mj Derry Aivaras Ratkevicius David A Blizard	BMC Genomics
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
Prediction of altered 3'- UTR miRNA-binding sites from RNA-Seq data: the swine leukocyte antigen complex (SLA) as a model region	2012-11-06	Marie-Laure Endale Ahanda Dario Beraldi Jordi Estellé Claire Rogel-Gaillard James M Reecy	Eric R Fritz Zhi-Liang Hu Ole Madsen Martien A M Groenen Ronan Kapetanovic David A Hume Robert R R Rowland Joan K Lunney Elisabetta Giuffra	PLOS ONE
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
Methods, Challenges and Potentials of Single Cell RNA-seq.	2012-11-16	Daniel Hebenstreit		Biology
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
Intron-centric estimation of alternative splicing from RNA-seq data.	2012-11-21	Roderic Guigó i Serra	Dmitri D Pervouchine David G Knowles	Bioinformatics
High-throughput sequencing of the melanoma genome.	2012-11-22	Janet Kelso	Manfred Kunz Michael Dannemann	Experimental Dermatology
A comprehensive analysis of the Manduca sexta immunotranscriptome.	2012-11-23	Haobo Jiang	Ramesh T Gunaratna	Developmental and Comparative Immunology
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 Michael Brudno	Aziz M Mezlini Eric J M Smith Marc Fiume Orion Buske Gleb L Savich Sohrab Shah Sam Aparicio Anna Goldenberg	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
The diverse applications of RNA-seq for functional genomic studies in Aspergillus fumigatus.	2012-12-01	Xiaofan Zhou Antonis Rokas	John G Gibbons Anne Beauvais Jean-Paul Latgé	Annals of the New York Academy of Sciences
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 Karl Kuchler	Anaïs F Bardet Clarissa J Nobile Andriy Petryshyn Walter Glaser Ulrike Schöck	PLOS Genetics
The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells.	2012-12-06	Wolf Reik Felix Krueger Bernard Thienpont Julia Arand	Stefanie Seisenberger Simon Andrews Jörn Walter Fátima Santos Christian Popp Wendy Dean	Molecular Cell
RNA-Seq vs dual- and single-channel microarray data: sensitivity analysis for differential expression and clustering	2012-12-10	Martin Crane	Alina Sîrbu Gráinne Kerr Heather J Ruskin	PLOS ONE
Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study.	2012-12-13	Andrew C Perkins Timothy L. Bailey	Lei Sun Zhihua Zhang Michael R Tallack Zhao Xu Hui Liu	BMC Bioinformatics
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
RNA-Seq analysis implicates dysregulation of the immune system in schizophrenia	2012-12-17	Xiangning Chen	Junzhe Xu Jingchun Sun Jingchun Chen Lily Wang Anna Li Matthew Helm Steven L Dubovsky Silviu-Alin Bacanu Zhongming Zhao	BMC Genomics
A specialized ABC efflux transporter GcABC-G1 confers monoterpene resistance to Grosmannia clavigera, a bark beetle-associated fungal pathogen of pine trees.	2012-12-17	Jörg Bohlmann	Ye Wang Lynette Lim Scott DiGuistini Gordon Robertson Colette Breuil	New Phytologist
Circular RNAs are abundant, conserved, and associated with ALU repeats.	2012-12-18	Norman 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
Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice.	2012-12-22	Guojun Lu	Tingting Lu Chuanrang Zhu Yunli Guo Yan Zhou Zhiyong Zhang Yan Zhao Wenjun Li Ying Lu Weihua Tang Qi Feng Bin Han	BMC Genomics
A comprehensive evaluation of alignment algorithms in the context of RNA-seq	2012-12-26	Caroline C Friedel	Robert Lindner	PLOS ONE
How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?	2012-12-27	Chad Nusbaum	Brian J Haas Melissa Chin Bruce W Birren Jonathan Livny	BMC Genomics
Correlates of relative resistance against low-dose rectal simian immunodeficiency virus challenges in peripheral blood mononuclear cells of vaccinated rhesus macaques.	2012-12-27	Sarah J. Ratcliffe	Raj Kurupati Steve Tuyishime Andrew V Kossenkov Marina Sazanovich Larissa H Haut Marcio O Lasaro Steven E Bosinger Diane G Carnathan Mark Lewis Louise C Showe Guido Silvestri Hildegund C J Ertl	Journal of Leukocyte Biology
Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data	2013	Matthias Kretzler Gil Omenn	Ridvan Eksi Hong-Dong Li Rajasree Menon Yuchen Wen Yuanfang Guan	PLOS Computational Biology
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
Transcriptome sequencing of tumor subpopulations reveals a spectrum of therapeutic options for squamous cell lung cancer	2013	Olivier Harismendy	Christian L Barrett Richard B Schwab HyunChul Jung Brian Crain Daniel J Goff Catriona H M Jamieson Patricia A Thistlethwaite Dennis A Carson Kelly A Frazer	PLOS ONE
RNA-Seq analysis of Cocos nucifera: transcriptome sequencing and de novo assembly for subsequent functional genomics approaches	2013	Yaodong Yang Annaliese S Mason	Haikuo Fan Yong Xiao Wei Xia Zhihui Xia Fei Qiao Songlin Zhao Haoru Tang	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
MicroRNA discovery by similarity search to a database of RNA-seq profiles	2013	Jan Gorodkin Sachin Pundhir		Frontiers in Genetics
Differential analysis of gene regulation at transcript resolution with RNA-seq	2013-01	John L. Rinn	Trapnell C Hendrickson DG Sauvageau M Goff L Pachter L	Nature Biotechnology
Interpreting personal transcriptomes: personalized mechanism-scale profiling of RNA-seq data	2013-01-01	Yves A. Lussier	Alan Perez-Rathke Haiquan Li	Pacific Symposium on Biocomputing
Analysis of RNA-Seq data with TopHat and Cufflinks for genome-wide expression analysis of jasmonate-treated plants and plant cultures.	2013-01-01	Stephane Rombauts Alain Goossens	Jacob Pollier	Methods in Molecular Biology
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
RNA-seq analysis of allele-specific expression, hybrid effects, and regulatory divergence in hybrids compared with their parents from natural populations.	2013-01-01	Loren H. Rieseberg	Graeme D M Bell Nolan C Kane Keith L Adams	Genome Biology and Evolution
Transcriptome sequencing reveals the character of incomplete dosage compensation across multiple tissues in flycatchers.	2013-01-01	Hans Ellegren	Severin Uebbing Axel Künstner Hannu Mäkinen	Genome Biology and Evolution
Genomic, RNAseq, and molecular modeling evidence suggests that the major allergen domain in insects evolved from a homodimeric origin	2013-01-01	Thomas A Randall Geoffrey A Mueller Lalith Perera	Robert E London	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
In vitro expansion of fetal neural progenitors as adherent cell lines.	2013-01-01	Steven M Pollard		Methods in Molecular Biology
Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics.	2013-01-07	Ching-Chia Yang Tsuyoshi Tanaka Takeshi Itoh	Hiroaki Sakai Sung Shin Lee Hisataka Numa Jungsok Kim Yoshihiro Kawahara Hironobu Wakimoto Masao Iwamoto Takashi Abe Yuko Yamada Akira Muto Hachiro Inokuchi Toshimichi Ikemura Takashi Matsumoto Takuji Sasaki	Plant and Cell Physiology
RNA-Seq analysis of the parietal cortex in Alzheimer's disease reveals alternatively spliced isoforms related to lipid metabolism.	2013-01-07	Pingzhao Hu Michael Janitz	James D Mills Thomas Nalpathamkalam Heidi I L Jacobs Caroline Janitz Daniele Merico	Neuroscience Letters
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
MMAPPR: mutation mapping analysis pipeline for pooled RNA-seq.	2013-01-08	Jonathon T Hill	Bradley L Demarest Brent W Bisgrove Bushra Gorsi Yi-Chu Su H Joseph Yost	Genome Research
SIBER: systematic identification of bimodally expressed genes using RNAseq data	2013-01-09	Kevin R. Coombes	Pan Tong Yong Chen Xiao Su	Bioinformatics
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
Dynamic DNA methylation across diverse human cell lines and tissues	2013-01-16	Gregory E Crawford John A Stamatoyannopoulos	Katherine E Varley Jason Gertz Kevin M Bowling Stephanie L Parker Timothy E Reddy Florencia Pauli-Behn Marie K Cross Brian A Williams Devin M Absher Barbara J Wold Richard M Myers	Genome Research
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 James F. Gusella	Hyung-Goo Kim Jill A Rosenfeld Yiping Shen Yves Lacassie Lawrence C Layman Lisa G Shaffer	Human Molecular Genetics
The evolutionary causes and consequences of sex-biased gene expression.	2013-02-01	Hans Ellegren	John Parsch	Nature Reviews Genetics
Comparative study of RNA-seq- and microarray-derived coexpression networks in Arabidopsis thaliana.	2013-02-01	Cristian Del Fabbro	Federico M Giorgi Francesco Licausi	Bioinformatics
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
Genetic screens: RNA-seq into the toolkit.	2013-02-05	Darren J. Burgess		Nature Reviews Genetics
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
The draft genome and transcriptome of Panagrellus redivivus are shaped by the harsh demands of a free-living lifestyle	2013-02-14	Paul W. Sternberg	Jagan Srinivasan Adler R Dillman Marissa G Macchietto Liisa Heikkinen Merja Lakso Kelley M Fracchia Igor Antoshechkin Ali Mortazavi Garry Wong	Genetics
mRNA expression, splicing and editing in the embryonic and adult mouse cerebral cortex.	2013-02-17	Dagmar Galter David N Hauser Mark R Cookson	Allissa A Dillman J Raphael Gibbs Michael A Nalls Melissa K McCoy Iakov N Rudenko	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
Zinc deficiency impacts CO2 assimilation and disrupts copper homeostasis in Chlamydomonas reinhardtii.	2013-02-25	Sabeeha Merchant Matteo Pellegrini David Casero	Davin Malasarn Janette Kropat Scott I Hsieh Giovanni Finazzi Joseph A Loo Francis-André Wollman	Journal of Biological Chemistry
Activity of a Py-Im polyamide targeted to the estrogen response element.	2013-02-26	Jerzy O Szablowski Peter Dervan	Nicholas G Nickols Amanda E Hargrove Benjamin C Li Jevgenij A Raskatov	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 Verma Gregory S. Pari	Margaret Tarrant-Elorza Pravinkumar Purushothaman	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
A comparison of methods for differential expression analysis of RNA-seq data	2013-03-09	Charlotte Soneson	Mauro Delorenzi	BMC Bioinformatics
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
The transcript catalogue of the short-lived fish Nothobranchius furzeri provides insights into age-dependent changes of mRNA levels.	2013-03-16	Matthias Platzer	Andreas Petzold Kathrin Reichwald Marco Groth Stefan Taudien Nils Hartmann Steffen Priebe Dmitry Shagin Christoph Englert	BMC Genomics
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
Zinc-mediated RNA fragmentation allows robust transcript reassembly upon whole transcriptome RNA-Seq.	2013-03-21	Maxime Wery Daniel Gautheret	Marc Descrimes Claude Thermes Antonin Morillon	Methods
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 Thomas Wicker Huanming Yang	Jizeng Jia Shancen Zhao Xiuying Kong Yingrui Li Guangyao Zhao Weiming He Rudi Appels Matthias Pfeifer Yong Tao Xueyong Zhang Ruilian Jing Chi Zhang Youzhi Ma Lifeng Gao Chuan Gao Manuel Spannagl Dong Li Shengkai Pan Fengya Zheng Qun Hu Xianchun Xia Jianwen Li Qinsi Liang Jie Chen Caiyun Gou Hanhui Kuang Genyun He Yadan Luo Beat Keller Qiuju Xia Peng Lu Hongfeng Zou Rongzhi Zhang Junyang Xu Jinlong Gao Christopher Middleton Zhiwu Quan Guangming Liu Jian Wang Xu Liu Zhonghu He Long Mao	Nature
RNAseq versus genome-predicted transcriptomes: a large population of novel transcripts identified in an Illumina-454 Hydra transcriptome	2013-03-25	Brigitte Galliot	Yvan Wenger	BMC Genomics
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
Differential expression analysis for paired RNA-Seq data	2013-03-27	Ruth R Montgomery	Lisa M Chung John P Ferguson Wei Zheng Feng Qian Vincent Bruno Hongyu Zhao	BMC Bioinformatics
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
Gene regulation by CcpA and catabolite repression explored by RNA-Seq in Streptococcus mutans	2013-03-28	Adam C. Siepel Robert A Burne	Lin Zeng Sang Chul Choi Charles G Danko Michael J Stanhope	PLOS ONE
Comprehensive molecular screening: from the RT-PCR to the RNA-seq.	2013-04-01	Rafael Rosell	Carlota Costa Ana Giménez-Capitán Niki Karachaliou	Translational lung cancer research
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
The transcriptome of Leishmania major in the axenic promastigote stage: transcript annotation and relative expression levels by RNA-seq.	2013-04-04	A Rastrojo Rosa M. Reguera	Fernando Carrasco-Ramiro Diana Martín Antonio Crespillo Begoña Aguado Jose M Requena	BMC Genomics
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 Kate Killick	Nicolas C Nalpas Stephen D E Park David A Magee Maria Taraktsoglou John A Browne Kevin M Conlon	BMC Genomics
Characterization of FUS mutations in amyotrophic lateral sclerosis using RNA-Seq.	2013-04-08	Marka van Blitterswijk Brad Friedman Leonard H van den Berg Jan H Veldink	Eric T Wang Pamela J Keagle Patrick Lowe Ashley Lyn Leclerc David E Housman John E Landers	PLOS ONE
Functional genomics based understanding of rice endosperm development.	2013-04-10	Shi-Rong Zhou	Lin-Lin Yin Hong-Wei Xue	Current Opinion in Plant Biology
Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo.	2013-04-11	Abhinav Nellore	Alexander D Ramos Aaron Diaz Ryan N Delgado Ki-Youb Park Gabriel Gonzales-Roybal Michael C Oldham Jun S Song Daniel A Lim	Cell Stem Cell
Accurate detection of differential RNA processing.	2013-04-12	Oliver Stegle Gunnar Rätsch Karsten M Borgwardt	Philipp Drewe Lisa Hartmann André Kahles Regina Bohnert Andreas Wachter	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
Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size.	2013-04-14	Wolfgang Huber	Danni Yu Olga Vitek	Bioinformatics
Faculty of 1000 evaluation for Transcriptome Profiling of Giardia intestinalis Using Strand-specific RNA-Seq	2013-04-16	Christen Rune Stensvold	C Graham Clark
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
Sprouts of RNA epigenetics: the discovery of mammalian RNA demethylases.	2013-04-17	Arne Klungland	Guanqun Zheng John Arne Dahl Yamei Niu Ye Fu Yun-Gui Yang Chuan He	RNA 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
Massively parallel sequencing, aCGH, and RNA-Seq technologies provide a comprehensive molecular diagnosis of Fanconi anemia.	2013-04-23	Elaine Ostrander Agata Smogorzewska Arleen D. Auerbach NISC Comparative Sequencing Program	Settara C Chandrasekharappa Francis P Lach Danielle C Kimble Aparna Kamat Jamie K Teer Frank X Donovan Elizabeth Flynn Shurjo K Sen Supawat Thongthip Erica Sanborn	Blood
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
RNAseq-based transcriptome analysis of Lactuca sativa infected by the fungal necrotroph Botrytis cinerea.	2013-04-26	Barbara De Coninck	Kaat De Cremer Janick Mathys Christine Vos Lutz Froenicke Richard W Michelmore Bruno P A Cammue	Plant, Cell and Environment
Prediction of transcribed PIWI-interacting RNAs from CHO RNAseq data.	2013-04-29	Johannes Grillari Alexandra B Graf Matthias Hackl Nicole Borth	Matthias Peter Gerstl	Journal of Biotechnology
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 Luyang Sun Yu Zhang	Xiuli Wang Fanyue Sun Jiaren Zhang Jianbin Feng Hong Liu K V Rajendran Yanliang Jiang Zhanjiang Liu	Physiological Genomics
Erratum: RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings	2013-05	Jun Wang Huanming Yang	Shancheng Ren Zhiyu Peng Jian-Hua Mao Yongwei Yu Changjun Yin Xin Gao Zilian Cui Jibin Zhang Kang Yi Weidong Xu Chao Chen Fubo Wang Xinwu Guo Ji Lu Jun Yang Min Wei Zhijian Tian Yinghui Guan Liang Tang Chuanliang Xu Linhui Wang Xu Gao Wei Tian Jian Wang Yinghao Sun	Cell Research
Glucocorticoid-induced changes in gene expression of airway smooth muscle in patients with asthma.	2013-05-01	Frank Baas Kees Fluiter	Ching Yong Yick Aeilko H Zwinderman Peter W Kunst Katrien Grünberg Thais Mauad Elisabeth H Bel René Lutter Peter J Sterk	American Journal of Respiratory and Critical Care Medicine
Transcription factors that convert adult cell identity are differentially polycomb repressed	2013-05-01	Sean Eddy Davis FP		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 Erik K Flemington	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	PLOS Pathogens
In vitro-differentiated neural cell cultures progress towards donor-identical brain tissue	2013-05-10	Thomas G Beach	Brooke E Hjelm Bodour Salhia Ahmet Kurdoglu Szabolcs Szelinger Rebecca A Reiman Lucia I Sue Matthew J Huentelman David W Craig	Human Molecular Genetics
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
Optimizing de novo assembly of short-read RNA-seq data for phylogenomics.	2013-05-14	Stephen A. Smith	Ya Yang	BMC Genomics
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 Stefan Scheu François Buscot	Sylvie Herrmann Lasse Feldhahn Sabine Recht Florence Kurth Sarah Mailänder Markus Bönn Maren Neef Oguzhan Angay Michael Bacht Marcel Graf Hazel Maboreke Frank Fleischmann Thorsten E E Grams Liliane Ruess Roland Brandl Silvia D Schrey Ivo Grosse	New Phytologist
Complexities of gammaherpesvirus transcription revealed by microarrays and RNAseq.	2013-05-16	Laurie T. Krug		Current opinion in virology
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
Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs	2013-06	Michael McManus	Matthew J Hangauer Ian W Vaughn	PLOS Genetics
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 Marcia Saraiva Julio C Vega-Arreguín Paul F Morris	Rays H Y Jiang Brian J Haas Rodrigo Belmonte Lars Löbach James Christie Arnaud Bottin Vincent Bulone Sara M Díaz-Moreno Lin Fan Elodie Gaulin Laura J Grenville-Briggs Joshua Z Levin Marco Mammella Harold J G Meijer Stan Oome Andrew J Phillips David van Rooyen Elzbieta Rzeszutek Chris J Secombes Joost H M Stassen Sean Sykes Herbert van den Berg Sarah K Young Qiandong Zeng Javier Dieguez-Uribeondo Brett M Tyler	PLOS Genetics
RNA-seq analysis reveals extensive transcriptional plasticity to temperature stress in a freshwater fish species.	2013-06-05	Steve Smith Luciano B. Beheregaray	Louis Bernatchez	BMC Genomics
Landscape of DNA virus associations across human malignant cancers: analysis of 3,775 cases using RNA-Seq	2013-06-05	Michelle D Williams Funda Meric-Bernstam	Joseph D Khoury Nizar M Tannir Yunxin Chen Hui Yao Jianping Zhang Erika J Thompson TCGA Network L Jeffrey Medeiros John N Weinstein Xiaoping Su	Journal of Virology
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
A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples	2013-06-10	Paolo Piazza Elizabeth M Batty Tanya Golubchik Kate E Dingle Paul Klenerman Daniel Wilson Eleanor Barnes	T H Nicholas Wong Amy Trebes Karène Argoud Moustafa Attar David Buck Camilla L C Ip Madeleine Cule Rory Bowden Charis Manganis A Sarah Walker David H Wyllie Tim E A Peto Derrick W Crook	PLOS ONE
Assessment of gene expression in peripheral blood using RNAseq before and after weight restoration in anorexia nervosa	2013-06-15	Cynthia M. Bulik	Yunjung Kim Sara E Trace James J Crowley Kimberly A Brownley Robert M Hamer David S Pisetsky Patrick F Sullivan	Psychiatry Research
Comprehensive High-Resolution Analysis of the Role of an Arabidopsis Gene Family in RNA Editing	2013-06-20	Stéphane Bentolila Maureen R. Hanson	Julyun Oh Robert Bukowski	PLOS Genetics
RNA-seq in the tetraploid Xenopus laevis enables genome-wide insight in a classic developmental biology model organism	2013-06-20	Erin Osborne	Nirav M Amin Panna Tandon Frank L Conlon	Methods
Cellular source and mechanisms of high transcriptome complexity in the mammalian testis.	2013-06-20	Anamaria Necsulea	Magali Soumillon Manuela Weier David Brawand Xiaolan Zhang Hongcang Gu Pauline Barthès Maria Kokkinaki Serge Nef Andreas Gnirke Martin Dym Bernard de Massy Tarjei S Mikkelsen Henrik Kaessmann	Cell Reports
ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells.	2013-06-21	Avi Ma'ayan Caroline Baroukh	Huilei Xu Ruth Dannenfelser Edward Y Chen Christopher M Tan Yan Kou Yujin E Kim Ihor R Lemischka	Database
Global transcriptome profiles of Camellia sinensis during cold acclimation	2013-06-22	Qiong-Yi Zhao	Xin-Chao Wang Chun-Lei Ma Zong-Hong Zhang Hong-Li Cao Yi-Meng Kong Chuan Yue Xin-Yuan Hao Liang Chen Jian-Qiang Ma Ji-Qiang Jin Xuan Li Ya-Jun Yang	BMC Genomics
Evaluating the impact of sequencing depth on transcriptome profiling in human adipose	2013-06-24	Jane Ferguson Muredach P. Reilly	Yichuan Liu Chenyi Xue Ian M Silverman Brian Gregory Mingyao Li	PLOS ONE
Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets	2013-06-28	W. Richard McCombie	Xiao Xu Yuanhao Zhang Jennie Williams Eric Antoniou Song Wu Wei Zhu Nicholas O Davidson Paula Denoya Ellen Li	BMC Bioinformatics
Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation.	2013-07-01	Sayan Mukherjee Uwe Ohler	Dina Hafez Ting Ni Jun Zhu	Bioinformatics
Classification of topological domains based on gene expression and regulation.	2013-07-01	Nadav Ahituv	Jingjing Zhao Hongbo Shi	Genome
RNA-Seq-based analysis of the physiologic cold shock-induced changes in Moraxella catarrhalis gene expression.	2013-07-02	Stefan Wyder Christoph Aebi	Violeta Spaniol	PLOS ONE
Exonuclease hDIS3L2 specifies an exosome-independent 3'-5' degradation pathway of human cytoplasmic mRNA	2013-07-03	Andrzej Dziembowski Rafał Tomecki Torben Heick Jensen Dominik Cysewski	Michal Lubas Christian K Damgaard	The EMBO Journal
RNaseIII and T4 polynucleotide Kinase sequence biases and solutions during RNA-seq library construction	2013-07-04	Claus O. Wilke	Changhoon Lee R Adron Harris Jason K Wall R Dayne Mayfield	Biology Direct
Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution	2013-07-05	Mark Bender Gerstein	Gang Fang Karla D Passalacqua Jason Hocking Paula Montero Llopis Nicholas H Bergman Christine Jacobs-Wagner	BMC Genomics
Identification of novel point mutations in splicing sites integrating whole-exome and RNA-seq data in myeloproliferative diseases	2013-07-07	Carlo Gambacorti-Passerini Vera Magistroni	Roberta Spinelli Alessandra Pirola Sara Redaelli Nitesh Sharma Hima Raman Simona Valletta Rocco Piazza	Molecular genetics & genomic medicine
Identification of genes critical for resistance to infection by West Nile virus using RNA-Seq analysis.	2013-07-08	Sebastian Kurscheid Ruth R Montgomery Erol Fikrig Mark Bender Gerstein	Feng Qian Lisa Chung Wei Zheng Vincent Bruno Roger P Alexander Zhong Wang Xiaomei Wang Hongyu Zhao Michael Snyder	Viruses
Clear cell renal cell carcinoma associated microRNA expression signatures identified by an integrated bioinformatics analysis.	2013-07-10	Wenying Yan	Jiajia Chen Daqing Zhang Wenyu Zhang Yifei Tang Lingchuan Guo Bairong Shen	Journal of Translational Medicine
Vitamin D receptor ChIP-seq in primary CD4+ cells: relationship to serum 25-hydroxyvitamin D levels and autoimmune disease	2013-07-12	Geir Kjetil Sandve Gavin Giovannoni	Adam E Handel Giulio Disanto Antonio J Berlanga-Taylor Giuseppe Gallone Heather Hanwell Finn Drabløs George C Ebers Sreeram V Ramagopalan	BMC Medicine
Male-biased genes in catfish as revealed by RNA-Seq analysis of the testis transcriptome.	2013-07-12	Shikai Liu Ludmilla Kaltenboeck Luyang Sun Rex Dunham	Fanyue Sun Xiaoyu Gao Yanliang Jiang Dayan Perera Xiuli Wang Chao Li Jiaren Zhang Zhanjiang Liu	PLOS ONE
Senescence-associated lncRNAs: senescence-associated long noncoding RNAs.	2013-07-14	Kevin G. Becker Myriam Gorospe Kotb Abdelmohsen	Amaresh Panda Min-Ju Kang Jason Xu Roza Selimyan Je-Hyun Yoon Jennifer L Martindale Supriyo De William H Wood	Aging Cell
Transcriptome analysis of mouse brain infected with Toxoplasma gondii.	2013-07-15	Yoshifumi Nishikawa	Sachi Tanaka Maki Nishimura Fumiaki Ihara Junya Yamagishi Yutaka Suzuki	Infection and Immunity
Diversity in the complexity of phosphate starvation transcriptomes among rice cultivars based on RNA-Seq profiles.	2013-07-16	Hirokazu Handa Takeshi Itoh	Youko Oono Yoshihiro Kawahara Takayuki Yazawa Hiroyuki Kanamori Masato Kuramata Harumi Yamagata Satomi Hosokawa Hiroshi Minami Satoru Ishikawa Jianzhong Wu Baltazar Antonio Takashi Matsumoto	Plant Molecular Biology
Proteogenomic database construction driven from large scale RNA-seq data.	2013-07-17	Vineet Bafna	Sunghee Woo Seong Won Cha Gennifer Merrihew Yupeng He Natalie Castellana Clark Guest Michael MacCoss	Journal of Proteome Research
CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes	2013-07-18	Jennifer Doudna Lei S Qi Jonathan Weissman Noam Stern-Ginossar	Luke A Gilbert Matthew H Larson Leonardo Morsut Zairan Liu Gloria A Brar Sandra E Torres Onn Brandman Evan H Whitehead Wendell A Lim	Cell
Methylmercury exposure increases lipocalin related (lpr) and decreases activated in blocked unfolded protein response (abu) genes and specific miRNAs in Caenorhabditis elegans	2013-07-18	Natalia Vanduyn	Martina Rudgalvyte Vuokko Aarnio Liisa Heikkinen Juhani Peltonen Merja Lakso Richard Nass Garry Wong	Toxicology Letters
Using a periclinal chimera to unravel layer-specific gene expression in plants.	2013-07-19	James Abbott	Ioannis Filippis Rosa Lopez-Cobollo Sarah Butcher Gerard J Bishop	The Plant Journal
Gene networks and chromatin and transcriptional regulation of the phaseolin promoter in Arabidopsis.	2013-07-19	Lakshminarayan M. Iyer	Sabarinath Sundaram Sunee Kertbundit Eugene V Shakirov Lakshminarayan M Iyer Miloslav Jurícek Timothy C Hall	The Plant Cell
Enhanced expression of codon optimized interferon gamma in CHO cells.	2013-07-19	Dong-Yup Lee	Bevan Kai-Sheng Chung Faraaz N K Yusufi Mariati Yuansheng Yang	Journal of Biotechnology
GLiMMPS: robust statistical model for regulatory variation of alternative splicing using RNA-seq data.	2013-07-22	Zhi-xiang Lu	Keyan Zhao Juw Won Park Qing Zhou Yi Xing	Genome Biology
Replication protein A subunit 3 and the iron efficiency response in soybean.	2013-07-22	Dianne Cook	Sarah E Atwood Jamie A O'Rourke Gregory A Peiffer Tengfei Yin Mahbubul Majumder Chunquan Zhang Silvia R Cianzio John H Hill Steven A Whitham Randy C Shoemaker Michelle A Graham	Plant, Cell and Environment
Knockdown of CDKN1C (p57(kip2)) and PHLDA2 results in developmental changes in bovine pre-implantation embryos	2013-07-22	Francisco Peñagaricano Wen Huang	Ashley M Driver Jenna Kropp Hasan Khatib	PLOS ONE
Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome.	2013-07-22	Ulrich Omasits Christian H Ahrens Mark D. Robinson Christoph Dehio	Maxime Quebatte Daniel J Stekhoven Claudia Fortes Bernd Roschitzki	Genome Research
Pairwise comparisons of ten porcine tissues identify differential transcriptional regulation at the gene, isoform, promoter and transcription start site level.	2013-07-27	Christian Bendixen	Leila Farajzadeh Henrik Hornshøj Jamal Momeni Bo Thomsen Knud Larsen Jakob Hedegaard Lone Bruhn Madsen	Biochemical and Biophysical Research Communications
Basal polarization of the mucosal compartment in Flavobacterium columnare susceptible and resistant channel catfish (Ictalurus punctatus).	2013-07-27	Eric Peatman	Chao Li Brian C Peterson David L Straus Bradley D Farmer Benjamin H Beck	Molecular Immunology
Differential programming of B cells in AID deficient mice	2013-07-29	Bas van Steensel	Marc A Hogenbirk Marinus R Heideman Arno Velds Paul C M van den Berk Ron M Kerkhoven Heinz Jacobs	PLOS ONE
DNA methylation, genotype and gene expression: who is driving and who is along for the ride?	2013-07-29	Meaghan J Jones Michael S Kobor	Anthony P Fejes	Genome Biology
Global gene expression response of a population exposed to benzene: a pilot study exploring the use of RNA-sequencing technology	2013-08	Nathaniel Rothman	Reuben Thomas Cliona M McHale Qing Lan Alan E Hubbard Luoping Zhang Roel Vermeulen Guilan Li Stephen M Rappaport Songnian Yin Martyn T Smith	Environmental and Molecular Mutagenesis
Computational analysis of bacterial RNA-Seq data	2013-08	Paul Sumby	Ryan McClure Divya Balasubramanian Yan Sun Maksym Bobrovskyy Caroline A Genco Carin K Vanderpool Brian Tjaden	Nucleic Acids Research
The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line	2013-08-01	Jay Shendure Joshua N Burton	Andrew Adey Jacob O Kitzman Joseph B Hiatt Alexandra P Lewis Beth K Martin Ruolan Qiu Choli Lee	Nature
Increased BCAR1 predicts poor outcomes of non-small cell lung cancer in multiple-center patients.	2013-08-01	Zhifu Sun	Bo Deng Wampfler Jason Ping Yang	Annals of Surgical Oncology
RNA-Seq reveals early distinctions and late convergence of gene expression between diapause and quiescence in the Asian tiger mosquito, Aedes albopictus	2013-08-02	Christine G Elsik Monica F Poelchau	Julie A Reynolds David L Denlinger Peter A Armbruster	The Journal of Experimental Biology
Photoreceptor phagocytosis is mediated by phosphoinositide signaling.	2013-08-02	Krzysztof Palczewski	Debarshi Mustafi Brian M Kevany Christel Genoud Xiaodong Bai	FASEB Journal
Simultaneous profiling of 194 distinct receptor transcripts in human cells	2013-08-06	Kevin A. Janes	Byong H Kang Karin J Jensen Jaime A Hatch	Science Signaling
Masculinization of the x chromosome in the pea aphid.	2013-08-08	Solenn Stoeckel Fabrice Legeai Gaël Le Trionnaire Julie Jaquiéry Nathalie Prunier-Leterme Béatrice Ségurens Julie Poulain Denis Tagu Corinne Da Silva Claude Rispe	Denis Roze Lucie Mieuzet Béatrice Ségurens Jean-Christophe Simon	PLOS Genetics
BlackOPs: increasing confidence in variant detection through mappability filtering.	2013-08-08	Charles M. Perou	Christopher R Cabanski Matthew D Wilkerson Matthew Soloway Joel S Parker Jinze Liu Jan F Prins J S Marron D Neil Hayes	Nucleic Acids Research
Genome-wide transcriptional response of Trichoderma reesei to lignocellulose using RNA sequencing and comparison with Aspergillus niger	2013-08-09	Stéphane Delmas Steven T. Pullan	Laure Ries Sunir Malla Martin J Blythe David B Archer	BMC Genomics
Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons.	2013-08-12	Cameron Brennan David Haussler Lynda Chin	J Zachary Sanborn Sofie R Salama Mia Grifford Tom Mikkelsen Suresh Jhanwar Sol Katzman	Cancer Research
Developing nuclear DNA phylogenetic markers in the angiosperm genus Leucadendron (Proteaceae): a next-generation sequencing transcriptomic approach.	2013-08-13	Emmanuel J. P. Douzery	Jeanne Tonnabel Isabelle Olivieri Agnès Mignot Anthony Rebelo Fabienne Justy Sylvain Santoni Stéfanie Caroli Laure Sauné Olivier Bouchez	Molecular Phylogenetics and Evolution
Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp. citri provide insights into mechanisms of bacterial virulence and host range.	2013-08-14	Joao Carlos Setubal Maxuel O Andrade	Neha Jalan Dibyendu Kumar Fahong Yu Jeffrey B Jones James H Graham Frank F White Nian Wang	BMC Genomics
Next-generation sequencing of advanced prostate cancer treated with androgen-deprivation therapy.	2013-08-14	Owen J Sansom Chris Ponting Andreas Heger Ian Sudbery Imran Ahmad Joanne Edwards Hing Y Leung Prabhakar Rajan	M Eugenia M Villasevil Ernest Mui Janis Fleming Mark Davis David Sims Rhona M McMenemin Ian D Pedley	European Urology
Adaptive responses to glucose restriction enhance cell survival, antioxidant capability, and autophagy of the protozoan parasite Trichomonas vaginalis.	2013-08-17	Petrus Tang	Kuo-Yang Huang Yi-Ywan Margaret Chen Yi-Kai Fang Wei-Hung Cheng Chih-Chieh Cheng Yu-Chuen Chen Tiffany E Wu Fu-Man Ku Shih-Chieh Chen Rose Lin	Biochimica et Biophysica Acta
Shaping development through mechanical strain: the transcriptional basis of diet-induced phenotypic plasticity in a cichlid fish.	2013-08-19	Helen M Gunter Paolo Franchini Axel Meyer Carmelo Fruciano	Shaohua Fan Fan Xiong	Molecular Ecology
Mechanisms of macroevolution: polyphagous plasticity in butterfly larvae revealed by RNA-Seq.	2013-08-19	Niklas Janz Sören Nylin Maria de la Paz Celorio-Mancera	Christopher W Wheat Heiko Vogel Lina Söderlind	Molecular Ecology
Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data.	2013-08-20	Quanhu Sheng David C Samuels	Yan Guo Jiang Li Fei Ye Yu Shyr	PLOS ONE
A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments.	2013-08-21	Pedro Puig	Mikel Esnaola David Gonzalez Robert Castelo Juan R Gonzalez	BMC Bioinformatics
Whole transcriptome RNA-Seq allelic expression in human brain	2013-08-22	Wolfgang Sadee	Ryan M Smith Amy Webb Audrey C Papp Leslie C Newman Samuel K Handelman Adam Suhy Roshan Mascarenhas John Oberdick	BMC Genomics
Jumping and gliding rodents: mitogenomic affinities of Pedetidae and Anomaluridae deduced from an RNA-Seq approach.	2013-08-23	Knud A. Jønsson Emmanuel J. P. Douzery	Pierre-Henri Fabre	Gene
Profiling microRNA expression in bovine alveolar macrophages using RNA-seq.	2013-08-24	Daniel G. Bradley Peter Vegh David J. Lynn David E. MacHugh Stephen V. Gordon	Amir B K Foroushani David A Magee Matthew S McCabe John A Browne Nicolas C Nalpas Kevin M Conlon	Veterinary Immunology and Immunopathology
Transcriptome analysis and SNP identification in SCC of horn in (Bos indicus) Indian cattle.	2013-08-24	Subhash J Jakhesara Chaitanya G. Joshi	Prakash G Koringa Vaibhav D Bhatt Anand B Patel Debabrata Dash	Gene
MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples.	2013-08-25	Gunnar Rätsch	Jonas Behr André Kahles Yi Zhong Vipin T Sreedharan Philipp Drewe	Bioinformatics
Complete mitochondrial genome of the medicinal mushroom Ganoderma lucidum	2013-08-26	Jianhui Zhang	Jianqin Li Haimei Chen Xiangdong Chen Jin Lan Chang Liu	PLOS ONE
Breakpoint features of genomic rearrangements in neuroblastoma with unbalanced translocations and chromothripsis.	2013-08-26	Isabelle Janoueix-Lerosey Valérie Combaret Valentina Boeva Emmanuel Barillot Olivier Delattre	Stéphanie Jouannet Romain Daveau Cécile Pierre-Eugène Alex Cazes Caroline Louis-Brennetot Gudrun Schleiermacher Sandrine Ferrand Gaëlle Pierron Alban Lermine Thomas Rio Frio Virginie Raynal Gilles Vassal	PLOS ONE
Remodeling of membrane lipids in iron-starved Chlamydomonas.	2013-08-27	David Casero Sabeeha Merchant Matteo Pellegrini Eugen Urzica Sean D Gallaher Astrid Vieler Christoph Benning	Anne Hong-Hermesdorf M Dudley Page Janette Kropat	Journal of Biological Chemistry
Characterization and comparative analyses of muscle transcriptomes in Dorper and small-tailed Han sheep using RNA-Seq technique.	2013-08-30	Jianmin Wang	Chunlan Zhang Guizhi Wang Zhibin Ji Zhaohuan Liu Xiushuang Pi Cunxian Chen	PLOS ONE
SNP development from RNA-seq data in a nonmodel fish: how many individuals are needed for accurate allele frequency prediction?	2013-08-31	Enrique Macpherson	C Schunter J C Garza M Pascual	Molecular Ecology Resources
SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization	2013-08-31	Shintaro Katayama Juha Kere Sten Linnarsson	Virpi Töhönen	Bioinformatics
Editorial for “Diversity of the non-coding transcriptomes revealed by RNA-seq technologies”	2013-09	Jean-Christophe Andrau	Antonin Morillon	Methods
Mutually exclusive signaling signatures define the hepatic and pancreatic progenitor cell lineage divergence.	2013-09-01	Nuria Cerdá-Esteban Nancy Mah Francesca Spagnoli	Elisa Rodríguez-Seguel Heike Naumann Igor M Pongrac Jean-Fred Fontaine Yongbo Wang Wei Chen Miguel A Andrade-Navarro	Genes & Development
Mining RNA-seq data for infections and contaminations.	2013-09-03	Caroline C Friedel Ralf Zimmer	Thomas Bonfert Gergely Csaba	PLOS ONE
RNA-Seq reveals infection-related gene expression changes in Phytophthora capsici.	2013-09-03	Xiao-Ren Chen	Yu-Ping Xing Yan-Peng Li Yun-Hui Tong Jing-You Xu	PLOS ONE
Trametes versicolor protein YZP activates regulatory B lymphocytes - gene identification through de novo assembly and function analysis in a murine acute colitis model.	2013-09-03	Fuu Sheu	Yen-Chou Kuan Ying-Jou Wu Chih-Liang Hung	PLOS ONE
Short-term feed deprivation alters immune status of surface mucosa in channel catfish (Ictalurus punctatus).	2013-09-04	Eric Peatman Lisa Liu	Chao Li Baofeng Su Benjamin H Beck	PLOS ONE
Copper response regulator1-dependent and -independent responses of the Chlamydomonas reinhardtii transcriptome to dark anoxia.	2013-09-06	David Casero Thomas Happe Sabeeha Merchant Matteo Pellegrini Anja Hemschemeier Christoph Benning	Bensheng Liu	The Plant Cell
Accelerating the design of biomimetic materials by integrating RNA-seq with proteomics and materials science.	2013-09-08	Yiqi Seow Shahrouz Amini Ali Miserez	Paul A Guerette Shawn Hoon Manfred Raida Admir Masic Fong T Wong Vincent H B Ho Kiat Whye Kong Melik C Demirel Abdon Pena-Francesch Gavin Z Tay Dawei Ding	Nature Biotechnology
Beta cell 5'-shifted isomiRs are candidate regulatory hubs in type 2 diabetes.	2013-09-09	Jeanette Baran-Gale	Emily E Fannin C Lisa Kurtz Praveen Sethupathy	PLOS ONE
U1 small nuclear ribonucleoprotein complex and RNA splicing alterations in Alzheimer's disease.	2013-09-10	Yuxin Li Drew R Jones Hao Wu Eric B Dammer David A Bennett	Bing Bai Chadwick M Hales Ping-Chung Chen Yair Gozal Jason J Fritz Xusheng Wang Qiangwei Xia Duc M Duong Craig Street Gloria Cantero Dongmei Cheng Zhiping Wu Ian Diner Craig J Heilman Howard D Rees Li Lin Keith E Szulwach Marla Gearing Elliott J Mufson Thomas J Montine Nicholas T Seyfried Thomas S Wingo Yi E Sun Peng Jin John Hanfelt Donna M Willcock Allan Levey James J Lah Junmin Peng	Proceedings of the National Academy of Sciences of the United States of America
Analysis of allele-specific expression in mouse liver by RNA-Seq: a comparison with Cis-eQTL identified using genetic linkage.	2013-09-11	Aldons Jake Lusis Eleazar Eskin Pierre-François Roux Sandrine Lagarrigue	Lisa Martin Farhad Hormozdiari Calvin Pan Atila van Nas Olivier Demeure Rita Cantor Anatole Ghazalpour	Genetics
Androgen receptor signaling regulates DNA repair in prostate cancers.	2013-09-11	Deyou Zheng Daniel E. Spratt Michael J Zelefsky	William R Polkinghorn Joel S Parker Man X Lee Elizabeth M Kass Phillip J Iaquinta Vivek K Arora Wei-Feng Yen Ling Cai Brett S Carver Yu Chen Philip A Watson Neel P Shah Sho Fujisawa Alexander G Goglia Anuradha Gopalan Haley Hieronymus John Wongvipat Peter T Scardino Maria Jasin Jayanta Chaudhuri Simon N Powell Charles L Sawyers	Cancer Discovery
A combination of improved differential and global RNA-seq reveals pervasive transcription initiation and events in all stages of the life-cycle of functional RNAs in Propionibacterium acnes, a major contributor to wide-spread human disease	2013-09-14	Kenneth J McDowall	Yu-fei Lin David Romero A Shuang Guan Lira Mamanova	BMC Genomics
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.	2013-09-15	Ann-Christine Syvänen Michael Sammeth Tuuli Lappalainen Xavier Estivill i Pallejà Peter A.C. 't Hoen Marc Friedlander Jeroen Laros	Jonas Almlöf Irina Pulyakhina Seyed Yahya Anvar Henk P J Buermans Olof Karlberg Mathias Brännvall GEUVADIS Consortium Johan T den Dunnen Gert-Jan B van Ommen Ivo G Gut Roderic Guigó Emmanouil T Dermitzakis	Nature Biotechnology
Localizing transcripts to single cells suggests an important role of uncultured deltaproteobacteria in the termite gut hydrogen economy	2013-09-16	Niles A. Pierce Xinning Zhang Vikas Trivedi	Adam Z Rosenthal Kaitlyn S Lucey Elizabeth A Ottesen Harry M T Choi Niles A Pierce Jared R Leadbetter	Proceedings of the National Academy of Sciences of the United States of America
RNA-Seq analysis of Mycobacterium avium non-coding transcriptome	2013-09-16	Dmitriy Ignatov Timofey Skvortsov Alexander S Apt	Sofia Malakho Konstantin Majorov Tatyana Azhikina	PLOS ONE
DEXUS: identifying differential expression in RNA-Seq studies with unknown conditions	2013-09-17	Sepp Hochreiter Günter Klambauer Thomas Unterthiner		Nucleic Acids Research
Analysis of the host transcriptome from demyelinating spinal cord of murine coronavirus-infected mice.	2013-09-18	Fan Li	Ruth Elliott Isabelle Dragomir Ming Ming W Chua Brian D Gregory Susan R Weiss	PLOS ONE
Differentiating progressive from nonprogressive T1 bladder cancer by gene expression profiling: applying RNA-sequencing analysis on archived specimens.	2013-09-18	John Quackenbush	Xuanhui Sharron Lin Lan Hu Kirley Sandy Mick Correll Chin-Lee Wu William Scott McDougal	Urologic Oncology
Epstein-Barr virus and human herpesvirus 6 detection in a non-Hodgkin's diffuse large B-cell lymphoma cohort by using RNA sequencing.	2013-09-18	Melody Baddoo Tina O'Grady Erik K Flemington	Michael J Strong Zhen Lin Guorong Xu Melody Baddoo Chris Parsons Kun Zhang Christopher M Taylor	Journal of Virology
Using transcriptomics to improve butanol tolerance of Synechocystis sp. strain PCC 6803.	2013-09-20	Jens Nielsen Mathias Uhlén Elton P. Hudson	Josefine Anfelt Björn Hallström	Applied and Environmental Microbiology
Accounting for technical noise in single-cell RNA-seq experiments.	2013-09-22	Simon Anders Vladimir Benes Sarah Teichmann John C Marioni Valentina Proserpio Marcus Heisler Jong Kyoung Kim	Philip Brennecke Aleksandra A Kołodziejczyk Xiuwei Zhang Bianka Baying	Nature Methods
Cryptic FUS-ERG fusion identified by RNA-sequencing in childhood acute myeloid leukemia.	2013-09-25	Sverre Heim Ioannis Panagopoulos	Ludmila Gorunova Bernward Zeller Anne Tierens	Oncology Reports
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 Robert Tjian	Haiying Zhou Ying He P Jeremy Wang	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 Zhen Chen	Shihong Mao Robert J Goodrich Steven M Schrader Stephen A Krawetz	Systems Biology in Reproductive Medicine
RNA-Seq of Bacillus licheniformis: active regulatory RNA features expressed within a productive fermentation	2013-10-01	Heiko Liesegang Sandra Wiegand Rolf Daniel	Sascha Dietrich Robert Hertel Johannes Bongaerts Stefan Evers Sonja Volland	BMC Genomics
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 Antony Bacic	Isabel E Moller Andrew Cassin Daniel F Jones Poh Ling Koh Sunil Ratnayake Cherie T Beahan Sarah M Wilson	PLOS ONE
Soft truncation thresholding for gene set analysis of RNA-seq data: application to a vaccine study	2013-10-09	Gregory Poland	Brooke L Fridley Gregory D Jenkins Diane E Grill Richard B Kennedy Ann L Oberg	Scientific Reports
mirCoX: a database of miRNA-mRNA expression correlations derived from RNA-seq meta-analysis.	2013-10-09	Mikhail G Dozmorov	Cory B Giles Reshmi Girija-Devi Jonathan D Wren	BMC Bioinformatics
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 Edward R. Dougherty	Noushin Ghaffari Mohammadmahdi R Yousefi Ivan Ivanov	BMC Bioinformatics
Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots.	2013-10-11	W. Richard McCombie Elena A Vidal Gabriel Krouk Milos Tanurdzic Rodrigo A Gutiérrez	Tomás C Moyano Manpreet S Katari Gloria M Coruzzi	BMC Genomics
GIIRA--RNA-Seq driven gene finding incorporating ambiguous reads.	2013-10-11	Bernhard Y Renard	Franziska Zickmann Martin S Lindner	Bioinformatics
F11R is a novel monocyte prognostic biomarker for malignant glioma	2013-10-11	Xi Feng Winnie W Pong Jaebok Choi Malachi Griffith Obi Griffith Greg N. Fuller David H Gutmann	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
SOAPfusion: a robust and effective computational fusion discovery tool for RNA-seq reads.	2013-10-11	Tak-Wah Lam Jun Wang Jikun Wu Zhiyu Peng	Wenqian Zhang Songbo Huang Zengquan He Yanbing Cheng Siu-Ming Yiu	Bioinformatics
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 Maurizio Prato	Sonia Zorzet Tatiana Da Ros	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
An RNA-seq transcriptome analysis of histone modifiers and RNA silencing genes in soybean during floral initiation process.	2013-10-16	Lim Chee Liew Mohan B. Singh Prem L. Bhalla		PLOS ONE
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 Jörn Kalinowski	Almut Mentz Armin Neshat Katharina Pfeifer-Sancar Christian Rückert	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 Herman P Spaink	Ron P Dirks Annemarie H Meijer André M Deelder	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 N. Ivanova Nikos C. Kyrpides Tanja Woyke Neha Varghese Konstantinos Billis Amrita Pati Marcel Huntemann Iain J. Anderson Konstantinos Mavromatis Krishna Palaniappan	Victor M Markowitz I-Min A Chen Ken Chu Ernest Szeto Manoj Pillay Anna Ratner Jinghua Huang	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 Quaid D Morris	Kyle Tsui Joyce Li Jack F Greenblatt Timothy R Hughes	Genome Research
Inferring polymorphism-induced regulatory gene networks active in human lymphocyte cell lines by weighted linear mixed model analysis of multiple RNA-Seq datasets.	2013-10-30	Erik K Flemington	Wensheng Zhang Andrea Edwards Kun Zhang	PLOS ONE
Probing bacterial metabolism during infection using high-resolution transcriptomics	2013-11	Marvin Whiteley	Peter Jorth Urvish Trivedi Kendra Rumbaugh	Journal of Bacteriology
An integrated model of the transcriptome of HER2-positive breast cancer.	2013-11-01	Kevin J Thompson Xiaojia Tang Krishna R Kalari Richard W. Joseph Zhifu Sun	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
RNA-seq-based comparative transcriptome analysis of the syngas-utilizing bacterium Clostridium ljungdahlii DSM 13528 grown autotrophically and heterotrophically.	2013-11-01	Fuli Li	Yang Tan Juanjuan Liu Xiaohua Chen Huajun Zheng	Molecular BioSystems
Global aspects of pacC regulation of pathogenicity genes in Colletotrichum gloeosporioides as revealed by transcriptome analysis.	2013-11-01	Michael Thon Serenella Sukno	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	Tim Hubbard Jennifer Harrow Felix Kokocinski Roderic Guigó i Serra Tamara Steijger Pär G Engström Josep F. Abril Paul Bertone	RGASP Consortium	Nature Methods
Model-based clustering for RNA-seq data.	2013-11-04	Thomas Brutnell	Yaqing Si Peng Liu Pinghua Li	Bioinformatics
The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations	2013-11-04	Gavin Sherlock Jennifer R Wortman Diane Inglis	Gustavo C Cerqueira Martha B Arnaud Marek S Skrzypek Gail Binkley Matt Simison Stuart R Miyasato Jonathan Binkley Joshua Orvis Prachi Shah Farrell Wymore	Nucleic Acids Research
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
Comparison of microarrays and RNA-seq for gene expression analyses of dose-response experiments.	2013-11-05	Russell S. Thomas Michael B Black	Bethany B Parks Linda Pluta Tzu-Ming Chu Bruce C Allen Russell D Wolfinger	Toxicological Sciences
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 José M Mato	Víctor Segura Juan Alberto Medina-Aunon Salvador Martínez-Bartolomé Oreto Antúnez Jesús M Arizmendi Mikel Azkargorta Silvia Barceló-Batllori Jabier Beaskoetxea Francisco Blanco Mariana B Monteiro David Cáceres Francesc Canals Monserrat Carrascal José Ignacio Casal Felipe Clemente Nuria Colomé Paula Díaz Félix Elortza Patricia Fernández-Puente Severine I Gharbi Carmen González-Tejedo María Luisa Hernáez Manuel Lombardía Maria Lopez-Lucendo Eliandre Oliveira Alberto Pascual-Montano Manuel M Sánchez del Pino Daniel Tabas-Madrid Maria L Valero Vital Vialas Joan Villanueva Juan Pablo Albar Fernando J Corrales	Journal of Proteome Research
Modeling alternative splicing variants from RNA-Seq data with isoform graphs.	2013-11-07	Gianluca Della Vedova	Stefano Beretta Paola Bonizzoni Yuri Pirola Raffaella Rizzi	Journal of Computational Biology
Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation.	2013-11-07	Alexander van Oudenaarden Wenqian Hu Jiahai Shi Harvey Lodish	Juan R Alvarez-Dominguez Bingbing Yuan Staphany S Park Austin A Gromatzky	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
Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki)	2013-11-09	David Sturgill	John H Malone Xia Sun Harold E Smith Leonard Rabinow Marie-Laure Samson Brian Oliver	BMC Bioinformatics
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
Accuracy of allele frequency estimation using pooled RNA-Seq.	2013-11-16	Mateusz Konczal Wieslaw Babik Jacek Radwan Paweł Koteja	M T Stuglik	Molecular Ecology Resources
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
Expression of Porphyromonas gingivalis small RNA in response to hemin availability identified using microarray and RNA-seq analysis.	2013-11-19	Ann Progulske-Fox	Priscilla Phillips Scott Grieshaber Nicole Grieshaber	FEMS Microbiology Letters
Global analysis of differentially expressed genes and proteins in the wheat callus infected by Agrobacterium tumefaciens	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 Erik K Flemington	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	Journal of Virology
Genome-wide mapping of transcriptional start sites defines an extensive leaderless transcriptome in Mycobacterium tuberculosis.	2013-11-21	Graham Rose Teresa Cortes Olga T Schubert Kristine B Arnvig Iñaki Comas Ruedi Aebersold	Douglas B Young	Cell Reports
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
RNA-seq profiles of immune related genes in the staghorn coral Acropora cervicornis infected with white band disease	2013-11-21	Silvia Libro	Stefan T Kaluziak Steven V Vollmer	PLOS ONE
Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia.	2013-11-21	Víctor Quesada Núria López-Bigas Alfonso Valencia Carlos López Otín Roderic Guigó i Serra Jean Monlong Panagiotis Papasaikas Simone Ecker Guillem Clot Sarah Djebali Pedro G Ferreira Rory Johnson Daniel Rico Gonzalo Gómez-López Xose S. Puente David G. Pisano María Rozman José I Martín-Subero Dolors Colomer Elias Campo	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 Siobhan Quenby	Yi-Wah Chan Hugo A van den Berg	Experimental Physiology
MMDiff: quantitative testing for shape changes in ChIP-Seq data sets	2013-11-24	Thomas Clouaire Adrian Peter Bird	Gabriele Schweikert Botond Cseke Guido Sanguinetti	BMC Genomics
Flexible analysis of RNA-seq data using mixed effects models.	2013-11-26	Ernest Turro	William J Astle Simon Tavaré	Bioinformatics
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
RNA-Seq analyses reveal CRISPR RNA processing and regulation patterns.	2013-12-01	Judith Zoephel L Randau	Judith Zoephel	Biochemical Society Transactions
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 Matthew Brooks	Sharda P Yadav Hong Hao Hyun-Jin Yang Marie-Audrey I Kautzmann 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
Comparison of software packages for detecting differential expression in RNA-seq studies.	2013-12-02	Laura L. Elo	Fatemeh Seyednasrollah Asta Laiho	Briefings in Bioinformatics
Integrated chromosome 19 transcriptomic and proteomic data sets derived from glioma cancer stem-cell lines.	2013-12-03	György Marko-Varga	Cheryl F Lichti Huiling Liu Alexander S Shavkunov Ekaterina Mostovenko Erik P Sulman Ravesanker Ezhilarasan Qianghu Wang Roger A Kroes Joseph C Moskal David Fenyö Betül Akgöl Oksuz Charles A Conrad Frederick F Lang Frode S Berven Akos Végvári Melinda Rezeli Sophia Hober Carol L Nilsson	Journal of Proteome Research
Joint estimation of isoform expression and isoform-specific read distribution using multisample RNA-Seq data.	2013-12-03	Stefano Calza	Chen Suo Agus Salim Yudi Pawitan	Bioinformatics
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 Todd Creasy	Michael S Humphrys Yezhou Sun Elliott F Drabek Umar Farooq Naomi Sengamalay Sandy Ott Huizhong Shou Patrik M Bavoil Anup Mahurkar Garry S A Myers	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 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	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
RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.	2013-12-06	Brian Scheffler Megan J Bowman Philip J Bauer	Wonkeun Park Joshua A Udall Justin T Page Joshua Raney Don C Jones B Todd Campbell	PLOS ONE
Co-expression network analysis identifies Spleen Tyrosine Kinase (SYK) as a candidate oncogenic driver in a subset of small-cell lung cancer	2013-12-09	John K. Field	Akshata R Udyavar Megan D Hoeksema Jonathan E Clark Yong Zou Zuojian Tang Zhiguo Li Ming Li Heidi Chen Alexander Statnikov Yu Shyr Daniel C Liebler Rosana Eisenberg Lourdes Estrada Pierre P Massion Vito Quaranta	BMC Systems Biology
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
TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes.	2013-12-13	Michiel Van Bel Klaas Vandepoele Yves Van de Peer	Sebastian Proost Christophe Van Neste Dieter Deforce Yves Van de Peer	Genome Biology
Identification of two putative reference genes from grapevine suitable for gene expression analysis in berry and related tissues derived from RNA-Seq data	2013-12-13	Ariel Orellana	Mauricio González-Agüero Miguel García-Rojas Alex Di Genova José Correa Alejandro Maass Patricio Hinrichsen	BMC Genomics
Transcriptome analysis of Pinus monticola primary needles by RNA-seq provides novel insight into host resistance to Cronartium ribicola.	2013-12-16	Jun-Jun Liu	Rona N Sturrock Ross Benton	BMC Genomics
Comprehensive analysis of the Corynebacterium glutamicum transcriptome using an improved RNAseq technique	2013-12-17	Jörn Kalinowski	Katharina Pfeifer-Sancar Almut Mentz Christian Rückert	BMC Genomics
RNA-Seq optimization with eQTL gold standards.	2013-12-17	Andrew B. West	Shannon E Ellis Simone Gupta Foram N Ashar Joel S Bader Dan E Arking	BMC Genomics
Studying Culicoides vectors of BTV in the post-genomic era: resources, bottlenecks to progress and future directions.	2013-12-17 2014-03-01	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 Robin Foà	Valentina Gianfelici Arun George Devasia Ellen Geerdens Nicole Mentens Sabina Chiaretti Kaat Durinck Anne Uyttebroeck Jacqueline Cloos 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
PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution	2013-12-20	Xianyun Mao Jane Ferguson Muredach P. Reilly	Yu Hu Yichuan Liu Cheng Jia Chenyi Xue Hongzhe Li Mingyao Li	Nucleic Acids Research
Correction: RNA-Seq-Based Analysis of the Physiologic Cold Shock-Induced Changes in Moraxella catarrhalis Gene Expression.	2013-12-20	Stefan Wyder	Violeta Spaniol Christoph Aebi	PLOS ONE
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	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 Tracey Davey Ian R. Adams John Greally	Donncha S Dunican Hazel A Cruickshanks Masako Suzuki Robert J Arceci Richard R Meehan	Genome Biology
Blind spots of quantitative RNA-seq: the limits for assessing abundance, differential expression, and isoform switching	2013-12-24	Lennart Opitz	Hubert Rehrauer Ge Tan Lina Sieverling Ralph Schlapbach	BMC Bioinformatics
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
Bulk segregant RNA-seq reveals expression and positional candidate genes and allele-specific expression for disease resistance against enteric septicemia of catfish.	2013-12-30	Luyang Sun Shikai Liu	Ruijia Wang Lisui Bao Jiaren Zhang Yanliang Jiang Jun Yao Lin Song Jianbin Feng Zhanjiang Liu	BMC Genomics
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 Sulev Kõks	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 Kurt Zatloukal	Vikash Pandey Marc Sultan Karl Kashofer Meryem Ralser Vyacheslav Amstislavskiy Julia Starmann Ingrid Osprian Hendrik Hache Holger Sültmann Michael Trauner 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 Michelle A. Petri	Lihua Shi Zhe Zhang Wei Wang Zhi Wei Ehtisham Akhter Kelly Maurer Li Song 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
Comparison between karyotyping-FISH-reverse transcription PCR and RNA-sequencing-fusion gene identification programs in the detection of KAT6A-CREBBP in acute myeloid leukemia	2014	Sverre Heim Ioannis Panagopoulos	Synne Torkildsen Ludmila Gorunova Anne Tierens Geir E Tjønnfjord	PLOS ONE
RNA families in Epstein-Barr virus	2014	Joan A. Steitz	Walter N Moss Nara Lee Genaro Pimienta	RNA Biology
Characterization of human pseudogene-derived non-coding RNAs for functional potential	2014	Deyou Zheng	Xingyi Guo Mingyan Lin Shira Rockowitz Herbert M Lachman	PLOS ONE
Oqtans: a multifunctional workbench for RNA-seq data analysis	2014	Gunnar Rätsch	Vipin T Sreedharan Sebastian J Schultheiss Géraldine Jean André Kahles Regina Bohnert Philipp Drewe Pramod Mudrakarta Nico Görnitz Georg Zeller	BMC Bioinformatics
Blood biomarkers of the late phase asthmatic response using RNA-Seq	2014	Louis-Philippe Boulet	Amrit Singh Casey P Shannon Gail M Gauvreau Paul M O'Byrne J FitzGerald Scott J Tebbutt	Allergy, Asthma & Clinical Immunology
Emerging RNA-Seq Applications in Food Science	2014	Alberto Valdés Virginia García-Cañas Carolina Simó	Clara Ibáñez
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 Cécile Neuvéglise	Can Wang Linda M Holland François Brunel 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
A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells	2014-01-01	Michael Stratton	Tony Ly Yasmeen Ahmad Adam Shlien Dominique Soroka Allie Mills Michael J Emanuele Angus I Lamond	eLife
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
A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages.	2014-01-01	Danielle Thierry-Mieg Lee Lancashire Heng Luo Nan Mei Jean Thierry-Mieg	Ying Yu James C Fuscoe Chen Zhao Chao Guo Meiwen Jia Tao Qing Desmond I Bannon Wenjun Bao Tingting Du Zhenqiang Su Wendell D Jones Carrie L Moland William S Branham Feng Qian Baitang Ning Yan Li Huixiao Hong Lei Guo Tieliu Shi Kevin Y Wang Russell D Wolfinger Yuri Nikolsky Stephen J Walker Penelope Duerksen-Hughes Christopher E Mason Weida Tong Leming Shi Charles Wang	Nature Communications
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 Carlos F Ibáñez	Genome Biology
RNA-Seq reveals novel transcriptional reorganization in human alcoholic brain.	2014-01-01	Sean P Farris	R Dayne Mayfield	International Review of Neurobiology
Discovery of Protein-lncRNA Interactions by Integrating Large-Scale CLIP-Seq and RNA-Seq Datasets	2014-01-01	Liang-Hu Qu	Jun-Hao Li Shun Liu Ling-Ling Zheng Jie Wu Wen-Ju Sun Ze-Lin Wang Hui Zhou Jian-Hua Yang	Frontiers in Bioengineering and Biotechnology
Next-generation sequencing applied to flower development: RNA-seq.	2014-01-01	Yuling Jiao	Jun He	Methods in Molecular Biology
Riboswitch discovery by combining RNA-seq and genome-wide identification of transcriptional start sites.	2014-01-01	Isabelle Rosinski-Chupin	Olga Soutourina Isabelle Martin-Verstraete	Methods in Enzymology
Plant and fungal gene expression in mycorrhizal protocorms of the orchid Serapias vomeracea colonized by Tulasnella calospora.	2014-01-01	Fabiano Sillo Silvia Perotto Raffaella Balestrini	Luca Nerva Mariangela Girlanda	Plant Signaling and Behavior
Shared transcription factors contribute to distinct cell fates	2014-01-01	Berthold Göttgens	Felicia S L Ng Fernando J Calero-Nieto	Transcription
Transcriptomic changes in brain development.	2014-01-01	Mark R Cookson	Allissa A Dillman	International Review of Neurobiology
RNA-Seq and Network Analysis Revealed Interacting Pathways in TGF-β-Treated Lung Cancer Cell Lines.	2014-01-01	Youping Deng	Yan Li Omid Rouhi Hankui Chen Rolando Ramirez Jeffrey A Borgia	Cancer Informatics
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
Quantitative transcriptome analysis using RNA-seq.	2014-01-01	Andrea Bräutigam	Canan Külahoglu	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
Differential expression analysis of RNA-seq data at single-base resolution	2014-01-06	Kasper D. Hansen Jeffrey T. Leek	Alyssa C Frazee Sarven Sabunciyan Rafael A Irizarry	Biostatistics
A unique missense allele of BAF155, a core BAF chromatin remodeling complex protein, causes neural tube closure defects in mice.	2014-01-09	Dawn E Watkins-Chow William J Pavan Lee Niswander	Laura Harmacek Jianfu Chen Kenneth L Jones J Michael Salbaum	Developmental Neurobiology
The histone-H3K4-specific demethylase KDM5B binds to its substrate and product through distinct PHD fingers.	2014-01-09	Brian D Strahl Scott B Rothbart	Brianna J Klein Lianhua Piao Yuanxin Xi Hector Rincon-Arano Danni Peng Hong Wen Connie Larson Xi Zhang Xia Zheng Michael A Cortazar Pedro V Peña Anthony Mangan David L Bentley Mark Groudine Wei Li Xiaobing Shi Tatiana G Kutateladze	Cell Reports
Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis.	2014-01-11	Georg Zeller Gunnar Rätsch	Vipin T Sreedharan Sebastian J Schultheiss Géraldine Jean André Kahles Regina Bohnert Philipp Drewe Pramod Mudrakarta Nico Görnitz	Bioinformatics
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
Transciptome analysis of the gill and swimbladder of Takifugu rubripes by RNA-Seq.	2014-01-16	Shikai Liu	Jun Cui Bing Zhang Hongdi Wang Hongjuan Sun Shuhui Song Xuemei Qiu Yang Liu Xiuli Wang Zhiqiang Jiang Zhanjiang Liu	PLOS ONE
Transcriptome analysis of psoriasis in a large case-control sample: RNA-seq provides insights into disease mechanisms	2014-01-17	A Johnston Lam C. Tsoi	Bingshan Li William R Swindell Johann E Gudjonsson Trilokraj Tejasvi Jun Ding Philip E Stuart Xianying Xing James J Kochkodan John J Voorhees Hyun M Kang Rajan P Nair Goncalo R Abecasis James T Elder	Journal of Investigative Dermatology
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 Narla Mohandas Xiuli An	Marilyn Parra Sherry Gee Dana Ghanem Jie Li 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
RNA-Seq transcriptome analysis of Spirodela dormancy without reproduction.	2014-01-23	Wenqin Wang Joachim Messing	Yongrui Wu	BMC Genomics
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 Stephen B McMahon	Ana Antunes-Martins Margarita Calvo John Grist Werner Rust Ramona Schmid Tobias Hildebrandt 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 Paul Kellam	Meleri Jones Inga R Dry Dan Frampton Manuraj Singh Ravinder K Kanda Michael B Yee 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 Marcin Imielinski Juliann Chmielecki Gad Getz Gordon Saksena	Angela N Brooks Peter S Choi Luc de Waal Tanaz Sharifnia Chandra Sekhar Pedamallu Andrey Sivachenko Michael S Lawrence David S DeLuca	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
Faculty of 1000 evaluation for Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells	2014-02-02	Marc S. Williams
voom: Precision weights unlock linear model analysis tools for RNA-seq read counts.	2014-02-03	Gordon K Smyth	Charity W Law Yunshun Chen Wei Shi	Genome Biology
Ultra deep sequencing of Listeria monocytogenes sRNA transcriptome revealed new antisense RNAs.	2014-02-03	Ramakanth Madhugiri Stefanie Widder Thomas Rattei	Sebastian Behrens Gopala Krishna Mannala Xiaoxing Qing Nathalie Kefer Mobarak Abu Mraheil Torsten Hain	PLOS ONE
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
RNA-seq reveals transcriptomic shock involving transposable elements reactivation in hybrids of young lake whitefish species.	2014-02-06	Sébastien Renaut Louis Bernatchez	Anne-Marie Dion-Côté Eric Normandeau	Molecular Biology and Evolution
Secondary cell wall composition and candidate gene expression in developing willow (Salix purpurea) stems.	2014-02-07	Keywan Hassani-Pak Angela Karp Huw Dylan Jones	Yongfang Wan Cristina Gritsch Theodora Tryfona Mike J Ray Ambrose Andongabo Paul Dupree Peter R Shewry Rowan A C Mitchell	Planta
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
Analysis of 52 Rab GTPases from channel catfish and their involvement in immune responses after bacterial infections.	2014-02-07	Luyang Sun Shikai Liu Yu Zhang	Ruijia Wang Chao Li Lisui Bao Jianbin Feng Zhanjiang Liu	Developmental and Comparative Immunology
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
SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads.	2014-02-13	Gane Ka-Shu Wong Ruibang Luo Tak-Wah Lam Jun Wang	Yinlong Xie Gengxiong Wu Jingbo Tang Jordan Patterson Shanlin Liu Weihua Huang Guangzhu He Shengchang Gu Shengkang Li Xin Zhou Yingrui Li Xun Xu	Bioinformatics
Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia.	2014-02-13	Ana Conesa Corey Nislow Eduardo Larriba José Martín-Nieto Luis V Lopez-Llorca	María D L A Jaime José Carbonell-Caballero Joaquín Dopazo	Fungal Genetics and Biology
Condition-specific target prediction from motifs and expression.	2014-02-14	Martin Vingron	Guofeng Meng	Bioinformatics
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
SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing.	2014-02-17	Xi Wang Murray J Cairns		Bioinformatics
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
Insight into insulin secretion from transcriptome and genetic analysis of insulin-producing cells of Drosophila	2014-02-20	Luis A Milla Wenxiu Ma Maria L Spletter	Jian Cao Julie Ni Vanessa Shiu Sangbin Park Sheng Tang Jun Zhang Xing Wei Seung K Kim Matthew P Scott	Genetics
Improving reliability and absolute quantification of human brain microarray data by filtering and scaling probes using RNA-Seq.	2014-02-24	Jeremy A Miller Vilas Menon Jeff Goldy Ajamete Kaykas Chang-Kyu Lee Kimberly A Smith Elaine H Shen John W Phillips Ed S Lein Mike J Hawrylycz		BMC Genomics
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 Julien Ablain Vincenzo Carafa	Floriana De Bellis Francesca Petraglia Filomena Matarese Kees-Jan Françoijs Rèmy Castellano Armelle Goubard Amit Mandoli Joost H A Martens Hendrik G Stunnenberg	Cancer Research
RNA CoMPASS: a dual approach for pathogen and host transcriptome analysis of RNA-seq datasets	2014-02-25	Erik K Flemington	Guorong Xu Michael J Strong Michelle R Lacey Carl Baribault Christopher M Taylor	PLOS ONE
Transcriptomic profiling of differential responses to drought in two freshwater mussel species, the giant floater Pyganodon grandis and the pondhorn Uniomerus tetralasmus.	2014-02-25	Eric Peatman	Yupeng Luo Chao Li Andrew Gascho Landis Guiling Wang James Stoeckel	PLOS ONE
FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions.	2014-02-25	Carlos Torroja Francesco Mazzarotto Enrique Lara-Pezzi Alberto Gatto	Stuart A Cook Paul J R Barton Fátima Sánchez-Cabo	Nucleic Acids Research
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
SnapShot-Seq: a method for extracting genome-wide, in vivo mRNA dynamics from a single total RNA sample	2014-02-26	Nimrod Miller Sarah A Boswell Yong-Chao Ma Nicole Cloonan Sean M. Grimmond	Jesse M Gray David A Harmin Thomas E Mullen Joseph J Ling Scott Kuersten Steven A McCarroll Michael Springer	PLOS ONE
Identification and initial functional characterization of a human vascular cell-enriched long noncoding RNA.	2014-02-27	Deyou Zheng	Robert D Bell Xiaochun Long Mingyan Lin Jan H Bergmann Vivek Nanda Sarah L Cowan Qian Zhou Yu Han David L Spector Joseph M Miano	Arteriosclerosis, Thrombosis, and Vascular Biology
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 Sabeeha Merchant Ursula Goodenough	Ian Blaby Carrie Goodson Jae-Hyeok Lee 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
ChIP-Seq and RNA-Seq reveal an AmrZ-mediated mechanism for cyclic di-GMP synthesis and biofilm development by Pseudomonas aeruginosa	2014-03-01	Yasuhiko Irie Peter White	Christopher J. Jones David Newsom Benjamin Kelly Laura K. Jennings Binjie Xu Dominique H. Limoli Joe J. Harrison Matthew R. Parsek Daniel J. Wozniak	PLOS Pathogens
The IncRNAs PCGEM1 and PRNCR1 are not implicated in castration resistant prostate cancer.	2014-03-01	Elai Davicioni	John R Prensner Anirban Sahu Matthew K Iyer Rohit Malik Benjamin Chandler Irfan A Asangani Anton Poliakov Ismael A Vergara Mohammed Alshalalfa Robert B Jenkins Felix Y Feng Arul M Chinnaiyan	Oncotarget
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 Mathias Uhlén	D Djureinovic B Hallström A Danielsson C Lindskog 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
Faculty of 1000 evaluation for SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads	2014-03-06	Steven Salzberg
Variation in RNA-Seq transcriptome profiles of peripheral whole blood from healthy individuals with and without globin depletion.	2014-03-07	Casey P. Shannon Robert Balshaw	Heesun Shin Nick Fishbane Jian Ruan Mi Zhou Janet E Wilson-McManus Raymond T Ng Bruce M McManus Scott J Tebbutt PROOF Centre of Excellence Team	PLOS ONE
Vicinal: a method for the determination of ncRNA ends using chimeric reads from RNA-seq experiments.	2014-03-12	Zhipeng Lu	A Gregory Matera	Nucleic Acids Research
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	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
Identification of novel point mutations in splicing sites integrating whole-exome and RNA-seq data in myeloproliferative diseases.	2014-03-13	Carlo Gambacorti-Passerini	Roberta Spinelli Alessandra Pirola Sara Redaelli Nitesh Sharma Hima Raman Simona Valletta Vera Magistroni Rocco Piazza	Molecular genetics & genomic medicine
Identification of candidate genes involved in coronary artery calcification by transcriptome sequencing of cell lines.	2014-03-14	NISC Comparative Sequencing Program Leslie G Biesecker Eric D. Green James C Mullikin	Shurjo K Sen Jennifer J Barb Praveen F Cherukuri David S Accame Abdel G Elkahloun Larry N Singh Shih-Queen Lee-Lin Frank D Kolodgie Qi Cheng XiaoQing Zhao Marcus Y Chen Andrew E Arai Peter J Munson	BMC Genomics
RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence.	2014-03-18	Hans J Nauwynck	Bouabid Badaoui Teresa Rutigliano Anna Anselmo Merijn Vanhee Elisabetta Giuffra Sara Botti	PLOS ONE
The human liver-specific proteome defined by transcriptomics and antibody-based profiling.	2014-03-19	Jens Nielsen Linn Fagerberg Mathias Uhlén	Caroline Kampf Adil Mardinoglu Björn M Hallström Karolina Edlund Emma Lundberg Fredrik Pontén	FASEB Journal
SNP discovery from transcriptome of the swimbladder of Takifugu rubripes	2014-03-20	Shikai Liu	Jun Cui Hongdi Wang Lifu Zhu Xuemei Qiu Zhiqiang Jiang Xiuli Wang Zhanjiang Liu	PLOS ONE
The highly conserved MraZ protein is a transcriptional regulator in Escherichia coli.	2014-03-21	Jesus M Eraso Ronald Taylor	Lye M Markillie Hugh D Mitchell Galya Orr William Margolin	Journal of Bacteriology
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
RNA sequencing reveals upregulation of RUNX1-RUNX1T1 gene signatures in clear cell renal cell carcinoma	2014-03-25	Jianfeng Xu	Zuquan Xiong Hongjie Yu Yan Ding Chenchen Feng Hanming Wei Sha Tao Dan Huang Siqun Lilly Zheng Jielin Sun Zujun Fang	BioMed Research International
De novo transcriptome analysis of Hevea brasiliensis tissues by RNA-seq and screening for molecular markers	2014-03-26	Luiz Gonzaga Paula de Almeida Dominique Garcia Daniel Guariz Pinheiro Antonio Figueira Luiz L Coutinho	Leonardo Rippel Salgado Daniela Martins Koop Ronan Rivallan Vincent Le Guen Marisa Fabiana Nicolás Viviani Ribeiro Rocha Milena Magalhães Alexandra Lehmkuhl Gerber Júlio Cézar de Mattos Cascardo AnaTereza Ribeiro de Vasconcelos Wilson Araújo Silva	BMC Genomics
De novo transcriptome assembly reveals sex-specific selection acting on evolving neo-sex chromosomes in Drosophila miranda.	2014-03-27	Doris Bachtrog	Vera B Kaiser	BMC Genomics
RNA-Seq reveals infection-induced gene expression changes in the snail intermediate host of the carcinogenic liver fluke, Opisthorchis viverrini.	2014-03-27	Thewarach Laha Smarn Tesana	Sattrachai Prasopdee Javier Sotillo Jutharat Kulsantiwong Matthew J Nolan Alex Loukas Cinzia Cantacessi	PLOS Neglected Tropical Diseases
Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing.	2014-03-27	Hideya Kawaji Masayoshi Itoh Piero Carninci Yoshihide Hayashizaki	Marina Lizio Mutsumi Kanamori-Katayama Ai Kaiho Hiromi Nishiyori-Sueki Jay W Shin Miki Kojima-Ishiyama Mitsuoki Kawano Mitsuyoshi Murata Noriko Ninomiya-Fukuda Sachi Ishikawa-Kato Sayaka Nagao-Sato Shohei Noma Alistair R R Forrest FANTOM Consortium	Genome Research
Transcriptome analysis of the gill of Takifugu rubripes using Illumina sequencing for discovery of SNPs.	2014-03-27	Shikai Liu	Jun Cui Hongdi Wang Xuemei Qiu Zhiqiang Jiang Xiuli Wang	Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics
RNA-seq dependent transcriptional analysis unveils gene expression profile in the intestine of sea cucumber Apostichopus japonicus during aestivation.	2014-03-27	Kenneth B. Storey	Ye Zhao Hongsheng Yang Muyan Chen	Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics
HDAC-regulated myomiRs control BAF60 variant exchange and direct the functional phenotype of fibro-adipogenic progenitors in dystrophic muscles.	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
The Period protein homolog LIN-42 negatively regulates microRNA biogenesis in C. elegans.	2014-03-31	Amy E Pasquinelli Priscilla M Van Wynsberghe	Emily F Finnegan Thomas Stark Evan P Angelus Kathryn E Homan Gene W Yeo	Developmental Biology
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
RNA-seq identifies clinically relevant fusion genes in leukemia including a novel MEF2D/CSF1R fusion responsive to imatinib.	2014-04	Henrik Lilljebjörn Hans Ehrencrona Thoas Fioretos	H Ågerstam C Orsmark-Pietras M Rissler L Nilsson J Richter	Leukemia
Odorant and gustatory receptors in the tsetse fly Glossina morsitans morsitans	2014-04	Daniel K. 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
RNA sequencing and proteogenomics reveal the importance of leaderless mRNAs in the radiation-tolerant bacterium Deinococcus deserti.	2014-04-01	Arjan de Groot Laurence Blanchard David Vallenet David Pignol Jean Armengaud	David Roche Bernard Fernandez Monika Ludanyi Stéphane Cruveiller	Genome Biology and Evolution
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
ZBED6 modulates the transcription of myogenic genes in mouse myoblast cells	2014-04-08	Lin Jiang Ola Wallerman Göran Andersson Leif Andersson	Shady Younis Carl-Johan Rubin Elizabeth R Gilbert Elisabeth Sundström Awaisa Ghazal Xiaolan Zhang Li Wang Tarjei S Mikkelsen	PLOS ONE
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 Mark R Cookson	Allissa A Dillman Jinhui Ding Yan Li	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
Comparison of transcriptional profiles of Clostridium thermocellum grown on cellobiose and pretreated yellow poplar using RNA-Seq.	2014-04-11	Michael E Himmel	Hui Wei Yan Fu Lauren Magnusson John O Baker Pin-Ching Maness Qi Xu Shihui Yang Andrew Bowersox Igor Bogorad Wei Wang Melvin P Tucker Shi-You Ding	Frontiers in Microbiology
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 Jonathan Weissman	Dale Muzzey	Genome Research
Heat shock alters the expression of schizophrenia and autism candidate genes in an induced pluripotent stem cell model of the human telencephalon	2014-04-15	Deyou Zheng	Mingyan Lin Dejian Zhao Anastasia Hrabovsky Erika Pedrosa Herbert M Lachman	PLOS ONE
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 Caroline Proux Vikas Yadav Cécile Neuvéglise Joseph Heitman	Damien Paulet Edmond J Byrnes Nandita Mullapudi Chung-Chau Hon R Blake Billmyre François Brunel Weidong Chen Eve W L Chow Jean-Yves Coppée Anna Floyd-Averette Claude Gaillardin Kimberly J Gerik Jonathan Goldberg Sara Gonzalez-Hilarion Sharvari Gujja Joyce L Hamlin Giuseppe Ianiri Chinnappa D Kodira Lukasz Kozubowski Woei Lam Marco Marra Larry D Mesner Frédérique Moyrand Kirsten Nielsen Jacqueline E Schein Sheng Sun Carolin Wollschlaeger Ian A Wood Qiandong Zeng Carol S Newlon John R Perfect Jennifer K Lodge James W Kronstad Fred S Dietrich	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 John M Mariadason	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	Cancer Research
RNA sequencing shows transcriptomic changes in rectosigmoid mucosa in patients with irritable bowel syndrome-diarrhea: a pilot case-control study.	2014-04-24	Michael Camilleri	Paula Carlson Andres Acosta Irene Busciglio Asha A Nair Simon J Gibbons Gianrico Farrugia Eric W Klee	American Journal of Physiology - Gastrointestinal and Liver Physiology
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
A novel highly divergent protein family identified from a viviparous insect by RNA-seq analysis: a potential target for tsetse fly-specific abortifacients.	2014-04-24	Geoffrey Attardo Aaron A Baumann Qirui Zhang Paul O. Mireji Serap Aksoy José M. Ribeiro	Joshua B Benoit Veronika Michalkova Tyler B Krause Jana Bohova Peter Takáč David L Denlinger	PLOS Genetics
A gene expression atlas of early craniofacial development	2014-04-26	Phillip Dexheimer	Eric W Brunskill Andrew S Potter Andrew Distasio Andrew Plassard Bruce J Aronow S Steven Potter	Developmental Biology
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 Luyang Sun Shikai Liu Yu Zhang	Jiaren Zhang Jun Yao Ruijia Wang 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 Robert A Holt	Scott D Brown Rene L Warren Ewan A Gibb John J Spinelli	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
Longer Reads Do Not Significantly Improve RNA-seq Results.	2014-05-01	Sagar Chhangawala	Gabe Rudy Po-Yen Wu Scott Tighe May D. Wang Don A. Baldwin George Grills Christopher E. Mason Jeffrey Rosenfeld	Journal of Biomolecular Techniques
From genome to function by studying eQTLs.	2014-05-04	Lude Franke	Harm-Jan Westra	Biochimica et Biophysica Acta
Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis.	2014-05-05	Gregory B. Gloor	Andrew D Fernandes Jennifer Ns Reid Jean M Macklaim Thomas A McMurrough David R Edgell	Microbiome
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 Lorena Landuzzi	Federica Riccardo Maddalena Arigoni Genny Buson Elisa Zago Alessandra Fiore Simona Nuzzo Patrizia Nanni	BMC Genomics
Genome sequencing and comparative genomics of the broad host-range pathogen Rhizoctonia solani AG8.	2014-05-08	Jana Sperschneider James K Hane Jonathan P Anderson Karam B. Singh	Angela H Williams	PLOS Genetics
lncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs.	2014-05-09	Wan Kyu Kim	Charny Park Namhee Yu Ikjung Choi Sanghyuk Lee	Bioinformatics
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
Dual RNA-seq transcriptional analysis of wheat roots colonized by Azospirillum brasilense reveals up-regulation of nutrient acquisition and cell cycle genes.	2014-05-16	Glaucio Valdameri Helisson Faoro Lucélia Donatti Leda S Chubatsu	Doumit Camilios-Neto Paloma Bonato Roseli Wassem Michelle Z Tadra-Sfeir Liziane C C Brusamarello-Santos Vinicius A Weiss Fábio O Pedrosa Emanuel M Souza	BMC Genomics
Estimates of allele-specific expression in Drosophila with a single genome sequence and RNA-seq data.	2014-05-19	Francis M Jiggins	Andrew Quinn Punita Juneja	Bioinformatics
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
Production, gene structure and characterization of two orthologs of leptin and a leptin receptor in tilapia.	2014-05-20	Tomer Ventura Berta Levavi-Sivan	Michal Shpilman Lian Hollander-Cohen Arieh Gertler	General and Comparative Endocrinology
A dynamic regulatory network explains ParaHox gene control of gut patterning in the sea urchin.	2014-05-21	Maria Ina Arnone	Rossella Annunziata	Development
Dual RNA-seq of parasite and host reveals gene expression dynamics during filarial worm-mosquito interactions	2014-05-22	George F Mayhew Matthew T Aliota	Young-Jun Choi Sara M Erickson Bruce M Christensen	PLOS Neglected Tropical Diseases
Transcriptome of Atoh7 retinal progenitor cells identifies new Atoh7-dependent regulatory genes for retinal ganglion cell formation.	2014-05-22	Xiuqian Mu	Zhiguang Gao Chai-An Mao Ping Pan William H Klein	Developmental Neurobiology
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
Sequential combination of karyotyping and RNA-sequencing in the search for cancer-specific fusion genes.	2014-05-23	Sverre Heim Ioannis Panagopoulos	Jim Thorsen Ludmila Gorunova Francesca Micci	International Journal of Biochemistry & Cell Biology
Selective and flexible depletion of problematic sequences from RNA-seq libraries at the cDNA stage.	2014-05-26	Thomas Preiss	Stuart K Archer Nikolay E Shirokikh	BMC Genomics
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
The PhoP-dependent ncRNA Mcr7 modulates the TAT secretion system in Mycobacterium tuberculosis.	2014-05-29	Luis Solans Jesús Gonzalo-Asensio Claudia Sala Carlos Martín	Andrej Benjak Swapna Uplekar Jacques Rougemont Christophe Guilhot Wladimir Malaga Stewart T Cole	PLOS Pathogens
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
RNA-seq: impact of RNA degradation on transcript quantification.	2014-05-30	Irene Gallego Romero	Athma A Pai Jenny Tung Yoav Gilad	BMC Biology
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
Differential RNA-seq: the approach behind and the biological insight gained.	2014-06-01	Cynthia Sharma Jörg Vogel		Current Opinion in Microbiology
Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling.	2014-06-02	Charles M. Perou	Wei Zhao Xiaping He Katherine A Hoadley Joel S Parker David Neil Hayes	BMC Genomics
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
Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series.	2014-06-03	Ana Conesa Sonia Tarazona María José Nueda		Bioinformatics
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
Transcriptome sequencing revealed the transcriptional organization at ribosome-mediated attenuation sites in Corynebacterium glutamicum and identified a novel attenuator involved in aromatic amino acid biosynthesis.	2014-06-06	Jörn Kalinowski	Armin Neshat Almut Mentz Christian Rückert	Journal of Biotechnology
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
Variable escape from X-chromosome inactivation: identifying factors that tip the scales towards expression	2014-06-10 2014-08-01	Allison M Cotton Carolyn J. Brown	Samantha B Peeters	BioEssays
An optimized method for the extraction of bacterial mRNA from plant roots infected with Escherichia coli O157:H7.	2014-06-10	Robert W Jackson Nicola Holden	Ashleigh Holmes Louise Birse	Frontiers in Microbiology
ARH-seq: identification of differential splicing in RNA-seq data	2014-06-11	Marie-Laure Yaspo Hans Lehrach Ralf Herwig	Axel Rasche Matthias Lienhard Marie-Laure Yaspo	Nucleic Acids Research
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
Annotation of long non-coding RNAs expressed in collaborative cross founder mice in response to respiratory virus infection reveals a new class of interferon-stimulated transcripts	2014-06-12	Ralph S Baric Yoshihiro Kawaoka	Laurence Josset Nicolas Tchitchek Lisa E Gralinski Martin T Ferris Amie J Eisfeld Richard R Green Matthew J Thomas Jennifer Tisoncik-Go Gary P Schroth Fernando Pardo Manuel de Villena Mark T Heise Xinxia Peng Michael G Katze	RNA Biology
A transcription factor network specifying inhibitory versus excitatory neurons in the dorsal spinal cord.	2014-06-12	Diogo S. Castro	Mark D Borromeo David M Meredith Joshua C Chang Kuang-Chi Tung Francois Guillemot Jane E Johnson	Development
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
miR-PREFeR: an accurate, fast and easy-to-use plant miRNA prediction tool using small RNA-Seq data.	2014-06-14	Jikai Lei	Yanni Sun	Bioinformatics
An integrative method to normalize RNA-Seq data.	2014-06-14	Klopp Christophe	Cyril Filloux Meersseman Cédric Philippe Romain Forestier Lionel Rocha Dominique Maftah Abderrahman Petit Daniel	BMC Bioinformatics
Mapping of HPV transcripts in four human cervical lesions using RNAseq suggests quantitative rearrangements during carcinogenic progression.	2014-06-14	Michael Poidinger	Jinmiao Chen Yuezhen Xue Thimothy Lim Sung Hock Chew Chai Ling Pang Jean-Pierre Abastado Françoise Thierry	Virology
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
RNA-Seq analysis implicates detoxification pathways in ovine mycotoxin resistance	2014-06-17	Jinbi Zhang	Zengxiang Pan Stephanie Moloney Allan Sheppard	PLOS ONE
The Chlamydomonas genome project: a decade on.	2014-06-17	David Goodstein Jane Grimwood Crysten E Blaby-Haas Sabeeha Merchant	Ian K Blaby Nicolas Tourasse Erik F Y Hom David Lopez Munevver Aksoy Arthur Grossman James Umen Susan Dutcher Mary Porter Stephen King George B Witman Mario Stanke Elizabeth H Harris Jane Grimwood Jeremy Schmutz Olivier Vallon Simon Prochnik	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 Amelia Casamassimi	Margherita Scarpato 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
A systems biology approach to the analysis of subset-specific responses to lipopolysaccharide in dendritic cells.	2014-06-20	Elena Shklovskaya Barbara Fazekas De St Groth	David G Hancock Thomas V Guy Reza Falsafi Chris D Fjell William Ritchie Robert E W Hancock	PLOS ONE
Genomic characterization of acute leukemias.	2014-06-20	Robin Foà	Sabina Chiaretti Valentina Gianfelici Giulia Ceglie	Medical Principles and Practice
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 Eleonora Adami	Henrike Maatz Sebastian Schafer Marieluise Kirchner Carola Rintisch Vita Dauksaite Matthias Selbach Paul J R Barton Stuart A Cook Norbert Hubner	Journal of Clinical Investigation
Comprehensive analysis of the whole transcriptomes from two different pig breeds using RNA-Seq method.	2014-06-24	Artur Gurgul Maria Oczkowicz Katarzyna Ropka-Molik Katarzyna Piórkowska	Kacper Zukowski Robert Eckert	Animal Genetics
A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.	2014-06-25	Richard Emes Joanna Moreton Stephen Dunham		Frontiers in Genetics
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
Requirements for Pseudomonas aeruginosa acute burn and chronic surgical wound infection	2014-07	Marvin Whiteley	Keith H Turner Jake Everett Urvish Trivedi Kendra P Rumbaugh	PLOS Genetics
The coding and noncoding architecture of the Caulobacter crescentus genome	2014-07	Bo Zhou Jared M Schrader Sean Crosson Jonathan Weissman	Gene-Wei Li Keren Lasker W Seth Childers Brandon Williams Tao Long Harley H McAdams Lucy Shapiro	PLOS Genetics
Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing	2014-07-01	Aviv Regev Rahul Satija Alex K. Shalek	John J. Trombetta David Gennert Diana Lu	Current protocols in molecular biology
Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data.	2014-07-01	Jingyi Jessica Li Steven E. Brenner	Haiyan Huang Peter J Bickel	Genome Research
SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models.	2014-07-01	Christoph W. Sensen	Ian Reid Nicholas O'Toole Omar Zabaneh Reza Nourzadeh Mahmoud Dahdouli Mostafa Abdellateef Paul M K Gordon Jung Soh Gregory Butler Adrian Tsang	BMC Bioinformatics
IMAGE GUIDED RNA-SEQ REVEALS SUBTYPE-SPECIFIC PATTERNS AT THE INFILTRATIVE MARGINS OF GLIOBLASTOMA.	2014-07-01	Michael B Sisti	Peter Canoll Peter Sims Brian Gil David Pisapia Hani Malone Hannah Goldstein Liang Lei Adam Sonabend Jonathan Yun Jorge Samanamud Jennifer Sims Andrew Teich Sameer Sheth Guy McKhann Jeffrey Bruce	Neuro-Oncology
Corrigendum: Differential expression analysis of RNA-seq data at single-base resolution.	2014-07-01	Kasper D. Hansen Jeffrey T. Leek	Frazee AC Sabunciyan S Irizarry RA	Biostatistics
Comprehensive high-throughput RNA sequencing analysis reveals contamination of multiple nasopharyngeal carcinoma cell lines with HeLa cell genomes.	2014-07-02	Melody Baddoo Asuka Nanbo	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
Exploring the stability of long intergenic non-coding RNA in K562 cells by comparative studies of RNA-Seq datasets	2014-07-05	Jing Tu	Lei Wang Dequan Zhou Yan Wang Zuhong Lu	Biology Direct
Large-scale transcriptional response to hypoxia in Aspergillus fumigatus observed using RNAseq identifies a novel hypoxia regulated ncRNA.	2014-07-05	Suman B Pakala Vinita S Joardar Bridget M Barker Nikhat Zafar	Liliana Losada Suchitra Pakala Stephanie Mounaud Natalie Fedorova William C Nierman Robert A Cramer	Mycopathologia
Enhanced whole genome sequence and annotation of Clostridium stercorarium DSM8532T using RNA-seq transcriptomics and high-throughput proteomics.	2014-07-07	Gerhard G Thallinger Richard Sparling Bernard Henrissat	John J Schellenberg Tobin J Verbeke Peter McQueen Oleg V Krokhin Xiangli Zhang Graham Alvare Brian Fristensky John A Wilkins David B Levin	BMC Genomics
De novo transcriptome sequencing and sequence analysis of the malaria vector Anopheles sinensis (Diptera: Culicidae).	2014-07-07	Liang Qiao	Bin Chen Yu-Juan Zhang Zhengbo He Wanshun Li Fengling Si Yao Tang Qiyi He Zhentian Yan Wenbo Fu Yanfei Che	Parasites & Vectors
Comparative Analysis of Glycogene Expression in Different Mouse Tissues Using RNA-Seq Data	2014-07-09	Vivekanand Jha Ahmad Firoz Sanjay Kumar Singh	Adeel Malik Amjad Ali	International Journal of Genomics
Occupancy of tissue-specific cis-regulatory modules by Otx2 and TLE/Groucho for embryonic head specification.	2014-07-09	Yuuri Yasuoka Yoshikazu Haramoto Makoto Asashima	Yutaka Suzuki Shuji Takahashi Haruka Someya Norihiro Sudou Ken W Cho Sumio Sugano Masanori Taira	Nature Communications
Analysis of the transcriptome and immune function of monocytes during IFNα-based therapy in chronic HCV revealed induction of TLR7 responsiveness.	2014-07-09	Andre Boonstra Wilfred F J van IJcken	Jun Hou Zwier M A Groothuismink Ludi Koning Robert Roomer Kim Kreefft Bi-Sheng Liu Harry L A Janssen Robert J de Knegt	Antiviral Research
Apomictic and sexual germline development differ with respect to cell cycle, transcriptional, hormonal and epigenetic regulation.	2014-07-10	Christian Sailer Ueli Grossniklaus	Anja Schmidt Marc W Schmid Ulrich C Klostermeier Weihong Qi Daniela Guthörl Manuel Waller Philip Rosenstiel Ueli Grossniklaus	PLOS Genetics
Expression pattern of immunoglobulin superfamily members in the silkworm, Bombyx mori.	2014-07-11	Moli Huang	Lei He Guangli Cao Renyu Xue Xiaolong Hu Chengliang Gong	Gene
A memory-efficient algorithm to obtain splicing graphs and de novo expression estimates from de Bruijn graphs of RNA-Seq data	2014-07-14	Aaron M. Tarone	Sing-Hoi Sze	BMC Genomics
Reference genes for RT-qPCR studies in Corynebacterium pseudotuberculosis identified through analysis of RNA-seq data.	2014-07-15	Bruno Bastos	Daiane M Carvalho Pablo H de Sá Thiago L P Castro Rodrigo D Carvalho Anne Pinto Danilo J P Gil Priscilla Bagano Lilia F M Costa Roberto Meyer Artur Silva Vasco Azevedo Rommel T J Ramos Luis G C Pacheco	Antonie van Leeuwenhoek
Roothairless5, which functions in maize (Zea mays L.) root hair initiation and elongation encodes a monocot-specific NADPH oxidase.	2014-07-15	Frank Hochholdinger	Josefine Nestler Sanzhen Liu Tsui-Jung Wen Anja Paschold Caroline Marcon Ho Man Tang Delin Li Li Li Robert B Meeley Hajime Sakai Wesley Bruce Patrick S Schnable	The Plant Journal
Whole transcriptome RNA-seq analysis: tumorigenesis and metastasis of melanoma.	2014-07-15	Songnian Hu	Hua Zhao Yongjun Li Shaobin Wang Yadong Yang Junyun Wang Xiuyan Ruan Yaran Yang Kan Cai Bing Zhang Peng Cui Jiangwei Yan Yongliang Zhao Edward K Wakeland Quanzhen Li Xiangdong Fang	Gene
SigFuge: single gene clustering of RNA-seq reveals differential isoform usage among cancer samples	2014-07-16	Charles M. Perou Liza Makowski Patrick K Kimes	Christopher R Cabanski Matthew D Wilkerson Ni Zhao Amy R Johnson Christopher A Maher Yufeng Liu J S Marron D Neil Hayes	Nucleic Acids Research
Differential gene expression in the respiratory tree of the sea cucumber Apostichopus japonicus during aestivation.	2014-07-16	Kenneth B. Storey	Ye Zhao Hongsheng Yang Muyan Chen	Marine Genomics
Polyphosphate accumulation is driven by transcriptome alterations that lead to near-synchronous and near-equivalent uptake of inorganic cations in an arbuscular mycorrhizal fungus.	2014-07-16	Katsuharu Saito Tatsuhiro Ezawa	Yusuke Kikuchi Nowaki Hijikata Kaede Yokoyama Ryo Ohtomo Yoshihiro Handa Masayoshi Kawaguchi	New Phytologist
Bioinformatic exploration of RIO protein kinases of parasitic and free-living nematodes.	2014-07-17	Pasi K. Korhonen Neil D. Young Andreas Hofmann Robin B. Gasser Aaron R Jex Paul W. Sternberg	Bert Breugelmans Stefano Mangiola Peter R Boag	International Journal for Parasitology
Developmental heterogeneity of cardiac fibroblasts does not predict pathological proliferation and activation.	2014-07-18	Kristy Red-Horse	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 Erin Bredeweg Matthew S. Sachs	Cheng Wu Fei Yang Kristina M Smith Matthew Peterson Rigzin Dekhang Ying Zhang Chandrashekara Mallappa Xiaoying Zhou Anna Lyubetskaya Jeffrey P Townsend James E Galagan Michael Freitag Jay C Dunlap Deborah Bell-Pedersen	G3
Sequence, structural and expression divergence of duplicate genes in the bovine genome.	2014-07-23	Graham Plastow Paul Stothard	Xiaoping Liao Hua Bao Yan Meng Stephen Moore	PLOS ONE
Hierarchical molecular events driven by oocyte-specific factors lead to rapid and extensive reprogramming	2014-07-24	Charles R Bradshaw Richard P Halley-Stott Vincent Pasque Kei Miyamoto John Gurdon	Jerome Jullien George E Allen Nigel J Garrett Hiroshi Kimura Keita Ohsumi	Molecular Cell
A new dataset of spermatogenic vs. oogenic transcriptomes in the nematode Caenorhabditis elegans.	2014-07-24	Marco A Ortiz Judith Kimble	Daniel Noble Elena P Sorokin	G3
Transcriptome Analysis of the Human Striatum in Tourette Syndrome.	2014-07-24	Gianfilippo Coppola Dean Palejev Flora M. Vaccarino Nenad Sestan	Jessica B Lennington Yuko Kataoka-Sasaki Thomas V Fernandez Yifan Li Anita Huttner Mihovil Pletikos Nenad Sestan James F Leckman	Biological Psychiatry
iRegulon: from a gene list to a gene regulatory network using large motif and track collections.	2014-07-24	Zeynep Kalender Atak Delphine Potier Stein Aerts Jean-Christophe Marine Bram Van de Sande Gert Hulselmans Marina N Sanchez	Rekin's Janky Annelien Verfaillie Hana Imrichová Laura Standaert Valerie Christiaens Koen Herten Dmitry Svetlichnyy Mark Fiers	PLOS Computational Biology
Characterization of long non-coding RNA transcriptome in clear-cell renal cell carcinoma by next-generation deep sequencing.	2014-07-25	Olivier Cussenot	Gabriel G Malouf Jianping Zhang Ying Yuan Eva Compérat Morgan Rouprêt Yunxin Chen Erika J Thompson Nizar M Tannir John N Weinstein Vicente Valero David Khayat Jean-Philippe Spano Xiaoping Su	Molecular Oncology
RNA-seq of the aging brain in the short-lived fish N. furzeri - conserved pathways and novel genes associated with neurogenesis.	2014-07-25	Eva Terzibasi Tozzini Francesco Spallotta Mario Baumgart Michela Ori Marco Groth Alessandro Cellerino Carlo Gaetano Matthias Platzer	Steffen Priebe Aurora Savino Giovanna Testa Andreas Dix Roberto Ripa Reinhard Guthke	Aging Cell
Utility of RNA-seq and GPMDB protein observation frequency for improving the sensitivity of protein identification by tandem MS	2014-07-28	Alexey I Nesvizhskii	Avinash K Shanmugam Anastasia K Yocum	Journal of Proteome Research
Genomes and transcriptomes of partners in plant-fungal-interactions between canola (Brassica napus) and two Leptosphaeria species.	2014-07-28	Jonathan Grandaubert Angela P Van de Wouw Barbara Jane Howlett	Rohan G T Lowe Andrew Cassin Bethany L Clark Thierry Rouxel	PLOS ONE
Transcriptome analysis reveals the same 17 S-locus F-box genes in two haplotypes of the self-incompatibility locus of Petunia inflata.	2014-07-28	Joshua P. Der Justin S Williams	Claude W dePamphilis Teh-Hui Kao	The Plant Cell
Genetic organization of interphase chromosome bands and interbands in Drosophila melanogaster	2014-07-29	Vladimir N. Babenko	Igor F Zhimulev Tatyana Yu Zykova Fyodor P Goncharov Varvara A Khoroshko Olga V Demakova Valeriy F Semeshin Galina V Pokholkova Lidiya V Boldyreva Darya S Demidova Sergey A Demakov Elena S Belyaeva	PLOS ONE
Molecular targets of chromatin repressive mark H3K9me3 in primate progenitor cells within adult neurogenic niches.	2014-07-30	Richard Sandstrom	Michael R Foret Christopher T Rhodes Yufeng Wang Mitchel S Berger Chin-Hsing Annie Lin	Frontiers in Genetics
Rbfox2-coordinated alternative splicing of Mef2d and Rock2 controls myoblast fusion during myogenesis.	2014-07-31	Zheng Xia Jernej Ule Ravi K. Singh Auinash Kalsotra	Christopher S Bland Marissa A Scavuzzo Tomaz Curk Wei Li Thomas A Cooper	Molecular Cell
Discovery of novel transcripts and gametophytic functions via RNA-seq analysis of maize gametophytic transcriptomes.	2014-07-31	Scott A. Givan	Antony M Chettoor Rex A Cole Clayton T Coker Erica Unger-Wallace Zuzana Vejlupkova Erik Vollbrecht John E Fowler Matthew Ms Evans	Genome Biology
Single-cell RNA-seq: advances and future challenges	2014-08 2014-08-01	Jörg Vogel Alexander Westermann	Antoine-Emmanuel Saliba Stanislaw A. Gorski	Nucleic Acids Research
Temporally and spatially restricted gene expression profiling	2014-08-01	Alexandra Tallafuss	Philip Washbourne John Postlethwait	Current Genomics
Characterization of distinct classes of differential gene expression in osteoblast cultures from non-syndromic craniosynostosis bone	2014-08-01	Rene Olivares-Navarrete	Monica L Rojas-Peña Sharon Hyzy Dalia Arafat Zvi Schwartz Barbara D Boyan Joseph Williams Greg Gibson	Journal of genomics
c-Jun promotes cell migration and drives expression of the motility factor ENPP2 in soft tissue sarcomas	2014-08-01	Massimo Loda	Stefano Sioletic Jeffrey Czaplinski Lan Hu Jonathan A Fletcher Christopher D M Fletcher Andrew J Wagner George D Demetri Ewa T Sicinska Eric L Snyder	The Journal of Pathology
In vivo mRNA profiling of uropathogenic Escherichia coli from diverse phylogroups reveals common and group-specific gene expression profiles	2014-08-05	Susanne Häussler Sarah Pohl Denitsa Eckweiler	Piotr Bielecki Uthayakumar Muthukumarasamy Agata Bielecka Ansgar Schanz Ute Niemeyer Tonio Oumeraci Nils von Neuhoff Jean-Marc Ghigo	mBio
Transcriptomic profiling revealed an important role of cell wall remodeling and ethylene signaling pathway during salt acclimation in Arabidopsis.	2014-08-05	Changle Ma	Xiaoyan Shen Zenglan Wang Xiaofeng Song Jiajia Xu Chunyun Jiang Yanxiu Zhao Hui Zhang	Plant Molecular Biology
Reduction of systematic bias in transcriptome data from human peripheral blood mononuclear cells for transportation and biobanking.	2014-08-07	Hideki Ohmomo	Tsuyoshi Hachiya Yu Shiwa Ryohei Furukawa Kanako Ono Shigeki Ito Yoji Ishida Mamoru Satoh Jiro Hitomi Kenji Sobue Atsushi Shimizu	PLOS ONE
MBASED: allele-specific expression detection in cancer tissues and cell lines.	2014-08-07	Jinfeng Liu	Oleg Mayba Houston N Gilbert Peter M Haverty Suchit Jhunjhunwala Zhaoshi Jiang Colin Watanabe Zemin Zhang	Genome Biology
Influence of RNA extraction methods and library selection schemes on RNA-seq data.	2014-08-11	Marie-Laure Yaspo Hans Lehrach	Marc Sultan Vyacheslav Amstislavskiy Thomas Risch Moritz Schuette Simon Dökel Meryem Ralser Daniela Balzereit Marie-Laure Yaspo	BMC Genomics
MRI-localized biopsies reveal subtype-specific differences in molecular and cellular composition at the margins of glioblastoma.	2014-08-11	Michael B Sisti	Brian J Gill David J Pisapia Hani R Malone Hannah Goldstein Liang Lei Adam Sonabend Jonathan Yun Jorge Samanamud Jennifer S Sims Matei Banu Athanassios Dovas Andrew F Teich Sameer A Sheth Guy M McKhann Jeffrey N Bruce Peter A Sims Peter Canoll	Proceedings of the National Academy of Sciences of the United States of America
SERPINB3/B4 contributes to early inflammation and barrier dysfunction in an experimental murine model of atopic dermatitis.	2014-08-11	Gurjit Khurana Hershey	Umasundari Sivaprasad Kayla G Kinker Mark B Ericksen Mark Lindsey Aaron M Gibson Stacey A Bass Nicolas S Hershey Jingyuan Deng Mario Medvedovic	Journal of Investigative Dermatology
A comparative study of techniques for differential expression analysis on RNA-Seq data.	2014-08-13	Naomi R. Wray Zong Hong Zhang Qiong-Yi Zhao Janette Edson Denis C Bauer	Dhanisha J Jhaveri Vikki M Marshall Ramesh K Narayanan Gregory J Robinson Andreas E Lundberg Perry F Bartlett	PLOS ONE
Interferon gene expression signature in rheumatoid arthritis neutrophils correlates with a good response to TNFi therapy.	2014-08-13	Helen L Wright	Huw B Thomas Robert J Moots Steven W Edwards	Rheumatology
Functional expression of dental plaque microbiota.	2014-08-14	Andrew I. Su Tobias Meißner	Scott N Peterson Erik Snesrud Ana C Ong Nicholas J Schork Walter A Bretz	Frontiers in cellular and infection microbiology
Discovering functional modules by topic modeling RNA-Seq based toxicogenomic data.	2014-08-14	Binsheng Gong	Ke Yu Mikyung Lee Zhichao Liu Joshua Xu Roger Perkins Weida Tong	Chemical Research in Toxicology
Itch-associated peptides: RNA-Seq and bioinformatic analysis of natriuretic precursor peptide B and gastrin releasing peptide in dorsal root and trigeminal ganglia, and the spinal cord.	2014-08-14	Danielle Thierry-Mieg Jean Thierry-Mieg	Samridhi C Goswami Santosh Mishra Mark A Hoon Andrew J Mannes Michael J Iadarola	Molecular Pain
De novo transcriptome assembly and comparative analysis of differentially expressed genes in Prunus dulcis Mill. in response to freezing stress.	2014-08-14	Arghavan Alisoltani	Sadegh Mousavi Behrouz Shiran Hossein Fallahi Esameil Ebrahimie Ali Imani Saadollah Houshmand	PLOS ONE
RNA-Rocket: An RNA-Seq Analysis Resource for Infectious Disease Research	2014-08-14	Leslie Birgit Vosshall Michael McClelland Cristina Aurrecoechea	Andrew S. Warren Brian Brunk Prerak Desai Scott Emrich Gloria I. Giraldo-Calderón Omar Harb Deborah Hix Daniel Lawson Dustin Machi Chunhong Mao Eric Nordberg Maulik Shukla Alice R. Wattam Rebecca Will Hyun Seung Yoo Bruno Sobral
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 Daryl P Shanley John C. Mathers	Catherine Meplan Sushma N Grellscheid Tom B L Kirkwood John E Hesketh	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 Vied Alexandre A S F Raposo David Feng	Yuting Wang	Frontiers in Neuroscience
Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations	2014-08-22	Pratik D. Jagtap	Gloria M Sheynkman James E Johnson Michael R Shortreed Getiria Onsongo Brian L Frey Timothy J Griffin Lloyd M Smith	BMC Genomics
MicroRNA and mRNA cargo of extracellular vesicles from porcine adipose tissue-derived mesenchymal stem cells.	2014-08-23	Lilach O. Lerman	Alfonso Eirin Scott M Riester Xiang-Yang Zhu Hui Tang Jared M Evans Daniel O'Brien Andre J van Wijnen	Gene
RNA-seq transcriptome profiling reveals that Medicago truncatula nodules acclimate N₂ fixation before emerging P deficiency reaches the nodules.	2014-08-23	Gabriela Salinas-Riester Claudia Pommerenke	Ricardo A Cabeza Rebecca Liese Annika Lingner Ilsabe von Stieglitz Janice Neumann Klaus Dittert Joachim Schulze	Journal of Experimental Botany
Normalization of RNA-seq data using factor analysis of control genes or samples	2014-08-24	Davide Risso	John Ngai Terence P Speed Sandrine Dudoit	Nature Biotechnology
The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance	2014-08-24	Danielle Thierry-Mieg Michele Filosi Roberto Visintainer Florian Caiment Samantha Riccadonna Marco Chierici Lee Lancashire Binsheng Gong Davide Albanese Jean Thierry-Mieg Giuseppe Jurman Jos Kleinjans	Charles Wang Pierre R Bushel Joshua Xu Hong Fang Huixiao Hong Jie Shen Zhenqiang Su Joe Meehan Xiaojin Li Lu Yang Haiqing Li Paweł P Łabaj David P Kreil Dalila Megherbi Stan Gaj Joost van Delft Andreas Scherer Viswanath Devanarayan Jian Wang Yong Yang Hui-Rong Qian Marina Bessarabova Yuri Nikolsky Cesare Furlanello Ke K Zhang Jianying Li Jui-Hua Hsieh Daniel L Svoboda James C Fuscoe Youping Deng Leming Shi Richard S Paules Scott S Auerbach Weida Tong	Nature Biotechnology
RNA-seq Transcriptional Profiling of Peripheral Blood Leukocytes from Cattle Infected with Mycobacterium bovis.	2014-08-26	Kévin Rue-Albrecht Karsten Hokamp Eamonn Gormley David E. MacHugh Stephen V. Gordon Kate Killick	Kirsten E McLoughlin Nicolas C Nalpas John A Browne David A Magee Stephen D E Park Kieran G Meade Cliona O'Farrelly	Frontiers in Immunology
Deletion of aryl hydrocarbon receptor AHR in mice leads to subretinal accumulation of microglia and RPE atrophy.	2014-08-26	Anand Swaroop Soo-Young Kim Wai T. Wong Robert N. Fariss Matthew Brooks Emily Chew	Hyun-Jin Yang Yi-Sheng Chang Jung-Woong Kim Rivka A Rachel Tiziana Cogliati Haohua Qian	Investigative Ophthalmology & Visual Science
Transcriptomic profiling of rat liver samples in a comprehensive study design by RNA-Seq.	2014-08-26	Danielle Thierry-Mieg Jean Thierry-Mieg	Binsheng Gong Charles Wang Zhenqiang Su Huixiao Hong Leming Shi Scott S Auerbach Weida Tong Joshua Xu	Scientific Data
Cross-platform ultradeep transcriptomic profiling of human reference RNA samples by RNA-Seq.	2014-08-26	Danielle Thierry-Mieg Jean Thierry-Mieg	Joshua Xu Zhenqiang Su Huixiao Hong David P Kreil Christopher E Mason Weida Tong Leming Shi	Scientific Data
RVboost: RNA-seq variants prioritization using a boosting method	2014-08-27	Andrew L Feldman	Chen Wang Jaime I Davila Saurabh Baheti Aditya V Bhagwate Xue Wang Jean-Pierre A Kocher Susan L Slager Anne J Novak James R Cerhan E Aubrey Thompson Yan W Asmann	Bioinformatics
RNA-Seq analysis reveals a six-gene SoxR regulon in Streptomyces coelicolor	2014-08-27	Joshua Shapiro Nawar Naseer	Monica Chander	PLOS ONE
Identification of sRNAs expressed by the human pathogen Neisseria gonorrhoeae under disparate growth conditions.	2014-08-28	Ryan S McClure	Brian Tjaden Caroline Genco	Frontiers in Microbiology
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 Siddharthan Chandran	Owain T James Matthew R Livesey Jing Qiu Bilada Bilican Ghazal Haghi Rinku Rajan Karen Burr	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
Identification of differentially expressed genes during development of the zebrafish pineal complex using RNA sequencing.	2014-08-28	Q85220273	Joshua T Gamse	Developmental Biology
Assessing the clinical use of clear cell renal cell carcinoma molecular subtypes identified by RNA expression analysis.	2014-08-28	Richard W. Joseph Thai Huu Ho	Jeanette E Eckel-Passow Daniel A Igel Daniel J Serie 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 Wolfgang R Streit	Dagmar Krysciak Jessica Grote Mariita Rodriguez Orbegoso Christian Utpatel Christel Schmeisser Hari B Krishnan	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 Erik K Flemington	Elizabeth C Martin Adrienne E Krebs Hope E Burks Steven Elliott Melody Baddoo Bridgette M Collins-Burow Matthew E Burow	Genes & Cancer
Genome-wide interrogation of longitudinal FEV1 in children with asthma	2014-09-01	Hae Kyung Im Nancy J Cox	Kehua Wu Eric R Gamazon Hae Kyung Im Paul Geeleher Steven R White Julian Solway George L Clemmer Scott T Weiss Kelan G Tantisira Mark J Ratain R Stephanie Huang	American Journal of Respiratory and Critical Care Medicine
Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function.	2014-09-01	Gregory E Crawford	James A Browne Rui Yang Lingyun Song Shih-Hsing Leir Ann Harris	Molecular Human Reproduction
The devil in the details of RNA-seq	2014-09-01	Anton Kratz Piero Carninci		Nature Biotechnology
Genome-wide distribution of Auts2 binding localizes with active neurodevelopmental genes.	2014-09-02	Ramon Y Birnbaum Nadav Ahituv	N Oksenberg G D E Haliburton W L Eckalbar I Oren S Nishizaki K Murphy K S Pollard	Translational Psychiatry
RNA-seq reveals aurora kinase-driven mTOR pathway activation in patients with sarcomatoid metastatic renal cell carcinoma.	2014-09-02	Tommy Tong Jeremy O Jones	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	Molecular Cancer Research
Transcriptomic dissection of the rice-Burkholderia glumae interaction.	2014-09-03	Teresia J Buza Peng Deng Daniel G. Peterson	Zenaida V Magbanua Mark Arick Chuan-Yu Hsu Kurt C Showmaker Philippe Chouvarine Shien Lu	BMC Genomics
Transcriptional profiles of bovine in vivo pre-implantation development.	2014-09-04	Junhong Luo	Zongliang Jiang Jiangwen Sun Hong Dong Xinbao Zheng Craig Obergfell Yong Tang Jinbo Bi Rachel O'Neill Yijun Ruan Jingbo Chen Xiuchun Cindy Tian	BMC Genomics
Whole transcriptome sequencing reveals extensive unspliced mRNA in metastatic castration-resistant prostate cancer.	2014-09-04	Adam G Sowalsky	Zheng Xia Liguo Wang Hao Zhao Shaoyong Chen Glenn J Bubley Steven P Balk Wei Li	Molecular Cancer Research
Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer.	2014-09-04	Elisa Ficarra Lasorella A Iavarone A Raul Rabadan	Francesco Abate Sakellarios Zairis Andrea Acquaviva Chris H Wiggins Veronique Frattini Giorgio Inghirami	BMC Systems Biology
Caught in the act: RNA-Seq provides novel insights into mRNA degradation.	2014-09-04	Jörg Stülke	Jan Gerwig	Molecular Microbiology
Transcriptome profiling of spinal muscular atrophy motor neurons derived from mouse embryonic stem cells	2014-09-05	Matthew E R Butchbach	Miho Maeda Ashlee W Harris Brewster F Kingham Casey J Lumpkin Lynn M Opdenaker Suzanne M McCahan Wenlan Wang	PLOS ONE
Progressive increase in mtDNA 3243A>G heteroplasmy causes abrupt transcriptional reprogramming.	2014-09-05	Paweł Golik	Martin Picard Jiangwen Zhang Saege Hancock Olga Derbeneva Ryan Golhar Sean O'Hearn Shawn Levy Prasanth Potluri Maria Lvova Antonio Davila Chun Shi Lin Juan Carlos Perin Eric F Rappaport Hakon Hakonarson Ian A Trounce Vincent Procaccio Douglas C Wallace	Proceedings of the National Academy of Sciences of the United States of America
Transcriptome profiling of Vitis amurensis, an extremely cold-tolerant Chinese wild Vitis species, reveals candidate genes and events that potentially connected to cold stress.	2014-09-05	Weirong Xu	Ruimin Li Ningbo Zhang Fuli Ma Yuntong Jiao Zhenping Wang	Plant Molecular 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
The sialotranscriptome of Amblyomma triste, Amblyomma parvum and Amblyomma cajennense ticks, uncovered by 454-based RNA-seq.	2014-09-08	Luiz Gustavo Gardinassi José M. Ribeiro Beatriz R Ferreira C L Mafra Matias Pablo Juan Szabó Sandra Regina Maruyama	Gustavo Rocha Garcia Elen Anatriello Higo Nasser Santanna Moreira Maria Marlene Martins Isabel Kinney Ferreira de Miranda-Santos	Parasites & Vectors
RNA-Seq analysis of the multipartite genome of Rhizobium etli CE3 shows different replicon contributions under heat and saline shock.	2014-09-08	Q85275267 Santiago Castillo-Ramírez	Maria Luisa Tabche Alfredo Mendoza-Vargas Miguel A Ramírez-Romero Guillermo Dávila	BMC Genomics
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
Transcriptome characteristics of filamentous fungi deduced using high-throughput analytical technologies.	2014-09-11	Lucía Ramírez	Martha Lucía Meijueiro Francisco Santoyo Antonio G Pisabarro	Briefings in functional genomics
GSAASeqSP: a toolset for gene set association analysis of RNA-Seq data	2014-09-12	Terrence S. Furey	Qing Xiong Sayan Mukherjee	Scientific Reports
Transcriptomic analysis identifies gene networks regulated by estrogen receptor α (ERα) and ERβ that control distinct effects of different botanical estrogens	2014-09-12	Zeynep Madak-Erdogan	Ping Gong Jilong Li Jianlin Cheng C Michael Greenlief William Helferich John A Katzenellenbogen Benita S Katzenellenbogen	Nuclear Receptor Signaling
TELP, a sensitive and versatile library construction method for next-generation sequencing	2014-09-15	Feng Xu	Xu Peng Jingyi Wu Reinhard Brunmeir Sun-Yee Kim Qiongyi Zhang Chunming Ding Weiping Han Wei Xie	Nucleic Acids Research
Onecut1 and Onecut2 redundantly regulate early retinal cell fates during development.	2014-09-16	Xiuqian Mu	Darshan Sapkota Hemabindu Chintala Fuguo Wu Steven J Fliesler Zihua Hu	Proceedings of the National Academy of Sciences of the United States of America
Using normalization to resolve RNA-Seq biases caused by amplification from minimal input.	2014-09-16	Christiaan V. Henkel Finn-Arne Weltzien	Eirill Ager-Wick Trude M Haug	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
Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis.	2014-09-18	Francesca Finotello	Barbara Di Camillo	Briefings in functional genomics
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
Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli.	2014-09-18	Kenneth J McDowall	Justin E Clarke Louise Kime David Romero A	Nucleic Acids Research
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
Error estimates for the analysis of differential expression from RNA-seq count data.	2014-09-23	Conrad J Burden	Sumaira E Qureshi Susan R Wilson	PeerJ
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 Everett E Vokes	Johannes Brägelmann Michaela K Keck Mohamed El Dinali Christopher D Brown Thomas Stricker Anish Munagala Ezra E W Cohen Mark W Lingen Kevin P White Tanguy Y Seiwert	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
Transcriptome profile analysis reveals specific signatures of pollutants in Atlantic eels.	2014-09-26	Louis Bernatchez Hélène Budzinski	Lucie Baillon Fabien Pierron Raphaël Coudret Eric Normendeau Antoine Caron Laurent Peluhet Pierre Labadie Gilles Durrieu Jérôme Sarraco Pierre Elie Patrice Couture Magalie Baudrimont	Ecotoxicology
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
RNA-Seq gene profiling--a systematic empirical comparison.	2014-09-30	Nuno A. Fonseca Alvis Brazma John C Marioni		PLOS ONE
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
Genome-wide discovery of drug-dependent human liver regulatory elements	2014-10	Marcelo Rizzatti Luizon Nadav Ahituv	Robin P Smith Walter L Eckalbar Kari M Morrissey Thomas J Hoffmann Xuefeng Sun Stacy L Jones Shelley Force Aldred Anuradha Ramamoorthy Zeruesenay Desta Yunlong Liu Todd C Skaar Nathan D Trinklein Kathleen M Giacomini	PLOS Genetics
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 Sulev Kõks	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
RNA-seq analysis of the rat placentation site reveals maternal obesity-associated changes in placental and offspring thyroid hormone signaling.	2014-10-05	Kartik Shankar	J Saben P Kang Y Zhong K M Thakali H Gomez-Acevedo S J Borengasser A Andres T M Badger	Placenta
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 Alberto Kornblihtt	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	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
RNA-seq reveals the pan-transcriptomic impact of attenuating the gliotoxin self-protection mechanism in Aspergillus fumigatus	2014-10-14	David A Fitzpatrick Gary W Jones Thomas M Keane Sean Doyle	Grainne O'Keeffe Stephen Hammel Rebecca A Owens	BMC Genomics
Quality Control for RNA-Seq (QuaCRS): An Integrated Quality Control Pipeline.	2014-10-15	James S Blachly	Karl W Kroll Nima E Mokaram Alexander R Pelletier David E Frankhouser Maximillian S Westphal Paige A Stump Cameron L Stump Ralf Bundschuh Pearlly Yan	Cancer Informatics
Rcount: simple and flexible RNA-Seq read counting.	2014-10-15	Ueli Grossniklaus	Marc W Schmid Ueli Grossniklaus	Bioinformatics
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 James F. Gusella	Aarathi Sugathan Ian Blumenthal Poornima Manavalan Ashok Ragavendran Harrison Brand Diane Lucente Judith Miles Steven D Sheridan Alexei Stortchevoi	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 Matthew Suderman	Jane J Pappas Sophie Petropoulos Majid Iqbal Vasilis Moisiadis Stephen G Matthews Moshe Szyf	PLOS ONE
In vivo proximity labeling for the detection of protein-protein and protein-RNA interactions.	2014-10-29	Roberto Bonasio Michiel Vermeulen	David B Beck Varun Narendra William J Drury Ryan Casey Pascal W T C Jansen Zuo-Fei Yuan Benjamin A Garcia	Journal of Proteome Research
Transcriptional adaptations during long-term persistence of Staphylococcus aureus in the airways of a cystic fibrosis patient.	2014-10-29	Boyke Bunk Barbara C. Kahl Alexander Mellmann Cathrin Spröer	Nadine Windmüller Anika Witten Desirée Block	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
GeneFriends: a human RNA-seq-based gene and transcript co-expression database	2014-10-31	Thomas Craig	Sipko van Dam João Pedro de Magalhães	Nucleic Acids Research
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
Several fusion genes identified by whole transcriptome sequencing in a spindle cell sarcoma with rearrangements of chromosome arm 12q and MDM2 amplification	2014-11	Sverre Heim Ioannis Panagopoulos	Bodil Bjerkehagen Ludmila Gorunova Jeanne-Marie Berner Kjetil Boye	International Journal of Oncology
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
Whole transcriptome analysis for T cell receptor-affinity and IRF4-regulated clonal expansion of T cells	2014-11-01	Gordon K Smyth	Wei Shi Kevin Man Stephen L Nutt Axel Kallies	Genomics Data
Increasing gene discovery and coverage using RNA-seq of globin RNA reduced porcine blood samples.	2014-11-04	Paul Stothard	Igseo Choi Hua Bao Arun Kommadath Afshin Hosseini Xu Sun Yan Meng Graham S Plastow Christopher K Tuggle James M Reecy Eric Fritz-Waters Samuel M Abrams Joan K Lunney Le Luo Guan	BMC Genomics
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
The landscape of microRNA, Piwi-interacting RNA, and circular RNA in human saliva.	2014-11-06	Xianzhi Lin Feng Li Xinshu Xiao	Jae Hoon Bahn Qing Zhang Tak-Ming Chan Yong Kim David T W Wong	Clinical Chemistry
Biochemical and molecular changes associated with heteroxylan biosynthesis in Neolamarckia cadamba (Rubiaceae) during xylogenesis	2014-11-07	Antony Bacic	Xianhai Zhao Kunxi Ouyang Siming Gan Wei Zeng Lili Song Shuai Zhao Juncheng Li Monika S Doblin Xiao-Yang Chen Alan Marchant Xiaomei Deng Ai-Min Wu	Frontiers in Plant Science
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
COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems.	2014-11-11	Yasunobu Okamura Shu Tadaka	Yuichi Aoki Takeshi Obayashi Satoshi Ito Takafumi Narise Kengo Kinoshita	Nucleic Acids Research
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 Andrew C Tolonen Adriana Alberti	Magali Boutard Tristan Cerisy Pierre-Yves Nogue Marcel Salanoubat	PLOS Genetics
RNA-seq analysis of Quercus pubescens Leaves: de novo transcriptome assembly, annotation and functional markers development.	2014-11-13	Alessio Fini Federico Sebastiani Cecilia Brunetti Massimiliano Tattini	Sara Torre Silvia Fineschi Francesco Ferrini	PLOS ONE
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 Fredrik Pontén	Journal of Histochemistry & Cytochemistry
Aberrant expression of miR-218 and miR-204 in human mesial temporal lobe epilepsy and hippocampal sclerosis-convergence on axonal guidance.	2014-11-19	Anne Yael Nossent Kees Fluiter A Sabers Lisbeth Birk Møller Asli Silahtaroglu Rikke S Møller Niels Tommerup Eleonora Aronica	Sanne S Kaalund Morten T Venø Mads Bak Henning Laursen Flemming Madsen Helle Broholm Bjørn Quistorff Peter Uldall Sakari Kauppinen Jørgen Kjems Zeynep Tümer	Epilepsia
ChiTaRS 2.1--an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts	2014-11-20	Alfonso Valencia Alessandro Gorohovski Milana Frenkel-Morgenstern	Dunja Vucenovic Lorena Maestre	Nucleic Acids Research
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 Ikuo Igarashi Xuenan Xuan Yoshifumi Nishikawa	Hiroyuki Wakaguri Shin-ichiro Kawazu Makoto Matsubayashi Fumiya Kawahara Naotoshi Tsuji Shinuo Cao Fujiko Sunaga Kazuhiro Okubo Josef Tuda Arthur E Mongan Yuki Eshita Ryuichiro Maeda Wojciech Makałowski Yutaka Suzuki Junya Yamagishi	Nucleic Acids Research
The TCF C-clamp DNA binding domain expands the Wnt transcriptome via alternative target recognition.	2014-11-20	Pierre Baldi	Nate P Hoverter Michael D Zeller Miriam M McQuade Angela Garibaldi Anke Busch Elizabeth M Selwan Klemens J Hertel Marian L Waterman	Nucleic Acids Research
The mechanisms of genome-wide target gene regulation by TCF7L2 in liver cells	2014-11-20	Ralph A DeFronzo	Luke Norton Xi Chen Marcel Fourcaudot Nikhil K Acharya Sami Heikkinen	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 Daohua Lou Jesper Haeggström Olga Kharchenko Peter V Kharchenko	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
Identification of Salt-Stress-Induced Genes from the RNA-Seq Data of Reaumuria trigyna Using Differential-Display Reverse Transcription PCR.	2014-11-26	Shu-Biao Wu	Zhen-Hua Dang Qi Qi Hui-Rong Zhang Hao-Yu Li Ying-Chun Wang	International Journal of Genomics
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 Yoshihiro Kawaoka	Xinxia Peng Amie J Eisfeld Scott R Tyler Jennifer Tisoncik-Go G Lynn Law Nives Skunca Masato Hatta David J Gasper Sara M Kelly Jean Chang Matthew J Thomas Jeremy Johnson Aaron M Berlin Pamela Russell Ross Swofford Jason Turner-Maier Sarah Young Steve Searle Xingshen Sun Yaling Yi M Suresh Terrence M Tumpey Samantha M Wisely Bruce W Birren Robert E Palermo Michael G Katze	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
Identifying direct targets of transcription factor Rfx2 that coordinate ciliogenesis and cell movement	2014-12-01	Taejoon Kwon	Mei-I Chung Rakhi Gupta Julie C Baker John B Wallingford	Genomics Data
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 David Edwards Ove Hoegh-Guldberg	Paulina Kaniewska Edmund Yew Siang Ling	BMC Genomics
An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era	2014-12-03	Lee Lancashire	Zhenqiang Su Hong Fang Huixiao Hong Leming Shi Wenqian Zhang Wenwei Zhang Yanyan Zhang Zirui Dong Marina Bessarabova Xi Yang Baitang Ning Binsheng Gong Joe Meehan Joshua Xu Weigong Ge Roger Perkins Matthias Fischer Weida Tong	Genome Biology
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
RNA-seq analysis of oil palm under cold stress reveals a different C-repeat binding factor (CBF) mediated gene expression pattern in Elaeis guineensis compared to other species.	2014-12-05	Yaodong Yang Annaliese S Mason	Xintao Lei Yong Xiao Wei Xia Zilong Ma Ming Peng	PLOS ONE
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
MCMC implementation of the optimal Bayesian classifier for non-Gaussian models: model-based RNA-Seq classification.	2014-12-10	Edward R. Dougherty	Jason M Knight Ivan Ivanov	BMC Bioinformatics
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
UPF2, a nonsense-mediated mRNA decay factor, is required for prepubertal Sertoli cell development and male fertility by ensuring fidelity of the transcriptome.	2014-12-11	Wei Yan Shuiqiao Yuan Jianqiang Bao Bo Torben Porse	Chong Tang	Development
Whole exome sequencing of a single osteosarcoma case--integrative analysis with whole transcriptome RNA-seq data.	2014-12-11	Sulev Kõks	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 Liewei Wang E Aubrey Thompson	Nucleic Acids Research
Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems.	2014-12-16	Julie Dickerson	Ruolin Liu Ann E Loraine	BMC Bioinformatics
Advances in translational bioinformatics facilitate revealing the landscape of complex disease mechanisms	2014-12-16	Youping Deng	Jack Y Yang A Dunker Jun S Liu Xiang Qin Hamid R Arabnia William Yang Andrzej Niemierko Zhongxue Chen Zuojie Luo Liangjiang Wang Yunlong Liu Dong Xu Weida Tong Mary Yang	BMC Bioinformatics
Identification of genes and pathways involved in kidney renal clear cell carcinoma	2014-12-16	Youping Deng	William Yang Kenji Yoshigoe Xiang Qin Jun S Liu Jack Y Yang Andrzej Niemierko Yunlong Liu A Dunker Zhongxue Chen Liangjiang Wang Dong Xu Hamid R Arabnia Weida Tong Mary Yang	BMC Bioinformatics
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
A note on an exon-based strategy to identify differentially expressed genes in RNA-seq experiments.	2014-12-26	Laura L. Elo	Asta Laiho	PLOS ONE
RNA-seq profiling of small numbers of Drosophila neurons.	2014-12-26	Michael Rosbash E Nagoshi Xiao Chen	Katharine Abruzzi 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
Comparisons of de novo transcriptome assemblers in diploid and polyploid species using peanut (Arachis spp.) RNA-Seq data.	2014-12-31	Ratan Chopra	Gloria Burow Andrew Farmer Joann Mudge Charles E Simpson Mark D Burow	PLOS ONE
Subgroup-elimination transcriptomics identifies signaling proteins that define subclasses of TRPV1-positive neurons and a novel paracrine circuit.	2014-12-31	Tim Hucho	Jörg Isensee Carsten Wenzel Rene Buschow Robert Weissmann Andreas W Kuss	PLOS ONE
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 Lesley Bell-Sakyi	Sabine Weisheit Marina Popara Julia Loecherbach Daniel Růžek Libor Grubhoffer	Parasites & Vectors
Dynamics in Transcriptomics: Advancements in RNA-seq Time Course and Downstream Analysis	2015	Daniel Spies Constance Ciaudo		Computational and Structural Biotechnology Journal
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 Grant Cramer	Stefan Czemmel Erin R Galarneau Renaud Travadon 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 Cristina Ovilo	Miriam Ayuso Almudena Fernández Yolanda Núñez Beatriz Isabel Carmen Barragán Ana Isabel Fernández Juan F Medrano Ángela Cánovas Antonio González-Bulnes Clemente López-Bote	PLOS ONE
From Insect to Man: Photorhabdus Sheds Light on the Emergence of Human Pathogenicity	2015	Helge Bode Nicholas J Tobias Michael L. Beeton Richard ffrench-Constant	Geraldine Mulley Paul Wilkinson Isabella Vlisidou Nina Ockendon-Powell Alexia Hapeshi Friederike I Nollmann Jean van den Elsen Nicholas R Waterfield	PLOS ONE
Decreased SMAD4 expression is associated with induction of epithelial-to-mesenchymal transition and cetuximab resistance in head and neck squamous cell carcinoma.	2015	Ruchira Ranaweera Elana J. Fertig	Haixia Cheng Hiroyuki Ozawa Hiromitsu Hatakeyama Jason D Howard Jimena Perez Michael Considine Manjusha Thakar Gabriel Krigsfeld Christine H Chung	Cancer Biology and Therapy
A cell-based systems biology assessment of human blood to monitor immune responses after influenza vaccination	2015	Nripesh Prasad Parimal Samir Sebastian Joyce Shawn Levy Q52577914	Kristen L Hoek Leigh M Howard Xinnan Niu Allison Galassie Qi Liu Tara M Allos Kyle A Floyd Yan Guo Yu Shyr Andrew J Link	PLOS ONE
Activin-A and Bmp4 levels modulate cell type specification during CHIR-induced cardiomyogenesis	2015	Karl Stamm	Min-Su Kim Audrey Horst Steven Blinka Donna Mahnke James Schuman Rebekah Gundry Aoy Tomita-Mitchell John Lough	PLOS ONE
mRNA profiling reveals determinants of trastuzumab efficiency in HER2-positive breast cancer	2015	Manuel Nietert Gabriela Salinas-Riester Silvia von der Heyde	Steve Wagner Alexander Czerny Fabian Ludewig Dorit Arlt Tim Beißbarth	PLOS ONE
The exosome component Rrp6 is required for RNA polymerase II termination at specific targets of the Nrd1-Nab3 pathway	2015	Amber L. Mosley	Melanie J Fox Hongyu Gao Whitney R Smith-Kinnaman Yunlong Liu	PLOS Genetics
A Genome-Wide Association Study for Culm Cellulose Content in Barley Reveals Candidate Genes Co-Expressed with Members of the CELLULOSE SYNTHASE A Gene Family	2015	Diane Mather Rachel A Burton Brian Steffenson Kanwarpal S Dhugga Robbie Waugh	Kelly Houston Beata Sznajder Antoni J Rafalski Jillian Taylor Geoffrey B Fincher	PLOS ONE
Differential Expression Analysis by RNA-Seq Reveals Perturbations in the Platelet mRNA Transcriptome Triggered by Pathogen Reduction Systems	2015	Abdimajid Osman Patrick Provost Adam Ameur	Walter E Hitzler	PLOS ONE
Asparagus Spears as a Model to Study Heteroxylan Biosynthesis during Secondary Wall Development	2015	Kelsey L. Picard Wei Zeng Edwin R. Lampugnani Antony Bacic	Lili Song Aimin Wu Roshan Cheetamun Cherie Beahan Andrew Cassin Andrew Lonsdale Monika S Doblin	PLOS ONE
Global Gene Expression Profiling through the Complete Life Cycle of Trypanosoma vivax	2015	Matthew Berriman Mandy Sanders Sophie Goyard Andrew P Jackson Dong Xia Paola Minoprio	Bernardo J Foth Jonathan M Wastling	PLOS Neglected Tropical Diseases
Gene Expression Ratios Lead to Accurate and Translatable Predictors of DR5 Agonism across Multiple Tumor Lineages	2015	John Monahan	Anupama Reddy Joseph D Growney Nick S Wilson Caroline M Emery Jennifer A Johnson Rebecca Ward Kelli A Monaco Joshua Korn Mark D Stump Felipa A Mapa Christopher J Wilson Janine Steiger Jebediah Ledell Richard J Rickles Vic E Myer Seth A Ettenberg Robert Schlegel William R Sellers Heather A Huet Joseph Lehár	PLOS ONE
RNA-Seq Analysis of Human Trigeminal and Dorsal Root Ganglia with a Focus on Chemoreceptors	2015	Janine Altmüller Hanns Hatt Günter Gisselmann	Caroline Flegel Nicole Schöbel Christian Becker Andrea Tannapfel Günter Gisselmann	PLOS ONE
Whole Body Melanoma Transcriptome Response in Medaka	2015	Manfred Schartl	Yingjia Shen Katja Maurus Ron Walter Chad Tomlinson Richard K Wilson John Postlethwait Wesley C Warren	PLOS ONE
OperomeDB: A Database of Condition-Specific Transcription Units in Prokaryotic Genomes	2015	Sarath Chandra Janga	Kashish Chetal Sarath Chandra Janga	BioMed Research International
Genome-wide transcriptional analysis suggests hydrogenase- and nitrogenase-mediated hydrogen production in Clostridium butyricum CWBI 1009	2015	Annick Wilmotte	Magdalena Calusinska Christopher Hamilton Pieter Monsieurs Gregory Mathy Natalie Leys Fabrice Franck Bernard Joris Philippe Thonart Serge Hiligsmann	Biotechnology for Biofuels
Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data	2015	Detlef Weigel Korbinian Schneeberger Vimal Rawat	Ahmed Abdelsamad Björn Pietzenuk Danelle K Seymour Daniel Koenig Ales Pecinka	PLOS ONE
Using RNA-Seq Data to Evaluate Reference Genes Suitable for Gene Expression Studies in Soybean	2015	Hon-Ming Lam	Aldrin Kay-Yuen Yim Johanna Wing-Hang Wong Yee-Shan Ku Hao Qin Ting-Fung Chan	PLOS ONE
274: Next generation sequencing (RNA-seq) of the human decidual and placental villous transcriptomes in intra-amniotic infection (IAI) induced preterm birth (PTB)	2015-01	Antonis Rokas	William Ackerman Irina Buhimschi Haley Eidem David Rinker Kara Rood Guomao Zhao Taryn Summerfield Mark Landon Catalin Buhimschi	American Journal of Obstetrics and Gynecology
Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli	2015-01-01	Thorsten Bischler Alexander Herbig Cynthia Sharma Konrad Förstner	Maureen K Thomason Sara K Eisenbart Aixia Zhang Kay Nieselt Gisela Storz	Journal of Bacteriology
A pan-cancer analysis of prognostic genes.	2015-01-01	Stefan Bekiranov Wei-Min Chen Anindya Dutta	Jordan Anaya Brian Reon Stefan Bekiranov	PeerJ
The transcription factor Nerfin-1 prevents reversion of neurons into neural stem cells	2015-01-01	Anthony T. Papenfuss Chen-Fang Weng Louise Y. Cheng	Francesca Froldi Milan Szuperak Wei Shi	Genes & Development
Quantifying entire transcriptomes by aligned RNA-seq data.	2015-01-01	Raffaele A. Calogero	Francesca Zolezzi	Methods in Molecular Biology
Exploring the RNA editing potential of RNA-Seq data by ExpEdit.	2015-01-01	Graziano Pesole Anna Maria D'Erchia Ernesto Picardi	Mattia D'Antonio Tiziana Castrignanò	Methods in Molecular Biology
Integrated whole transcriptome and DNA methylation analysis identifies gene networks specific to late-onset Alzheimer's disease.	2015-01-01	Margaret A. Pericak-Vance	Crystal E Humphries Martin A Kohli Lubov Nathanson Patrice Whitehead Gary Beecham Eden Martin Deborah C Mash John Gilbert	Journal of Alzheimer's Disease
Translating Ribosome Affinity Purification (TRAP) followed by RNA sequencing technology (TRAP-SEQ) for quantitative assessment of plant translatomes.	2015-01-01	María Eugenia Zanetti	Mauricio A Reynoso Piyada Juntawong Marcos Lancia Flavio A Blanco Julia Bailey-Serres	Methods in Molecular Biology
Nuclear transcriptome profiling of induced pluripotent stem cells and embryonic stem cells identify non-coding loci resistant to reprogramming	2015-01-01	Piero Carninci	Alexandre Fort Daisuke Yamada Kosuke Hashimoto Haruhiko Koseki	Cell Cycle
Plasticity of DNA methylation in a nerve injury model of pain.	2015-01-01	Julie M. Cunningham	Meike Gölzenleuchter Rahul Kanwar Manal Zaibak Fadi Al Saiegh Theresa Hartung Jana Klukas Regenia L Smalley Maria E Figueroa Gary P Schroth Terry M Therneau Michaela S Banck Andreas S Beutler	Epigenetics
Interferon regulatory factor 1 and histone H4 acetylation in systemic lupus erythematosus.	2015-01-01	Michelle A. Petri	Yiu Tak Leung Lihua Shi Kelly Maurer Li Song Zhe Zhang Kathleen E Sullivan	Epigenetics
Identification of secretaglobin Scgb2a1 as a target for developmental reprogramming by BPA in the rat prostate	2015-01-01	Kurunthachalam Kannan	Rebecca Lee Yean Wong Quan Wang Lindsey S Treviño Maarten C Bosland Jing Chen Mario Medvedovic Gail S Prins Shuk-Mei Ho Cheryl Lyn Walker	Epigenetics
Characterization of the Olfactory Receptors Expressed in Human Spermatozoa	2015-01-01	Hanns Hatt Günter Gisselmann	Caroline Flegel Felix Vogel Adrian Hofreuter Benjamin S P Schreiner Sandra Osthold Sophie Veitinger Christian Becker Norbert H Brockmeyer Michael Muschol Gunther Wennemuth Janine Altmüller Günter Gisselmann	Frontiers in molecular biosciences
MicroRNA profiling of the bovine alveolar macrophage response to Mycobacterium bovis infection suggests pathogen survival is enhanced by microRNA regulation of endocytosis and lysosome trafficking.	2015-01-01	Kenneth Bryan Daniel G. Bradley David J. Lynn David E. MacHugh Stephen V. Gordon	Peter Vegh David A Magee Nicolas C Nalpas Matthew S McCabe John A Browne Kevin M Conlon	Tuberculosis
Noncoding regions of C. elegans mRNA undergo selective adenosine to inosine deamination and contain a small number of editing sites per transcript.	2015-01-01	Michael C Washburn	Emily C Wheeler Francois Major Douglas B Rusch Heather A Hundley	RNA Biology
Investigating CRISPR RNA Biogenesis and Function Using RNA-seq.	2015-01-01	Jörg Vogel Cynthia Sharma Gaurav Dugar Nadja Heidrich		Methods in Molecular Biology
Integrative genome-wide analysis of the determinants of RNA splicing in kidney renal clear cell carcinoma.	2015-01-01	Oliver Stegle Cyriac Kandoth Nikolaus Schultz	Kjong-Van Lehmann André Kahles William Lee Gunnar Rätsch	Pacific Symposium on Biocomputing
Analysis of alternative splicing events in custom gene datasets by AStalavista.	2015-01-01	Sylvain Foissac Michael Sammeth		Methods in Molecular Biology
Computer-assisted annotation of small RNA transcriptomes.	2015-01-01	Grant W Hennig Wei Yan	Nicole Ortogero Dickson Luong	Methods in Molecular Biology
First insights into the giant panda (Ailuropoda melanoleuca) blood transcriptome: a resource for novel gene loci and immunogenetics.	2015-01-02	Bisong Yue	Lianming Du Wujiao Li Zhenxin Fan Fujun Shen Mingyu Yang Zili Wang Zuoyi Jian Rong Hou Xiuyue Zhang	Molecular Ecology Resources
Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data.	2015-01-05	Åslaug Helland Lynnette Fernandez-Cuesta Joachim H Clement Martin Peifer Stefan Haas Gavin Wright Peter Nürnberg Steinar Solberg Martin Vingron Elisabeth Brambilla	Ruping Sun Roopika Menon Julie George Susanne Lorenz Leonardo A Meza-Zepeda Dennis Plenker Johannes M Heuckmann Frauke Leenders Thomas Zander Ilona Dahmen Mirjam Koker Jakob Schöttle Roland T Ullrich Christian Becker Henrik Seidel Diana Böhm Friederike Göke Sascha Ansén Prudence A Russell Zoe Wainer Benjamin Solomon Iver Petersen Jörg Sänger Odd-Terje Brustugun Marius Lund-Iversen Reinhard Buettner Jürgen Wolf Sven Perner Roman K Thomas	Genome Biology
Characterization of human cyclin-dependent kinase 12 (CDK12) and CDK13 complexes in C-terminal domain phosphorylation, gene transcription, and RNA processing	2015-01-05	Laurence Florens Michael P. Washburn	Kaiwei Liang Xin Gao Joshua M Gilmore Edwin Smith Ali Shilatifard	Molecular and Cellular Biology
rbamtools: an R interface to samtools enabling fast accumulative tabulation of splicing events over multiple RNA-seq samples.	2015-01-05	Wolfgang Kaisers	Wolfgang Kaisers Heiner Schaal Holger Schwender	Bioinformatics
iRNA-seq: computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data	2015-01-06	Susanne Mandrup Bjørk Ditlev Larsen Søren Fisker Schmidt	Jesper Grud Skat Madsen Anne Loft Ronni Nielsen	Nucleic Acids Research
Astrovirus VA1/HMO-C: an increasingly recognized neurotropic pathogen in immunocompromised patients	2015-01-07	Vincent Plagnol Divya Shah Sofia Morfopoulou Julianne R Brown Judith Breuer Waseem Qasim	Jonathan Hubb Warren A Emmett Winnie Ip Tony Brooks Simon M L Paine Glenn Anderson Alex Virasami C Y William Tong Duncan A Clark Thomas S Jacques Mike Hubank	Clinical Infectious Diseases
RNA-Rocket: an RNA-Seq analysis resource for infectious disease research	2015-01-07	Andrew Warren Omar S. Harb Daniel Lawson Leslie Birgit Vosshall Michael McClelland Cristina Aurrecoechea	Brian Brunk Prerak Desai Scott Emrich Gloria I Giraldo-Calderón Deborah Hix Dustin Machi Chunhong Mao Eric Nordberg Maulik Shukla Alice R Wattam Rebecca Will Hyun Seung Yoo Bruno Sobral	Bioinformatics
Systems biology with high-throughput sequencing reveals genetic mechanisms underlying the metabolic syndrome in the Lyon hypertensive rat.	2015-01-08	Man Chun John Ma Anne E Kwitek	Jinkai Wang Amanda K Mennie Janette M Pettus Yang Xu Lan Lin Matthew G Traxler Jessica Jakoubek Santosh S Atanur Timothy J Aitman Yi Xing	Circulation: Cardiovascular Genetics
Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli.	2015-01-12	Xiaoliang Sunney Xie	Huiyi Chen Katsuyuki Shiroguchi Hao Ge	Molecular Systems Biology
Defining the transcriptomic landscape of Candida glabrata by RNA-Seq.	2015-01-13	Oliver Kurzai Reinhard Guthke	Jörg Linde Seána Duggan Michael Weber Fabian Horn Patricia Sieber Daniela Hellwig Konstantin Riege Manja Marz Ronny Martin	Nucleic Acids Research
Deep sequencing of the murine olfactory receptor neuron transcriptome.	2015-01-15	Hanns Hatt Günter Gisselmann Christian H. Wetzel Eva M. Neuhaus	Ninthujah Kanageswaran Marilen Demond Maximilian Nagel Benjamin S P Schreiner Sabrina Baumgart Paul Scholz Janine Altmüller Christian Becker Julia F Doerner Heike Conrad Sonja Oberland Günter Gisselmann	PLOS ONE
Reprogramming of Yersinia from virulent to persistent mode revealed by complex in vivo RNA-seq analysis.	2015-01-15	Kemal Avican Mikael Huss	Anna Fahlgren Ann Kathrin Heroven Michael Beckstette Petra Dersch Maria Fällman	PLOS Pathogens
Blocking miRNA Biogenesis in Adult Forebrain Neurons Enhances Seizure Susceptibility, Fear Memory, and Food Intake by Increasing Neuronal Responsiveness.	2015-01-16	Angel Barco	Anna Fiorenza Jose P Lopez-Atalaya Victor Rovira Marilyn Scandaglia Emilio Geijo-Barrientos	Cerebral Cortex
Partial dosage compensation in Strepsiptera, a sister group of beetles.	2015-01-18	Doris Bachtrog	Shivani Mahajan	Genome Biology and Evolution
Integrated modeling of protein-coding genes in the Manduca sexta genome using RNA-Seq data from the biochemical model insect.	2015-01-20	Xiaolong Cao Haobo Jiang		Insect Biochemistry and Molecular Biology
Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation in Caenorhabditis elegans intestine and muscles.	2015-01-20	Marco Mangone	Stephen M Blazie Cody Babb Henry Wilky Alan Rawls Jin G Park	BMC Biology
Combining RNA and protein profiling data with network interactions identifies genes associated with spermatogenesis in mouse and human.	2015-01-21	Bernard Jégou Fatima Smagulova Soazik P Jamin Fabrice G Petit Emmanuelle Becker Frédéric Chalmel Michael Primig	Christine Kervarrec Chunxiang Hao Bernard Jégou	Biology of Reproduction
Claudin multigene family in channel catfish and their expression profiles in response to bacterial infection and hypoxia as revealed by meta-analysis of RNA-Seq datasets.	2015-01-21	Luyang Sun Shikai Liu	Lisui Bao Yun Li Jianbin Feng Zhanjiang Liu	Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics
Quantitative visualization of alternative exon expression from RNA-seq data.	2015-01-22	Schraga Schwartz Jill P. Mesirov Helga Thorvaldsdóttir	Yarden Katz Eric T Wang Jacob Silterra Bang Wong Helga Thorvaldsdóttir James T Robinson Edoardo M Airoldi Christopher B Burge	Bioinformatics
RNA-Seq reveals a role for NFAT-signaling in human retinal microvascular endothelial cells treated with TNFα.	2015-01-24	Colin A Bretz	Sara R Savage John S Penn	PLOS ONE
Blocking yersiniabactin import attenuates extraintestinal pathogenic Escherichia coli in cystitis and pyelonephritis and represents a novel target to prevent urinary tract infection.	2015-01-26	Harry L T Mobley	Ariel R Brumbaugh Sara N Smith Sargurunathan Subashchandrabose Stephanie D Himpsl Tracy H Hazen David A Rasko	Infection and Immunity
The long intergenic noncoding RNA landscape of human lymphocytes highlights the regulation of T cell differentiation by linc-MAF-4.	2015-01-26	Sergio Abrignani Massimiliano Pagani	Valeria Ranzani Grazisa Rossetti Ilaria Panzeri Alberto Arrigoni Raoul Jp Bonnal Serena Curti Paola Gruarin Elena Provasi Elisa Sugliano Maurizio Marconi Raffaele De Francesco Jens Geginat Beatrice Bodega	Nature Immunology
Next-Generation Sequencing Reveals Low-Dose Effects of Cationic Dendrimers in Primary Human Bronchial Epithelial Cells	2015-01-27	Pekka Kohonen Hanna L. Karlsson Bengt Fadeel Neus Feliu Yuning Zhang	Neus Feliu Jie Ji Lena Palmberg Andreas Nyström	ACS Nano
Age dependent changes in the LPS induced transcriptome of bovine dermal fibroblasts occurs without major changes in the methylome	2015-01-27	Stephanie McKay	Benjamin B Green David E Kerr	BMC Genomics
Computational and analytical challenges in single-cell transcriptomics.	2015-01-28	Sarah Teichmann John C Marioni Oliver Stegle		Nature Reviews Genetics
The transcriptional stress response of Candida albicans to weak organic acids.	2015-01-29	Norman Pavelka Michael Poidinger	Fabien Cottier Alrina Shin Min Tan Jinmiao Chen Josephine Lum Francesca Zolezzi	G3
The avian transcriptome response to malaria infection	2015-01-29	Olof Hellgren Gediminas Valkiūnas Elin Videvall Vaidas Palinauskas	Charlie K Cornwallis	Molecular Biology and Evolution
Saccharomyces cerevisiae transcriptional reprograming due to bacterial contamination during industrial scale bioethanol production.	2015-01-30	Melline F Noronha Luciana S Mofatto Juan Lucas Argueso Piotr A Mieczkowski	Osmar V Carvalho-Netto Marcelo F Carazzolle Paulo J P L Teixeira Luige A L Calderón Gonçalo A G Pereira	Microbial Cell Factories
RNA-seq SSRs and small RNA-seq SSRs: new approaches in cancer biomarker discovery.	2015-01-30	Arghavan Alisoltani	Arghavan Alisoltani Hossein Fallahi Behrouz Shiran Anousheh Alisoltani Esmaeil Ebrahimie	Gene
RNA-Seq analysis of rye-grass transcriptomic response to an herbicide inhibiting acetolactate-synthase identifies transcripts linked to non-target-site-based resistance.	2015-01-31	Jérôme Gouzy	Arnaud Duhoux Sébastien Carrère Ludovic Bonin Christophe Délye	Plant Molecular Biology
Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data.	2015-02-01	Federico Comoglio	Cem Sievers Renato Paro	BMC Bioinformatics
Fertility and genomics: comparison of gene expression in contrasting reproductive tissues of female cattle.	2015-02-01	Trudee Fair Niamh Forde John R. Roche	P A McGettigan J A Browne S D Carrington M A Crowe B J Loftus A Lohan P Lonergan K Pluta S Mamo A Murphy S W Walsh C J Creevey B Earley S Keady D A Kenny D Matthews M McCabe D Morris A O'Loughlin S Waters M G Diskin A C O Evans	Reproduction, Fertility and Development
The role of TP53 in miRNA loading onto AGO2 and in remodelling the miRNA-mRNA interaction network.	2015-02-01	Teresa Colombo Valerio Fulci	Jonathan Krell Justin Stebbing Adam Enver Frampton Claudia Carissimi Victoria Harding Alexander De Giorgio Giuseppe Macino Leandro Castellano	The Lancet
Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers.	2015-02-02	Laura Clarke Paul Flicek Xabier Agirre Michael I Robson Marien Pascual Avik Datta Renée Beekman David Richardson Giancarlo Castellano Juan R Rodriguez-Madoz José I Martín-Subero Norma C. Gutiérrez José M García-Verdugo Elias Campo Simon Heath Felipe Prosper Eric C Schirmer Reiner Siebert	Marta Kulis Victor Segura Anke Bergmann Anna Esteve Angelika Merkel Emanuele Raineri Lidia Agueda Julie Blanc Nuria Russiñol Ana C Queirós Edurne San José-Enériz Fang Fang Elisabeth Guruceaga Joost H A Martens Marta Gut Maria J Calasanz Jesús F San Miguel Ari Melnick Hendrik G Stunnenberg Ivo G Gut	Genome Research
Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling.	2015-02-02	Jens Nielsen Mathias Uhlén	Pouyan Ghaffari Adil Mardinoglu Anna Asplund Saeed Shoaie Caroline Kampf	Scientific Reports
The genomic landscape of phaeochromocytoma.	2015-02-02	Stephen B. Fox Richard W. Tothill Rodney J. Hicks Aidan Flynn Jason Li Grant McArthur Roderick J Clifton-Bligh	Diana Benn Bruce Robinson Alison H Trainer Paul James Annette Hogg Kelly Waldeck Joshy George Anthony J Gill	The Journal of Pathology
Analysis of the Bovine Monocyte-Derived Macrophage Response to Mycobacterium avium Subspecies Paratuberculosis Infection Using RNA-seq.	2015-02-04	Karsten Hokamp David E. MacHugh Kate Killick	Maura E Casey Kieran G Meade Nicolas C Nalpas Maria Taraktsoglou John A Browne Stephen D E Park Eamonn Gormley David A Magee	Frontiers in Immunology
Comparison of larval and adult Drosophila astrocytes reveals stage-specific gene expression profiles	2015-02-04	Yanmei Huang	Fanny S Ng F Rob Jackson	G3
Integrating transcriptomics and proteomics to show that tanshinone IIA suppresses cell growth by blocking glucose metabolism in gastric cancer cells.	2015-02-05	Chia-Lang Hsu Hsuan-Cheng Huang Hsueh-Fen Juan	Li-Ling Lin Chieh-Ren Hsia	BMC Genomics
Computational prediction of molecular pathogen-host interactions based on dual transcriptome data.	2015-02-06	Reinhard Guthke	Sylvie Schulze Sebastian G Henkel Dominik Driesch Jörg Linde	Frontiers in Microbiology
Vision from next generation sequencing: multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease	2015-02-07	Anand Swaroop Rinki Ratnapriya	Hyun-Jin Yang Tiziana Cogliati Jung-Woong Kim	Progress in Retinal and Eye Research
Regulatory small RNAs from the 3' regions of bacterial mRNAs.	2015-02-09	Jörg Vogel Masatoshi Miyakoshi Yanjie Chao		Current Opinion in Microbiology
Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome.	2015-02-10	Catherine Feuillet Etienne Paux Frédéric Choulet Adriana Alberti	Lise Pingault Natasha Glover Patrick Wincker	Genome Biology
Rapid changes in gene expression direct rapid shifts in intestinal form and function in the Burmese python after feeding.	2015-02-10	David D. Pollock	Audra L Andrew Daren C Card Robert P Ruggiero Drew R Schield Richard H Adams Stephen M Secor Todd A Castoe	Physiological Genomics
Bridger: a new framework for de novo transcriptome assembly using RNA-seq data.	2015-02-11	Cody Ashby	Zheng Chang Guojun Li Juntao Liu Yu Zhang Deli Liu Carole L Cramer Xiuzhen Huang	Genome Biology
Distinct Transcriptomic Features are Associated with Transitional and Mature B-Cell Populations in the Mouse Spleen.	2015-02-11	Daria Salyakina Jean-Christophe Renauld	Eden Kleiman Magali De Heusch Kristen L Hoek Joan M Llanes Iris Castro Jacqueline A Wright Emily S Clark Derek M Dykxhoorn Enrico Capobianco Akiko Takeda Wasif N Khan	Frontiers in Immunology
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
SplicingTypesAnno: annotating and quantifying alternative splicing events for RNA-Seq data.	2015-02-14	Gaurav Sablok	Xiaoyong Sun Fenghua Zuo Yuanbin Ru Jiqiang Guo Xiaoyan Yan	Computer Methods and Programs in Biomedicine
Transcriptome analysis of thermophilic methylotrophic Bacillus methanolicus MGA3 using RNA-sequencing provides detailed insights into its previously uncharted transcriptional landscape	2015-02-14	Jörn Kalinowski	Marta Irla Armin Neshat Trygve Brautaset Christian Rückert Volker F Wendisch	BMC Genomics
Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli.	2015-02-14	Vânia Pobre Cecília Maria Arraiano		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 Bonnie Bassler Konrad Förstner	Jian-Ping Cong	Proceedings of the National Academy of Sciences of the United States of America
DNA methylation-based subtype prediction for pediatric acute lymphoblastic leukemia.	2015-02-17	Ann-Christine Syvänen Christofer L. Bäcklin Ann Nordgren Jonas Abrahamsson Trond Flægstad Kjeld Schmiegelow Rolf Larsson	Jessica Nordlund Vasilios Zachariadis Lucia Cavelier Johan Dahlberg Ingegerd Öfverholm Gisela Barbany Elin Övernäs Mats M Heyman Ólafur G Jónsson Jukka Kanerva Josefine Palle Mats G Gustafsson Gudmar Lönnerholm Erik Forestier	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 Charlotte Rolny Gonçalo Castelo-Branco Christer Betsholtz	Amit Zeisel Ana B Muñoz-Manchado Simone Codeluppi Anna Juréus Sueli Marques Liqun He	Science
Flexible expressed region analysis for RNA-seq with derfinder	2015-02-19	Michael I Love Leonardo Collado-Torres Jeffrey T. Leek Ben Langmead Abhinav Nellore	Alyssa C Frazee Christopher Wilks Rafael A Irizarry Andrew E Jaffe
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
Inferring bona fide transfrags in RNA-Seq derived-transcriptome assemblies of non-model organisms.	2015-02-21	Peter van Heusden Uljana Hesse Alan Christoffels	Stanley Kimbung Mbandi	BMC Bioinformatics
A phylogenetic backbone for Bivalvia: an RNA-seq approach	2015-02-22	Casey W. Dunn Sónia C S Andrade Rüdiger Bieler Gonzalo Giribet John D. Taylor	Vanessa L González Timothy M Collins Paula M Mikkelsen	Proceedings of the Royal Society B
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 George A. Calin Michael J. Keating	Eric Londin Phillipe Loher Kevin Quann Yi Jing Eleftheria Hatzimichael Shozo Honda Bharat Ramratnam Clay E S Comstock Leonard Gomella George L Spaeth Lisa Hark L Jay Katz Agnieszka Witkiewicz Abdolmohamad Rostami Sergio A Jimenez Michael A Hollingsworth Jen Jen Yeh Chad A Shaw Steven E McKenzie Paul Bray Peter T Nelson Simona Zupo Katrien Van Roosbroeck Charles Yeo Masaya Jimbo Joseph Cozzitorto Jonathan R Brody Kathleen Delgrosso Paolo Fortina	Proceedings of the National Academy of Sciences of the United States of America
Polyribosomal RNA-Seq reveals the decreased complexity and diversity of the Arabidopsis translatome.	2015-02-23	Vivek Krishnakumar	Xingtan Zhang Benjamin D Rosen Haibao Tang Christopher D Town	PLOS ONE
RNA-seq analysis of the response of the halophyte, Mesembryanthemum crystallinum (ice plant) to high salinity.	2015-02-23	Hironaka Tsukagoshi Sumie Ishiguro	Takamasa Suzuki Kouki Nishikawa Sakae Agarie Tetsuya Higashiyama	PLOS ONE
Overlapping and unique signatures in the proteomic and transcriptomic responses of the nematode Caenorhabditis elegans toward pathogenic Bacillus thuringiensis.	2015-02-23	Andreas Tholey	Wentao Yang Katja Dierking Daniela Esser Matthias Leippe Philip Rosenstiel Hinrich Schulenburg	Developmental and Comparative Immunology
Guidance for RNA-seq co-expression network construction and analysis: safety in numbers.	2015-02-24	Jesse Gillis	S Ballouz W Verleyen	Bioinformatics
RNAseq reveals weed-induced PIF3-like as a candidate target to manipulate weed stress response in soybean.	2015-02-25	Brian Scheffler Ronald Pierik	David P Horvath Stephanie A Hansen Janet P Moriles-Miller Changhui Yan David E Clay Sharon A Clay	New Phytologist
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
Simultaneous generation of many RNA-seq libraries in a single reaction	2015-03-02	Georgia Giannoukos Jenny Chen Alper Kucukural	Alexander A Shishkin Dawn Ciulla Michele Busby Christine Surka Roby P Bhattacharyya Robert F Rudy Milesh M Patel Nathaniel Novod Deborah T Hung Andreas Gnirke Manuel Garber Mitchell Guttman Jonathan Livny	Nature Methods
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
Systems approach for exploring the intricate associations between sweetness, color and aroma in melon fruits	2015-03-03	Shiri Freilich	Shery Lev Itay Gonda Eli Reuveni Vitaly Portnoy Elad Oren Marc Lohse Navot Galpaz Einat Bar Galil Tzuri Guy Wissotsky Ayala Meir Joseph Burger Yaakov Tadmor Arthur Schaffer Zhangjun Fei James Giovannoni Efraim Lewinsohn Nurit Katzir	BMC Plant Biology
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 Rengul Cetin-Atalay	Nazli Keskin Emre Deniz Jitka Eryilmaz Manolya Un Tugce Batur Tulin Ersahin 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
Nuclear genomic signals of the 'microturbellarian' roots of platyhelminth evolutionary innovation	2015-03-12	Andreas Hejnol Gonzalo Giribet	Christopher E Laumer	eLife
Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum	2015-03-12	Qin Ma	Wen-Chi Chou Shihui Yang Sha Cao Dawn M Klingeman Steven D Brown Ying Xu	Nucleic Acids Research
RNA-seq analysis of Macrobrachium rosenbergii hepatopancreas in response to Vibrio parahaemolyticus infection.	2015-03-14	Jun Wang	Rama Rao Ya Bing Zhu Tahereh Alinejad Suma Tiruvayipati Kwai Lin Thong Subha Bhassu	Gut Pathogens
Modifying effects of vitamin E on chlorpyrifos toxicity in atlantic salmon	2015-03-16	Pål A. Olsvik	Marc H G Berntssen Liv Søfteland	PLOS ONE
Cyclic GMP balance is critical for malaria parasite transmission from the mosquito to the mammalian host	2015-03-17	Sebastian A. Mikolajczak	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 Christian Neri	Mayada Achour Stéphanie Le Gras Céline Keime Frédéric Parmentier François-Xavier Lejeune Anne-Laurence Boutillier 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
Escape from X inactivation varies in mouse tissues.	2015-03-18	Jay Shendure	Joel B Berletch Wenxiu Ma Fan Yang William S Noble Christine M Disteche Xinxian Deng	PLOS Genetics
Immunoglobulin transcript sequence and somatic hypermutation computation from unselected RNA-seq reads in chronic lymphocytic leukemia.	2015-03-18	Albert de la Chapelle John C Byrd	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	Proceedings of the National Academy of Sciences of the United States of America
A comparative study of RNA-seq analysis strategies.	2015-03-18	Ernest Turro Alexandra M. Lewin	Jürgen Jänes Fengyuan Hu	Briefings in Bioinformatics
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
Preclinical activity of combined HDAC and KDM1A inhibition in glioblastoma.	2015-03-19	Michelle Craig Barton	Melissa M Singh Blake Johnson Avinashnarayan Venkatarayan Elsa R Flores Jianping Zhang Xiaoping Su Frederick Lang Joya Chandra	Neuro-Oncology
GLI2 inhibition abrogates human leukemia stem cell dormancy.	2015-03-21	John McPherson Tannishtha Reya	Anil Sadarangani Gabriel Pineda Kathleen M Lennon Hye-Jung Chun Alice Shih Annelie E Schairer Angela C Court Daniel J Goff Sacha L Prashad Ifat Geron Russell Wall Richard A Moore Minya Pu Lei Bao Amy Jackson-Fisher Michael Munchhof Todd VanArsdale Sheldon R Morris Mark D Minden Karen Messer Hanna K A Mikkola Marco A Marra Thomas J Hudson Catriona H M Jamieson	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 Lucila Ohno-Machado	Pedro A F Galante Elisabeth Limbeck Patrick Möhnle Raphael B Parmigiani 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 Peter A.C. 't Hoen Jeroen Laros	Irina Pulyakhina Isabella Gazzoli Nisha Verwey Johan T den Dunnen	Nucleic Acids Research
A cytochrome P450, OsDSS1, is involved in growth and drought stress responses in rice (Oryza sativa L.).	2015-03-24	Hideo Matsumura	Muluneh Tamiru Jerwin R Undan Hiroki Takagi Akira Abe Kakoto Yoshida Jesusa Q Undan Satoshi Natsume Aiko Uemura Hiromasa Saitoh Naoya Urasaki Takao Yokota Ryohei Terauchi	Plant Molecular Biology
The RNAi machinery controls distinct responses to environmental signals in the basal fungus Mucor circinelloides.	2015-03-25	Victoriano 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 Yoshihide Hayashizaki	Hiroko Ohmiya Susumu Hara Satoshi Kawasaki FANTOM consortium Motokazu Tsujikawa	PLOS ONE
Correction: Reprogramming of Yersinia from virulent to persistent mode revealed by complex in vivo RNA-seq analysis.	2015-03-25	PLOS Pathogens Staff		PLOS Pathogens
Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols.	2015-03-26	Michael Eisen Peter A Combs		PeerJ
SplAdder: Identification, quantification and testing of alternative splicing events from RNA-Seq data	2015-03-26	Gunnar Rätsch	Andre Kahles Cheng Soon Ong Yi Zhong
Assessing allele-specific expression across multiple tissues from RNA-seq read data	2015-03-27	Tuuli Lappalainen Matti Pirinen Mark McCarthy Peter Donnelly	Noah A Zaitlen GTEx Consortium Emmanouil T Dermitzakis Manuel A Rivas	Bioinformatics
Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels	2015-03-27	Cisca Wijmenga Daria V. Zhernakova Kristin Abbott Patrick Deelen Jingyuan Fu Marc Jan Bonder Morris A Swertz	Mark de Haan Marijke van der Sijde Juha Karjalainen K Joeri van der Velde Richard J Sinke 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
BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis.	2015-03-28	Yang Pan	Quan Wan Hayley Dingerdissen Yu Fan Naila Gulzar Tsung-Jung Wu Cheng Yan Haichen Zhang Raja Mazumder	Database
The Listeria monocytogenes strain 10403S BioCyc database.	2015-03-28	Teresa M Bergholz Kathryn J Boor Martin Wiedmann	Renato H Orsi	Database
Linear mRNA amplification approach for RNAseq from limited amount of RNA.	2015-03-28	Maria A Nagai Dirce Carraro Helena Brentani Renata Pasqualini	Elisa Napolitano Ferreira Gustavo de Campos Molina Renato David Puga Antônio Hugo José Froes Marques Campos Gustavo Cardoso Guimarães Diana Noronha Nunes Wadih Arap Emmanuel Dias-Neto Ricardo R Brentani	Gene
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 Eleonora Aronica	James D Mills Jieqiong Chen Woojin S Kim Paul D Waters Avanita S Prabowo Michael Janitz	Neurogenetics
Assessing the consistency of public human tissue RNA-seq data sets.	2015-03-30	David Gomez-Cabrero Mikael Huss	Frida Danielsson Tojo James	Briefings in Bioinformatics
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 Alessandra Dal Molin	Felice Contaldi Maria Raffaella Ercolano Valentina Grosso Massimo Iorizzo Filippo Tatino Luciano Xumerle 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 Igor Smirnov	James C Cronk Noël C Derecki Emily Ji Yang Xu Aaron E Lampano Wendy Baker Geoffrey T Norris Ioana Marin Nathan Coddington Yochai Wolf Alan Aderem Alexander L Klibanov Vladimir Litvak	Immunity
p53 Enables metabolic fitness and self-renewal of nephron progenitor cells	2015-04-01	Melody Baddoo Yumei Feng	Yuwen Li Jiao Liu Wencheng Li Aaron Brown Melody Baddoo Marilyn Li Thomas Carroll Leif Oxburgh 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 Gordon K Smyth	Julie M Sheridan Sarah A Best Kun Jiang Tamara J Beck François Vaillant Kevin Liu 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
Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum.	2015-04-06	Alexias Safi Gregory E Crawford	Christopher L Frank Fang Liu Ranjula Wijayatunge Lingyun Song Matthew T Biegler Marty G Yang Christopher M Vockley Charles A Gersbach Anne E West	Nature Neuroscience
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
The immune signaling pathways of Manduca sexta	2015-04-07	Haobo Jiang	Xiaolong Cao Yan He Yingxia Hu Yang Wang Yun-Ru Chen Bart Bryant Rollie J Clem Lawrence M Schwartz Gary Blissard	Insect Biochemistry and Molecular Biology
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 Kim Overvad Augustine Kong Peter Rudnai Patrick Sulem Daniel F Gudbjartsson Kári Stefánsson	Simon N Stacey Hannes Helgason Sigurjon A Gudjonsson Florian Zink Asgeir Sigurdsson Birte Kehr Julius Gudmundsson Bardur Sigurgeirsson Kristrun R Benediktsdottir Kristin Thorisdottir Rafn Ragnarsson Victoria Fuentelsaz Cristina Corredera Matilde Grasa Dolores Planelles Onofre Sanmartin Eugene Gurzau Kvetoslava Koppova Bjørn A Nexø Jon G Jonasson Anna M Kristinsdottir Gisli Masson Olafur T Magnusson Bjarni V Halldorsson José I Mayordomo Jon H Olafsson	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 Claire M. Fraser	Yaoping Liu L Latey Bradford Wenjie Xu Qyunh T Phan Priti Kumari Anup Mahurkar Aaron P Mitchell 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
Decreased expression of endogenous feline leukemia virus in cat lymphomas: a case control study.	2015-04-10	Reinhard Ertl Fritz Sedlazeck Regina Hofmann-Lehmann	Milica Krunic Benedikt Hagen Arndt von Haeseler Dieter Klein	BMC Veterinary Research
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
A serine-arginine-rich (SR) splicing factor modulates alternative splicing of over a thousand genes in Toxoplasma gondii.	2015-04-13	Giel G van Dooren Stuart A Ralph	Lee M Yeoh Christopher D Goodman Nathan E Hall Geoffrey I McFadden	Nucleic Acids Research
RNA-Seq analysis of the wild barley (H. spontaneum) leaf transcriptome under salt stress.	2015-04-13	Ahmed Bahieldin	Ahmed Atef Jamal S M Sabir Nour O Gadalla Sherif Edris Ahmed M Alzohairy Nezar A Radhwan Mohammed N Baeshen Ahmed M Ramadan Hala F Eissa Sabah M Hassan Nabih A Baeshen Osama Abuzinadah Magdy A Al-Kordy Fotouh M El-Domyati Robert K Jansen	Comptes Rendus Biologies
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
Antagonistic regulation of mRNA expression and splicing by CELF and MBNL proteins.	2015-04-16	Amanda J Ward Jimena Giudice	Eric T Wang Jennifer M Cherone Thomas T Wang Daniel J Treacy Nicole J Lambert Peter Freese Tanvi Saxena Thomas A Cooper Christopher B Burge	Genome Research
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 Nicola J Waddell Anil K Madugundu	Shivashankar H Nagaraj Scott Wood Alun Jones Ramya A Mandyam Katia Nones John V Pearson	Journal of Proteome Research
ContextMap 2: fast and accurate context-based RNA-seq mapping	2015-04-17	Ralf Zimmer	Thomas Bonfert Evelyn Kirner Gergely Csaba Caroline C Friedel	BMC Bioinformatics
High throughput profiling of the cotton bollworm Helicoverpa armigera immunotranscriptome during the fungal and bacterial infections	2015-04-18	Haobo Jiang	Guang-Hua Xiong Long-Sheng Xing Zhe Lin Tusar T Saha Chengshu Wang Zhen Zou	BMC Genomics
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
Transcriptome analysis reveals the host response to Schmallenberg virus in bovine cells and antagonistic effects of the NSs protein	2015-04-19	Alain Kohl	Anne-Lie Blomström Quan Gu Gerald Barry Gavin Wilkie Jessica K Skelton Margaret Baird Melanie McFarlane Esther Schnettler Richard M Elliott Massimo Palmarini	BMC Genomics
A RNA-Seq Analysis of the Rat Supraoptic Nucleus Transcriptome: Effects of Salt Loading on Gene Expression.	2015-04-21	David Murphy	Kory R Johnson C C T Hindmarch Yasmmyn D Salinas YiJun Shi Michael Greenwood See Ziau Hoe Harold Gainer	PLOS ONE
Functional and mechanistic studies of XPC DNA-repair complex as transcriptional coactivator in embryonic stem cells.	2015-04-21	Robert Tjian Claudia Cattoglio	Elisa T Zhang Ivan Grubisic Kunitoshi Chiba Yick W Fong	Proceedings of the National Academy of Sciences of the United States of America
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
Integrated RNA-Seq and sRNA-Seq Analysis Identifies Chilling and Freezing Responsive Key Molecular Players and Pathways in Tea Plant (Camellia sinensis).	2015-04-22	Chao Zheng	Lei Zhao Yu Wang Jiazhi Shen Yinfei Zhang Sisi Jia Yusheng Li Zhaotang Ding	PLOS ONE
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
De Novo Reconstruction of Adipose Tissue Transcriptomes Reveals Long Non-coding RNA Regulators of Brown Adipocyte Development.	2015-04-23	Nikolai Slavov Harvey Lodish	Juan R Alvarez-Dominguez Zhiqiang Bai Dan Xu Bingbing Yuan Kinyui Alice Lo Myeong Jin Yoon Yen Ching Lim Marko Knoll Shuai Chen Chen Peng Lei Sun	Cell Metabolism
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 Kuliński Paul Datlinger	M Rita T Casari Philipp M Guenzl Daniel Wenzel Daniel Andergassen Anastasiya Hladik 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 Annegret Kohler	Fabien Baldacci-Cresp Jihad Moussawi Jean-Charles Leplé Rebecca Van Acker Julie Candiracci Laure Twyffels Antanas V Spokevicius Gerd Bossinger Françoise Laurans Nicole Brunel Marjorie Vermeersch Mondher El Jaziri Marie Baucher	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
Polyester: simulating RNA-seq datasets with differential transcript expression.	2015-04-28	Jeffrey T. Leek Andrew E Jaffe Ben Langmead	Alyssa C Frazee	Bioinformatics
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 Erik K Flemington	Subing Cao Walter Moss Monica Concha Xia Wang Yi Yu Melody Baddoo Kun Zhang Claire Fewell Zhen Lin Yan Dong	Journal of Virology
Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses.	2015-04-29	Gordon K Smyth	Ruijie Liu Aliaksei Z Holik Shian Su Natasha Jansz Kelan Chen Huei San Leong Marnie E Blewitt Marie-Liesse Asselin-Labat Matthew E Ritchie	Nucleic Acids Research
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 Catrina Fronick	Cara Lunn Shirai James N Ley Brian S White Sanghyun Kim Justin Tibbitts Jin Shao Matthew Ndonwi Brian Wadugu Eric J Duncavage Theresa Okeyo-Owuor Tuoen Liu Vincent Magrini Robert S Fulton Michelle O'Laughlin Matthew J Walter	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 Marisa Jaconi Biljana Dumevska	Alexis Bosman Audrey Letourneau Martina Del Lungo Flavio Ronzoni Rostyslav Kuziakiv Virpi Tohonen Marco Zucchelli Federico Santoni Michel Guipponi Outi Hovatta	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 Guillermo Garcia-Manero	Derrick Sek Tong Ong Yamini Ogoti Nipun A Mistry Karen Clise-Dwyer Sonny A Ang Andrea Viale Kathryn Ruisaard Irene Ganan Gomez Christopher A Bristow David C Weksberg Yan Wing Ho Baoli Hu Giannicola Genovese Piergiorgio Pettazzoni Asha S Multani Shan Jiang Sujun Hua Michael C Ryan Alessandro Carugo Luigi Nezi Yue Wei Hui Yang Li Zhang Sarah Gaddis Ting Gong James W Horner Timothy P Heffernan Philip Jones Laurence J N Cooper Han Liang Y Alan Wang Carlos Bueso-Ramos Ronald A DePinho	Cancer Cell
regionReport: Interactive reports for region-level and feature-level genomic analyses.	2015-05-01	Leonardo Collado-Torres Andrew E Jaffe Jeffrey T. Leek		F1000Research
A bioinformatics approach to distinguish plant parasite and host transcriptomes in interface tissue by classifying RNA-Seq reads.	2015-05-03	Tomoaki Sakamoto	Daisuke Ikeue Christian Schudoma Wenna Zhang Yoshiyuki Ogata Tetsuya Kurata Takeshi Furuhashi Friedrich Kragler Koh Aoki	Plant Methods
Bariatric Surgery Induces Disruption in Inflammatory Signaling Pathways Mediated by Immune Cells in Adipose Tissue: A RNA-Seq Study	2015-05-04	Yuna Blum Karine Clément	Christine Poitou Claire Perret François Mathieu Vinh Truong Hervé Durand Rohia Alili Nadjim Chelghoum Véronique Pelloux Judith Aron-Wisnewsky Adriana Torcivia Jean-Luc Bouillot Brian W Parks Ewa Ninio Laurence Tiret	PLOS ONE
The Transcriptome and Terpene Profile of Eucalyptus grandis Reveals Mechanisms of Defense Against the Insect Pest, Leptocybe invasa.	2015-05-05	Bernard Slippers	Caryn N Oates Carsten Külheim Alexander A Myburg Sanushka Naidoo	Plant and Cell Physiology
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
Rail-RNA: Scalable analysis of RNA-seq splicing and coverage	2015-05-07	Jeffrey T. Leek Ben Langmead Abhinav Nellore	Leonardo Collado-Torres Andrew E Jaffe José Alquicira-Hernández Jacob Pritt James Morton
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
Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data.	2015-05-12	Angelika N Christ Nicole Cloonan Sean M. Grimmond	David L A Wood Katia Nones Anita Steptoe Ivon Harliwong Felicity Newell Timothy J C Bruxner David Miller	PLOS ONE
Probe Region Expression Estimation for RNA-Seq Data for Improved Microarray Comparability.	2015-05-12	Antti Honkela	Karolis Uziela Antti Honkela	PLOS ONE
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
Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data.	2015-05-14	Frank Emmert-Streib	Ricardo de Matos Simoes Sabine Dalleau Kate E Williamson	BMC Systems Biology
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
Genome-wide analysis links NFATC2 with asparaginase hypersensitivity.	2015-05-18	Seth Karol Laura B Ramsey Charles G. Mullighan Ching-Hon Pui Stephen P Hunger	Christian A Fernandez Colton Smith Wenjian Yang Chunxu Qu Eric Larsen W Paul Bowman Chengcheng Liu Tamara Chang Mignon L Loh Elizabeth A Raetz Naomi J Winick William L Carroll Sima Jeha William E Evans Meenakshi Devidas Mary V Relling	Blood
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	Q85197310 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 Anthony R Green Berthold Göttgens Carlos Caldas	Nicola K Wilson Mona Shehata Manuel Sánchez Castillo Evangelia Diamanti Reiner Schulte Thierry Voet John Stingl	Cell Stem Cell
Effects of Tris(1,3-dichloro-2-propyl) Phosphate (TDCPP) in Tetrahymena Thermophila: Targeting the Ribosome.	2015-05-21	John P Giesy	Jing Li Liqin Yu Guangyu Li Chunsheng Liu	Scientific Reports
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
TRUFA: A User-Friendly Web Server for de novo RNA-seq Analysis Using Cluster Computing.	2015-05-24	Julio Rozas Rafael Zardoya	Etienne Kornobis Luis Cabellos Fernando Aguilar Cristina Frías-López Jesús Marco	Evolutionary Bioinformatics
RNA-seq Transcriptional Profiling of an Arbuscular Mycorrhiza Provides Insights into Regulated and Coordinated Gene Expression in Lotus japonicus and Rhizophagus irregularis.	2015-05-25	Masayoshi Kawaguchi	Yoshihiro Handa Hiroyo Nishide Naoya Takeda Yutaka Suzuki Katsuharu Saito	Plant and Cell Physiology
A Comprehensive Analysis of Codon Usage Patterns in Blunt Snout Bream (Megalobrama amblycephala) Based on RNA-Seq Data	2015-05-26	Shaokui Yi	Xiaoke Duan Xianwu Guo Weimin Wang	International Journal of Molecular Sciences
Systematic transcriptome analysis reveals tumor-specific isoforms for ovarian cancer diagnosis and therapy	2015-05-26	Christopher DeBoever Frazer KA	Christian L Barrett Kristen Jepsen Cheryl C Saenz Dennis A Carson	Proceedings of the National Academy of Sciences of the United States of America
nagnag: Identification and quantification of NAGNAG alternative splicing using RNA-Seq data.	2015-05-27	Gaurav Sablok	Xiaoyan Yan Gang Feng Jiaxin Ma Hongwei Zhao Xiaoyong Sun	FEBS Letters
Cellular microRNA miR-26a suppresses replication of porcine reproductive and respiratory syndrome virus by activating innate antiviral immunity.	2015-05-27	Yuhai Bi	Xiaojuan Jia Jing Li Qing Xie Hanchun Yang Wenjun Liu	Scientific Reports
Towards Elucidating Carnosic Acid Biosynthesis in Lamiaceae: Functional Characterization of the Three First Steps of the Pathway in Salvia fruticosa and Rosmarinus officinalis	2015-05-28	Q85232174 Irini Pateraki Fani Chatzopoulou Albert Ferrer Alain Tissier Sotirios Kampranis Angelos K Kanellis	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
Identification of regulatory network hubs that control lipid metabolism in Chlamydomonas reinhardtii	2015-05-28	Leslie M. Hicks	Mahmoud Gargouri Jeong-Jin Park F Omar Holguin Min-Jeong Kim Hongxia Wang Rahul R Deshpande Yair Shachar-Hill David R Gang	Journal of Experimental Botany
Tracking global gene expression responses in T cell differentiation.	2015-05-28	Vincent Piras Kumar Selvarajoo	Oriane Simeoni Masaru Tomita	Gene
Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators	2015-05-29	Alexias Safi Gregory E Crawford	Lauren R Polstein Pablo Perez-Pinera D Dewran Kocak Christopher M Vockley Peggy Bledsoe Lingyun Song Timothy E Reddy Charles A Gersbach	Genome Research
Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus agalactiae	2015-05-30	Isabelle Rosinski-Chupin Patrick Trieu-Cuot Philippe Bouloc Marie-Agnès Dillies Marie-Frédérique Lartigue	Elisabeth Sauvage Odile Sismeiro Adrien Villain Violette Da Cunha Marie-Elise Caliot Philippe Glaser	BMC Genomics
Functionally defined therapeutic targets in diffuse intrinsic pontine glioma	2015-06	Wenchao Sun Jacques Grill Michelle Monje Javad Nazarian Maryam Fouladi Cynthia Hawkins	Catherine S Grasso Yujie Tang Nathalene Truffaux Noah E Berlow Lining Liu Marie-Anne Debily Michael J Quist Lara E Davis Elaine C Huang Pamelyn J Woo Anitha Ponnuswami Spenser Chen Tessa B Johung Mari Kogiso Yuchen Du Lin Qi Yulun Huang Marianne Hütt-Cabezas Katherine E Warren Ludivine Le Dret Paul S Meltzer Hua Mao Martha Quezado Dannis G van Vuurden Jinu Abraham Matthew N Svalina Nicholas Wang Marta M Alonso Eric H Raabe Esther Hulleman Paul T Spellman Xiao-Nan Li Charles Keller Ranadip Pal	Nature Medicine
3USS: a web server for detecting alternative 3'UTRs from RNA-seq experiments	2015-06-01	Anna Tramontano	Loredana Le Pera Mariagiovanna Mazzapioda	Bioinformatics
FourCSeq: analysis of 4C sequencing data.	2015-06-01	Yad Ghavi-Helm Wolfgang Huber Simon Anders Eileen E. M. Furlong	Felix A Klein Tibor Pakozdi	Bioinformatics
FunPat: function-based pattern analysis on RNA-seq time series data.	2015-06-01	Francesca Finotello Tiziana Sanavia	Barbara Di Camillo	BMC Genomics
Condensin-driven remodelling of X chromosome topology during dosage compensation.	2015-06-01	Rachel Patton McCord	Emily Crane Qian Bian Bryan R Lajoie Bayly S Wheeler Edward J Ralston Satoru Uzawa Job Dekker Barbara J Meyer	Nature
Dynamics of GATA1 binding and expression response in a GATA1-induced erythroid differentiation system	2015-06-01	Ross C Hardison Christapher S Morrissey Mitchell J Weiss	Deepti Jain Tejaswini Mishra Belinda M Giardine Cheryl A Keller Susan Magargee Christine M Dorman Maria Long	Genomics Data
RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application.	2015-06-01	Matteo Pallocca Anna Maria D'Erchia Ernesto Picardi Raffaele A. Calogero	Mattia D'Antonio Paolo D'Onorio De Meo Tiziana Castrignanò Graziano Pesole	BMC Genomics
Elucidating steroid alkaloid biosynthesis in Veratrum californicum: production of verazine in Sf9 cells.	2015-06-01	Gane Ka-Shu Wong Megan M Augustin	Dan R Ruzicka Ashutosh K Shukla Jörg M Augustin Courtney M Starks Mark O'Neil-Johnson Michael R McKain Bradley S Evans Matt D Barrett Ann Smithson Michael K Deyholos Patrick P Edger J Chris Pires James H Leebens-Mack David A Mann Toni M Kutchan	The Plant Journal
Detecting disease genes of non-small lung cancer based on consistently differential interactions.	2015-06-01	Xiaoping Liu Tao Zeng	Qianqian Shi William Wang Luonan Chen	Cancer and Metastasis Reviews
Immune cell profiling to guide therapeutic decisions in rheumatic diseases	2015-06-02	Deepak A Rao Soumya Raychaudhuri	Joerg Ermann Nikola C Teslovich Michael B Brenner	Nature Reviews Rheumatology
RNA-Seq analysis of isolated satellite cells in Prmt5 deficient mice.	2015-06-03	Carsten T Kuenne Mario Looso Thomas Braun	Stefan Guenther Ting Zhang Marcus Krueger Yonggang Zhou Johnny Kim	Genomics Data
CD24(+) cells fuel rapid tumor growth and display high metastatic capacity	2015-06-04	Derek LeRoith	Ran Rostoker Sagi Abelson Inna Genkin Sarit Ben-Shmuel Ravi Sachidanandam Eyal J Scheinman Keren Bitton-Worms Zila Shen Orr Avishay Caspi Maty Tzukerman	Breast Cancer Research
Defective pollen wall contributes to male sterility in the male sterile line 1355A of cotton.	2015-06-05	Ling Min Longfu Zhu Daojun Yuan Xianlong Zhang	Yuanlong Wu Zancheng Wu Li Yang Xiyan Yang Xiaoping Guo	Scientific Reports
The generation of macrophages with anti-inflammatory activity in the absence of STAT6 signaling.	2015-06-05	Najib El-sayed	Bryan D Fleming Prabha Chandrasekaran Laura A L Dillon Elizabeth Dalby Rahul Suresh Arup Sarkar David M Mosser	Journal of Leukocyte Biology
Scalable microfluidics for single-cell RNA printing and sequencing.	2015-06-06	Dana Pe'er Peter A Sims	Sayantan Bose Zhenmao Wan Ambrose Carr Abbas H Rizvi Gregory Vieira Dana Pe'er	Genome Biology
Flagellin Is Required for Host Cell Invasion and Normal Salmonella Pathogenicity Island 1 Expression by Salmonella enterica Serovar Paratyphi A	2015-06-08	Michael McClelland	Dana Elhadad Prerak Desai Galia Rahav Ohad Gal-Mor	Infection and Immunity
Infiltration of chitin by protein coacervates defines the squid beak mechanical gradient.	2015-06-08	Ali Miserez	YerPeng Tan Shawn Hoon Paul A Guerette Wei Wei Ali Ghadban Cai Hao J Herbert Waite	Nature Chemical Biology
hnRNP U protein is required for normal pre-mRNA splicing and postnatal heart development and function	2015-06-09	Rhonda Bassel-Duby Tom Maniatis Junqiang Ye Lindsey J. Macpherson	Nadine Beetz Sean O'Keeffe Juan Carlos Tapia Weisheng V. Chen Eric N. Olson	Proceedings of the National Academy of Sciences of the United States of America
From Glacier to Sauna: RNA-Seq of the Human Pathogen Black Fungus Exophiala dermatitidis under Varying Temperature Conditions Exhibits Common and Novel Fungal Response	2015-06-10	Barbara Blasi Hakim Tafer	Donatella Tesei Katja Sterflinger	PLOS ONE
Molecular characterization of two novel molecular chaperones in bacterial-challenged Apostichopus japonicus.	2015-06-10	Chenghua Li	Haihong Wang Yina Shao Weiwei Zhang Zhimeng Lv Chunhua Jin	Gene
RNA-Seq analysis of isolate- and growth phase-specific differences in the global transcriptomes of enteropathogenic Escherichia coli prototype isolates	2015-06-12	Sean C Daugherty	Tracy H Hazen Amol Shetty Anup A Mahurkar Owen White James B Kaper David A Rasko	Frontiers in Microbiology
The Impact of Normalization Methods on RNA-Seq Data Analysis.	2015-06-15	Marek Figlerowicz	J Zyprych-Walczak A Szabelska L Handschuh K Górczak K Klamecka I Siatkowski	BioMed Research International
Combined Targeted DNA Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using UNCseq and NGScopy, and RNA Sequencing Using UNCqeR for the Detection of Genetic Aberrations in NSCLC.	2015-06-15	Norman Sharpless Nirali M Patel Vonn Walter	Xiaobei Zhao Anyou Wang David A Eberhard Michele C Hayward Ashley H Salazar Heejoon Jo Matthew G Soloway Matthew D Wilkerson Joel S Parker Xiaoying Yin Guosheng Zhang Marni B Siegel Gary B Rosson H Shelton Earp Margaret L Gulley Karen E Weck D Neil Hayes Stergios J Moschos	PLOS ONE
Suppressing Sorbitol Synthesis Substantially Alters the Global Expression Profile of Stress Response Genes in Apple (Malus domestica) Leaves.	2015-06-15	Yi Zheng Abhaya Dandekar	Ting Wu Yi Wang Zhangjun Fei Kenong Xu Zhenhai Han Lailiang Cheng	Plant and Cell Physiology
Differential RNA-seq (dRNA-seq) for annotation of transcriptional start sites and small RNAs in Helicobacter pylori.	2015-06-16	Cynthia Sharma	Thorsten Bischler Hock Siew Tan Kay Nieselt	Methods
RNASequel: accurate and repeat tolerant realignment of RNA-seq reads.	2015-06-16	Lincoln Stein	Gavin W Wilson	Nucleic Acids Research
YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut.	2015-06-17	Abhaya Dandekar	Sandeep Chakraborty Monica Britton Jill Wegrzyn Timothy Butterfield Pedro José Martínez-García Russell L Reagan Basuthkar J Rao Charles A Leslie Mallikarjuna Aradhaya David Neale Keith Woeste	F1000Research
RNA-seq analysis of an apical meristem time series reveals a critical point in Arabidopsis thaliana flower initiation	2015-06-18	Anna V Klepikova Sergey E. Dmitriev	Maria D Logacheva Aleksey A Penin	BMC Genomics
RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications.	2015-06-18	Gane Ka-Shu Wong Udo Gowik	Ming-Ju Amy Lyu Steve Kelly Sarah Covshoff Julia Mallmann Peter Westhoff Julian M Hibberd Matt Stata Rowan F Sage Haorong Lu Xiaofeng Wei Xin-Guang Zhu	BMC Evolutionary Biology
Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens	2015-06-19	Dario Cantu	Abraham Morales-Cruz Katherine C H Amrine Barbara Blanco-Ulate Daniel P Lawrence Renaud Travadon Philippe E Rolshausen Kendra Baumgartner	BMC Genomics
PAT-seq: a method to study the integration of 3'-UTR dynamics with gene expression in the eukaryotic transcriptome.	2015-06-19	Thomas Preiss Traude H. Beilharz David Powell Ana Traven Torsten Seemann	Paul F Harrison Jennifer L Clancy Peter R Boag	RNA
Benchmarking Transcriptome Quantification Methods for Duplicated Genes in Xenopus laevis.	2015-06-19	Taejoon Kwon		Cytogenetics and Genome Research
RNA-Seq analysis of resistant and susceptible potato varieties during the early stages of potato virus Y infection.	2015-06-20	Jeff H. Chang	Aymeric Goyer Launa Hamlin James M Crosslin Alex Buchanan	BMC Genomics
Marrying microfluidics and microwells for parallel, high-throughput single-cell genomics.	2015-06-20	Alex K. Shalek	Marc H Wadsworth Travis K Hughes	Genome Biology
Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data.	2015-06-22	Bonnie Berger	Sean Simmons Jian Peng Jadwiga Bienkowska	Journal of Computational Biology
ArcA Controls Metabolism, Chemotaxis, and Motility Contributing to the Pathogenicity of Avian Pathogenic Escherichia coli.	2015-06-22	Eve Syrkin Wurtele Dan Nettleton	Fengwei Jiang Chunxia An Yinli Bao Xuefeng Zhao Robert L Jernigan Andrew Lithio Ling Li Lisa K Nolan Chengping Lu Ganwu Li	Infection and Immunity
RNA Seq profiling reveals a novel expression pattern of TGF-β target genes in human blood eosinophils.	2015-06-22	Stephane Esnault	Zhong-Jian Shen Jie Hu Igor Dozmorov James S Malter	Immunology Letters
RNA-seq Reveals Complicated Transcriptomic Responses to Drought Stress in a Nonmodel Tropic Plant, Bombax ceiba L.	2015-06-23	Yuan Chen Liuyang Wang	Zhili Zhou Huancheng Ma Kevin Lin Youjie Zhao Zhi Xiong Bin Tian	Evolutionary Bioinformatics
An integrated RNA-Seq and network study reveals a complex regulation process of rice embryo during seed germination.	2015-06-23	Songnian Hu	Ting Wei Zilong He XinYu Tan Xue Liu Xiao Yuan Yingfeng Luo	Biochemical and Biophysical Research Communications
Systematically evaluating interfaces for RNA-seq analysis from a life scientist perspective.	2015-06-23	Alicia Poplawski Federico Marini	Moritz Hess Tanja Zeller Johanna Mazur Harald Binder	Briefings in Bioinformatics
How Many Genes Are Expressed in a Transcriptome? Estimation and Results for RNA-Seq.	2015-06-24	Luis Fernando García-Ortega Octavio Martínez		PLOS ONE
Gene expression analysis of skin grafts and cultured keratinocytes using synthetic RNA normalization reveals insights into differentiation and growth control.	2015-06-25	Juha Kere Eeva-Mari Jouhilahti Sten Linnarsson Peter Lönnerberg Tiina Skoog Shintaro Katayama Esko Kankuri	H Annika Siitonen Kristo Nuutila Mari H Tervaniemi Jyrki Vuola Anna Johnsson Outi Elomaa	BMC Genomics
Comparison of RNA-seq and microarray-based models for clinical endpoint prediction.	2015-06-25	Benedikt Brors Danielle Thierry-Mieg Falk Hertwig Weihong Xu Marco Chierici Lee Lancashire Richard G Grundy Heng Luo Davide Albanese Martin Peifer Jean Thierry-Mieg Jun Wang Zhiyu Peng Jo Vandesompele	Wenqian Zhang Ying Yu Wenwei Zhang Jian Wang Cesare Furlanello Viswanath Devanarayan Jie Cheng Youping Deng Barbara Hero Huixiao Hong Meiwen Jia Li Li Simon M Lin Yuri Nikolsky André Oberthuer Tao Qing Zhenqiang Su Ruth Volland Charles Wang May D Wang Junmei Ai Shahab Asgharzadeh Smadar Avigad Wenjun Bao Marina Bessarabova Murray H Brilliant Tzu-Ming Chu Jibin Zhang Min Max He Scott Hebbring Howard L Kaufman Samir Lababidi Yan Li Xin X Lu Xiwen Ma Baitang Ning Rosa Noguera John H Phan Frederik Roels Carolina Rosswog Susan Shao Jie Shen Jessica Theissen Gian Paolo Tonini Po-Yen Wu Wenzhong Xiao Joshua Xu Jiekun Xuan Yong Yang Zhan Ye Zirui Dong Ke K Zhang Ye Yin Chen Zhao Yuanting Zheng Russell D Wolfinger Tieliu Shi Linda H Malkas Frank Berthold Weida Tong Leming Shi Matthias Fischer	Genome Biology
AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana.	2015-06-25	Eduardo Eyras Allan B. James Yamile Marquez Maria Kalyna Hugh G. Nimmo Andrea Barta	Runxuan Zhang Cristiane P G Calixto Nikoleta A Tzioutziou Craig G Simpson Wenbin Guo Rob Patro John W S Brown	New Phytologist
Correction: A RNA-Seq Analysis of the Rat Supraoptic Nucleus Transcriptome: Effects of Salt Loading on Gene Expression.	2015-06-25	David Murphy	Kory R Johnson C C T Hindmarch Yasmmyn D Salinas YiJun Shi Michael Greenwood See Ziau Hoe Harold Gainer	PLOS ONE
Intratumoral morphologic and molecular heterogeneity of rhabdoid renal cell carcinoma: challenges for personalized therapy.	2015-06-26	Lalit Patel	Rajesh R Singh Paari Murugan Horatiu Voicu Suk-Young Yoo Tadeusz Majewski Meenakshi Mehrotra Khalida Wani Nizar Tannir Jose A Karam Eric Jonasch Christopher G Wood Chad J Creighton L Jeffrey Medeiros Russell R Broaddus Pheroze Tamboli Keith A Baggerly Kenneth D Aldape Bogdan Czerniak Rajyalakshmi Luthra Kanishka Sircar	Modern Pathology
Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium.	2015-06-27	Hideya Kawaji Mathias Uhlén Nancy Y Yu Linn Fagerberg Piero Carninci Yoshihide Hayashizaki	Björn M Hallström Fredrik Ponten Alistair R R Forrest Fantom Consortium Carsten O Daub	Nucleic Acids Research
Sex hormone-dependent tRNA halves enhance cell proliferation in breast and prostate cancers.	2015-06-29	Yohei Kirino	Shozo Honda Phillipe Loher Megumi Shigematsu Juan P Palazzo Ryusuke Suzuki Issei Imoto Isidore Rigoutsos	Proceedings of the National Academy of Sciences of the United States of America
Gene fusion detection in formalin-fixed paraffin-embedded benign fibrous histiocytomas using fluorescence in situ hybridization and RNA sequencing.	2015-06-29	David Gisselsson Fredrik Mertens	Charles Walther Jakob Hofvander Jenny Nilsson Linda Magnusson Henryk A Domanski Johnbosco Tayebwa Leona A Doyle Christopher D M Fletcher	Laboratory Investigation
A nested parallel experiment demonstrates differences in intensity-dependence between RNA-seq and microarrays.	2015-06-30	John D. Storey	David G Robinson Jean Y Wang	Nucleic Acids Research
Phylogenetic analysis and expression profiling of the pattern recognition receptors: Insights into molecular recognition of invading pathogens in Manduca sexta	2015-07	Xiaolong Cao Haobo Jiang	Xiufeng Zhang Yan He Ramesh T Gunaratna Yun-ru Chen Gary Blissard Michael R Kanost	Insect Biochemistry and Molecular Biology
Isoform-level brain expression profiling of the spermidine/spermine N1-Acetyltransferase1 (SAT1) gene in major depression and suicide	2015-07	Victoria Arango Peter L Nagy	Spiro P Pantazatos Stuart J Andrews Jane Dunning-Broadbent Jiuhong Pang Yung-Yu Huang J John Mann	Neurobiology of Disease
The Discovery, Distribution, and Evolution of Viruses Associated with Drosophila melanogaster	2015-07	Giada Ferrari Fergal M Waldron Jewelna Osei-Poku Elizabeth H Bayne Ben Longdon Amy H Buck Darren J. Obbard	Claire L Webster Shaun Robertson Daisy Crowson Juan F Quintana Jean-Michel Brouqui Brian P Lazzaro Penelope R Haddrill	PLOS Biology
Computational assignment of cell-cycle stage from single-cell transcriptome data.	2015-07-01	Sarah Teichmann Valentina Proserpio Kedar N Natarajan Antonio Scialdone Florian Buettner Luis R. Saraiva Oliver Stegle John C Marioni		Methods
The 3'-5' exoribonuclease Dis3 regulates the expression of specific microRNAs in Drosophila wing imaginal discs.	2015-07-01	Christopher Jones Sandra Cristina Viegas Cecília Maria Arraiano	Benjamin P Towler Patricia Apura Joseph A Waldron Sarah K Smalley Sarah F Newbury	RNA Biology
Gene and miRNA expression changes in squamous cell carcinoma of larynx and hypopharynx.	2015-07-01	Prachi Jain	Jayalakshmi Nair Udita Chandola Vinayak Palve N R Harsha Vardhan Ram Bhupal Reddy Vikram D Kekatpure Amritha Suresh Moni Abraham Kuriakose Binay Panda	Genes & Cancer
Positional RNA-Seq identifies candidate genes for phenotypic engineering of sexual traits.	2015-07-03	Peter Ladurner Eugene Berezikov	Roberto Arbore Kiyono Sekii Christian Beisel Lukas Schärer	Frontiers in Zoology
Quantitative and functional interrogation of parent-of-origin allelic expression biases in the brain.	2015-07-03	Catherine Dulac	Julio D Perez Nimrod D Rubinstein Daniel E Fernandez Stephen W Santoro Leigh A Needleman Olivia Ho-Shing John J Choi Mariela Zirlinger Shau-Kwaun Chen Jun S Liu	eLife
"Pocket-sized RNA-Seq": A Method to Capture New Mature microRNA Produced from a Genomic Region of Interest.	2015-07-03	Florent Hube	Claire Francastel	Non-coding RNA
Age-Related Gene Expression Differences in Monocytes from Human Neonates, Young Adults, and Older Adults.	2015-07-06	Tobias Kollmann	Michelle M Lissner Brandon J Thomas Kathleen Wee Ann-Jay Tong Stephen T Smale	PLOS ONE
Transcriptomic Responses of the Heart and Brain to Anoxia in the Western Painted Turtle.	2015-07-06	Cyriac Kandoth	Sarah W Keenan Craig A Hill Leslie T Buck Daniel E Warren	PLOS ONE
Cytoplasmic LSM-1 protein regulates stress responses through the insulin/IGF-1 signaling pathway in Caenorhabditis elegans	2015-07-06	Denis Dupuy Eric Cornes J Cerón	Montserrat Porta-De-La-Riva David Aristizábal-Corrales Ana María Brokate-Llanos Francisco Javier García-Rodríguez Iris Ertl Mònica Díaz Laura Fontrodona Kadri Reis Robert Johnsen David Baillie Manuel J Muñoz Mihail Sarov	RNA
Transcriptomic profiling of gene expression and RNA processing during Leishmania major differentiation.	2015-07-06	Najib El-sayed	Laura A L Dillon Kwame Okrah V Keith Hughitt Rahul Suresh Yuan Li Maria Cecilia Fernandes A Trey Belew Hector Corrada Bravo David M Mosser	Nucleic Acids Research
Biphasic components of sarcomatoid clear cell renal cell carcinomas are molecularly similar to each other, but distinct from, non-sarcomatoid renal carcinomas	2015-07-07	Lalit Patel	Kanishka Sircar Suk-Young Yoo Tadeusz Majewski Khalida Wani Horatiu Voicu Wandaliz Torres-Garcia Roel G W Verhaak Nizar Tannir Jose A Karam Eric Jonasch Christopher G Wood Pheroze Tamboli Keith A Baggerly Kenneth D Aldape Bogdan Czerniak	The journal of pathology. Clinical research
Transcriptional landscape of trans-kingdom communication between Candida albicans and Streptococcus gordonii.	2015-07-07	Sophie Shaw Howard F. Jenkinson Angela H Nobbs	L C Dutton K H Paszkiewicz R J Silverman P R Splatt R J Lamont M Ramsdale	Molecular Oral Microbiology
Tungsten-induced carcinogenesis in human bronchial epithelial cells.	2015-07-08	Steven Shen Maria Antonietta Zoroddu Massimiliano Peana	Freda Laulicht Jason Brocato Laura Cartularo Joshua Vaughan Feng Wu Thomas Kluz Hong Sun Betul Akgol Oksuz Serenella Medici Max Costa	Toxicology and Applied Pharmacology
Impact of feed additives on surface mucosal health and columnaris susceptibility in channel catfish fingerlings, Ictalurus punctatus.	2015-07-08	Eric Peatman Wilawan Thongda	Honggang Zhao Chao Li Benjamin H Beck Ran Zhang Wilawan Thongda D Allen Davis	Fish and Shellfish Immunology
Revealing Missing Human Protein Isoforms Based on Ab Initio Prediction, RNA-seq and Proteomics	2015-07-09	Parvathy Venugopal Bergithe E Oftedal Zhiqiang Hu Chaochun Wei David L. Adelson Hamish S. Scott	Guangrong Qin Guangyong Zheng Xixia Chu Lu Xie Milena Babic Christopher N Hahn Bing Zhang Xiaojing Wang Nan Li	Scientific Reports
Evolutionary Divergence of Gene and Protein Expression in the Brains of Humans and Chimpanzees.	2015-07-10	Chet C. Sherwood	Amy L Bauernfeind Erik J Soderblom Meredith E Turner M Arthur Moseley John J Ely Patrick R Hof Gregory A Wray Courtney C Babbitt	Genome Biology and Evolution
Drosophila anti-nematode and antibacterial immune regulators revealed by RNA-Seq	2015-07-11	Upasana Shokal Julio Cesar Castillo Todd Creasy	Priti Kumari Amol Shetty Luke J Tallon Ioannis Eleftherianos	BMC Genomics
Differential and coherent processing patterns from small RNAs	2015-07-13	Jan Gorodkin Sachin Pundhir		Scientific Reports
Microbes & neurodevelopment--Absence of microbiota during early life increases activity-related transcriptional pathways in the amygdala.	2015-07-13	Roman Stilling Feargal J Ryan Marcus J Claesson Gerard Clarke Timothy G. Dinan John F. Cryan	Alan E Hoban Fergus Shanahan	Brain, Behavior, and Immunity
Opposing roles of STAT1 and STAT3 in IL-21 function in CD4+ T cells	2015-07-13	Majid Kazemian	Chi-Keung Wan Allison B Andraski Rosanne Spolski Peng Li Jangsuk Oh Leigh Samsel Phillip A Swanson Dorian B McGavern Elizabeth P Sampaio Alexandra F Freeman Joshua D Milner Steven M Holland Warren J Leonard	Proceedings of the National Academy of Sciences of the United States of America
Physiology and immunology of mucosal barriers in catfish (Ictalurus spp.)	2015-07-15	Eric Peatman	Miles Lange Honggang Zhao Benjamin H Beck	Tissue Barriers
Leveraging transcript quantification for fast computation of alternative splicing profiles.	2015-07-15	Eduardo Eyras	Gael P Alamancos Amadís Pagès Juan L Trincado Nicolás Bellora	RNA
Correction: De novo Transcriptome Analysis of Portunus trituberculatus Ovary and Testis by RNA-Seq: Identification of Genes Involved in Gonadal Development.	2015-07-15	PLOS ONE staff		PLOS ONE
Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package	2015-07-16	María José Nueda Antonio Di Pietro	Sonia Tarazona Pedro Furió-Tarí David Turrà Alberto Ferrer Ana Conesa	Nucleic Acids Research
Widespread Inducible Transcription Downstream of Human Genes.	2015-07-16	Joan A. Steitz	Anna Vilborg Maria C Passarelli Therese A Yario Kazimierz T Tycowski	Molecular Cell
Expression of an estrogen-regulated variant transcript of the peroxisomal branched chain fatty acid oxidase ACOX2 in breast carcinomas	2015-07-17	Anne-Lise Børresen-Dale Surendra Kumar Vessela Kristensen Bjørn Naume	Sunniva Stordal Bjørklund Michael Seiler Grethe I Grenaker Alnæs Yao Ming John Kerrigan Ravi Sachidanandam Gyan Bhanot Shridar Ganesan	BMC Cancer
A nonlethal sampling method to obtain, generate and assemble whole blood transcriptomes from small, wild mammals.	2015-07-17	Emma C. Teeling Sébastien J. Puechmaille Michaël Bekaert	Zixia Huang Aurore Gallot Nga T Lao Nicole M Foley David Jebb	Molecular Ecology Resources
Genome-wide association analysis on normal hearing function identifies PCDH20 and SLC28A3 as candidates for hearing function and loss.	2015-07-17	Dragana Vuckovic Sally J. Dawson Giorgia Girotto Anne Viljanen Taina Rantanen Marina Ciullo Diego Vozzi Teresa Nutile Ginevra Biino Anu Loukola	Deborah I Scheffer Anna Morgan Mariateresa Di Stazio Maria P Concas Lisa Nolan Aileen Bahl Adrian Davis David P Corey Mario Pirastu Paolo Gasparini	Human Molecular Genetics
Integrative analyses of RNA editing, alternative splicing, and expression of young genes in human brain transcriptome by deep RNA sequencing.	2015-07-17	David M. Irwin	Dong-Dong Wu Ling-Qun Ye Yan Li Yan-Bo Sun Yi Shao Chunyan Chen Zhu Zhu Li Zhong Lu Wang Yong E Zhang Ya-Ping Zhang	Journal of molecular cell biology
QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments	2015-07-19	James C Mullikin	Stephen W Hartley	BMC Bioinformatics
How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets	2015-07-21	Shane G. Poplawski Lucia Peixoto Davide Risso Ted Abel	Mathieu E Wimmer Terence P Speed Marcelo A Wood	Nucleic Acids Research
Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data.	2015-07-21	Tomasz Kuliński	Daniel Andergassen Christoph P Dotter Philipp M Guenzl Philipp C Bammer Denise P Barlow Florian M Pauler Quanah J Hudson	Nucleic Acids Research
Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data.	2015-07-23	Mihaela Zavolan Andreas R Gruber Foivos Gypas Alexander Kanitz	Georges Martin	Genome Biology
Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment.	2015-07-23	Geoffrey J. Barton Gordon G Simpson Nicholas Schurch Christian Cole Tom Owen-Hughes Karim Gharbi Mark Blaxter	Marek Gierliński Pietà Schofield Alexander Sherstnev Vijender Singh Nicola Wrobel	Bioinformatics
TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets.	2015-07-23	Oliver H Tam	Ying Jin Eric Paniagua Molly Hammell	Bioinformatics
TANRIC: An Interactive Open Platform to Explore the Function of lncRNAs in Cancer.	2015-07-24	Lingxiang Liu Jun Li Leng Han	Paul Roebuck Lixia Diao Yuan Yuan John N Weinstein Han Liang	Cancer Research
Experimental validation of methods for differential gene expression analysis and sample pooling in RNA-seq.	2015-07-25	Per Qvist Anto P. Rajkumar Mette Nyegaard Ole Mors	Ross Lazarus Francesco Lescai Jia Ju Anders D Børglum Qibin Li Jane H Christensen	BMC Genomics
Identifying new sex-linked genes through BAC sequencing in the dioecious plant Silene latifolia.	2015-07-25	Alex Widmer Nicolas Blavet Niklaus Zemp Jos Käfer	H Blavet A Muyle R Cegan C Deschamps S Mousset S Aubourg R Bergero D Charlesworth R Hobza G A B Marais	BMC Genomics
Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17 Human Proteome Project.	2015-07-28	Gil Omenn	Hong-Dong Li Rajasree Menon Brandon Govindarajoo Bharat Panwar Yang Zhang Yuanfang Guan	Journal of Proteome Research
Transcriptional profiling of macrophages derived from monocytes and iPS cells identifies a conserved response to LPS and novel alternative transcription	2015-07-30	Siamon Gordon	Kaur Alasoo Fernando O Martinez Christine Hale Fiona Powrie Gordon Dougan Subhankar Mukhopadhyay Daniel J Gaffney	Scientific Reports
Transcriptome Dynamics of Developing Photoreceptors in Three-Dimensional Retina Cultures Recapitulates Temporal Sequence of Human Cone and Rod Differentiation Revealing Cell Surface Markers and Gene Networks	2015-07-31	Anand Swaroop Kohei Homma Jizhong Zou Matthew Brooks	Rossukon Kaewkhaw Koray Dogan Kaya Vijender Chaitankar Mahendra Rao	Stem Cells
DNA hypomethylation-mediated activation of Cancer/Testis Antigen 45 (CT45) genes is associated with disease progression and reduced survival in epithelial ovarian cancer.	2015-08-01	Kunle Odunsi	Wa Zhang Carter J Barger Petra A Link Paulette Mhawech-Fauceglia Austin Miller Stacey N Akers Adam R Karpf	Epigenetics
Analysis of the Human Prostate-Specific Proteome Defined by Transcriptomics and Antibody-Based Profiling Identifies TMEM79 and ACOXL as Two Putative, Diagnostic Markers in Prostate Cancer	2015-08-03	Mathias Uhlén Linn Fagerberg William M Gallagher Karin Jirström	Gillian O'Hurley Christer Busch Björn M Hallström Charlotte Stadler Anna Tolf Emma Lundberg Jochen M Schwenk Anders Bjartell Fredrik Pontén	PLOS ONE
Similarities in Gene Expression Profiles during In Vitro Aging of Primary Human Embryonic Lung and Foreskin Fibroblasts.	2015-08-03	Peter Hemmerich Reinhard Guthke	Shiva Marthandan Steffen Priebe Mario Baumgart Marco Groth Alessandro Cellerino Stephan Diekmann	BioMed Research International
Dynamics of gene silencing during X inactivation using allele-specific RNA-seq.	2015-08-03	Tahsin Stefan Barakat Hendrik Marks Wouter de Laat Austin Smith	Hindrik H D Kerstens Erik Splinter René A M Dirks Guido van Mierlo Onkar Joshi Shuang-Yin Wang Tomas Babak Cornelis A Albers Tüzer Kalkan Alice Jouneau Joost Gribnau Hendrik G Stunnenberg	Genome Biology
RNA-seq reveals the critical role of OtpR in regulating Brucella melitensis metabolism and virulence under acidic stress.	2015-08-05	Yongqun He	Wenxiao Liu Hao Dong Jing Li Qixing Ou Yujin Lv Xiaolei Wang Zuoshuang Xiang Qingmin Wu	Scientific Reports
Transcriptome response to heat stress in a chicken hepatocellular carcinoma cell line.	2015-08-05	Carl J Schmidt	Liang Sun Susan J Lamont Amanda M Cooksey Fiona McCarthy Catalina O Tudor K Vijay-Shanker Rachael M DeRita Max Rothschild Chris Ashwell Michael E Persia	Cell Stress & Chaperones
RNASeq in C. elegans Following Manganese Exposure.	2015-08-06	Michael Aschner	Nancy L Parmalee Shahina B Maqbool Bin Ye Brent Calder Aaron B Bowman	Current protocols in toxicology / editorial board, Mahin D. Maines (editor-in-chief) ... [et al.]
Comprehensive assembly of novel transcripts from unmapped human RNA-Seq data and their association with cancer	2015-08-07	Majid Kazemian	Min Ren Jian-Xin Lin Wei Liao Rosanne Spolski Warren J Leonard	Molecular Systems Biology
An RNA-Seq-based reference transcriptome for Citrus.	2015-08-11	Terol J	Francisco Tadeo Daniel Ventimilla Manuel Talon	Plant Biotechnology Journal
ROTS: reproducible RNA-seq biomarker detector-prognostic markers for clear cell renal cell cancer.	2015-08-11	Laura L. Elo Panu M Jaakkola	Fatemeh Seyednasrollah Krista Rantanen	Nucleic Acids Research
Transcriptome profiling of larvae of the marine medaka Oryzias melastigma by Illumina RNA-seq.	2015-08-11	Jae-Seong Lee	Bo-Mi Kim Beom-Soon Choi Hui-Soo Kim Jae-Sung Rhee Doris W T Au Rudolf S S Wu Ik-Young Choi	Marine Genomics
Galaxy Integrated Omics: Web-based Standards-Compliant Workflows for Proteomics Informed by Transcriptomics.	2015-08-12	Jun Fan Fawaz Ghali David A. Matthews Andrew Jones	Shyamasree Saha Gary Barker Kate J Heesom Conrad Bessant	Molecular & Cellular Proteomics
Host and non-host roots in rice: cellular and molecular approaches reveal differential responses to arbuscular mycorrhizal fungi.	2015-08-13	Paola Bonfante	Valentina Fiorilli Marta Vallino Chiara Biselli Antonella Faccio Paolo Bagnaresi	Frontiers in Plant Science
Comparative RNA-seq analysis of the Tritrichomonas foetus PIG30/1 isolate from pigs reveals close association with Tritrichomonas foetus BP-4 isolate 'bovine genotype'.	2015-08-14	Ana Conesa	Victoria Morin-Adeline Kai Mueller Jan Šlapeta	Veterinary Parasitology
The identification and characterization of novel transcripts from RNA-seq data.	2015-08-17	Stefanie Dimmeler Tyler Weirick Shizuka Uchida	Giuseppe Militello Raphael Müller David John	Briefings in Bioinformatics
Lost in Translation: Pitfalls in Deciphering Plant Alternative Splicing Transcripts.	2015-08-18	Andrea Barta Yamile Marquez Maria Kalyna Geoffrey Michael Gadd	John W S Brown Craig G Simpson	The Plant Cell
The mRNA expression of soluble urokinase plasminogen activator surface receptor in human adipose tissue is positively correlated with body mass index.	2015-08-18	Kok Gan Chan	Hien Fuh Ng Kin Fah Chin Yun Fong Ngeow	Genome
Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis.	2015-08-19	Guo-Li Ming Hongjun Song Daniel A Berg David Nauen	Jaehoon Shin Yunhua Zhu Joseph Y Shin Juan Song Michael A Bonaguidi Grigori Enikolopov Kimberly M Christian	Cell Stem Cell
Assembly and Analysis of Differential Transcriptome Responses of Hevea brasiliensis on Interaction with Microcyclus ulei.	2015-08-19	Ibonne Aydee García Romero Dolly Montoya Castaño Silvia Restrepo	Uriel Alonso Hurtado Páez Fabio Ancizar Aristizábal Gutiérrez	PLOS ONE
Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development.	2015-08-19	Dmitry A Ovchinnikov Deanne M. Taylor Ernst J. Wolvetang	Yu Hasegawa Laurence de Torrenté Jessica C Mar	PLOS Genetics
Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms	2015-08-19	Mihaela Pertea Steven Salzberg	Tsung-Cheng Chang Sungyul Lee Joshua T Mendell	Genome Research
Regulation of alternative splicing in Drosophila by 56 RNA binding proteins.	2015-08-20	Steven E. Brenner Brenton R. Graveley	Angela N Brooks Michael O Duff Gemma May Li Yang Mohan Bolisetty Jane Landolin Ken Wan Jeremy Sandler Benjamin W Booth Susan E Celniker	Genome Research
Defining the three cell lineages of the human blastocyst by single-cell RNA-seq.	2015-08-20	Tim Xiaoming Hu Ignacio del Valle Kay Elder Paul Robson	Paul Blakeley Norah M E Fogarty Sissy E Wamaitha Philip Snell Leila Christie Kathy K Niakan	Development
Full-length de novo assembly of RNA-seq data in pea (Pisum sativum L.) provides a gene expression atlas and gives insights into root nodulation in this species.	2015-08-22	Jérôme Gouzy Pascal Gamas Corinne Da Silva	Susete Alves-Carvalho Grégoire Aubert Sébastien Carrère Corinne Cruaud Anne-Lise Brochot Françoise Jacquin Anthony Klein Chantal Martin Karen Boucherot Jonathan Kreplak Sandra Moreau Patrick Wincker Judith Burstin	The Plant Journal
Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments	2015-08-24	Christina Kendziorski	Ning Leng Li-Fang Chu Chris Barry Yuan Li Jeea Choi Xiaomao Li Peng Jiang Ron M Stewart James A Thomson	Nature Methods
Novel insights into the molecular events linking to cell death induced by tetracycline in the amitochondriate protozoan Trichomonas vaginalis.	2015-08-24	Po-Jung Huang Petrus Tang	Kuo-Yang Huang Fu-Man Ku Wei-Hung Cheng Chi-Ching Lee Lichieh Julie Chu Chih-Chieh Cheng Yi-Kai Fang Hsueh-Hsia Wu	Antimicrobial Agents and Chemotherapy
Time-Course RNA-Seq Analysis Reveals Transcriptional Changes in Rice Plants Triggered by Rice stripe virus Infection.	2015-08-25	Jin Kyo Jung	Won Kyong Cho Sen Lian Sang-Min Kim Bo Yoon Seo Kook-Hyung Kim	PLOS ONE
Identification of miRNAs in Bovine Endometrium through RNAseq and Prediction of Regulated Pathways.	2015-08-25	Soroush Sharbati	S E Palma-Vera R Einspanier	Reproduction in Domestic Animals
MetaRNA-Seq: An Interactive Tool to Browse and Annotate Metadata from RNA-Seq Studies.	2015-08-25	Karsten Suhre Anja M Billing Anna Halama	Pankaj Kumar Shahina Hayat Manish Gupta Noha A Yousri Gregory M Smith	BioMed Research International
Fast and accurate approximate inference of transcript expression from RNA-seq data.	2015-08-26	Antti Honkela	James Hensman Panagiotis Papastamoulis Peter Glaus Antti Honkela Magnus Rattray	Bioinformatics
Stimulation of Innate and Adaptive Immunity by Using Filamentous Bacteriophage fd Targeted to DEC-205	2015-08-26	Piergiuseppe De Berardinis	Luciana D'Apice Valerio Costa Rossella Sartorius Maria Trovato Marianna Aprile	Journal of Immunology Research
Altered Exosomal RNA Profiles in Bronchoalveolar Lavage from Lung Transplants with Acute Rejection	2015-08-26	Aric Gregson David Sayah	Aki Hoji Patil Injean Steven T Poynter Claudia Briones Vyacheslav Palchevskiy S Sam Weigt Michael Y Shino Ariss Derhovanessian Rajan Saggar David Ross Abbas Ardehali Joseph P Lynch John A Belperio	American Journal of Respiratory and Critical Care Medicine
Genome-wide RNA-Seq of Human Motor Neurons Implicates Selective ER Stress Activation in Spinal Muscular Atrophy.	2015-08-26	Natalia Rodríguez-Muela Shi-Yan Ng Lee L Rubin John L. Rinn	Boon Seng Soh David G Hendrickson Feodor Price	Cell Stem Cell
RNAseq analysis of Aspergillus fumigatus in blood reveals a just wait and see resting stage behavior	2015-08-27	Ana Conesa Sven Krappmann Gerhard H Braus	Henriette Irmer Sonia Tarazona Christoph Sasse Patrick Olbermann Jürgen Loeffler	BMC Genomics
The coelomic epithelium transcriptome from a clonal sea star, Coscinasterias muricata.	2015-08-27	Josep F. Abril Pedro Martinez	Jonatan L Gabre Helen Nilsson Sköld Olga Ortega-Martinez	Marine Genomics
RNA-Seq analysis of urea nutrition responsive transcriptome of Oryza sativa elite indica cultivar RP Bio 226.	2015-08-28	K Ulaganathan	Mettu Madhavi Reddy	Genomics Data
Chromatin features, RNA polymerase II and the comparative expression of lens genes encoding crystallins, transcription factors, and autophagy mediators	2015-08-28	Deyou Zheng Ales Cvekl	Jian Sun Shira Rockowitz Daniel Chauss Ping Wang Marc Kantorow	Molecular Vision
Concordance between RNA-sequencing data and DNA microarray data in transcriptome analysis of proliferative and quiescent fibroblasts	2015-09	Brett Trost Anthony Kusalik	Catherine A Moir Zoe E Gillespie Jennifer A Mitchell Christopher H Eskiw	Royal Society Open Science
Relationships within Cladobranchia (Gastropoda: Nudibranchia) based on RNA-Seq data: an initial investigation	2015-09	Jessica A Goodheart Allen Collins	Adam L Bazinet Michael P Cummings	Royal Society Open Science
Cullin4 Is Pro-Viral during West Nile Virus Infection of Culex Mosquitoes.	2015-09-01	Peter Walker Julio Rodriguez-Andres Jean-bernard Duchemin	Prasad N Paradkar Lee Trinidad	PLOS Pathogens
RNA-Seq analysis identifies key genes associated with haustorial development in the root hemiparasite Santalum album.	2015-09-01	Oliver Berkowitz James Whelan	Xinhua Zhang Jaime A Teixeira da Silva Muhan Zhang Guohua Ma Jun Duan	Frontiers in Plant Science
Integrated methylome and transcriptome analysis reveals novel regulatory elements in pediatric acute lymphoblastic leukemia.	2015-09-01	Kristen H Taylor Stephanie McKay	Md Almamun Benjamin T Levinson Annette C van Swaay Nathan T Johnson Gerald L Arthur J Wade Davis	Epigenetics
Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses	2015-09-02	Aviv Regev Rahul Satija Roi Avraham Alex K. Shalek	Nathan Haseley Douglas Brown Cristina Penaranda Humberto B Jijon John J Trombetta Ramnik J Xavier Deborah T Hung	Cell
RNAseq expression analysis of resistant and susceptible mice after influenza A virus infection identifies novel genes associated with virus replication and important for host resistance to infection	2015-09-02	Claudia Pommerenke	Esther Wilk Ashutosh K Pandey Sarah Rebecca Leist Bastian Hatesuer Matthias Preusse Junxi Wang Klaus Schughart	BMC Genomics
Allele-Selective Transcriptome Recruitment to Polysomes Primed for Translation: Protein-Coding and Noncoding RNAs, and RNA Isoforms.	2015-09-02	Wolfgang Sadee	Roshan Mascarenhas Maciej Pietrzak Ryan M Smith Amy Webb Danxin Wang Audrey C Papp Julia K Pinsonneault Michal Seweryn Grzegorz Rempala	PLOS ONE
Cell type-specific transcriptomics of hypothalamic energy-sensing neuron responses to weight-loss	2015-09-02	Scott M Sternson Henry FE Ken Sugino Tozer A Branco T		eLife
HiCdat: a fast and easy-to-use Hi-C data analysis tool.	2015-09-03	Ueli Grossniklaus Stefan Grob Marc W Schmid		BMC Bioinformatics
Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data	2015-09-03	Katharina E. Hayer Gregory R Grant	Angel Pizarro Nicholas F Lahens John B Hogenesch	Bioinformatics
Errors in RNA-Seq quantification affect genes of relevance to human disease.	2015-09-03	Mick Watson	Christelle Robert	Genome Biology
Transcriptomic Features of Bovine Blastocysts Derived by Somatic Cell Nuclear Transfer.	2015-09-03	Namshin Kim	Byungkuk Min Sunwha Cho Jung Sun Park Yun-Gyeong Lee Yong-Kook Kang	G3
Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline	2015-09-04	Frank Emmert-Streib	Yasir Rahmatallah Galina Glazko	Briefings in Bioinformatics
Transcriptome analysis of the white pine blister rust pathogen Cronartium ribicola: de novo assembly, expression profiling, and identification of candidate effectors.	2015-09-04	Jun-Jun Liu	Rona N Sturrock Richard A Sniezko Holly Williams Ross Benton Arezoo Zamany	BMC Genomics
Function and Regulation of Cph2 in Candida albicans.	2015-09-04	Pierre Baldi	Shelley Lane Pietro Di Lena Kati Tormanen Haoping Liu	Eukaryotic Cell
RNA-seq analysis of the whole transcriptome of MDA-MB-231 mammary carcinoma cells exposed to the antimetastatic drug NAMI-A.	2015-09-04	Alberto Pallavicini	Alberta Bergamo Marco Gerdol Marianna Lucafò Chiara Pelillo Marilena Battaglia Gianni Sava	Metallomics
Gene Ranking of RNA-Seq Data via Discriminant Non-Negative Matrix Factorization.	2015-09-08	Michael R. Barnes	Zhilong Jia Xiang Zhang Naiyang Guan Xiaochen Bo Zhigang Luo	PLOS ONE
Systematic identification of factors for provirus silencing in embryonic stem cells	2015-09-09	George Q. Daley Chadi A El Farran Yinghui Li Matthew C. Lorincz	Bin Xia Yang Hong Chao Guo Tao Yu Hai Tong Fang Hao Fei Wang Sharon Schlesinger Yu Fen Samantha Seah Germaine Yen Lin Goh Suat Peng Neo Vinay Tergaonkar Tit-Meng Lim Lingyi Chen Jayantha Gunaratne James J Collins Stephen P Goff Hu Li Frederic A Bard Yuin-Han Loh	Cell
Molecular analyses of juvenile granulosa cell tumors bearing AKT1 mutations provide insights into tumor biology and therapeutic leads.	2015-09-11	Aurélie Auguste S Caburet Sabine Sarnacki	Laurianne Bessière Anne-Laure Todeschini Jaime Prat Emanuela D'angelo Pierre De La Grange Olivier Ariste Fréderic Lemoine Bérangère Legois Charles Sultan Alain Zider Louise Galmiche Nicolas Kalfa Reiner A Veitia	Human Molecular Genetics
Genome-wide RNA sequencing analysis of quorum sensing-controlled regulons in the plant-associated Burkholderia glumae PG1 strain.	2015-09-11	Andreas Knapp Rolf Daniel	Rong Gao Dagmar Krysciak Katrin Petersen Christian Utpatel Christel Schmeisser Sonja Voget Karl-Erich Jaeger Wolfgang R Streit	Applied and Environmental Microbiology
The role of antigen presenting cells in the induction of HIV-1 latency in resting CD4(+) T-cells.	2015-09-11	Vanessa A Evans David Powell Sharon R. Lewin	Nitasha A Kumar Karey Cheong Candida da Fonseca Pereira Jenny Anderson Paul U Cameron	Retrovirology
The reverse transcription signature of N-1-methyladenosine in RNA-Seq is sequence dependent	2015-09-13	Andreas Hildebrandt Marie-Luise Winz Sunny Sharma Yuri Motorin Mark Helm	Ralf Hauenschild Lyudmil Tserovski Katharina Schmid Kathrin Thüring Karl-Dieter Entian Ludivine Wacheul Denis L J Lafontaine James Anderson Juan Alfonzo Andres Jäschke	Nucleic Acids Research
Ancient gene duplications have shaped developmental stage-specific expression in Pristionchus pacificus.	2015-09-15	Christian Rödelsperger P Baskaran Gabriel V. Markov	Christian Rödelsperger Neel Prabh Vahan Serobyan Antje Hirsekorn Christoph Dieterich	BMC Evolutionary Biology
Identification of candidate gonadal sex differentiation genes in the chicken embryo using RNA-seq	2015-09-16	Alicia Oshlack Nadia M Davidson Craig A. Smith Andrew H Sinclair	Katie L Ayers Luke S Lambeth	BMC Genomics
RNA-seq analysis of Pichia anomala reveals important mechanisms required for survival at low pH	2015-09-16	Jens Nielsen Verena Siewers SungSoo Kim	Eugene Fletcher Amir Feizi	Microbial Cell Factories
A novel workflow correlating RNA-seq data to Phythophthora infestans resistance levels in wild Solanum species and potato clones.	2015-09-17	Estelle Proux-Wéra Erik Andreasson	Itziar Frades Kibrom B Abreha Åsa Lankinen Erik Alexandersson	Frontiers in Plant Science
Tools and best practices for data processing in allelic expression analysis.	2015-09-17	Tuuli Lappalainen Pejman Mohammadi	Stephane E Castel Ami Levy-Moonshine Eric Banks	Genome Biology
RNA-seq analyses of changes in the Anopheles gambiae transcriptome associated with resistance to pyrethroids in Kenya: identification of candidate-resistance genes and candidate-resistance SNPs.	2015-09-17	Eric Ochomo Mariangela Bonnizoni Guiyun Yan	William Augustine Dunn Monica Britton Yaw Afrane Guofa Zhou Joshua Hartsel Ming-Chieh Lee Jiabao Xu Andrew Githeko Joseph Fass	Parasites & Vectors
Codon and Amino Acid Usage Are Shaped by Selection Across Divergent Model Organisms of the Pancrustacea	2015-09-17	Cassandra G. Extavour	Carrie A Whittle	G3
RNAseq Analysis Highlights Specific Transcriptome Signatures of Yeast and Mycelial Growth Phases in the Dutch Elm Disease Fungus Ophiostoma novo-ulmi.	2015-09-17	Louis Bernier	Martha Nigg Jérôme Laroche Christian R Landry	G3
In vivo Monitoring of Transcriptional Dynamics After Lower-Limb Muscle Injury Enables Quantitative Classification of Healing	2015-09-18	Alexander Meissner	Carlos A Aguilar Anna Shcherbina Darrell O Ricke Ramona Pop Christopher T Carrigan Casey A Gifford Maria L Urso Melissa A Kottke	Scientific Reports
Early transcriptional events linked to induction of diapause revealed by RNAseq in larvae of drosophilid fly, Chymomyza costata.	2015-09-21	Jan Provazník Konrad Schöttner Rodolphe Poupardin	Jaroslava Korbelová David Doležel Dinko Pavlinic Vladimír Beneš Vladimír Koštál	BMC Genomics
Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells.	2015-09-21	Sarah Teichmann Aleksandra A Kolodziejczyk Florian Buettner	Jason C H Tsang Yong Yu Shannon Burke Cui Wang Liming Lu Pentao Liu	Genome Biology
Semantic Assembly and Annotation of Draft RNAseq Transcripts without a Reference Genome.	2015-09-22	Andrey Ptitsyn	Ramzi Temanni Christelle Bouchard Peter A V Anderson	PLOS ONE
Dynamic transcriptional symmetry-breaking in pre-implantation mammalian embryo development revealed by single-cell RNA-seq.	2015-09-22	Qi Chen	Junchao Shi Xin Li Xiudeng Zheng Ying Zhang Jie Qiao Fuchou Tang Yi Tao Qi Zhou Enkui Duan	Development
Transcriptome Profiling of Pediatric Core Binding Factor AML.	2015-09-23	George Komatsoulis	Chih-Hao Hsu Cu Nguyen Chunhua Yan Rhonda E Ries Qing-Rong Chen Ying Hu Fabiana Ostronoff Derek L Stirewalt George Komatsoulis Shawn Levy Daoud Meerzaman Soheil Meshinchi	PLOS ONE
Gene expression changes in the salivary glands of Anopheles coluzzii elicited by Plasmodium berghei infection	2015-09-23	Luis Pedro Coelho Ana Domingos Alejandro Cabezas-Cruz	Renato Pinheiro-Silva Lara Borges James J Valdés Virgílio do Rosário José de la Fuente	Parasites & Vectors
Molecular mechanisms of D-cycloserine in facilitating fear extinction: insights from RNAseq.	2015-09-23	Soraya Seedat	Stefanie Malan-Müller Lorren Fairbairn Willie M U Daniels Mahjoubeh Jalali Sefid Dashti Edward J Oakeley Marc Altorfer Martin Kidd Junaid Gamieldien Sîan Megan Joanna Hemmings	Metabolic Brain Disease
RNA-Seq in Mytilus galloprovincialis: comparative transcriptomics and expression profiles among different tissues.	2015-09-24	David Posada Rebeca Moreira Carlos Canchaya	Patricia Pereiro Antonio Figueras Beatriz Novoa	BMC Genomics
Whose Gene Is It Anyway? The Effect of Preparation Purity on Neutrophil Transcriptome Studies	2015-09-24	Helen L Wright	Huw B Thomas Robert J Moots Steven W Edwards	PLOS ONE
Harnessing Next Generation Sequencing in Climate Change: RNA-Seq Analysis of Heat Stress-Responsive Genes in Wheat (Triticum aestivum L.).	2015-09-25	RANJEET RANJAN KUMAR Viswanathan Chinnusamy	Suneha Goswami Sushil K Sharma Yugal K Kala Gyanendra K Rai Dwijesh C Mishra Monendra Grover Gyanendra P Singh Himanshu Pathak Anil Rai Raj D Rai	OMICS: A Journal of Integrative Biology
Comprehensive Identification of Sexual Dimorphism-Associated Differentially Expressed Genes in Two-Way Factorial Designed RNA-Seq Data on Japanese Quail (Coturnix coturnix japonica).	2015-09-29	Heebal Kim	Kelsey Caetano-Anolles Minseok Seo Sandra Rodriguez-Zas Jae-Don Oh Jae Yong Han Kichoon Lee Tae Sub Park Sangsu Shin Zhang Jiao Jiao Mrinmoy Ghosh Dong Kee Jeong Seoae Cho Ki-Duk Song Hak-Kyo Lee	PLOS ONE
De novo transcriptome profiling of highly purified human lymphocytes primary cells	2015-09-29	Sergio Abrignani Massimiliano Pagani Grazisa Rossetti Ilaria Panzeri	Raoul J P Bonnal Valeria Ranzani Alberto Arrigoni Serena Curti Paola Gruarin	Scientific Data
Transcriptome Characteristics and X-Chromosome Inactivation Status in Cultured Rat Pluripotent Stem Cells.	2015-09-29	Irina S. Zakharova Sergey P Medvedev Fedor Kolpakov Suren M Zakian Alexander Karaskov	Evgeniya A Vaskova Anastasiya E Sorokina Artem A Nemudryy Evgeniy A Elisaphenko Alexander I Shevchenko Elena A Kizilova Antonina I Zhelezova Ivan S Evshin Ruslan N Sharipov Julia M Minina Natalia S Zhdanova Igor I Khegay Gennadiy T Sukhikh Evgeniy A Pokushalov Valentin V Vlasov Ludmila N Ivanova	Stem Cells and Development
Detecting Multivariate Gene Interactions in RNA-Seq Data Using Optimal Bayesian Classification.	2015-10-01	Edward R. Dougherty	Jason Knight Ivan Ivanov Karen Triff Robert Chapkin	IEEE/ACM Transactions on Computational Biology and Bioinformatics
Functional Impact and Evolution of a Novel Human Polymorphic Inversion That Disrupts a Gene and Creates a Fusion Transcript.	2015-10-01	Tõnu Esko Carla Giner-Delgado Marta Puig Magdalena Gayà-Vidal David Castellano	Lorena Pantano David Izquierdo José Ignacio Lucas-Lledó Chikashi Terao Fumihiko Matsuda Mario Cáceres	PLOS Genetics
SRSF1-Regulated Alternative Splicing in Breast Cancer	2015-10-01	Frédéric H-T Allain Adrian Robert Krainer Antoine Cléry	Olga Anczuków Martin Akerman Jie Wu Chen Shen Nitin H Shirole Amanda Raimer Shuying Sun Mads A Jensen Yimin Hua	Molecular Cell
Prdm12 specifies V1 interneurons through cross-repressive interactions with Dbx1 and Nkx6 genes in Xenopus.	2015-10-01	Carine Van Lint Benoît Van Driessche Julie Hanotel Ian Quigley Aurore Thelie Alessandra Pierani Michael Schubert	Simon Desiderio Benoit Van Driessche Anthony Rodari Mark D Borromeo Sadia Kricha François Lahaye Jenifer Croce Gustavo Cerda-Moya Jesús Ordoño Fernandez Barbara Bolle Katharine E Lewis Maike Sander Jane E Johnson Christopher R Kintner Tomas Pieler Kristine A Henningfeld Eric J Bellefroid Claude Van Campenhout	Development
Different exercise modalities have distinct effects on the integrin-linked kinase (ILK) and Ca2+ signaling pathways in the male rat bone.	2015-10-01	Dharani M Sontam Peter Tsai	Elwyn C Firth Mark H Vickers Justin M O'Sullivan	Physiological Reports
Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells.	2015-10-01	Aviv Regev Itay Tirosh	Monika S Kowalczyk Itay Tirosh Dirk Heckl Tata Nageswara Rao Atray Dixit Brian J Haas Rebekka K Schneider Amy J Wagers Benjamin L Ebert	Genome Research
Complete hematologic response of early T-cell progenitor acute lymphoblastic leukemia to the γ-secretase inhibitor BMS-906024: genetic and epigenetic findings in an outlier case.	2015-10-01	Matthew Meyerson Andrew L. Kung	Birgit Knoechel Ami Bhatt Li Pan Chandra S Pedamallu Eric Severson Alejandro Gutierrez David M Dorfman Frank C Kuo Michael Kluk Patrick Zweidler-McKay Stephen C Blacklow Daniel J DeAngelo Jon C Aster	Cold Spring Harbor molecular case studies
Dynamic expression of long noncoding RNAs and repeat elements in synaptic plasticity.	2015-10-01	Marcel E. Dinger	Jesper L V Maag Debabrata Panja Ida Sporild Sudarshan Patil Dominik C Kaczorowski Clive R Bramham Karin Wibrand	Frontiers in Neuroscience
BrowserGenome.org: web-based RNA-seq data analysis and visualization.	2015-10-01	Jonathan Schmid-Burgk Veit Hornung		Nature Methods
Defining the three cell lineages of the human blastocyst by single-cell RNA-seq.	2015-10-01	Tim Xiaoming Hu	Paul Blakeley Norah M E Fogarty Ignacio Del Valle Sissy E Wamaitha Kay Elder Philip Snell Leila Christie Paul Robson Kathy K Niakan	Development
Functional development of the adult ovine mammary gland--insights from gene expression profiling.	2015-10-05	Amy M Paten Sam W Peterson Elizabeth J. Duncan Peter Dearden	Sarah J Pain Paul R Kenyon Hugh T Blair	BMC Genomics
Discovery of progenitor cell signatures by time-series synexpression analysis during Drosophila embryonic cell immortalization.	2015-10-05	Norbert Perrimon	Mary-Lee Dequéant Delphine Fagegaltier Yanhui Hu Kerstin Spirohn Amanda Simcox Gregory J Hannon	Proceedings of the National Academy of Sciences of the United States of America
RNA-Seq analysis for indigo biosynthesis pathway genes in Indigofera tinctoria and Polygonum tinctorium.	2015-10-05	Sanjog T Thul	Bijaya K Sarangi Yoshiko Minami	Genomics Data
Giving Time Purpose: The Synechococcus elongatus Clock in a Broader Network Context.	2015-10-05	Spencer Diamond	Ryan K Shultzaberger Joseph S Boyd Ralph J Greenspan Susan S Golden	Annual Review of Genetics
Hierarchical Modeling and Differential Expression Analysis for RNA-seq Experiments with Inbred and Hybrid Genotypes.	2015-10-05	Dan Nettleton	Andrew Lithio	Journal of Agricultural, Biological, and Environmental Statistics
Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues.	2015-10-05	Susan Fanayan Ling Yen Lee	Julia Fangfei Yan Hoguen Kim Seul-Ki Jeong Hyoung-Joo Lee Manveen K Sethi Ronald C Beavis Hogune Im Michael P Snyder Matan Hofree Trey Ideker Shiaw-Lin Wu Young-Ki Paik William S Hancock	Journal of Proteome Research
Global analysis of physical and functional RNA targets of hnRNP L reveals distinct sequence and epigenetic features of repressed and enhanced exons.	2015-10-05	Samuel J Allon	Brian S Cole Iulia Tapescu Michael J Mallory Jinsong Qiu Robert J Lake Hua-Ying Fan Xiang-Dong Fu Kristen W Lynch	RNA
Alternative Splicing Signatures in RNA-seq Data: Percent Spliced in (PSI).	2015-10-06	Matthias Heinig	Sebastian Schafer Kui Miao Craig C Benson Stuart A Cook Norbert Hubner	Current protocols in human genetics / editorial board, Nicholas C, Dracapoli ... [et al.]
Transition from somatic embryo to friable embryogenic callus in cassava: dynamic changes in cellular structure, physiological status, and gene expression profiles.	2015-10-06	Peng Zhang	Qiuxiang Ma Wenzhi Zhou	Frontiers in Plant Science
Chromatin-Remodelling Complex NURF Is Essential for Differentiation of Adult Melanocyte Stem Cells.	2015-10-06	Dana Koludrovic Gabrielle Mengus Irwin Davidson	Patrick Laurette Thomas Strub Céline Keime Madeleine Le Coz Sebastien Coassolo Lionel Larue	PLOS Genetics
Model of fibrolamellar hepatocellular carcinomas reveals striking enrichment in cancer stem cells	2015-10-06	Vincenzo Cardinale Guido Carpino Domenico Alvaro	Tsunekazu Oikawa Eliane Wauthier Timothy A Dinh Sara R Selitsky Andrea Reyna-Neyra Ronald Levine David Klimstra Eugenio Gaudio Nancy Carrasco Praveen Sethupathy Lola M Reid	Nature Communications
Identification of functional networks associated with cell death in the retina of OXYS rats during the development of retinopathy.	2015-10-06	Oyuna S. Kozhevnikova	Darya V Telegina Elena E Korbolina Nikita I Ershov Nataliya G Kolosova	Cell Cycle
A Semi-parametric Bayesian Approach for Differential Expression Analysis of RNA-seq Data.	2015-10-07	Chong Wang	Fangfang Liu Peng Liu	Journal of Agricultural, Biological, and Environmental Statistics
RNA-Seq Analysis of Abdominal Fat in Genetically Fat and Lean Chickens Highlights a Divergence in Expression of Genes Controlling Adiposity, Hemostasis, and Lipid Metabolism	2015-10-07	Chuming Chen Larry A. Cogburn Michel J Duclos	Christopher W Resnyk Hongzhan Huang Cathy H Wu Jean Simon Elisabeth Le Bihan-Duval	PLOS ONE
The androgen receptor controls expression of the cancer-associated sTn antigen and cell adhesion through induction of ST6GalNAc1 in prostate cancer.	2015-10-07	Daniel Vodák David J Elliott Hing Y Leung Rolf Inge Skotheim	Jennifer Munkley Sebastian Oltean Brian T Wilson Karen E Livermore Yan Zhou Eleanor Star Vasileios I Floros Bjarne Johannessen Bridget Knight Paul McCullagh John McGrath Malcolm Crundwell Craig N Robson Lorna W Harries Prabhakar Rajan Ian G Mills	Oncotarget
The membrane proteome of male gametophyte in Solanum lycopersicum.	2015-10-08	Enrico Schleiff Arindam Ghatak Palak Chaturvedi Wolfram Weckwerth	Puneet Paul Mario Selymesi Anida Mesihovic Klaus-Dieter Scharf Stefan Simm	Journal of Proteomics
B-Cell and Monocyte Contribution to Systemic Lupus Erythematosus Identified by Cell-Type-Specific Differential Expression Analysis in RNA-Seq Data.	2015-10-08	Joel M Guthridge Judith A. James	Mikhail G Dozmorov Nicolas Dominguez Krista Bean Susan R Macwana Virginia Roberts Edmund Glass	Bioinformatics and Biology Insights
Profiling RNA editing in human tissues: towards the inosinome Atlas	2015-10-09	Graziano Pesole Anna Maria D'Erchia Ernesto Picardi	Caterina Manzari Francesca Mastropasqua Italia Aiello	Scientific Reports
Molecular genetic response to varied wavelengths of light in Xiphophorus maculatus skin	2015-10-09	Jordan Chang	Yuan Lu William T Boswell Mikki Boswell Kaela L Caballero Ronald B Walter	Comparative Biochemistry and Physiology C: Toxicology and Pharmacology
Novel RNA variants in colorectal cancers.	2015-10-12	Andreas M Hoff Torfinn Nome Ragnhild A. Lothe Rolf Inge Skotheim	Bjarne Johannessen Sharmini Alagaratnam Sen Zhao Marthe Løvf Anne C Bakken Merete Hektoen Anita Sveen	Oncotarget
A basal stem cell signature identifies aggressive prostate cancer phenotypes.	2015-10-12	Robert Baertsch	Bryan A Smith Artem Sokolov Vladislav Uzunangelov Yulia Newton Kiley Graim Colleen Mathis Donghui Cheng Joshua M Stuart Owen N Witte	Proceedings of the National Academy of Sciences of the United States of America
Hepatic Long Intergenic Noncoding RNAs: High Promoter Conservation and Dynamic, Sex-Dependent Transcriptional Regulation by Growth Hormone.	2015-10-12	David J Waxman	Tisha Melia Pengying Hao Feyza Yilmaz	Molecular and Cellular Biology
RNA-Seq mediated root transcriptome analysis of Chlorophytum borivilianum for identification of genes involved in saponin biosynthesis.	2015-10-12	Avneesh Kumar Jagdeep Kaur	Sunil Kumar Shikha Kalra Baljinder Singh Kashmir Singh	Functional and Integrative Genomics
RNAseq by Total RNA Library Identifies Additional RNAs Compared to Poly(A) RNA Library.	2015-10-12	Brian D Lehmann David C Samuels	Yan Guo Shilin Zhao Quanhu Sheng Mingsheng Guo Jennifer Pietenpol Yu Shyr	BioMed Research International
Assessing Transcription Regulatory Elements To Evaluate the Expression Status of Missing Protein Genes on Chromosomes 11 and 19.	2015-10-12	Zhe Ren Shaohang Xu	Nannan Kong Yang Zhou Yamei Deng Yang Fan Yue Zhang Liang Lin Yan Ren Quanhui Wang Jin Zi Bo Wen Siqi Liu	Journal of Proteome Research
FOXM1 cistrome predicts breast cancer metastatic outcome better than FOXM1 expression levels or tumor proliferation index.	2015-10-12	Charles J Vaske Stephen Benz	Christina Yau Laurence Meyer Gary Scott Brian Egan Paul Labhart Nader Pourmand Christopher C Benz	Breast Cancer Research and Treatment
Spatially distinct neutrophil responses within the inflammatory lesions of pneumonic plague	2015-10-13	Nikolas M Stasulli William E. Goldman	Kara R Eichelberger Paul A Price Roger D Pechous Stephanie A Montgomery Joel S Parker	mBio
Extensive tissue-specific transcriptomic plasticity in maize primary roots upon water deficit	2015-10-13	Waqas Ahmed Malik Dan Nettleton Hans-Peter Piepho	Nina Opitz Caroline Marcon Anja Paschold Andrew Lithio Ronny Brandt Frank Hochholdinger	Journal of Experimental Botany
Computational analysis of stochastic heterogeneity in PCR amplification efficiency revealed by single molecule barcoding.	2015-10-13	James M Heather Benny Chain	Katharine Best Theres Oakes John Shawe-Taylor	Scientific Reports
Dynamic association rules for gene expression data analysis	2015-10-14	Wen-Hsiung Li	Shu-Chuan Chen Tsung-Hsien Tsai Cheng-Han Chung	BMC Genomics
Insights into the role of immunosenescence during varicella zoster virus infection (shingles) in the aging cell model	2015-10-14	Mukesh Kumar	Ji-Ae Kim Seul-Ki Park Chan-Hee Lee Ok Sarah Shin	Oncotarget
Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies.	2015-10-14	Jörg Vogel Lars Barquist		Annual Review of Genetics
RNA-Seq workflow: gene-level exploratory analysis and differential expression.	2015-10-14	Simon Anders Wolfgang Huber Michael I Love	Vladislav Kim	F1000Research
Decay-Initiating Endoribonucleolytic Cleavage by RNase Y Is Kept under Tight Control via Sequence Preference and Sub-cellular Localisation.	2015-10-16	Peter Redder Julien Prados	Vanessa Khemici Patrick Linder	PLOS Genetics
Genome-wide analysis on Chlamydomonas reinhardtii reveals the impact of hydrogen peroxide on protein stress responses and overlap with other stress transcriptomes.	2015-10-16	Sabeeha Merchant Stefan Schmollinger María Esther Pérez-Pérez Crysten E Blaby-Haas Stéphane D Lemaire	Ian K Blaby Sorel Fitz-Gibbon	The Plant Journal
Effect of heparin on the biological properties and molecular signature of human mesenchymal stem cells	2015-10-17	Rebekah M Samsonraj Drew M Titmarsh Emily T Camilleri	Ling Ling Torben Helledie Ren Jie Chua Oliver Dreesen Christian Dombrowski David A Rider Mario Galindo Ian Lee Wanjin Hong James H Hui Victor Nurcombe Andre J van Wijnen Simon M Cool	Gene
CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in neurodevelopment.	2015-10-19	Deyou Zheng	Ping Wang Mingyan Lin Erika Pedrosa Anastasia Hrabovsky Zheng Zhang Wenjun Guo Herbert M Lachman	Molecular Autism
Elucidating drivers of oral epithelial dysplasia formation and malignant transformation to cancer using RNAseq.	2015-10-19	Jennifer L Graham Rebecca Chalkley Alastair Droop	Caroline Conway Preetha Chengot Catherine Daly Lisa Ross Pamela Rabbitts Lucy F Stead	Oncotarget
Functional analysis of NtMPK2 uncovers its positive role in response to Pseudomonas syringae pv. tomato DC3000 in tobacco.	2015-10-19	Qingyou Xia	Xingtan Zhang Genhong Wang Junping Gao Mengyun Nie Wenshan Liu	Plant Molecular Biology
Identification of a novel fusion transcript between human relaxin-1 (RLN1) and human relaxin-2 (RLN2) in prostate cancer.	2015-10-20	Sean D McGrath Marcel E. Dinger Elizabeth D. Williams Gregor Tevz Jyotsna Batra	Ryan Demeter Vincent Magrini Varinder Jeet Anja Rockstroh Stephen McPherson John Lai Nenad Bartonicek Jiyuan An Melanie L Lehman Colleen C Nelson	Molecular and Cellular Endocrinology
Comparative RNA seq analysis of the New Zealand glowworm Arachnocampa luminosa reveals bioluminescence-related genes.	2015-10-21	Peter Dearden	Miriam L Sharpe Gregory Gimenez Kurt L Krause	BMC Genomics
Modeling of autosomal-dominant retinitis pigmentosa in Caenorhabditis elegans uncovers a nexus between global impaired functioning of certain splicing factors and cell type-specific apoptosis.	2015-10-21	Karinna Rubio-Peña Sylvain Foissac Eric Cornes J Cerón	Laura Fontrodona David Aristizábal-Corrales Silvia Torres Francisco J García-Rodríguez Xènia Serrat David González-Knowles Montserrat Porta-De-La-Riva	RNA
The Human Endometrium-Specific Proteome Defined by Transcriptomics and Antibody-Based Profiling.	2015-10-21	Linn Fagerberg Mathias Uhlén	Agata Zieba Evelina Sjöstedt Matts Olovsson Björn M Hallström Linda Oskarsson Karolina Edlund Anna Tolf Fredrik Ponten	OMICS: A Journal of Integrative Biology
Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.	2015-10-22	Aleksandra A Kolodziejczyk John C Marioni Sarah Teichmann Jong Kyoung Kim	Tomislav Ilicic	Nature Communications
A Diencephalic Dopamine Source Provides Input to the Superior Colliculus, where D1 and D2 Receptors Segregate to Distinct Functional Zones.	2015-10-22	Martha Constantine-Paton Rory Kirchner Yasunobu Murata Sung-Yon Kim	Andrew D Bolton Andrew Young Tru Dang Yuchio Yanagawa	Cell Reports
HENMT1 and piRNA Stability Are Required for Adult Male Germ Cell Transposon Repression and to Define the Spermatogenic Program in the Mouse.	2015-10-23	Jeffrey R Mann David L. Adelson Lee H Wong Hamish S. Scott Moira O'bryan	Shu Ly Lim Zhi Peng Qu R Daniel Kortschak David M Lawrence Joel Geoghegan Anna-Lena Hempfling Martin Bergmann Christopher C Goodnow Christopher J Ormandy Duangporn Jamsai	PLOS Genetics
Menadione-Induced Oxidative Stress Re-Shapes the Oxylipin Profile of Aspergillus flavus and Its Lifestyle.	2015-10-23	Walter Sanseverino	Marco Zaccaria Matteo Ludovici Simona Marianna Sanzani Antonio Ippolito Riccardo Aiese Cigliano Marzia Scarpari Valeria Scala Corrado Fanelli Massimo Reverberi	Toxins
Circularization restores signal recognition particle RNA functionality in Thermoproteus	2015-10-24	L Randau	André Plagens Michael Daume Julia Wiegel	eLife
Mapping 3' transcript ends in the bank vole (Clethrionomys glareolus) mitochondrial genome with RNA-Seq.	2015-10-26	Petr Kotlík	Silvia Marková Karolína Filipi Jeremy B Searle	BMC Genomics
IRAK1 is a novel DEK transcriptional target and is essential for head and neck cancer cell survival.	2015-10-26	Phillip Dexheimer	Allie K Adams Lyndsey C Bolanos Rebekah A Karns Bruce J Aronow Kakajan Komurov Anil G Jegga Keith A Casper Yash J Patil Keith M Wilson Daniel T Starczynowski Susanne I Wells	Oncotarget
Identification of Genes Related to Growth and Lipid Deposition from Transcriptome Profiles of Pig Muscle Tissue.	2015-10-27	Hao Zhang	Zhixiu Wang Qinggang Li Yangzom Chamba Bo Zhang Peng Shang Changxin Wu	PLOS ONE
A Database of microRNA Expression Patterns in Xenopus laevis	2015-10-27	Sara Lopez-Gomollon Simon Moxon Tamas Dalmay	Ayisha Ahmed Nicole J Ward Camille Viaut Matthew L Tomlinson Ilya Patrushev Michael J Gilchrist Dario Dotlic Andrea E Münsterberg Grant N Wheeler	PLOS ONE
RNA-Seq of Tumor-Educated Platelets Enables Blood-Based Pan-Cancer, Multiclass, and Molecular Pathway Cancer Diagnostics.	2015-10-27	Bauke Ylstra Pieter Wesseling Jan Koster	Myron G Best Nik Sol Irsan Kooi Jihane Tannous Bart A Westerman François Rustenburg Pepijn Schellen Heleen Verschueren Edward Post Najim Ameziane Josephine Dorsman Egbert F Smit Henk M Verheul David P Noske Jaap C Reijneveld R Jonas A Nilsson Bakhos A Tannous Thomas Wurdinger	Cancer Cell
Transcriptomic Changes in Coral Holobionts Provide Insights into Physiological Challenges of Future Climate and Ocean Change.	2015-10-28	Nedeljka N. Rosic David I Kline Chon-Kit Kenneth Chan Sophie Dove David Edwards Ove Hoegh-Guldberg	Paulina Kaniewska Edmund Yew Siang Ling	PLOS ONE
Strand-Specific RNA-Seq Analyses of Fruiting Body Development in Coprinopsis cinerea	2015-10-28	Igor V Grigoriev Kazuo Ishii Yuichi Sakamoto Kerrie Barry	Hajime Muraguchi Kiwamu Umezawa Mai Niikura Makoto Yoshida Toshinori Kozaki Kiyota Sakai Motoyuki Shimizu Kiyoshi Nakahori Cindy Choi Chew Yee Ngan Eika Lindquist Anna Lipzen Andrew Tritt Sajeet Haridas Patricia J Pukkila	PLOS ONE
Sxl-Dependent, tra/tra2-Independent Alternative Splicing of the Drosophila melanogaster X-Linked Gene found in neurons.	2015-10-28	David Sturgill	Xia Sun Haiwang Yang Brian Oliver Leonard Rabinow Marie-Laure Samson	G3
Transcriptomic analysis of global changes in cytokine expression in mouse spleens following acute Toxoplasma gondii infection.	2015-10-28	Xing-Quan Zhu Si-Yang Huang Dong-Hui Zhou	Jun-Jun He Jun Ma Hui-Qun Song Jin-Lei Wang	Parasitology Research
A high-throughput RNA-seq approach to profile transcriptional responses	2015-10-29	Xiaoquan Wen Francesca Luca Roger Pique-Regi	G A Moyerbrailean G O Davis C T Harvey D Watza	Scientific Reports
RNA Editing in Chloroplasts of Spirodela polyrhiza, an Aquatic Monocotelydonous Species	2015-10-30	Wenqin Wang Joachim Messing	Wei Zhang Yongrui Wu Pal Maliga	PLOS ONE
ccmGDB: a database for cancer cell metabolism genes	2015-10-30	Feixiong Cheng	Pora Kim Junfei Zhao Zhongming Zhao	Nucleic Acids Research
The vitamin D-dependent transcriptome of human monocytes.	2015-10-30	Veijo Nurminen Antonio Neme Carsten Carlberg	Sabine Seuter	The Journal of Steroid Biochemistry and Molecular Biology
Activation of AhR-mediated toxicity pathway by emerging pollutants polychlorinated diphenyl sulfides.	2015-10-30	John P Giesy Pu Xia Rui Zhang Guanyong Su Zunyao Wang Xiaowei Zhang	Junjiang Zhang Yang Wu Jie Xia Jiamin Zhang Daniel L Villeneuve Hongxia Yu	Chemosphere
Cross-platform normalization of microarray and RNA-seq data for machine learning applications	2015-10-30	Casey S. Greene	Jeffrey A Thompson Jie Tan
Cross-platform normalization of microarray and RNA-seq data for machine learning applications	2015-10-30	Casey S. Greene	Jeffrey A Thompson Jie Tan
Comparative blood transcriptome analysis in idiopathic and LRRK2 G2019S-associated Parkinson's disease.	2015-10-31	Carlos Prieto	Jon Infante María Sierra Pascual Sánchez-Juan Isabel González-Aramburu Coro Sánchez-Quintana José Berciano Onofre Combarros Jesús Sainz	Neurobiology of Aging
Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems	2015-11	Silvana Konermann Eugene Koonin	Sergey Shmakov Omar O. Abudayyeh Kira S. Makarova Yuri I. Wolf Jonathan S. Gootenberg Ekaterina Semenova Leonid Minakhin Julia Joung Konstantin Severinov Feng Zhang	Molecular Cell
LEDGF/p75 interacts with mRNA splicing factors and targets HIV-1 integration to highly spliced genes.	2015-11-01	Mamuka Kvaratskhelia Stephen H. Hughes	Parmit Kumar Singh Matthew R Plumb Andrea L Ferris James R Iben Xiaolin Wu Hind J Fadel Brian T Luke Caroline Esnault Eric M Poeschla Henry L Levin	Genes & Development
Global Analysis of mRNA, Translation, and Protein Localization: Local Translation Is a Key Regulator of Cell Protrusions.	2015-11-01	Faraz Khosravi Mardakheh	Angela Paul Sandra Kümper Amine Sadok Hugh Paterson Afshan Mccarthy Yinyin Yuan Christopher J Marshall	Developmental Cell
SOX9 modulates the expression of key transcription factors required for heart valve development.	2015-11-02	Olivia Alder Pamela A. Hoodless	Victoria C Garside Rebecca Cullum Daphne Y Lu Ryan Vander Werff Mikhail Bilenky Yongjun Zhao Steven J M Jones Marco A Marra T Michael Underhill	Development
Global Transcriptome Analysis of Primary Cerebrocortical Cells: Identification of Genes Regulated by Triiodothyronine in Specific Cell Types.	2015-11-02	Juan Bernal	Pilar Gil-Ibañez Francisco García-García Joaquín Dopazo Beatriz Morte	Cerebral Cortex
Multi-Scale Molecular Deconstruction of the Serotonin Neuron System.	2015-11-04	Rachael Brust	Benjamin W Okaty Morgan E Freret Benjamin D Rood Morgan L Hennessy Danielle deBairos Jun Chul Kim Melloni N Cook Susan M Dymecki	Neuron
The Orthology Clause in the Next Generation Sequencing Era: Novel Reference Genes Identified by RNA-seq in Humans Improve Normalization of Neonatal Equine Ovary RT-qPCR Data.	2015-11-04	Dragos Scarlet Reinhard Ertl Christine Aurich	Ralf Steinborn	PLOS ONE
Spatio-Temporal Gene Expression Profiling during In Vivo Early Ovarian Folliculogenesis: Integrated Transcriptomic Study and Molecular Signature of Early Follicular Growth.	2015-11-05	Bertrand Servin	Agnes Bonnet Philippe Mulsant Beatrice Mandon-Pepin	PLOS ONE
Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells	2015-11-05	Zhikun Zhao Qichao Yu Liang Wu Yong Hou Karsten Kristiansen Huanming Yang Xiuqing Zhang	Xiaolong Zhang Ling Wang Bo Li Guibo Li Michael Dean Yanhui Wang Xinxin Lin Weijian Rao Zhanlong Mei Yang Li Runze Jiang Huan Yang Fuqiang Li Guoyun Xie Liqin Xu Kui Wu Jie Zhang Jianghao Chen Ting Wang Yingrui Li Jian Wang Xun Xu	GigaScience
A multi-omic analysis of human naïve CD4+ T cells.	2015-11-06	Danielle Thierry-Mieg Tai-Chung Huang Sneha M Pinto Jun Zhong Luigi Marchionni Jean Thierry-Mieg Min-Sik Kim	Christopher J Mitchell Derese Getnet Srikanth S Manda Praveen Kumar Raja Sekhar Nirujogi Mio Iwasaki Patrick G Shaw Xinyan Wu Raghothama Chaerkady Arivusudar Marimuthu Babylakshmi Muthusamy Nandini A Sahasrabuddhe Rajesh Raju Caitlyn Bowman Ludmila Danilova Jevon Cutler Dhanashree S Kelkar Charles G Drake T S Keshava Prasad Peter N Murakami Alan F Scott Leming Shi Rafael Irizarry Leslie Cope Yasushi Ishihama Charles Wang Harsha Gowda Akhilesh Pandey	BMC Systems Biology
Proper Use of Allele-Specific Expression Improves Statistical Power for cis-eQTL Mapping with RNA-Seq Data	2015-11-07	Charles M. Perou	Yi-Juan Hu Wei Sun Jung-Ying Tzeng	Journal of the American Statistical Association
Host Transcriptional Profiling at Early and Later Stages of the Compatible Interaction Between Phaseolus vulgaris and Meloidogyne incognita.	2015-11-09	Mário Massayuki Inomoto Maria Lucia Carneiro Vieira	Luciane Santini Carla de Freitas Munhoz Mauro Ferreira Bonfim Marcelo Mendes Brandão	Phytopathology
RNA sequencing of Sleeping Beauty transposon-induced tumors detects transposon-RNA fusions in forward genetic cancer screens	2015-11-09	Jesse D Riordan Adam J. Dupuy	Nuri A Temiz Branden S Moriarity Natalie K Wolf David A Largaespada Aaron L Sarver	Genome Research
Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers.	2015-11-09	Albin Sandelin Timo Lassmann Bogumil Kaczkowski Hideya Kawaji Masayoshi Itoh Piero Carninci Yoshihide Hayashizaki Robin Andersson	Yuji Tanaka Alistair R R Forrest FANTOM5 Consortium	Cancer Research
Highly proliferative primitive fetal liver hematopoietic stem cells are fueled by oxidative metabolic pathways.	2015-11-09	Ruben Boon Alex van Vliet Sarah-maria Fendt Nick van Gastel Catherine Verfaillie Peter Carmeliet	Javed K Manesia Zhuofei Xu Dorien Broekaert Guy Eelen Thomas Vanwelden Steve Stegen Alberto Pascual-Montano Geert Carmeliet Satish Khurana	Stem Cell Research
STEM-22LARGE-SCALE SINGLE-CELL RNA-seq REVEALS A DEVELOPMENTAL CELLULAR HIERARCHY IN HUMAN OLIGODENDROGLIOMA.	2015-11-09	Aviv Regev	Andrew Venteicher Itay Tirosh Christine Hebert Leah Escalante Brian Nahed Daniel Cahill William Curry Robert Martuza Bradley Bernstein David Louis Mario Suva	Neuro-Oncology
A resource of ribosomal RNA-depleted RNA-Seq data from different normal adult and fetal human tissues.	2015-11-10	Nicolas Bertin	Jocelyn Y H Choy Priscilla L S Boon Melissa J Fullwood	Scientific Data
An effective analytic method for detecting tissue-specific genes in RNA-seq experiments.	2015-11-10	Xiaohua Douglas Zhang	Guoqing Zhao Qiao Li I-Ming Wang Xiaoqiao Liu Xiangzhong Fang	Pharmacogenomics
Cancer genetics: RNA-seq for blood-based pan-cancer diagnostics.	2015-11-10	Liesbet Lieben		Nature Reviews Genetics
REST-Governed Gene Expression Profiling in a Neuronal Cell Model Reveals Novel Direct and Indirect Processes of Repression and Up-Regulation.	2015-11-10	Davide Cittaro	Jose M Garcia-Manteiga Silvia Bonfiglio Lucrezia Folladori Maria L Malosio Dejan Lazarevic Elia Stupka Jacopo Meldolesi	Frontiers in Cellular Neuroscience
Saccular Transcriptome Profiles of the Seasonal Breeding Plainfin Midshipman Fish (Porichthys notatus), a Teleost with Divergent Sexual Phenotypes.	2015-11-11	Joseph A. Sisneros	Joshua Faber-Hammond Manoj P Samanta Elizabeth A Whitchurch Dustin Manning Allison B Coffin	PLOS ONE
A Comprehensive RNA Sequencing Analysis of the Adeno-Associated Virus (AAV) Type 2 Transcriptome Reveals Novel AAV Transcripts, Splice Variants, and Derived Proteins	2015-11-11	Andreas Gogol-Döring	Catrin Stutika Laura Botschen Mario Mietzsch Stefan Weger Mirjam Feldkamp Wei Chen Regine Heilbronn	Journal of Virology
Genome-Wide Transcriptome Analysis During Anthesis Reveals New Insights into the Molecular Basis of Heat Stress Responses in Tolerant and Sensitive Rice Varieties.	2015-11-11	Ludovico Dreni Massimo Galbiati Lucia Colombo Martin M. Kater	Nahuel González-Schain Lovely M F Lawas Sigrid Heuer Krishna S V Jagadish	Plant and Cell Physiology
RNA-seq Brings New Insights to the Intra-Macrophage Transcriptome of Salmonella Typhimurium	2015-11-12	Shabarinath Srikumar Siân V Owen Carsten Kröger Karsten Hokamp	Magali Hébrard Aoife Colgan Sathesh K Sivasankaran Andrew D S Cameron Jay C D Hinton	PLOS Pathogens
Molecular response of chorioretinal endothelial cells to complement injury: implications for macular degeneration.	2015-11-13	Luke A. Wiley Budd A. Tucker Todd E. Scheetz Robert F. Mullins Elliott H Sohn Edwin M. Stone	Shemin Zeng S Scott Whitmore Megan J Riker	The Journal of Pathology
Diagnosis: RNA-seq for blood-based pan-cancer diagnostics.	2015-11-13	Liesbet Lieben		Nature Reviews Cancer
Molecular tools for studying the major malaria vector Anopheles funestus: improving the utility of the genome using a comparative poly(A) and Ribo-Zero RNAseq analysis	2015-11-14	Gareth D Weedall	Helen Irving Margaret A Hughes Charles S Wondji	BMC Genomics
miRge - A Multiplexed Method of Processing Small RNA-Seq Data to Determine MicroRNA Entropy	2015-11-16	Marc K. Halushka	Alexander S Baras Christopher J Mitchell Jason R Myers Simone Gupta Lien-Chun Weng John M Ashton Toby C Cornish Akhilesh Pandey	PLOS ONE
Tumor Repression of VCaP Xenografts by a Pyrrole-Imidazole Polyamide.	2015-11-16	Peter Dervan	Amanda E Hargrove Thomas F Martinez Alissa A Hare Alexis A Kurmis John W Phillips Sudha Sud Kenneth J Pienta	PLOS ONE
Interaction of Arabidopsis Trihelix-Domain Transcription Factors VFP3 and VFP5 with Agrobacterium Virulence Protein VirF.	2015-11-16	Vitaly Citovsky	Elena García-Cano Shimpei Magori Qi Sun Zehong Ding Sondra G Lazarowitz	PLOS ONE
High-throughput mRNA and miRNA profiling of epithelial-mesenchymal transition in MDCK cells	2015-11-16	Mathias Müller	Priyank Shukla Claus Vogl Barbara Wallner Doris Rigler Sabine Macho-Maschler	BMC Genomics
Dual RNA-seq of Nontypeable Haemophilus influenzae and Host Cell Transcriptomes Reveals Novel Insights into Host-Pathogen Cross Talk	2015-11-17	Buket Baddal Raffaele A. Calogero	Alessandro Muzzi Stefano Censini Giulia Torricelli Silvia Guidotti Anna R Taddei Antonello Covacci Mariagrazia Pizza Rino Rappuoli Marco Soriani Alfredo Pezzicoli	mBio
RNA-seq is a valuable complement of conventional diagnostic tools in newly diagnosed AML patients	2015-11-17	Vera Magistroni Carlo Gambacorti-Passerini	Rocco Piazza Caterina Cecchetti Alessandra Pirola