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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
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Brian J Raney
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Timothy R Dreszer
Katrina Learned
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Laurence R Meyer
Cricket A Sloan
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Nucleic Acids Research
Insights into global mechanisms and disease by gene expression profiling. 2011-01-01 Hubert Hackl
Johannes Rainer
Ana Dopazo
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Zlatko Trajanoski
Methods in Molecular Biology
Identifying mRNA editing deaminase targets by RNA-Seq. 2011-01-01 Nina Papavasiliou Brad R Rosenberg
Scott Dewell
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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
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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
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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
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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
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Jacqueline E Villalta
Gary P Schroth
Shujun Luo
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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
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Connie Weaver
Alex G Waterson
Emily Days
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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
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Marco A Marra
Martin Hirst
Joseph F Costello
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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
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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
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Nathalie A Johnson
Yongjun Zhao
Adele Telenius
Susana Ben Neriah
Andrew McPherson
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Mark Sun
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Joseph M Connors
David G Huntsman
Kerry J Savage
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Nature
A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii. 2011-03-21 Sabeeha Merchant
Matteo Pellegrini
David Casero
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Petr Ent
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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
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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
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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
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Thomas Kluz
Adriana Arita
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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
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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
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PLOS ONE
Genome-wide analysis of the 5' and 3' ends of vaccinia virus early mRNAs delineates regulatory sequences of annotated and anomalous transcripts. 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
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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
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Biometrics
Contribution of Hfq to photooxidative stress resistance and global regulation in Rhodobacter sphaeroides. 2011-04-27 Cynthia Sharma
Jörg Vogel
Gabriele Klug
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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
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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
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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
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Nataliya Melnyk
Marina Pacheco
Marco A Marra
Martin Hirst
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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
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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
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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
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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
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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
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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
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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
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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
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Raktima Raychowdhury
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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
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Bioinformatics
Global transcriptome changes underlying colony growth in the opportunistic human pathogen Aspergillus fumigatus. 2011-07-01 Antonis Rokas John G Gibbons
Anne Beauvais
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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
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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
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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
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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
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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
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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
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Ann-Ying Lee
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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
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Bioinformatics
RseqFlow: workflows for RNA-Seq data analysis. 2011-07-27 Ewa Deelman Ying Wang
Gaurang Mehta
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Bioinformatics
Detection of splicing events and multiread locations from RNA-seq data based on a geometric-tail (GT) distribution of intron length 2011-07-27 Jing Woei Li
Stephen Kwok-Wing Tsui
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Hao Qin
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Bing Ni
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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
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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
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Nallasivam Palanisamy
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Javed Siddiqui
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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
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Cell Host & Microbe
AlleleSeq: analysis of allele-specific expression and binding in a network framework. 2011-08-02 Yong Kong
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Molecular Systems Biology
Synthetic spike-in standards for RNA-seq experiments. 2011-08-04 Thomas R. Gingeras Lichun Jiang
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Genome Research
Quantitative RNA-seq analysis of the Campylobacter jejuni transcriptome 2011-08-04 Paul P. Gardner
Roy R Chaudhuri
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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
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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
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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
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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
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Frontiers in Neuroscience
Local and global factors affecting RNA sequencing analysis. 2011-08-16 Graham D Johnson Edward Sendler
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Analytical Biochemistry
Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma 2011-08-18 Martin Hirst
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Nature
An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype 2011-08-18 Michele Balsamo Irina M Shapiro
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PLOS Genetics
Transcriptional profiling of psoriasis using RNA-seq reveals previously unidentified differentially expressed genes. 2011-08-18 Ali Jabbari Mayte Suárez-Fariñas
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Journal of Investigative Dermatology
The disequilibrium of nucleosomes distribution along chromosomes plays a functional and evolutionarily role in regulating gene expression 2011-08-19 Songnian Hu Peng Cui
Qiang Lin
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PLOS ONE
Lignin metabolism has a central role in the resistance of cotton to the wilt fungus Verticillium dahliae as revealed by RNA-Seq-dependent transcriptional analysis and histochemistry. 2011-08-23 Daojun Yuan
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Bioaccumulation and effects of CdTe/CdS quantum dots on Chlamydomonas reinhardtii - nanoparticles or the free ions? 2011-08-25 Rute F. Domingos
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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
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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
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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
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Genome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factor erythroid Kruppel-like factor during erythrocyte differentiation. 2011-09-06 Ross C Hardison
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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
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Proteomic and phosphoproteomic comparison of human ES and iPS cells. 2011-09-11 Justin Brumbaugh Douglas H Phanstiel
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Identification of common carp innate immune genes with whole-genome sequencing and RNA-Seq data. 2011-09-12 Elia Stupka
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Integrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes. 2011-09-13 Jurian Schuijers
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Integrative approach involving RNA-Seq, foliar traits and growth measurements revealed genotype-specific plasticity on Eucalyptus subjected to seasonal water shortage. 2011-09-13 Christophe Plomion Emilie Villar
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Pronounced and extensive microtubule defects in a Saccharomyces cerevisiae DIS3 mutant. 2011-09-15 Daniel L Kiss Sarah B Smith
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Differential Expression for RNA Sequencing (RNA-Seq) Data: Mapping, Summarization, Statistical Analysis, and Experimental Design 2011-09-22 Davis J McCarthy
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Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals. 2011-09-25 Vincent Lynch
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From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.). 2011-09-28 Thomas Schmutzer
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Accurate identification of A-to-I RNA editing in human by transcriptome sequencing. 2011-09-29 Jae-Hyung Lee
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Genome-wide transcriptome analysis in murine neural retina using high-throughput RNA sequencing. 2011-10-01 Ece D. Gamsiz
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RNA-Seq analysis in MeV. 2011-10-05 John Quackenbush Eleanor A Howe
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RNA-seq analysis of small RNPs in Trypanosoma brucei reveals a rich repertoire of non-coding RNAs 2011-10-05 Tirza Doniger Shulamit Michaeli
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GENE-counter: a computational pipeline for the analysis of RNA-Seq data for gene expression differences. 2011-10-06 Jeff H. Chang
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S-MART, a software toolbox to aid RNA-Seq data analysis 2011-10-06 Hadi Quesneville Matthias Zytnicki PLOS ONE
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The role of CYP3A4 mRNA transcript with shortened 3'-untranslated region in hepatocyte differentiation, liver development, and response to drug induction. 2011-10-13 Gaedigk R
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RNA-Seq for Plant Pathogenic Bacteria. 2011-10-13 Jeffrey A Kimbrel
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Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens. 2011-10-18 Charles D. Johnson
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The crystal structure of necrosis- and ethylene-inducing protein 2 from the causal agent of cacao's Witches' Broom disease reveals key elements for its activity 2011-10-21 Paulo José Pereira Lima Teixeira
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Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster. 2011-10-23 Thomas R. Gingeras
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Nature Genetics
Identification of gene fusion transcripts by transcriptome sequencing in BRCA1-mutated breast cancers and cell lines 2011-10-27 Anne Vincent-Salomon
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RNA-Seq reveals an integrated immune response in nucleated erythrocytes. 2011-10-27 Nerea Roher
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The transcriptome of the reference potato genome Solanum tuberosum Group Phureja clone DM1-3 516R44. 2011-10-28 Giovanni Giuliano
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RNA-Seq reveals genotype-specific molecular responses to water deficit in eucalyptus 2011-11-02 Christophe Plomion
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RNA-Seq improves annotation of protein-coding genes in the cucumber genome. 2011-11-02 Zhen Li
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BMC Genomics
deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns. 2011-11-03 Peter F. Stadler
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Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain. 2011-11-06 Adam Ameur
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Nature Structural & Molecular Biology
Exploring the gonad transcriptome of two extreme male pigs with RNA-seq 2011-11-08 Giovanni Bussotti
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Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq. 2011-11-08 Ming Hu
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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
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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
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Journal of Visualized Experiments
ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets. 2011-11-16 Jeffrey T. Leek
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Identification of new viral genes and transcript isoforms during Epstein-Barr virus reactivation using RNA-Seq. 2011-11-16 Melody Baddoo
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Genetic variation of pre-mRNA alternative splicing in human populations 2011-11-17 Zhi-xiang Lu Peng Jiang
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Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. 2011-11-22 Aviv Regev
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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
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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
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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
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Plant Physiology
Transposase mediated construction of RNA-seq libraries. 2011-11-29 Jason Gertz
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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
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Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in Anabaena sp. PCC7120 2011-11-30 Agustín Vioque
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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
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EpiRegNet: constructing epigenetic regulatory network from high throughput gene expression data for humans. 2011-12-01 Jing Qin
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RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.). 2011-12-02 Jérôme Salse Caroline Pont
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Genome Biology
X-chromosome hyperactivation in mammals via nonlinear relationships between chromatin states and transcription 2011-12-04 Ruslan I Sadreyev Eda Yildirim
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Nature Structural & Molecular Biology
Isoform diversity and its importance for axon regeneration. 2011-12-13 John L. Bixby
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Protein identification using customized protein sequence databases derived from RNA-Seq data. 2011-12-14 David Tabb
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Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. 2011-12-14 Qiong-Yi Zhao Yi Wang
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GC-content normalization for RNA-Seq data 2011-12-17 Gavin Sherlock
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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
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BMC Genomics
Characterization of a highly conserved histone related protein, Ydl156w, and its functional associations using quantitative proteomic analyses. 2011-12-22 Laurence Florens
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Molecular & Cellular Proteomics
Statistical methods on detecting differentially expressed genes for RNA-seq data. 2011-12-23 Saralees Nadarajah Zhongxue Chen
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BMC Systems Biology
Modulation of NF-κB-dependent gene transcription using programmable DNA minor groove binders 2011-12-27 Jordan L Meier
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Detection, annotation and visualization of alternative splicing from RNA-Seq data with SplicingViewer. 2011-12-28 Fangqing Zhao Qi Liu
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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
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PLOS ONE
Isoform diversity and regulation in peripheral and central neurons revealed through RNA-Seq 2012 John L. Bixby
Vance P. Lemmon
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PLOS ONE
Genes associated with MUC5AC expression in small airway epithelium of human smokers and non-smokers 2012 Jacqueline Salit Guoqing Wang
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BMC Medical Genomics
The transcriptional landscape of the deep-sea bacterium Photobacterium profundum in both a toxR mutant and its parental strain 2012 Andrea Telatin
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BMC Genomics
Computational analysis of noncoding RNAs 2012 Manolis Kellis
Stefan Washietl
Bonnie Berger
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Transcriptome analysis reveals strain-specific and conserved stemness genes in Schmidtea mediterranea 2012 Brenton R. Graveley Alissa M Resch
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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
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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
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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
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PLOS Genetics
Gene expression profiling of liver cancer stem cells by RNA-sequencing 2012 Timothy Wan David W Y Ho
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Nrac, a novel nutritionally-regulated adipose and cardiac-enriched gene 2012 Feng Gao
Abdul B Abou-Samra
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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
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PLOS ONE
Stable gene targeting in human cells using single-strand oligonucleotides with modified bases 2012 George M. Church Xavier Rios
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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
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PLOS ONE
Comparing Bowtie and BWA to Align Short Reads from a RNA-Seq Experiment 2012 Honghuang Lin N. Medina-Medina
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Nucleic Acids Research
Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes 2012-01-01 Andreas Gnirke
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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
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Farah Jaber-Hijazi
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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
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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
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Nature Communications
Computational analysis of RNA-seq. 2012-01-01 Scott A. Givan Christopher A Bottoms
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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
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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
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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
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Bioinformatics
IQSeq: integrated isoform quantification analysis based on next-generation sequencing. 2012-01-06 Andrea Sboner
Mark Bender Gerstein
Jiang Du
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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
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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
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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
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GENIE Consortium
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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
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BMC Genomics
FX: an RNA-Seq analysis tool on the cloud. 2012-01-17 Young Seok Ju
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Bioinformatics
MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data. 2012-01-20 Zhi-xiang Lu
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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
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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
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PLOS ONE
Comparison between Normalised and Unnormalised 454-Sequencing Libraries for Small-Scale RNA-Seq Studies. 2012-01-26 Robert Ekblom
Jon Slate
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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
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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
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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
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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
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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
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D Luiselli
A Boattini
P Garagnani
A Vitale
F Pane
M Baccarani
M Delledonne
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Blood Cancer Journal
An Interspecies Regulatory Network Inferred from Simultaneous RNA-seq of Candida albicans Invading Innate Immune Cells. 2012-03-12 Sascha Brunke
Karl Kuchler
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
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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
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M D Welch
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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
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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
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Zhihua Zhang
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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
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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
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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
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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
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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
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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
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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
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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
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Kelly Thomas
Christopher Cardinale
Gholson J Lyon
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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
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Jonathan R Dry
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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
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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
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Sauvageau M
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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
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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
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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
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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
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Giovanni Finazzi
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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
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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
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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
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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
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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
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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
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Begoña Aguado
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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
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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
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European Urology
Adaptive responses to glucose restriction enhance cell survival, antioxidant capability, and autophagy of the protozoan parasite Trichomonas vaginalis. 2013-08-17 Petrus Tang Kuo-Yang Huang
Yi-Ywan Margaret Chen
Yi-Kai Fang
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Biochimica et Biophysica Acta
Shaping development through mechanical strain: the transcriptional basis of diet-induced phenotypic plasticity in a cichlid fish. 2013-08-19 Helen M Gunter
Paolo Franchini
Axel Meyer
Carmelo Fruciano
Shaohua Fan
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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
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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
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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
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Debabrata Dash
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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
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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
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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
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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
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Ian Diner
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Howard D Rees
Li Lin
Keith E Szulwach
Marla Gearing
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Thomas J Montine
Nicholas T Seyfried
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Peng Jin
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Donna M Willcock
Allan Levey
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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
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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
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Cancer Discovery
A combination of improved differential and global RNA-seq reveals pervasive transcription initiation and events in all stages of the life-cycle of functional RNAs in Propionibacterium acnes, a major contributor to wide-spread human disease 2013-09-14 Kenneth J McDowall Yu-fei Lin
David Romero A
Shuang Guan
Lira Mamanova
BMC Genomics
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. 2013-09-15 Ann-Christine Syvänen
Michael Sammeth
Tuuli Lappalainen
Xavier Estivill i Pallejà
Peter A.C. 't Hoen
Marc Friedlander
Jeroen Laros
Jonas Almlöf
Irina Pulyakhina
Seyed Yahya Anvar
Henk P J Buermans
Olof Karlberg
Mathias Brännvall
GEUVADIS Consortium
Johan T den Dunnen
Gert-Jan B van Ommen
Ivo G Gut
Roderic Guigó
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Nature Biotechnology
Localizing transcripts to single cells suggests an important role of uncultured deltaproteobacteria in the termite gut hydrogen economy 2013-09-16 Niles A. Pierce
Xinning Zhang
Vikas Trivedi
Adam Z Rosenthal
Kaitlyn S Lucey
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Niles A Pierce
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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
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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
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PLOS ONE
Taf7l cooperates with Trf2 to regulate spermiogenesis. 2013-09-30 Ke Zheng
Ivan Grubisic
Tommy Kaplan
Robert Tjian
Haiying Zhou
Ying He
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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
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Integrative Biology
Human housekeeping genes, revisited 2013-10 Eli Eisenberg Erez Y. Levanon Trends in Genetics
Evaluation of the effectiveness of semen storage and sperm purification methods for spermatozoa transcript profiling 2013-10 Russ Hauser
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
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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
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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
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Nucleic Acids Research
Differential expression of olfactory genes in the southern house mosquito and insights into unique odorant receptor gene isoforms. 2013-10-28 Walter S Leal Young-Moo Choo
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
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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
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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
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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
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Molecular Plant-Microbe Interactions
Systematic evaluation of spliced alignment programs for RNA-seq data 2013-11-03 Jennifer Harrow
Roderic Guigó i Serra
Tamara Steijger
Pär G Engström
Gregory R Grant
Gunnar Rätsch
Nick Goldman
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Botond Sipos
André Kahles
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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
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Stuart R Miyasato
Jonathan Binkley
Joshua Orvis
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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
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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
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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
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Journal of Computational Biology
Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation. 2013-11-07 Alexander van Oudenaarden
Wenqian Hu
Jiahai Shi
Harvey Lodish
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
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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
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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
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Anwesha Dey
Thomas Trimarchi
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Cem Kuscu
Todd Hricik
Delphine Ndiaye-Lobry
Lindsay M Lafave
Richard Koche
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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
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Genes, Brain and Behavior
Early T helper cell programming of gene expression in human 2013-11-15 Riitta Lahesmaa Soile Tuomela Seminars in Immunology
Resolving chromosome-centric human proteome with translating mRNA analysis: a strategic demonstration. 2013-11-15 Yizhi Cui
Qing-Yu He
Gong Zhang
Tong Wang
Jiayong Zhong
Jiahui Guo
Zhipeng Chen
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Journal of Proteome Research
Accuracy of allele frequency estimation using pooled RNA-Seq. 2013-11-16 Mateusz Konczal
Wieslaw Babik
Jacek Radwan
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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
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Ming Li
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Cancer Research
Expression of Porphyromonas gingivalis small RNA in response to hemin availability identified using microarray and RNA-seq analysis. 2013-11-19 Ann Progulske-Fox 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
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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
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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
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Proceedings of the National Academy of Sciences of the United States of America
Transcriptional regulation of two conceptus interferon tau genes expressed in Japanese black cattle during peri-implantation period. 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
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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
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Cell Host & Microbe
The transcription-splicing protein NonO/p54nrb and three NonO-interacting proteins bind to distal enhancer region and augment rhodopsin expression. 2013-12-02 Anand Swaroop
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
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Ivana Kurelac
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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
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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
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Martin Zwahlen
IngMarie Olsson
Sanjay Navani
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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
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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
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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
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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
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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
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Daniel Lawson
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Dana Nayduch
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Christopher Saski
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Virus Research
Combining DGE and RNA-sequencing data to identify new polyA+ non-coding transcripts in the human genome 2013-12-18 Eric Rivals Nicolas Philippe
Elias Bou Samra
Anthony Boureux
Alban Mancheron
Florence Rufflé
Qiang Bai
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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
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Filip C W Van Nieuwerburgh
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BMC Plant Biology
PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution 2013-12-20 Xianyun Mao
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Muredach P. Reilly
Yu Hu
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Cheng Jia
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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
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Gioele La Manno
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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
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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
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Nucleic Acids Research
Mycorrhizal phosphate uptake pathway in maize: vital for growth and cob development on nutrient poor agricultural and greenhouse soils. 2013-12-26 Jan Jansa Martin Willmann
Nina Gerlach
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Eva Koebke
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Frontiers in Plant Science
Nutritional impacts on gene expression in the surface mucosa of blue catfish (Ictalurus furcatus). 2013-12-28 Eric Peatman Chao Li
Benjamin H Beck
Developmental and Comparative Immunology
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
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Paula Reemann
Sten Ilmjärv
Orm Porosaar
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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
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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
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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
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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
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Christine Wasylyk
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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
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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
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Pramod Mudrakarta
Nico Görnitz
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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
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Allergy, Asthma & Clinical Immunology
Emerging RNA-Seq Applications in Food Science 2014 Alberto Valdés
Virginia García-Cañas
Carolina Simó
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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
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Cécile Neuvéglise
Can Wang
Linda M Holland
François Brunel
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PLOS Genetics
CellFinder: a cell data repository 2014-01 Stefanie Seltmann
Fritz Lekschas
Mariana Lara Neves
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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
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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
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B Hallström
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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
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BMC Bioinformatics
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. 2014-03-23 John L. Rinn Cole Trapnell
Davide Cacchiarelli
Jonna Grimsby
Prapti Pokharel
Shuqiang Li
Michael Morse
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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
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Dan Huang
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Jielin Sun
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BioMed Research International
De novo transcriptome analysis of Hevea brasiliensis tissues by RNA-seq and screening for molecular markers 2014-03-26 Luiz Gonzaga Paula de Almeida
Dominique Garcia
Daniel Guariz Pinheiro
Antonio Figueira
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Marisa Fabiana Nicolás
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Milena Magalhães
Alexandra Lehmkuhl Gerber
Júlio Cézar de Mattos Cascardo
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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
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Sachi Ishikawa-Kato
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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
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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
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Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics
HDAC-regulated myomiRs control BAF60 variant exchange and direct the functional phenotype of fibro-adipogenic progenitors in dystrophic muscles. 2014-03-28 Janet Rossant
Gianmaria Frigè
Lorenzo Giordani
Alberto Termanini
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Iros Barozzi
Martina Sandoná
Tammy Ryan
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Luca Madaro
Pasquale Fasanaro
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Mark Mercola
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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
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Developmental Biology
Small regulatory RNAs in Archaea. 2014-03-31 L Randau
Jörg Soppa
Julia Babski
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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
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Leukemia
Odorant and gustatory receptors in the tsetse fly Glossina morsitans morsitans 2014-04 Daniel K. Masiga
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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
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Bioinformatics
RNA sequencing and proteogenomics reveal the importance of leaderless mRNAs in the radiation-tolerant bacterium Deinococcus deserti. 2014-04-01 Arjan de Groot
Laurence Blanchard
David Vallenet
David Pignol
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David Roche
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Genome Biology and Evolution
Genome-wide transcriptomic responses of the seagrasses Zostera marina and Nanozostera noltii under a simulated heatwave confirm functional types. 2014-04-03 Erich Bornberg-Bauer
Susanne U Franssen
Jenny Gu
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Marine Genomics
LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq. 2014-04-07 Daniel C. Jeffares
Graeme C Smith
Charalampos Rallis
Jürg Bähler
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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
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PLOS ONE
Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-Seq and ESTs. 2014-04-10 Gordon G Simpson
Nicholas Schurch
Christian Cole
Sara J Brown
Geoffrey J. Barton
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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
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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
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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
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Shihui Yang
Andrew Bowersox
Igor Bogorad
Wei Wang
Melvin P Tucker
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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
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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
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Giovanni Blandino
Maurizio Fanciulli
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The Journal of Steroid Biochemistry and Molecular Biology
Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans. 2014-04-14 Gavin Sherlock
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
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Transcriptome profiling to identify genes involved in pathogenicity of Valsa mali on apple tree. 2014-04-16 Zhiyuan Yin Xiwang Ke
Na Song
Qingqing Dai
Ralf T Voegele
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Haiying Wang
Xiaoning Gao
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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
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James Fraser
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Kaustuv Sanyal
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Steven Jones
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Caroline Proux
Vikas Yadav
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Damien Paulet
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Nandita Mullapudi
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François Brunel
Weidong Chen
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Jean-Yves Coppée
Anna Floyd-Averette
Claude Gaillardin
Kimberly J Gerik
Jonathan Goldberg
Sara Gonzalez-Hilarion
Sharvari Gujja
Joyce L Hamlin
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Lukasz Kozubowski
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Marco Marra
Larry D Mesner
Frédérique Moyrand
Kirsten Nielsen
Jacqueline E Schein
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Carolin Wollschlaeger
Ian A Wood
Qiandong Zeng
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John R Perfect
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PLOS Genetics
IKKα restoration via EZH2 suppression induces nasopharyngeal carcinoma differentiation. 2014-04-17 Eric W-F Lam Min Yan
Yan Zhang
Bin He
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Zi-feng Wang
Fei-meng Zheng
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Yu-liang Zhu
Hai-jun Wen
Xiang-bo Wan
Cai-feng Yue
Na Yang
Wei Zhang
Jia-liang Zhang
Jing Wang
Yang Wang
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Nature Communications
Colorectal cancer cell lines are representative models of the main molecular subtypes of primary cancer. 2014-04-22 Diego Arango
Walter Bodmer
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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
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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
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Joshua B Benoit
Xin Zhao
Amy F Savage
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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
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Tyler B Krause
Jana Bohova
Peter Takáč
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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
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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
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Jiaren Zhang
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Ruijia Wang
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Biochimica et Biophysica Acta
An improved genome release (version Mt4.0) for the model legume Medicago truncatula. 2014-04-27 Haibao Tang
Vivek Krishnakumar
Laurent Gentzbittel
Kevin L. Childs
Shelby Bidwell
Benjamin Rosen
Agnes Chan
Shiguo Zhou
Mark Yandell
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Klaus F X Mayer
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BMC Genomics
Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival. 2014-04-29 Spencer D. Martin
Brad H Nelson
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Genome Research
Microfluidic single-cell whole-transcriptome sequencing. 2014-04-29 Liang Zhao
Yanyi Huang
Aaron M Streets
Xiannian Zhang
Chen Cao
Yuhong Pang
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Lu Yang
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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
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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
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Thomas A McMurrough
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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
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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
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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
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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
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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
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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
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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
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Current Biology
Oak root response to ectomycorrhizal symbiosis establishment: RNA-Seq derived transcript identification and expression profiling 2014-05-23 Bruno M Vieira
Octávio S. Paulo
Filipa Monteiro
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
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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
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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
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Chiara Migliore
Sabrina Carrella
Raffaella Avellino
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Nucleic Acids Research
RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri. 2014-06-06 Nicholas Thomson Marta Vergara-Irigaray
Maria C Fookes
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BMC Genomics
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
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Schraga Schwartz
Raktima Raychowdhury
Alex K. Shalek
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Dave Gennert
Diana Lu
Peilin Chen
Rona S Gertner
Jellert T Gaublomme
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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
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Christopher P Wardell
Brian A. Walker
Alexander Murison
Lauren I Aronson
Sarah J Hanrahan
Jacqueline H L Fok
Martin F Kaiser
Faith E Davies
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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
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Jennifer Tisoncik-Go
Gary P Schroth
Fernando Pardo Manuel de Villena
Mark T Heise
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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
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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
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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
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Nucleic Acids Research
Differential gene expression in the respiratory tree of the sea cucumber Apostichopus japonicus during aestivation. 2014-07-16 Kenneth B. Storey Ye Zhao
Hongsheng Yang
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
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Allergy
Genome-wide characterization of light-regulated genes in Neurospora crassa. 2014-07-21 Jeremy Zucker
Erin Bredeweg
Matthew S. Sachs
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
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Proceedings of the National Academy of Sciences of the United States of America
Differential expression of endogenous plant cell wall degrading enzyme genes in the stick insect (Phasmatodea) midgut. 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
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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
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Pascal W T C Jansen
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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
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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
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Proceedings of the National Academy of Sciences of the United States of America
GeneFriends: a human RNA-seq-based gene and transcript co-expression database 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
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Sharon E Plon
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Dolores López-Terrada
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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
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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
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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
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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
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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
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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
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BMC Genomics
Identification of a candidate prognostic gene signature by transcriptome analysis of matched pre- and post-treatment prostatic biopsies from patients with advanced prostate cancer. 2014-12-18 Chris Ponting
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
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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
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S W Walsh
C J Creevey
B Earley
S Keady
D A Kenny
D Matthews
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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
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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
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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
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Frontiers in Immunology
Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. 2015-02-12 Je Hyuk Lee
George M. Church
Evan R Daugharthy
Jonathan Scheiman
Reza Kalhor
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Richard Terry
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Joyce L Yang
Ho Suk Lee
John Aach
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Nature Protocols
The herbicide linuron inhibits cholesterol biosynthesis and induces cellular stress responses in brown trout. 2015-02-12 Eduarda M. Santos
Tamsyn M Uren Webster
Mandy H Perry Environmental Science & Technology
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
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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
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Jukka Kanerva
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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
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Glia
Molecular characterization and transcriptome analysis of orange head Chinese cabbage (Brassica rapa L. ssp. pekinensis). 2015-02-17 Barry J Pogson Junxiang Zhang
Hui Yuan
Zhangjun Fei
Lugang Zhang
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Planta
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads 2015-02-18 Steven Salzberg
Mihaela Pertea
Geo M Pertea
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
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BMC Genomics
Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. 2015-02-19 Sten Linnarsson
Peter Lönnerberg
Jens Hjerling-Leffler
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
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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
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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
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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
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Kenian Chen
Jia Qian Wu
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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
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Guy Wissotsky
Ayala Meir
Joseph Burger
Yaakov Tadmor
Arthur Schaffer
Zhangjun Fei
James Giovannoni
Efraim Lewinsohn
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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
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PLOS ONE
Activation of an endogenous retrovirus-associated long non-coding RNA in human adenocarcinoma. 2015-03-05 Gregg B Morin Ewan A Gibb
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
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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
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Gethin Thomas
Tim R Mercer
Katelin R Haynes
Marion E Brunck
Kim-Anh Lê Cao
Wendy Y Chen
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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
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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
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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
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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
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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
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Frederick Lang
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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
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Angela C Court
Daniel J Goff
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Ifat Geron
Russell Wall
Richard A Moore
Minya Pu
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Amy Jackson-Fisher
Michael Munchhof
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Sheldon R Morris
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Karen Messer
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Journal of Translational Medicine
Alternative polyadenylation allows differential negative feedback of human miRNA miR-579 on its host gene ZFR. 2015-03-23 Ludwig Christian Hinske
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
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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
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Takao Yokota
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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
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BMC Genomics
Discovery of molecular markers to discriminate corneal endothelial cells in the human body. 2015-03-25 Masahito Yoshihara
Hideya Kawaji
Masayoshi Itoh
Kohji Nishida
Yoshihide Hayashizaki
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
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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
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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
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Laura Lewis-Tuffin
Jennifer M Kachergus
Xochiquetzal J Geiger
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Daniel J O'Shannessy
Julia D Maltzman
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PLOS ONE
Functional characterization of BC039389-GATM and KLK4-KRSP1 chimeric read-through transcripts which are up-regulated in renal cell cancer 2015-03-27 Mark Rubin Dorothee Pflueger
Christiane Mittmann
Silvia Dehler
Holger Moch
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BMC Genomics
BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis. 2015-03-28 Yang Pan Quan Wan
Hayley Dingerdissen
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The Listeria monocytogenes strain 10403S BioCyc database. 2015-03-28 Teresa M Bergholz
Kathryn J Boor
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Linear mRNA amplification approach for RNAseq from limited amount of RNA. 2015-03-28 Maria A Nagai
Dirce Carraro
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Elisa Napolitano Ferreira
Gustavo de Campos Molina
Renato David Puga
Antônio Hugo José Froes Marques Campos
Gustavo Cardoso Guimarães
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UV irradiation responses in Giardia intestinalis. 2015-03-28 Karin Troell
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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
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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
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Massimo Iorizzo
Filippo Tatino
Luciano Xumerle
Carla Avanzato
Alberto Ferrarini
Massimo Delledonne
Luigi Frusciante
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The Plant Cell
Methyl-CpG Binding Protein 2 Regulates Microglia and Macrophage Gene Expression in Response to Inflammatory Stimuli. 2015-04-01 Jonathan Kipnis
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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
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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
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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
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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
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Genes & Development
Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum. 2015-04-06 Alexias Safi
Gregory E Crawford
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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
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Bart Bryant
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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
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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
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Molecular Genetics and Genomics
Purification and Transcriptomic Analysis of Mouse Fetal Leydig Cells Reveals Candidate Genes for Specification of Gonadal Steroidogenic Cells. 2015-04-08 Alicia Oshlack
Josephine Bowles
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Biology of Reproduction
New basal cell carcinoma susceptibility loci. 2015-04-09 Laufey Tryggvadottir
Unnur Þorsteinsdóttir
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Nature Communications
New signaling pathways govern the host response to C. albicans infection in various niches. 2015-04-09 Jacques Ravel
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Genome Research
Allelic Imbalance Is a Prevalent and Tissue-Specific Feature of the Mouse Transcriptome. 2015-04-09 Bernhard Payer
David Colognori
Ruslan I Sadreyev
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Genetics
Decreased expression of endogenous feline leukemia virus in cat lymphomas: a case control study. 2015-04-10 Reinhard Ertl
Fritz Sedlazeck
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Milica Krunic
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BMC Veterinary Research
High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin. 2015-04-13 Kaia Achim
Daria Gavriouchkina
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Nature Biotechnology
Spatial reconstruction of single-cell gene expression data. 2015-04-13 Aviv Regev
Rahul Satija
Jeffrey A Farrell
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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
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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
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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
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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
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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
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Nezar A Radhwan
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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
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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
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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
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Thomas T Wang
Daniel J Treacy
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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
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Cristina Cotobal
François Bachand
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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
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Eran Meshorer
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Cell Reports
First description of small proteins encoded by spRNAs in Methanosarcina mazei strain Gö1. 2015-04-16 Ruth Schmitz-Streit
Dörte Becher
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Biochimie
PGTools: A Software Suite for Proteogenomic Data Analysis and Visualization. 2015-04-17 Sean M. Grimmond
Nicola J Waddell
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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
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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
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Michael Greenwood
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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
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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
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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
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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
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Amrith Rodrigues
Jennifer Tabita-Martinez
John S Millar
Marina Cuchel
Evanthia E Pashos
Ying Liu
Ruilan Yan
Wenli Yang
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Daniel VanDorn
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Mingyao Li
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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
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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
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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
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Timothy J Stasevich
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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
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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
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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
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Peadar Ó Gaora
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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
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Brian S White
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Justin Tibbitts
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Brian Wadugu
Eric J Duncavage
Theresa Okeyo-Owuor
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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
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Bibha Chaudhary
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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
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Biljana Dumevska
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Audrey Letourneau
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Virpi Tohonen
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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
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Baoli Hu
Giannicola Genovese
Piergiorgio Pettazzoni
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Shan Jiang
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Yue Wei
Hui Yang
Li Zhang
Sarah Gaddis
Ting Gong
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Timothy P Heffernan
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Cancer Cell
regionReport: Interactive reports for region-level and feature-level genomic analyses. 2015-05-01 Leonardo Collado-Torres
Andrew E Jaffe
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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
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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
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Chunxu Qu
Eric Larsen
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Chengcheng Liu
Tamara Chang
Mignon L Loh
Elizabeth A Raetz
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William L Carroll
Sima Jeha
William E Evans
Meenakshi Devidas
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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
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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
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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
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Albert Ferrer
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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
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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
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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
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Marie-Anne Debily
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Marianne Hütt-Cabezas
Katherine E Warren
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Hua Mao
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Matthew N Svalina
Nicholas Wang
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Eric H Raabe
Esther Hulleman
Paul T Spellman
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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
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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
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Barbara J Meyer
Nature
Dynamics of GATA1 binding and expression response in a GATA1-induced erythroid differentiation system 2015-06-01 Ross C Hardison
Christapher S Morrissey
Mitchell J Weiss
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Genomics Data
RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application. 2015-06-01 Matteo Pallocca
Anna Maria D'Erchia
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Mattia D'Antonio
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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
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The Plant Journal
Detecting disease genes of non-small lung cancer based on consistently differential interactions. 2015-06-01 Xiaoping Liu
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Cancer and Metastasis Reviews
Immune cell profiling to guide therapeutic decisions in rheumatic diseases 2015-06-02 Deepak A Rao
Soumya Raychaudhuri
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Nature Reviews Rheumatology
RNA-Seq analysis of isolated satellite cells in Prmt5 deficient mice. 2015-06-03 Carsten T Kuenne
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Genomics Data
CD24(+) cells fuel rapid tumor growth and display high metastatic capacity 2015-06-04 Derek LeRoith Ran Rostoker
Sagi Abelson
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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
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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
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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
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Gregory Vieira
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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
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Infection and Immunity
Infiltration of chitin by protein coacervates defines the squid beak mechanical gradient. 2015-06-08 Ali Miserez YerPeng Tan
Shawn Hoon
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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
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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
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PLOS ONE
Molecular characterization of two novel molecular chaperones in bacterial-challenged Apostichopus japonicus. 2015-06-10 Chenghua Li Haihong Wang
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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
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Frontiers in Microbiology
The Impact of Normalization Methods on RNA-Seq Data Analysis. 2015-06-15 Marek Figlerowicz J Zyprych-Walczak
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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
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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
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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
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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
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Russell L Reagan
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David Neale
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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
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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
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Matt Stata
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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
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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
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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
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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
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Lisa K Nolan
Chengping Lu
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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
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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
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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
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Biochemical and Biophysical Research Communications
Systematically evaluating interfaces for RNA-seq analysis from a life scientist perspective. 2015-06-23 Alicia Poplawski
Federico Marini
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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
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Kristo Nuutila
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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
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Richard G Grundy
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Davide Albanese
Martin Peifer
Jean Thierry-Mieg
Jun Wang
Zhiyu Peng
Jo Vandesompele
Wenqian Zhang
Ying Yu
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Jian Wang
Cesare Furlanello
Viswanath Devanarayan
Jie Cheng
Youping Deng
Barbara Hero
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Li Li
Simon M Lin
Yuri Nikolsky
André Oberthuer
Tao Qing
Zhenqiang Su
Ruth Volland
Charles Wang
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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
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Frank Berthold
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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
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Runxuan Zhang
Cristiane P G Calixto
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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
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Michael Greenwood
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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
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Eric Jonasch
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Chad J Creighton
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Russell R Broaddus
Pheroze Tamboli
Keith A Baggerly
Kenneth D Aldape
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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
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Björn M Hallström
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Fantom Consortium
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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
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Issei Imoto
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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
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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
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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
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Jiuhong Pang
Yung-Yu Huang
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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
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PLOS Biology
Computational assignment of cell-cycle stage from single-cell transcriptome data. 2015-07-01 Sarah Teichmann
Valentina Proserpio
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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
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RNA Biology
Gene and miRNA expression changes in squamous cell carcinoma of larynx and hypopharynx. 2015-07-01 Prachi Jain Jayalakshmi Nair
Udita Chandola
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Genes & Cancer
Positional RNA-Seq identifies candidate genes for phenotypic engineering of sexual traits. 2015-07-03 Peter Ladurner
Eugene Berezikov
Roberto Arbore
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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
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Leigh A Needleman
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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
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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
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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
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Montserrat Porta-De-La-Riva
David Aristizábal-Corrales
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Francisco Javier García-Rodríguez
Iris Ertl
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Transcriptomic profiling of gene expression and RNA processing during Leishmania major differentiation. 2015-07-06 Najib El-sayed Laura A L Dillon
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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
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Keith A Baggerly
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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
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Molecular Oral Microbiology
Tungsten-induced carcinogenesis in human bronchial epithelial cells. 2015-07-08 Steven Shen
Maria Antonietta Zoroddu
Massimiliano Peana
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Jason Brocato
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Thomas Kluz
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Serenella Medici
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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
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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
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Xixia Chu
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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
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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
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Amol Shetty
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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
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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
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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
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Tissue Barriers
Leveraging transcript quantification for fast computation of alternative splicing profiles. 2015-07-15 Eduardo Eyras Gael P Alamancos
Amadís Pagès
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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
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Nucleic Acids Research
Widespread Inducible Transcription Downstream of Human Genes. 2015-07-16 Joan A. Steitz Anna Vilborg
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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
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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
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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
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Taina Rantanen
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Diego Vozzi
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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
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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
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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
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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
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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