TopHat: discovering splice junctions with RNA-Seq

Bioinformatics
Cole TrapnellSteven L Salzberg

Abstract

A new protocol for sequencing the messenger RNA in a cell, known as RNA-Seq, generates millions of short sequence fragments in a single run. These fragments, or 'reads', can be used to measure levels of gene expression and to identify novel splice variants of genes. However, current software for aligning RNA-Seq data to a genome relies on known splice junctions and cannot identify novel ones. TopHat is an efficient read-mapping algorithm designed to align reads from an RNA-Seq experiment to a reference genome without relying on known splice sites. We mapped the RNA-Seq reads from a recent mammalian RNA-Seq experiment and recovered more than 72% of the splice junctions reported by the annotation-based software from that study, along with nearly 20,000 previously unreported junctions. The TopHat pipeline is much faster than previous systems, mapping nearly 2.2 million reads per CPU hour, which is sufficient to process an entire RNA-Seq experiment in less than a day on a standard desktop computer. We describe several challenges unique to ab initio splice site discovery from RNA-Seq reads that will require further algorithm development. TopHat is free, open-source software available from http://tophat.cbcb.umd.edu. Supplementary da...Continue Reading

References

Nov 12, 1996·Proceedings of the National Academy of Sciences of the United States of America·N MorinagaM Vaughan
Apr 5, 2002·Genome Research·W James Kent
Feb 25, 2005·Bioinformatics·Thomas D Wu, Colin K Watanabe
Mar 25, 2006·BMC Bioinformatics·Vincent Le TexierThangavel Alphonse Thanaraj
Oct 31, 2006·Trends in Genetics : TIG·Uberto PozzoliManuela Sironi
Jan 11, 2008·BMC Bioinformatics·Andreas DöringKnut Reinert
Jan 22, 2008·Nature Methods·LaDeana W HillierElaine R Mardis
Mar 20, 2008·Genome Research·Daniel R Zerbino, Ewan Birney
Jun 3, 2008·Nature Methods·Ali MortazaviBarbara Wold
Jun 3, 2008·Nature Methods·Nicole CloonanSean M Grimmond
Aug 12, 2008·Bioinformatics·Fabio De BonaGunnar Rätsch
Nov 4, 2008·Nature·Eric T WangChristopher B Burge
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg

Citations

Oct 28, 2009·Cellular and Molecular Life Sciences : CMLS·Samuel Marguerat, Jürg Bähler
Mar 7, 2013·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Hiroshi MizunoTakashi Matsumoto
Nov 17, 2011·Applied Microbiology and Biotechnology·Tiezheng YuanBin Yao
Apr 28, 2012·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Monika S KowalczykDouglas R Higgs
Nov 10, 2013·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Meenakshi RoyRobert Wayne
Feb 22, 2012·Molecular Genetics and Genomics : MGG·Martin R JonesAnn M Rose
Nov 12, 2013·Breast Cancer Research and Treatment·Johanna TuomelaKatri S Selander
Jun 21, 2013·Plant Molecular Biology·Lu WangYuepeng Han
Oct 10, 2013·Plant Molecular Biology·Ting ZhangZhikang Li
Dec 25, 2012·Journal of Molecular Neuroscience : MN·Tomas KavanaghMichael Janitz
Mar 14, 2013·Trends in Plant Science·Marcel C Van VerkSaskia C M Van Wees
Mar 24, 2012·Animal : an International Journal of Animal Bioscience·D P BerryC J Creevey
Nov 23, 2011·Journal of Proteome Research·Xiaojing WangBing Zhang
Dec 21, 2012·Journal of Proteome Research·Zohreh JangraviGhasem Hosseini Salekdeh
Aug 24, 2013·Journal of Proteome Research·Katarzyna CiesielskaBart Devreese
Mar 22, 2012·Molecular Therapy : the Journal of the American Society of Gene Therapy·Lijun WangHuating Wang
Oct 21, 2011·Nature·David BrawandHenrik Kaessmann
May 31, 2013·Nature·Philip J SpenceJean Langhorne
May 17, 2011·Nature Biotechnology·M G GrabherrAviv Regev
Nov 15, 2011·Nature Biotechnology·Tim R MercerJohn L Rinn
May 15, 2012·Nature Biotechnology·Jeffrey L BennetzenKatrien M Devos
May 12, 2009·Nature Biotechnology·Cole Trapnell, Steven L Salzberg
May 12, 2010·Nature Biotechnology·Brian Haas, Michael C Zody
Oct 11, 2012·Nature Communications·Zhiwei ZhuZongbao K Zhao
Dec 29, 2012·Nature Communications·Qixiang ZhangJun Wang
Feb 7, 2013·Nature Communications·Yu FanYong-Gang Yao
Jan 31, 2013·Nature Communications·Aiping ZhengPing Li
Jun 14, 2013·Nature Communications·Haiyun GanFuchou Tang
Aug 13, 2013·Nature Communications·Hidetoshi SazeTetsuji Kakutani
Sep 28, 2013·Nature Communications·Sudhir ThakurelaVijay K Tiwari
Nov 22, 2013·Nature Communications·Tao MaLiu Jianquan
Jul 4, 2012·Nature Genetics·Qiang QiuJianquan Liu
Nov 28, 2012·Nature Genetics·Qiang XuYijun Ruan
Dec 12, 2012·Nature Genetics·Rocco PiazzaCarlo Gambacorti-Passerini
Jul 23, 2013·Nature Genetics·Jacob L MuellerDavid C Page
Nov 26, 2013·Nature Genetics·Hyung-Soon YimJung-Hyun Lee
Nov 3, 2010·Nature Genetics·Pinghua LiThomas P Brutnell
Jul 19, 2011·Nature Genetics·Cornelis A AlbersWillem H Ouwehand
Sep 10, 2013·Nature Immunology·Hilde SchjervenStephen T Smale
Apr 3, 2012·Nature Medicine·Wei GuoMichael Gotthardt
Jan 8, 2013·Nature Medicine·Leilei ChenXin-Yuan Guan
Nov 3, 2009·Nature Methods·Shirley PepkeAli Mortazavi
Jun 15, 2010·Nature Methods·Charles PlessyPiero Carninci
Sep 14, 2010·Nature Methods·Malachi GriffithMarco A Marra
Oct 12, 2010·Nature Methods·Gordon Robertsonİnanç Birol
Nov 9, 2010·Nature Methods·Yarden KatzChristopher B Burge
May 31, 2011·Nature Methods·Manuel GarberCole Trapnell
May 21, 2013·Nature Methods·Xian AdiconisJoshua Z Levin
Oct 22, 2013·Nature Methods·Angela R WuStephen R Quake
Nov 5, 2013·Nature Methods·Tamara SteijgerPaul Bertone
Nov 5, 2013·Nature Methods·Pär G EngströmRGASP Consortium
Nov 26, 2013·Nature Methods·Rui ZhangJin Billy Li
Sep 18, 2012·Nature Neuroscience·Brian R HerbAndrew P Feinberg
Feb 6, 2010·Nature Protocols·Brian T WilhelmJürg Bähler
Dec 31, 2010·Nature Reviews. Genetics·Fatih Ozsolak, Patrice M Milos
Nov 30, 2011·Nature Reviews. Genetics·Todd J Treangen, Steven L Salzberg
Apr 19, 2013·Nature Reviews. Genetics·Bonnie BergerMona Singh
Jan 25, 2011·Nature Structural & Molecular Biology·Brad R RosenbergF Nina Papavasiliou
Dec 6, 2011·Nature Structural & Molecular Biology·Eda YildirimJeannie T Lee
Jun 19, 2012·Nature Structural & Molecular Biology·Allison J TaggartWilliam G Fairbrother
Feb 5, 2013·Nature Structural & Molecular Biology·Benjamin HerquelIrwin Davidson
Feb 8, 2011·Integrative Biology : Quantitative Biosciences From Nano to Macro·Karin S KassahnSean M Grimmond
Sep 9, 2010·Proceedings of the National Academy of Sciences of the United States of America·Philip A WatsonCharles L Sawyers
Mar 15, 2012·Proceedings of the National Academy of Sciences of the United States of America·Ronnie de JongeBart P H J Thomma
May 10, 2012·Proceedings of the National Academy of Sciences of the United States of America·Hooman K MoghadamJudith E Mank
Jul 11, 2012·Proceedings of the National Academy of Sciences of the United States of America·Ramakrishna K ChodavarapuMatteo Pellegrini
Aug 21, 2012·Proceedings of the National Academy of Sciences of the United States of America·Qingqing LiuHarvey F Lodish
Apr 9, 2013·Proceedings of the National Academy of Sciences of the United States of America·Ruslan I SadreyevJeannie T Lee
Dec 1, 2012·Proceedings of the National Academy of Sciences of the United States of America·Nicholas M TeetsDavid L Denlinger
Jan 9, 2013·Proceedings of the National Academy of Sciences of the United States of America·Joseph RodriguezMichael Rosbash
Feb 6, 2013·Proceedings of the National Academy of Sciences of the United States of America·Alla A SigovaRichard A Young
Oct 17, 2013·Proceedings of the National Academy of Sciences of the United States of America·Stephen R PiccoloW Evan Johnson
May 23, 2013·Proceedings of the National Academy of Sciences of the United States of America·Stéphane HacquardEmiel Ver Loren van Themaat
Aug 13, 2013·Proceedings of the National Academy of Sciences of the United States of America·Ayla ErgunImmGen Consortium
Nov 28, 2013·Proceedings of the National Academy of Sciences of the United States of America·Kin Fai AuWing Hung Wong
Aug 17, 2011·The Journal of Biological Chemistry·Junko TomikawaTakuya Imamura
Jun 5, 2012·The Journal of Biological Chemistry·Emmanuel MoutierIrwin Davidson
Sep 26, 2012·The Journal of Biological Chemistry·Junko OkanoMaria I Morasso
Jun 12, 2012·Molecular & Cellular Proteomics : MCP·Christopher M RoseJoshua J Coon
Jul 10, 2012·Molecular & Cellular Proteomics : MCP·Jeremy D VolkeningMichael R Sussman
Dec 18, 2013·The Journal of Cell Biology·Congying WuJames E Bear
Apr 5, 2012·The Journal of Experimental Medicine·Bojan VilagosMeinrad Busslinger
Mar 10, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Jianxing FengTao Jiang
Sep 29, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Wei LiTao Jiang
Feb 4, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Thomas SakoparnigNiko Beerenwinkel
Jun 16, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Wenyuan LiXianghong Jasmine Zhou
Aug 22, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Steven N HartJean-Pierre Kocher
Jul 19, 2013·Genetic Testing and Molecular Biomarkers·Cheng ZhangShiwei Duan
Jun 19, 2012·Omics : a Journal of Integrative Biology·Dongyu ZhaoJun Yu
Sep 23, 2011·Molecular Biology of the Cell·Judith A SharpMichael D Blower
Feb 5, 2010·Briefings in Functional Genomics·Lin WangThomas P Brutnell
Mar 11, 2011·Briefings in Functional Genomics·Nicole C RoyWarren C McNabb
Dec 21, 2011·Briefings in Functional Genomics·Hong C LeeDavid Edwards
Dec 14, 2011·Briefings in Functional Genomics·Mukesh Jain
Oct 30, 2009·Briefings in Bioinformatics·David Stephen HornerGraziano Pesole
May 13, 2010·Briefings in Bioinformatics·Heng Li, Nils Homer
Jan 19, 2012·Briefings in Bioinformatics·Tim CarverJacqueline A McQuillan
Mar 27, 2012·Briefings in Bioinformatics·Iain MilneDavid Marshall
Jul 27, 2012·Briefings in Bioinformatics·Chang F QuoGil Alterovitz
Apr 2, 2013·Briefings in Bioinformatics·Benilton S Carvalho, Gabriella Rustici
Sep 29, 2009·Bioinformatics·Michael BrudnoFrancisco M De La Vega
Feb 12, 2010·Bioinformatics·Thomas D Wu, Serban Nacu
Apr 23, 2010·Bioinformatics·Douglas W BryantTodd C Mockler
Jun 26, 2010·Bioinformatics·Yin HuJinze Liu
Dec 15, 2010·Bioinformatics·Kana Shimizu, Koji Tsuda
Jan 15, 2011·Bioinformatics·Ângela GonçalvesMisha Kapushesky
Feb 19, 2011·Bioinformatics·Marcus KinsellaVineet Bafna
Mar 24, 2011·Bioinformatics·Ernesto PicardiGraziano Pesole
Jun 15, 2011·Bioinformatics·Ofer IsakovNoam Shomron
Jun 24, 2011·Bioinformatics·Adam RobertsLior Pachter
Nov 5, 2011·Bioinformatics·David LangenbergerJan Gorodkin
Jun 13, 2012·Bioinformatics·Thomas ConwayBryan Beresford-Smith
May 18, 2012·Bioinformatics·Jun HuKejun Liu
Jun 13, 2012·Bioinformatics·Chandana TennakoonWing-Kin Sung
Aug 24, 2012·Bioinformatics·Fernando García-AlcaldeAna Conesa
Sep 8, 2012·Bioinformatics·Robert C McLeayTimothy L Bailey
Oct 13, 2012·Bioinformatics·Nuno A FonsecaJohn C Marioni
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
Feb 23, 2013·Bioinformatics·Ning LengChristina Kendziorski
Mar 2, 2013·Bioinformatics·Moritz AschoffRainer König
Mar 16, 2013·Bioinformatics·Ergude BaoThomas Girke
Apr 17, 2013·Bioinformatics·Jia MengYufei Huang
Jun 22, 2013·Bioinformatics·Julie NocqBrian T Wilhelm
Jun 25, 2013·Bioinformatics·Ei-Wen YangTao Jiang
Sep 21, 2013·Bioinformatics·Adam B OlshenBarry S Taylor
Jun 5, 2013·Database : the Journal of Biological Databases and Curation·Charles A StewardJennifer Harrow
Jul 12, 2013·Database : the Journal of Biological Databases and Curation·Valerio BianchiManuela Helmer-Citterich
Sep 14, 2013·Database : the Journal of Biological Databases and Curation·Lei KongHong Qu
Oct 12, 2011·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Kil Hyun KimSuk-Ha Lee
May 10, 2013·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Hideki NagasakiYasukazu Nakamura
Oct 12, 2011·Genome Biology and Evolution·Vera B KaiserDoris Bachtrog
Mar 10, 2012·Genome Biology and Evolution·Robert S YoungChris P Ponting
Apr 19, 2012·Genome Biology and Evolution·Meng-Shin ShiaoWen-Hsiung Li
Nov 26, 2013·Genome Biology and Evolution·Raquel López-DíezBegoña Aguado
Oct 8, 2009·Human Molecular Genetics·Elaine R Mardis, Richard K Wilson
Nov 24, 2012·Human Molecular Genetics·Adrian G ToddElliot J Androphy
Apr 9, 2013·Human Molecular Genetics·Debarshi MustafiKrzysztof Palczewski
May 15, 2013·Human Molecular Genetics·Brooke E HjelmDavid W Craig
Mar 31, 2010·Molecular Biology and Evolution·Richard P MeiselStephen W Schaeffer
Feb 10, 2012·Molecular Biology and Evolution·R M GrazeLauren M McIntyre
Mar 22, 2013·Molecular Biology and Evolution·Patrick C BrunnerBruce A McDonald
Dec 9, 2009·Nucleic Acids Research·Jun-ichi TakedaSumio Sugano
Apr 8, 2010·Nucleic Acids Research·Kin Fai AuWing Hung Wong
Aug 31, 2010·Nucleic Acids Research·Kai WangJinze Liu
Feb 15, 2011·Nucleic Acids Research·Nan DengDongxiao Zhu
Dec 3, 2011·Nucleic Acids Research·Karine MegyVectorBase Consortium
Dec 6, 2011·Nucleic Acids Research·Philippe LameschEva Huala
Dec 6, 2011·Nucleic Acids Research·Li-Ming XuLiping Wei
Dec 27, 2011·Nucleic Acids Research·Leslie Y ChenLeroy Hood
Jul 9, 2011·Nucleic Acids Research·Muhammad A TariqNader Pourmand
Aug 2, 2011·Nucleic Acids Research·Weichun HuangLeping Li
Nov 30, 2012·Nucleic Acids Research·Sooyoung ChoSanghyuk Lee
Dec 22, 2012·Nucleic Acids Research·Chung-Chau HonNancy Guillen
Dec 27, 2012·Nucleic Acids Research·Touati BenoukrafRichie Soong
Dec 21, 2012·Nucleic Acids Research·Yang LiJian Ma
Jan 18, 2013·Nucleic Acids Research·Sílvia CarvalhoSérgio Fernandes de Almeida
Apr 13, 2012·Nucleic Acids Research·Chengyang WangX Shirley Liu
May 16, 2012·Nucleic Acids Research·Ravi Vijaya SatyaJaques Reifman
Aug 3, 2012·Nucleic Acids Research·Gilbert L HenrySean R Eddy
Aug 28, 2012·Nucleic Acids Research·Satish SatiShantanu Sengupta
Sep 4, 2012·Nucleic Acids Research·Jonatan HalvardsonLars Feuk
Sep 4, 2012·Nucleic Acids Research·Hui-wen LiuJeffrey D Parvin
Sep 12, 2012·Nucleic Acids Research·Shi-Jian ZhangChuan-Yun Li
Sep 12, 2012·Nucleic Acids Research·Line M NordstrandArne Klungland
Feb 15, 2013·Nucleic Acids Research·Richard Patryk Ngondo-MbongoPhilippe Carbon
Feb 15, 2013·Nucleic Acids Research·Danai FimereliTomasz Konopka
Apr 16, 2013·Nucleic Acids Research·Philipp DreweGunnar Rätsch
Apr 6, 2013·Nucleic Acids Research·Yang LiaoWei Shi
Apr 6, 2013·Nucleic Acids Research·Hai-Son LeZiv Bar-Joseph
Apr 11, 2013·Nucleic Acids Research·Jie WuChaolin Zhang
Sep 17, 2013·Nucleic Acids Research·Ralf SchmidDavid J Elliott
Jan 10, 2013·Plant & Cell Physiology·Michał Wojciech SzcześniakIzabela Makałowska
Mar 16, 2013·Plant & Cell Physiology·Alex Van MoerkerckeAlain Goossens
Apr 20, 2012·Proceedings. Biological Sciences·Sandy J MacdonaldAngela E Douglas
Dec 14, 2011·Genes & Development·Yevgenia L KhodorMichael Rosbash
Feb 4, 2012·Genes & Development·Markus KretzPaul A Khavari
May 3, 2012·Genes & Development·Jung-Shin LeeAli Shilatifard
Jun 21, 2012·Genes & Development·Darwin S Dichmann, Richard M Harland
Sep 14, 2012·Genes & Development·Jason DolesWilliam M Keyes
Jul 23, 2013·Genes & Development·Wei-Yi ChenRobert G Roeder
Dec 17, 2009·Genome Research·Ran BlekhmanYoav Gilad
Dec 24, 2010·Genome Research·Roger A HoskinsSusan E Celniker
May 4, 2011·Genome Research·Jonathan M ToungVivian G Cheung
Aug 6, 2011·Genome Research·Lichun JiangBrian Oliver
Sep 10, 2011·Genome Research·Sonia TarazonaAna Conesa
Nov 24, 2011·Genome Research·Wenli ZhangJiming Jiang
Apr 14, 2012·Genome Research·Roberto FerrariSiavash K Kurdistani
Nov 24, 2011·Genome Research·Andrea PauliAlexander F Schier
Jun 23, 2012·Genome Research·Simon AndersWolfgang Huber
Sep 8, 2012·Genome Research·Cédric HowaldAlexandre Reymond
Jul 28, 2012·Genome Research·Michael R TallackAndrew C Perkins
Jun 23, 2012·Genome Research·Igor UlitskyDavid P Bartel
Jun 19, 2012·Genome Research·Jin-Wu Nam, David P Bartel
Dec 4, 2012·Genome Research·Aziz M MezliniMichael Brudno
Jun 21, 2013·Genome Research·Timothy Sterne-WeilerJeremy R Sanford
May 21, 2013·Genome Research·Ronnie de JongeBart P H J Thomma
May 25, 2013·Genome Research·Laura E DeMareJames P Noonan
Aug 31, 2013·Genome Research·Ioanna FloutsakouBrian McStay
Aug 26, 2010·Plant Physiology·Pudota B BhaskarJiming Jiang
Feb 10, 2012·Plant Physiology·Gregory A PeifferRandy C Shoemaker
Jul 24, 2012·The Plant Cell·Kengo MorohashiErich Grotewold
Mar 7, 2013·The Plant Cell·Irina MakarevitchNathan M Springer
Nov 2, 2013·The Plant Cell·Anireddy Sn ReddyAndrea Barta
Dec 14, 2011·Neuropathology : Official Journal of the Japanese Society of Neuropathology·Jessica K LerchVance P Lemmon
Dec 22, 2012·Science·Jason MerkinChristopher B Burge
Dec 22, 2012·Science·Nuno L Barbosa-MoraisBenjamin J Blencowe
Oct 19, 2013·Science·Maya KasowskiMichael Snyder
Aug 31, 2012·Science Translational Medicine·Max JanRavindra Majeti
Aug 4, 2012·Eukaryotic Cell·Shailesh KumarKaliannan Ganesan
Oct 30, 2012·Eukaryotic Cell·Martijn Staats, Jan A L van Kan
Sep 7, 2013·Genome Announcements·Paula M MoolhuijzenDonald M Gardiner
Nov 16, 2012·Journal of Virology·Zhen LinErik K Flemington
Oct 18, 2012·MBio·Mohan BolisettyKaren Beemon
Apr 11, 2013·MBio·Jigar V DesaiAaron P Mitchell
Aug 2, 2012·Molecular and Cellular Biology·Jan RynesMirka Uhlirova
Oct 31, 2012·Molecular and Cellular Biology·Justine T Tigno-AranjuezDerek W Abbott
Jun 19, 2013·Molecular and Cellular Biology·Prashanth Kumar BajpeSidong Huang
Feb 23, 2012·Molecular and Cellular Biology·Kimberly A DittmarRussell P Carstens
Feb 23, 2013·Physiological Genomics·Richard H ChappleJeremy F Taylor
Jan 19, 2012·Molecular Cancer Research : MCR·Katherine B ChiappinelliPaul J Goodfellow
Jun 4, 2011·Cancer Prevention Research·Jennifer BeaneAvrum Spira
Feb 7, 2013·Cancer Discovery·Vishal KothariChandan Kumar-Sinha
Apr 5, 2012·Circulation. Cardiovascular Genetics·Jeffrey HsuJonathan D Smith
Oct 30, 2010·Circulation Research·Scot J MatkovichGerald W Dorn
Oct 25, 2012·The Journal of Clinical Investigation·Marie van DijkCees B M Oudejans
May 27, 2011·BMC Bioinformatics·Anna Leśniewska, Michał J Okoniewski
Jul 21, 2011·BMC Bioinformatics·Wei ZhengHongyu Zhao
Mar 5, 2011·BMC Bioinformatics·Sung-Chou LiWen-Chang Lin
Dec 23, 2011·BMC Bioinformatics·Aleksandra A Markovets, Damir Herman
Nov 15, 2012·BMC Bioinformatics·Brendan A VeenemanArul M Chinnaiyan
Jan 18, 2013·BMC Bioinformatics·Guoshuai CaiShoudan Liang
May 2, 2012·BMC Bioinformatics·Thomas BonfertCaroline C Friedel
Mar 28, 2013·BMC Bioinformatics·Lisa ChungHongyu Zhao
Apr 6, 2013·BMC Bioinformatics·Shaojun Tang, Alberto Riva
Jan 31, 2013·BMC Bioinformatics·Ellis PatrickYee Hwa Yang
Jun 14, 2013·BMC Bioinformatics·Li Song, Liliana Florea
Nov 7, 2012·BMC Developmental Biology·Manabu OzawaPeter J Hansen
Apr 13, 2013·BMC Developmental Biology·María Galardi-CastillaLeandro Sastre
Dec 21, 2010·BMC Genomics·Wen Huang, Hasan Khatib
Apr 1, 2011·BMC Genomics·Jun WangGe Gao
Jun 8, 2011·BMC Genomics·Lauren M McIntyreSergey V Nuzhdin
Jan 22, 2011·BMC Genomics·Matthew BookerNorbert Perrimon
Nov 10, 2011·BMC Genomics·Anna Esteve-CodinaMiguel Pérez-Enciso
Sep 11, 2012·BMC Genomics·Jérôme MarietteChristophe Klopp
Jan 11, 2013·BMC Genomics·Hatice Gulcin OzerKun Huang
Mar 21, 2013·BMC Genomics·Brian J AbrahamKeji Zhao
Apr 30, 2013·BMC Genomics·Jean-Michel CarterCasper J Breuker
May 10, 2013·BMC Genomics·Chia-Chun YangChun-Chi Liu
Jan 19, 2013·BMC Genomics·Chad E NiederhuthJohn C Walker
Jun 14, 2013·BMC Genomics·Alessio ColantoniFabrizio Ferrè
Sep 11, 2013·BMC Genomics·Dechassa DuressaSteven J Klosterman
Sep 13, 2013·BMC Genomics·Yong LongZongbin Cui
Feb 5, 2013·BMC Genomics·Ahmad Yamin Abdul RahmanMaqsudul Alam
Nov 13, 2013·BMC Genomics·Traver HartDaniel R Salomon
Dec 18, 2013·BMC Genomics·Danielle G LemayJ Bruce German
Feb 15, 2013·Biological Procedures Online·Derek Shyr, Qi Liu
Jun 2, 2011·BMC Biology·John H Malone, Brian Oliver
Apr 21, 2011·Algorithms for Molecular Biology : AMB·Marius NicolaeAlex Zelikovsky
Nov 21, 2013·Algorithms for Molecular Biology : AMB·Sebastian Deorowicz, Szymon Grabowski
Jan 15, 2011·Source Code for Biology and Medicine·Guorong XuDongxiao Zhu
Oct 12, 2012·BMC Systems Biology·Chao DaiXianghong Jasmine Zhou
Feb 26, 2014·BMC Systems Biology·Jingde BuZhong Jin
Jun 8, 2012·Biotechnology for Biofuels·Jacob ValenzuelaMatthew W Fields
Feb 13, 2013·BMC Medical Genomics·Liran JuanYunlong Liu
Jan 8, 2013·BMC Research Notes·Eric S TorstensonChun Li
Nov 28, 2013·Epigenetics & Chromatin·Günter RaddatzFrank Lyko
Nov 28, 2012·Journal of Clinical Bioinformatics·Subhashini SrinivasanRaghunathan Srivatsan
Nov 7, 2012·Cell & Bioscience·Catherine Lee, Nobuaki Kikyo
Dec 25, 2012·Cell & Bioscience·Daniel P HeruthShui Qing Ye
Sep 11, 2012·Journal of Animal Science and Biotechnology·Yongsheng BaiJames Cavalcoli
Nov 26, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Dec 24, 2010·Genome Biology·Alicia OshlackMatthew D Young
Mar 20, 2010·Genome Biology·Adam AmeurUlf Gyllensten
Jul 6, 2010·Genome Biology·Elizabeth T CirulliCenter for HIV/AIDS Vaccine Immunology (CHAVI)
Jun 17, 2010·Genome Biology·Thomas HornMichael Boutros
Aug 13, 2010·Genome Biology·Ben LangmeadJeffrey T Leek
Mar 18, 2011·Genome Biology·Adam RobertsLior Pachter
Aug 13, 2011·Genome Biology·Daehwan Kim, Steven L Salzberg
Aug 19, 2011·Genome Biology·Thomas SandmannKerstin Bartscherer
Nov 2, 2012·Genome Biology·Yogesh SaletoreChristopher E Mason
Jun 19, 2012·Genome Biology·Christoffer NellåkerChris P Ponting
Mar 30, 2013·Genome Biology·Nicolas PhilippeEric Rivals
Jun 19, 2013·Genome Biology·Nicolas SierroNikolai V Ivanov
Jul 31, 2013·Genome Biology·Gretchen M EhrenkauferUpinder Singh
Sep 5, 2013·Genome Biology·Eduardo LeeSuzanna E Lewis
Jul 27, 2012·RNA·Claudia L KleinmanJacek Majewski
Jul 4, 2012·RNA·Jonathan B PreallGregory J Hannon
May 27, 2010·PLoS Biology·Harm van BakelTimothy R Hughes
Jul 19, 2011·PLoS Biology·Michael B ClarkJohn S Mattick
Jan 12, 2012·PLoS Biology·Robert K BradleyChristopher B Burge
Sep 11, 2013·PLoS Biology·Sulakshana P MukherjeeGourisankar Ghosh
Apr 13, 2012·PLoS Computational Biology·Onur SakaryaAsim S Siddiqui
Apr 5, 2013·PLoS Computational Biology·Oscar FranzénStaffan G Svärd
Jun 6, 2014·PLoS Computational Biology·Ondrej PodlahaFranziska Michor
Jun 13, 2014·PLoS Computational Biology·Shira RockowitzDeyou Zheng
Jul 25, 2014·PLoS Computational Biology·Rekin's JankyStein Aerts
Dec 15, 2010·PLoS Genetics·Joseph K PickrellJonathan K Pritchard
Jun 23, 2011·PLoS Genetics·Anatole GhazalpourAldons J Lusis
Jun 4, 2011·PLoS Genetics·Patrick Schorderet, Denis Duboule
Jul 31, 2012·PLoS Genetics·Claudia KutterAna C Marques