Ewan Birney

Ewan Birney

Joint Associate Director and Senior Scientist

Dr Birney is one of the founders of the Ensembl genome browser. Together with Dr Rolf Apweiler, he has strategic responsibility and oversight for bioinformatics services at EMBL-EBI. Dr Birney played a vital role in annotating the genome sequences of the human, mouse, chicken and several other organisms; this work has had a profound impact on our understanding of genomic biology. He led the analysis group for the ENCODE project, which is defining functional elements in the human genome. Ewan’s main areas of research include functional genomics, assembly algorithms, statistical methods to analyse genomic information (in particular information associated with individual differences) and compression of sequence information. He completed his PhD at the Wellcome Trust Sanger Institute with Richard Durbin, and worked in the laboratories of leading scientists Adrian Krainer, Toby Gibson and Iain Campbell. Ewan has received a number of prestigious awards including the 2003 Francis Crick Award from the Royal Society, the 2005 Overton Prize from the International Society for Computational Biology and the 2005 Benjamin Franklin Award for contributions in Open Source Bioinformatics.

ORCID iD: 0000-0001-8314-8497

Tel:+44 (0)1223 494 420 / Fax:+44 (0)1223 494 468

Research

Find out about research activity in the Birney research group

Birney projects

There are two teams involved in EBI Services that report directly to Ewan Birney. The Technology & Science Integration team focuses on exploring new technologies for service provision, in particular in the context of pan-European initiatives. The HUGO Gene Nomenclature Team is the global authority for assigning human gene names and the coordinator, Elspeth Bruford reports directly to Ewan Birney.

Publications

2014

Archaic humans: Four makes a party.
Birney E, Pritchard JK.
Nature Volume 505 (2014) p.32-34
DOI: 10.1038/nature12847

Defining functional DNA elements in the human genome.
Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC.
Proc Natl Acad Sci U S A Volume 111 (2014) p.6131-6138
DOI: 10.1073/pnas.1318948111

The European Bioinformatics Institute's data resources 2014.
Brooksbank C, Bergman MT, Apweiler R, Birney E, Thornton J.
Nucleic Acids Res Volume 42 (2014) p.d18-25
DOI: 10.1093/nar/gkt1206

The Reactome pathway knowledgebase.
Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, Caudy M, Garapati P, Gillespie M, Kamdar MR, Jassal B, Jupe S, Matthews L, May B, Palatnik S, Rothfels K, Shamovsky V, Song H, Williams M, Birney E, Hermjakob H, Stein L, D'Eustachio P.
Nucleic Acids Res Volume 42 (2014) p.d472-7
DOI: 10.1093/nar/gkt1102

Genomic and phenotypic characterization of a wild medaka population: towards the establishment of an isogenic population genetic resource in fish.
Spivakov M, Auer TO, Peravali R, Dunham I, Dolle D, Fujiyama A, Toyoda A, Aizu T, Minakuchi Y, Loosli F, Naruse K, Birney E, Wittbrodt J.
G3 (Bethesda) Volume 4 (2014) p.433-445
DOI: 10.1534/g3.113.008722

Integrative knowledge management to enhance pharmaceutical R&D.
Marti-Solano M, Birney E, Bril A, Della Pasqua O, Kitano H, Mons B, Xenarios I, Sanz F.
Nat Rev Drug Discov Volume 13 (2014) p.239-240
DOI: 10.1038/nrd4290

Ensembl 2014.
Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt S, Johnson N, Juettemann T, Kähäri AK, Keenan S, Kulesha E, Martin FJ, Maurel T, McLaren WM, Murphy DN, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, Riat HS, Ruffier M, Sheppard D, Taylor K, Thormann A, Trevanion SJ, Vullo A, Wilder SP, Wilson M, Zadissa A, Aken BL, Birney E, Cunningham F, Harrow J, Herrero J, Hubbard TJ, Kinsella R, Muffato M, Parker A, Spudich G, Yates A, Zerbino DR, Searle SM.
Nucleic Acids Res Volume 42 (2014) p.d749-55
DOI: 10.1093/nar/gkt1196

The EBI RDF platform: linked open data for the life sciences.
Jupp S, Malone J, Bolleman J, Brandizi M, Davies M, Garcia L, Gaulton A, Gehant S, Laibe C, Redaschi N, Wimalaratne SM, Martin M, Le Novère N, Parkinson H, Birney E, Jenkinson AM.
Bioinformatics Volume 30 (2014) p.1338-1339
DOI: 10.1093/bioinformatics/btt765

2013

Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium.
Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D, Birney E, Hung JH, Weng Z.
Nucleic Acids Res Volume 41 (2013) p.d171-6
DOI: 10.1093/nar/gks1221

Policy challenges of clinical genome sequencing.
Wright CF, Middleton A, Burton H, Cunningham F, Humphries SE, Hurst J, Birney E, Firth HV.
BMJ Volume 347 (2013) p.f6845
DOI: 10.1136/bmj.f6845

Ensembl 2013.
Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, García-Girón C, Gordon L, Hourlier T, Hunt S, Juettemann T, Kähäri AK, Keenan S, Komorowska M, Kulesha E, Longden I, Maurel T, McLaren WM, Muffato M, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, Riat HS, Ritchie GR, Ruffier M, Schuster M, Sheppard D, Sobral D, Taylor K, Thormann A, Trevanion S, White S, Wilder SP, Aken BL, Birney E, Cunningham F, Dunham I, Harrow J, Herrero J, Hubbard TJ, Johnson N, Kinsella R, Parker A, Spudich G, Yates A, Zadissa A, Searle SM.
Nucleic Acids Res Volume 41 (2013) p.d48-55
DOI: 10.1093/nar/gks1236

Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development.
Sanges R, Hadzhiev Y, Gueroult-Bellone M, Roure A, Ferg M, Meola N, Amore G, Basu S, Brown ER, De Simone M, Petrera F, Licastro D, Strähle U, Banfi S, Lemaire P, Birney E, Müller F, Stupka E.
Nucleic Acids Res Volume 41 (2013) p.3600-3618
DOI: 10.1093/nar/gkt030

Genome-wide meta-analysis identifies new susceptibility loci for migraine.
Anttila V, Winsvold BS, Gormley P, Kurth T, Bettella F, McMahon G, Kallela M, Malik R, de Vries B, Terwindt G, Medland SE, Todt U, McArdle WL, Quaye L, Koiranen M, Ikram MA, Lehtimäki T, Stam AH, Ligthart L, Wedenoja J, Dunham I, Neale BM, Palta P, Hamalainen E, Schürks M, Rose LM, Buring JE, Ridker PM, Steinberg S, Stefansson H, Jakobsson F, Lawlor DA, Evans DM, Ring SM, Färkkilä M, Artto V, Kaunisto MA, Freilinger T, Schoenen J, Frants RR, Pelzer N, Weller CM, Zielman R, Heath AC, Madden PA, Montgomery GW, Martin NG, Borck G, Göbel H, Heinze A, Heinze-Kuhn K, Williams FM, Hartikainen AL, Pouta A, van den Ende J, Uitterlinden AG, Hofman A, Amin N, Hottenga JJ, Vink JM, Heikkilä K, Alexander M, Muller-Myhsok B, Schreiber S, Meitinger T, Wichmann HE, Aromaa A, Eriksson JG, Traynor BJ, Trabzuni D, Rossin E, Lage K, Jacobs SB, Gibbs JR, Birney E, Kaprio J, Penninx BW, Boomsma DI, van Duijn C, Raitakari O, Jarvelin MR, Zwart JA, Cherkas L, Strachan DP, Kubisch C, Ferrari MD, van den Maagdenberg AM, Dichgans M, Wessman M, Smith GD, Stefansson K, Daly MJ, Nyholt DR, Chasman DI, Palotie A, North American Brain Expression Consortium, UK Brain Expression Consortium, International Headache Genetics Consortium.
Nat Genet Volume 45 (2013) p.912-917
DOI: 10.1038/ng.2676

Integrative annotation of chromatin elements from ENCODE data.
Hoffman MM, Ernst J, Wilder SP, Kundaje A, Harris RS, Libbrecht M, Giardine B, Ellenbogen PM, Bilmes JA, Birney E, Hardison RC, Dunham I, Kellis M, Noble WS.
Nucleic Acids Res Volume 41 (2013) p.827-841
DOI: 10.1093/nar/gks1284

Towards practical, high-capacity, low-maintenance information storage in synthesized DNA.
Goldman N, Bertone P, Chen S, Dessimoz C, LeProust EM, Sipos B, Birney E.
Nature Volume 494 (2013) p.77-80
DOI: 10.1038/nature11875

2012

VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics.
Megy K, Emrich SJ, Lawson D, Campbell D, Dialynas E, Hughes DS, Koscielny G, Louis C, Maccallum RM, Redmond SN, Sheehan A, Topalis P, Wilson D, VectorBase Consortium.
Nucleic Acids Res Volume 40 (2012) p.d729-34
DOI: 10.1093/nar/gkr1089

A transcription factor collective defines cardiac cell fate and reflects lineage history.
Junion G, Spivakov M, Girardot C, Braun M, Gustafson EH, Birney E, Furlong EE.
Cell Volume 148 (2012) p.473-486
DOI: 10.1016/j.cell.2012.01.030

Major submissions tool developments at the European Nucleotide Archive.
Amid C, Birney E, Bower L, Cerdeño-Tárraga A, Cheng Y, Cleland I, Faruque N, Gibson R, Goodgame N, Hunter C, Jang M, Leinonen R, Liu X, Oisel A, Pakseresht N, Plaister S, Radhakrishnan R, Reddy K, Rivière S, Rossello M, Senf A, Smirnov D, Ten Hoopen P, Vaughan D, Vaughan R, Zalunin V, Cochrane G.
Nucleic Acids Res Volume 40 (2012) p.d43-7
DOI: 10.1093/nar/gkr946

Ensembl 2012.
Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri AK, Keefe D, Keenan S, Kinsella R, Komorowska M, Koscielny G, Kulesha E, Larsson P, Longden I, McLaren W, Muffato M, Overduin B, Pignatelli M, Pritchard B, Riat HS, Ritchie GR, Ruffier M, Schuster M, Sobral D, Tang YA, Taylor K, Trevanion S, Vandrovcova J, White S, Wilson M, Wilder SP, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Harrow J, Herrero J, Hubbard TJ, Parker A, Proctor G, Spudich G, Vogel J, Yates A, Zadissa A, Searle SM.
Nucleic Acids Res Volume 40 (2012) p.d84-90
DOI: 10.1093/nar/gkr991

The future of DNA sequence archiving.
Cochrane G, Cook CE, Birney E.
Gigascience Volume 1 (2012) p.2
DOI: 10.1186/2047-217x-1-2

Understanding transcriptional regulation by integrative analysis of transcription factor binding data.
Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y, Davis CA, Carninci P, Lassman T, Gingeras TR, Guigó R, Birney E, Weng Z, Snyder M, Gerstein M.
Genome Res Volume 22 (2012) p.1658-1667
DOI: 10.1101/gr.136838.111

Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species.
Kersey PJ, Staines DM, Lawson D, Kulesha E, Derwent P, Humphrey JC, Hughes DS, Keenan S, Kerhornou A, Koscielny G, Langridge N, McDowall MD, Megy K, Maheswari U, Nuhn M, Paulini M, Pedro H, Toneva I, Wilson D, Yates A, Birney E.
Nucleic Acids Res Volume 40 (2012) p.d91-7
DOI: 10.1093/nar/gkr895

The making of ENCODE: Lessons for big-data projects.
Birney E.
Nature Volume 489 (2012) p.49-51
DOI: 10.1038/489049a

The genomic basis of adaptive evolution in threespine sticklebacks.
Jones FC, Grabherr MG, Chan YF, Russell P, Mauceli E, Johnson J, Swofford R, Pirun M, Zody MC, White S, Birney E, Searle S, Schmutz J, Grimwood J, Dickson MC, Myers RM, Miller CT, Summers BR, Knecht AK, Brady SD, Zhang H, Pollen AA, Howes T, Amemiya C, Broad Institute Genome Sequencing Platform & Whole Genome Assembly Team, Baldwin J, Bloom T, Jaffe DB, Nicol R, Wilkinson J, Lander ES, Di Palma F, Lindblad-Toh K, Kingsley DM.
Nature Volume 484 (2012) p.55-61
DOI: 10.1038/nature10944

Analysis of variation at transcription factor binding sites in Drosophila and humans.
Spivakov M, Akhtar J, Kheradpour P, Beal K, Girardot C, Koscielny G, Herrero J, Kellis M, Furlong EE, Birney E.
Genome Biol Volume 13 (2012) p.r49
DOI: 10.1186/gb-2012-13-9-r49

An integrated encyclopedia of DNA elements in the human genome.
ENCODE Project Consortium.
Nature Volume 489 (2012) p.57-74
DOI: 10.1038/nature11247

Paralogous annotation of disease-causing variants in long QT syndrome genes.
Ware JS, Walsh R, Cunningham F, Birney E, Cook SA.
Hum Mutat Volume 33 (2012) p.1188-1191
DOI: 10.1002/humu.22114

Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells.
Lee BK, Bhinge AA, Battenhouse A, McDaniell RM, Liu Z, Song L, Ni Y, Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR.
Genome Res Volume 22 (2012) p.9-24
DOI: 10.1101/gr.127597.111

Modeling gene expression using chromatin features in various cellular contexts.
Dong X, Greven MC, Kundaje A, Djebali S, Brown JB, Cheng C, Gingeras TR, Gerstein M, Guigó R, Birney E, Weng Z.
Genome Biol Volume 13 (2012) p.r53
DOI: 10.1186/gb-2012-13-9-r53

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels.
Schulz MH, Zerbino DR, Vingron M, Birney E.
Bioinformatics Volume 28 (2012) p.1086-1092
DOI: 10.1093/bioinformatics/bts094

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors.
Yip KY, Cheng C, Bhardwaj N, Brown JB, Leng J, Kundaje A, Rozowsky J, Birney E, Bickel P, Snyder M, Gerstein M.
Genome Biol Volume 13 (2012) p.r48
DOI: 10.1186/gb-2012-13-9-r48

Journey to the genetic interior. Interview by Stephen S Hall.
Birney E.
Sci Am Volume 307 (2012) p.80-2, 84

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors.
Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, Rando OJ, Birney E, Myers RM, Noble WS, Snyder M, Weng Z.
Genome Res Volume 22 (2012) p.1798-1812
DOI: 10.1101/gr.139105.112

2011

Assemblies: the good, the bad, the ugly.
Birney E.
Nat Methods Volume 8 (2011) p.59-60
DOI: 10.1038/nmeth0111-59

Ensembl 2011.
Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Larsson P, Longden I, McLaren W, Overduin B, Pritchard B, Riat HS, Rios D, Ritchie GR, Ruffier M, Schuster M, Sobral D, Spudich G, Tang YA, Trevanion S, Vandrovcova J, Vilella AJ, White S, Wilder SP, Zadissa A, Zamora J, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJ, Parker A, Proctor G, Vogel J, Searle SM.
Nucleic Acids Res Volume 39 (2011) p.d800-6
DOI: 10.1093/nar/gkq1064

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity.
Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, Sheffield NC, Gräf S, Huss M, Keefe D, Liu Z, London D, McDaniell RM, Shibata Y, Showers KA, Simon JM, Vales T, Wang T, Winter D, Zhang Z, Clarke ND, Birney E, Iyer VR, Crawford GE, Lieb JD, Furey TS.
Genome Res Volume 21 (2011) p.1757-1767
DOI: 10.1101/gr.121541.111

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.
Boyle AP, Song L, Lee BK, London D, Keefe D, Birney E, Iyer VR, Crawford GE, Furey TS.
Genome Res Volume 21 (2011) p.456-464
DOI: 10.1101/gr.112656.110

The European Nucleotide Archive.
Leinonen R, Akhtar R, Birney E, Bower L, Cerdeno-Tárraga A, Cheng Y, Cleland I, Faruque N, Goodgame N, Gibson R, Hoad G, Jang M, Pakseresht N, Plaister S, Radhakrishnan R, Reddy K, Sobhany S, Ten Hoopen P, Vaughan R, Zalunin V, Cochrane G.
Nucleic Acids Res Volume 39 (2011) p.d28-31
DOI: 10.1093/nar/gkq967

Mouse genomic variation and its effect on phenotypes and gene regulation.
Keane TM, Goodstadt L, Danecek P, White MA, Wong K, Yalcin B, Heger A, Agam A, Slater G, Goodson M, Furlotte NA, Eskin E, Nellåker C, Whitley H, Cleak J, Janowitz D, Hernandez-Pliego P, Edwards A, Belgard TG, Oliver PL, McIntyre RE, Bhomra A, Nicod J, Gan X, Yuan W, van der Weyden L, Steward CA, Bala S, Stalker J, Mott R, Durbin R, Jackson IJ, Czechanski A, Guerra-Assunção JA, Donahue LR, Reinholdt LG, Payseur BA, Ponting CP, Birney E, Flint J, Adams DJ.
Nature Volume 477 (2011) p.289-294
DOI: 10.1038/nature10413

RNAcentral: A vision for an international database of RNA sequences.
Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP, Gautheret D, Griffiths-Jones S, Harrow J, Herrero J, Holmes IH, Huang HD, Kelly KA, Kersey P, Kozomara A, Lowe TM, Marz M, Moxon S, Pruitt KD, Samuelsson T, Stadler PF, Vilella AJ, Vogel JH, Williams KP, Wright MW, Zwieb C.
RNA Volume 17 (2011) p.1941-1946
DOI: 10.1261/rna.2750811

Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses.
Vilella AJ, Birney E, Flicek P, Herrero J.
Genome Biol Volume 12 (2011) p.401
DOI: 10.1186/gb-2011-12-2-401

Chromatin and heritability: how epigenetic studies can complement genetic approaches.
Birney E.
Trends Genet Volume 27 (2011) p.172-176
DOI: 10.1016/j.tig.2011.02.005

Reactome: a database of reactions, pathways and biological processes.
Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, Matthews L, Caudy M, Garapati P, Gopinath G, Jassal B, Jupe S, Kalatskaya I, Mahajan S, May B, Ndegwa N, Schmidt E, Shamovsky V, Yung C, Birney E, Hermjakob H, D'Eustachio P, Stein L.
Nucleic Acids Res Volume 39 (2011) p.d691-7
DOI: 10.1093/nar/gkq1018

A user's guide to the encyclopedia of DNA elements (ENCODE).
ENCODE Project Consortium.
PLoS Biol Volume 9 (2011) p.e1001046
DOI: 10.1371/journal.pbio.1001046

A high-resolution map of human evolutionary constraint using 29 mammals.
Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC, Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA, Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK, Genome Institute at Washington University, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M.
Nature Volume 478 (2011) p.476-482
DOI: 10.1038/nature10530

Efficient storage of high throughput DNA sequencing data using reference-based compression.
Hsi-Yang Fritz M, Leinonen R, Cochrane G, Birney E.
Genome Res Volume 21 (2011) p.734-740
DOI: 10.1101/gr.114819.110

The variant call format and VCFtools.
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, 1000 Genomes Project Analysis Group.
Bioinformatics Volume 27 (2011) p.2156-2158
DOI: 10.1093/bioinformatics/btr330

2010

Ensembl variation resources.
Chen Y, Cunningham F, Rios D, McLaren WM, Smith J, Pritchard B, Spudich GM, Brent S, Kulesha E, Marin-Garcia P, Smedley D, Birney E, Flicek P.
BMC Genomics Volume 11 (2010) p.293
DOI: 10.1186/1471-2164-11-293

EMMA--mouse mutant resources for the international scientific community.
Wilkinson P, Sengerova J, Matteoni R, Chen CK, Soulat G, Ureta-Vidal A, Fessele S, Hagn M, Massimi M, Pickford K, Butler RH, Marschall S, Mallon AM, Pickard A, Raspa M, Scavizzi F, Fray M, Larrigaldie V, Leyritz J, Birney E, Tocchini-Valentini GP, Brown S, Herault Y, Montoliu L, de Angelis MH, Smedley D.
Nucleic Acids Res Volume 38 (2010) p.d570-6
DOI: 10.1093/nar/gkp799

The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance.
Atanur SS, Birol I, Guryev V, Hirst M, Hummel O, Morrissey C, Behmoaras J, Fernandez-Suarez XM, Johnson MD, McLaren WM, Patone G, Petretto E, Plessy C, Rockland KS, Rockland C, Saar K, Zhao Y, Carninci P, Flicek P, Kurtz T, Cuppen E, Pravenec M, Hubner N, Jones SJ, Birney E, Aitman TJ.
Genome Res Volume 20 (2010) p.791-803
DOI: 10.1101/gr.103499.109

A draft sequence of the Neandertal genome.
Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Z, Gusic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PL, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S.
Science Volume 328 (2010) p.710-722
DOI: 10.1126/science.1188021

A database and API for variation, dense genotyping and resequencing data.
Rios D, McLaren WM, Chen Y, Birney E, Stabenau A, Flicek P, Cunningham F.
BMC Bioinformatics Volume 11 (2010) p.238
DOI: 10.1186/1471-2105-11-238

The systematic annotation of the three main GPCR families in Reactome.
Jassal B, Jupe S, Caudy M, Birney E, Stein L, Hermjakob H, D'Eustachio P.
Database (Oxford) Volume 2010 (2010) p.baq018
DOI: 10.1093/database/baq018

Allele-specific and heritable chromatin signatures in humans.
Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR.
Hum Mol Genet Volume 19 (2010) p.r204-9
DOI: 10.1093/hmg/ddq404

A small-cell lung cancer genome with complex signatures of tobacco exposure.
Pleasance ED, Stephens PJ, O'Meara S, McBride DJ, Meynert A, Jones D, Lin ML, Beare D, Lau KW, Greenman C, Varela I, Nik-Zainal S, Davies HR, Ordoñez GR, Mudie LJ, Latimer C, Edkins S, Stebbings L, Chen L, Jia M, Leroy C, Marshall J, Menzies A, Butler A, Teague JW, Mangion J, Sun YA, McLaughlin SF, Peckham HE, Tsung EF, Costa GL, Lee CC, Minna JD, Gazdar A, Birney E, Rhodes MD, McKernan KJ, Stratton MR, Futreal PA, Campbell PJ.
Nature Volume 463 (2010) p.184-190
DOI: 10.1038/nature08629

A new strategy for genome assembly using short sequence reads and reduced representation libraries.
Young AL, Abaan HO, Zerbino D, Mullikin JC, Birney E, Margulies EH.
Genome Res Volume 20 (2010) p.249-256
DOI: 10.1101/gr.097956.109

The consequence of natural selection on genetic variation in the mouse.
Reuveni E, Birney E, Gross CT.
Genomics Volume 95 (2010) p.196-202
DOI: 10.1016/j.ygeno.2010.02.004

Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes, and mitochondria.
Gnad F, Forner F, Zielinska DF, Birney E, Gunawardena J, Mann M.
Mol Cell Proteomics Volume 9 (2010) p.2642-2653
DOI: 10.1074/mcp.m110.001594

An effective model for natural selection in promoters.
Hoffman MM, Birney E.
Genome Res Volume 20 (2010) p.685-692
DOI: 10.1101/gr.096719.109

Modeling Competition of Transcription Factors for DNA Binding Sites Improves Binding Site Predictions
Hestand MS, Hoffman MM, Birney E, van Ommen G-JB, den Dunnen JT, A.C. ’t Hoen P.
Volume (2010) p.45-62

Improvements to services at the European Nucleotide Archive.
Leinonen R, Akhtar R, Birney E, Bonfield J, Bower L, Corbett M, Cheng Y, Demiralp F, Faruque N, Goodgame N, Gibson R, Hoad G, Hunter C, Jang M, Leonard S, Lin Q, Lopez R, Maguire M, McWilliam H, Plaister S, Radhakrishnan R, Sobhany S, Slater G, Ten Hoopen P, Valentin F, Vaughan R, Zalunin V, Zerbino D, Cochrane G.
Nucleic Acids Res Volume 38 (2010) p.d39-45
DOI: 10.1093/nar/gkp998

An international bioinformatics infrastructure to underpin the Arabidopsis community.
International Arabidopsis Informatics Consortium.
Plant Cell Volume 22 (2010) p.2530-2536
DOI: 10.1105/tpc.110.078519

Heritable individual-specific and allele-specific chromatin signatures in humans.
McDaniell R, Lee BK, Song L, Liu Z, Boyle AP, Erdos MR, Scott LJ, Morken MA, Kucera KS, Battenhouse A, Keefe D, Collins FS, Willard HF, Lieb JD, Furey TS, Crawford GE, Iyer VR, Birney E.
Science Volume 328 (2010) p.235-239
DOI: 10.1126/science.1184655

Finding and sharing: new approaches to registries of databases and services for the biomedical sciences.
Smedley D, Schofield P, Chen CK, Aidinis V, Ainali C, Bard J, Balling R, Birney E, Blake A, Bongcam-Rudloff E, Brookes AJ, Cesareni G, Chandras C, Eppig J, Flicek P, Gkoutos G, Greenaway S, Gruenberger M, Hériché JK, Lyall A, Mallon AM, Muddyman D, Reisinger F, Ringwald M, Rosenthal N, Schughart K, Swertz M, Thorisson GA, Zouberakis M, Hancock JM.
Database (Oxford) Volume 2010 (2010) p.baq014
DOI: 10.1093/database/baq014

Locus Reference Genomic sequences: an improved basis for describing human DNA variants.
Dalgleish R, Flicek P, Cunningham F, Astashyn A, Tully RE, Proctor G, Chen Y, McLaren WM, Larsson P, Vaughan BW, Béroud C, Dobson G, Lehväslaiho H, Taschner PE, den Dunnen JT, Devereau A, Birney E, Brookes AJ, Maglott DR.
Genome Med Volume 2 (2010) p.24
DOI: 10.1186/gm145

Genomic information infrastructure after the deluge.
Parkhill J, Birney E, Kersey P.
Genome Biol Volume 11 (2010) p.402
DOI: 10.1186/gb-2010-11-7-402

Ensembl's 10th year.
Flicek P, Aken BL, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Gräf S, Haider S, Hammond M, Howe K, Jenkinson A, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Koscielny G, Kulesha E, Lawson D, Longden I, Massingham T, McLaren W, Megy K, Overduin B, Pritchard B, Rios D, Ruffier M, Schuster M, Slater G, Smedley D, Spudich G, Tang YA, Trevanion S, Vilella A, Vogel J, White S, Wilder SP, Zadissa A, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJ, Parker A, Proctor G, Smith J, Searle SM.
Nucleic Acids Res Volume 38 (2010) p.d557-62
DOI: 10.1093/nar/gkp972

International network of cancer genome projects.
International Cancer Genome Consortium, Hudson TJ, Anderson W, Artez A, Barker AD, Bell C, Bernabé RR, Bhan MK, Calvo F, Eerola I, Gerhard DS, Guttmacher A, Guyer M, Hemsley FM, Jennings JL, Kerr D, Klatt P, Kolar P, Kusada J, Lane DP, Laplace F, Youyong L, Nettekoven G, Ozenberger B, Peterson J, Rao TS, Remacle J, Schafer AJ, Shibata T, Stratton MR, Vockley JG, Watanabe K, Yang H, Yuen MM, Knoppers BM, Bobrow M, Cambon-Thomsen A, Dressler LG, Dyke SO, Joly Y, Kato K, Kennedy KL, Nicolás P, Parker MJ, Rial-Sebbag E, Romeo-Casabona CM, Shaw KM, Wallace S, Wiesner GL, Zeps N, Lichter P, Biankin AV, Chabannon C, Chin L, Clément B, de Alava E, Degos F, Ferguson ML, Geary P, Hayes DN, Hudson TJ, Johns AL, Kasprzyk A, Nakagawa H, Penny R, Piris MA, Sarin R, Scarpa A, Shibata T, van de Vijver M, Futreal PA, Aburatani H, Bayés M, Botwell DD, Campbell PJ, Estivill X, Gerhard DS, Grimmond SM, Gut I, Hirst M, López-Otín C, Majumder P, Marra M, McPherson JD, Nakagawa H, Ning Z, Puente XS, Ruan Y, Shibata T, Stratton MR, Stunnenberg HG, Swerdlow H, Velculescu VE, Wilson RK, Xue HH, Yang L, Spellman PT, Bader GD, Boutros PC, Campbell PJ, Flicek P, Getz G, Guigó R, Guo G, Haussler D, Heath S, Hubbard TJ, Jiang T, Jones SM, Li Q, López-Bigas N, Luo R, Muthuswamy L, Ouellette BF, Pearson JV, Puente XS, Quesada V, Raphael BJ, Sander C, Shibata T, Speed TP, Stein LD, Stuart JM, Teague JW, Totoki Y, Tsunoda T, Valencia A, Wheeler DA, Wu H, Zhao S, Zhou G, Stein LD, Guigó R, Hubbard TJ, Joly Y, Jones SM, Kasprzyk A, Lathrop M, López-Bigas N, Ouellette BF, Spellman PT, Teague JW, Thomas G, Valencia A, Yoshida T, Kennedy KL, Axton M, Dyke SO, Futreal PA, Gerhard DS, Gunter C, Guyer M, Hudson TJ, McPherson JD, Miller LJ, Ozenberger B, Shaw KM, Kasprzyk A, Stein LD, Zhang J, Haider SA, Wang J, Yung CK, Cros A, Liang Y, Gnaneshan S, Guberman J, Hsu J, Bobrow M, Chalmers DR, Hasel KW, Joly Y, Kaan TS, Kennedy KL, Knoppers BM, Lowrance WW, Masui T, Nicolás P, Rial-Sebbag E, Rodriguez LL, Vergely C, Yoshida T, Grimmond SM, Biankin AV, Bowtell DD, Cloonan N, deFazio A, Eshleman JR, Etemadmoghadam D, Gardiner BB, Kench JG, Scarpa A, Sutherland RL, Tempero MA, Waddell NJ, Wilson PJ, McPherson JD, Gallinger S, Tsao MS, Shaw PA, Petersen GM, Mukhopadhyay D, Chin L, DePinho RA, Thayer S, Muthuswamy L, Shazand K, Beck T, Sam M, Timms L, Ballin V, Lu Y, Ji J, Zhang X, Chen F, Hu X, Zhou G, Yang Q, Tian G, Zhang L, Xing X, Li X, Zhu Z, Yu Y, Yu J, Yang H, Lathrop M, Tost J, Brennan P, Holcatova I, Zaridze D, Brazma A, Egevard L, Prokhortchouk E, Banks RE, Uhlén M, Cambon-Thomsen A, Viksna J, Ponten F, Skryabin K, Stratton MR, Futreal PA, Birney E, Borg A, Børresen-Dale AL, Caldas C, Foekens JA, Martin S, Reis-Filho JS, Richardson AL, Sotiriou C, Stunnenberg HG, Thoms G, van de Vijver M, van't Veer L, Calvo F, Birnbaum D, Blanche H, Boucher P, Boyault S, Chabannon C, Gut I, Masson-Jacquemier JD, Lathrop M, Pauporté I, Pivot X, Vincent-Salomon A, Tabone E, Theillet C, Thomas G, Tost J, Treilleux I, Calvo F, Bioulac-Sage P, Clément B, Decaens T, Degos F, Franco D, Gut I, Gut M, Heath S, Lathrop M, Samuel D, Thomas G, Zucman-Rossi J, Lichter P, Eils R, Brors B, Korbel JO, Korshunov A, Landgraf P, Lehrach H, Pfister S, Radlwimmer B, Reifenberger G, Taylor MD, von Kalle C, Majumder PP, Sarin R, Rao TS, Bhan MK, Scarpa A, Pederzoli P, Lawlor RA, Delledonne M, Bardelli A, Biankin AV, Grimmond SM, Gress T, Klimstra D, Zamboni G, Shibata T, Nakamura Y, Nakagawa H, Kusada J, Tsunoda T, Miyano S, Aburatani H, Kato K, Fujimoto A, Yoshida T, Campo E, López-Otín C, Estivill X, Guigó R, de Sanjosé S, Piris MA, Montserrat E, González-Díaz M, Puente XS, Jares P, Valencia A, Himmelbauer H, Quesada V, Bea S, Stratton MR, Futreal PA, Campbell PJ, Vincent-Salomon A, Richardson AL, Reis-Filho JS, van de Vijver M, Thomas G, Masson-Jacquemier JD, Aparicio S, Borg A, Børresen-Dale AL, Caldas C, Foekens JA, Stunnenberg HG, van't Veer L, Easton DF, Spellman PT, Martin S, Barker AD, Chin L, Collins FS, Compton CC, Ferguson ML, Gerhard DS, Getz G, Gunter C, Guttmacher A, Guyer M, Hayes DN, Lander ES, Ozenberger B, Penny R, Peterson J, Sander C, Shaw KM, Speed TP, Spellman PT, Vockley JG, Wheeler DA, Wilson RK, Hudson TJ, Chin L, Knoppers BM, Lander ES, Lichter P, Stein LD, Stratton MR, Anderson W, Barker AD, Bell C, Bobrow M, Burke W, Collins FS, Compton CC, DePinho RA, Easton DF, Futreal PA, Gerhard DS, Green AR, Guyer M, Hamilton SR, Hubbard TJ, Kallioniemi OP, Kennedy KL, Ley TJ, Liu ET, Lu Y, Majumder P, Marra M, Ozenberger B, Peterson J, Schafer AJ, Spellman PT, Stunnenberg HG, Wainwright BJ, Wilson RK, Yang H.
Nature Volume 464 (2010) p.993-998
DOI: 10.1038/nature08987

The BioPAX community standard for pathway data sharing.
Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Ruebenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Le Novère N, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD.
Nat Biotechnol Volume 28 (2010) p.935-942
DOI: 10.1038/nbt.1666

Ensembl Genomes: extending Ensembl across the taxonomic space.
Kersey PJ, Lawson D, Birney E, Derwent PS, Haimel M, Herrero J, Keenan S, Kerhornou A, Koscielny G, Kähäri A, Kinsella RJ, Kulesha E, Maheswari U, Megy K, Nuhn M, Proctor G, Staines D, Valentin F, Vilella AJ, Yates A.
Nucleic Acids Res Volume 38 (2010) p.d563-9
DOI: 10.1093/nar/gkp871

2009

MAPU 2.0: high-accuracy proteomes mapped to genomes.
Gnad F, Oroshi M, Birney E, Mann M.
Nucleic Acids Res Volume 37 (2009) p.d902-6
DOI: 10.1093/nar/gkn773

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates.
Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E.
Genome Res Volume 19 (2009) p.327-335
DOI: 10.1101/gr.073585.107

ENFIN--A European network for integrative systems biology.
Kahlem P, Clegg A, Reisinger F, Xenarios I, Hermjakob H, Orengo C, Birney E.
C R Biol Volume 332 (2009) p.1050-1058
DOI: 10.1016/j.crvi.2009.09.003

Petabyte-scale innovations at the European Nucleotide Archive.
Cochrane G, Akhtar R, Bonfield J, Bower L, Demiralp F, Faruque N, Gibson R, Hoad G, Hubbard T, Hunter C, Jang M, Juhos S, Leinonen R, Leonard S, Lin Q, Lopez R, Lorenc D, McWilliam H, Mukherjee G, Plaister S, Radhakrishnan R, Robinson S, Sobhany S, Hoopen PT, Vaughan R, Zalunin V, Birney E.
Nucleic Acids Res Volume 37 (2009) p.d19-25
DOI: 10.1093/nar/gkn765

Reactome knowledgebase of human biological pathways and processes.
Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B, Kanapin A, Lewis S, Mahajan S, May B, Schmidt E, Vastrik I, Wu G, Birney E, Stein L, D'Eustachio P.
Nucleic Acids Res Volume 37 (2009) p.d619-22
DOI: 10.1093/nar/gkn863

Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment.
Paten B, Herrero J, Beal K, Birney E.
Bioinformatics Volume 25 (2009) p.295-301
DOI: 10.1093/bioinformatics/btn630

Sense from sequence reads: methods for alignment and assembly.
Flicek P, Birney E.
Nat Methods Volume 6 (2009) p.s6-s12
DOI: 10.1038/nmeth.1376

Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler.
Zerbino DR, McEwen GK, Margulies EH, Birney E.
PLoS One Volume 4 (2009) p.e8407
DOI: 10.1371/journal.pone.0008407

Correction: Reactome: a knowledge base of biologic pathways and processes.
Vastrik I, D'Eustachio P, Schmidt E, Gopinath G, Croft D, de Bono B, Gillespie M, Jassal B, Lewis S, Matthews L, Wu G, Birney E, Stein L.
Genome Biol Volume 10 (2009) p.402-402

Ensembl 2009.
Hubbard TJ, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Clarke L, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Graf S, Haider S, Hammond M, Holland R, Howe K, Jenkinson A, Johnson N, Kahari A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Rios D, Schuster M, Slater G, Smedley D, Spooner W, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wilder S, Zadissa A, Birney E, Cunningham F, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Kasprzyk A, Proctor G, Smith J, Searle S, Flicek P.
Nucleic Acids Res Volume 37 (2009) p.d690-7
DOI: 10.1093/nar/gkn828

Visualising the Epigenome
Flicek P, Birney E.
Volume (2009) p.55-66
DOI: 10.1007/978-1-4020-9187-2_4

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt.
Durinck S, Spellman PT, Birney E, Huber W.
Nat Protoc Volume 4 (2009) p.1184-1191
DOI: 10.1038/nprot.2009.97

VectorBase: a data resource for invertebrate vector genomics.
Lawson D, Arensburger P, Atkinson P, Besansky NJ, Bruggner RV, Butler R, Campbell KS, Christophides GK, Christley S, Dialynas E, Hammond M, Hill CA, Konopinski N, Lobo NF, MacCallum RM, Madey G, Megy K, Meyer J, Redmond S, Severson DW, Stinson EO, Topalis P, Birney E, Gelbart WM, Kafatos FC, Louis C, Collins FH.
Nucleic Acids Res Volume 37 (2009) p.d583-7
DOI: 10.1093/nar/gkn857

Prepublication data sharing.
Toronto International Data Release Workshop Authors, Birney E, Hudson TJ, Green ED, Gunter C, Eddy S, Rogers J, Harris JR, Ehrlich SD, Apweiler R, Austin CP, Berglund L, Bobrow M, Bountra C, Brookes AJ, Cambon-Thomsen A, Carter NP, Chisholm RL, Contreras JL, Cooke RM, Crosby WL, Dewar K, Durbin R, Dyke SO, Ecker JR, El Emam K, Feuk L, Gabriel SB, Gallacher J, Gelbart WM, Granell A, Guarner F, Hubbard T, Jackson SA, Jennings JL, Joly Y, Jones SM, Kaye J, Kennedy KL, Knoppers BM, Kyrpides NC, Lowrance WW, Luo J, MacKay JJ, Martín-Rivera L, McCombie WR, McPherson JD, Miller L, Miller W, Moerman D, Mooser V, Morton CC, Ostell JM, Ouellette BF, Parkhill J, Raina PS, Rawlings C, Scherer SE, Scherer SW, Schofield PN, Sensen CW, Stodden VC, Sussman MR, Tanaka T, Thornton J, Tsunoda T, Valle D, Vuorio EI, Walker NM, Wallace S, Weinstock G, Whitman WB, Worley KC, Wu C, Wu J, Yu J.
Nature Volume 461 (2009) p.168-170
DOI: 10.1038/461168a

Genomic resources for invertebrate vectors of human pathogens, and the role of VectorBase.
Megy K, Hammond M, Lawson D, Bruggner RV, Birney E, Collins FH.
Infect Genet Evol Volume 9 (2009) p.308-313
DOI: 10.1016/j.meegid.2007.12.007

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.
Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ, Hart E, Suner MM, Landrum MJ, Aken B, Ayling S, Baertsch R, Fernandez-Banet J, Cherry JL, Curwen V, Dicuccio M, Kellis M, Lee J, Lin MF, Schuster M, Shkeda A, Amid C, Brown G, Dukhanina O, Frankish A, Hart J, Maidak BL, Mudge J, Murphy MR, Murphy T, Rajan J, Rajput B, Riddick LD, Snow C, Steward C, Webb D, Weber JA, Wilming L, Wu W, Birney E, Haussler D, Hubbard T, Ostell J, Durbin R, Lipman D.
Genome Res Volume 19 (2009) p.1316-1323
DOI: 10.1101/gr.080531.108

2008

Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database.
Cochrane G, Akhtar R, Aldebert P, Althorpe N, Baldwin A, Bates K, Bhattacharyya S, Bonfield J, Bower L, Browne P, Castro M, Cox T, Demiralp F, Eberhardt R, Faruque N, Hoad G, Jang M, Kulikova T, Labarga A, Leinonen R, Leonard S, Lin Q, Lopez R, Lorenc D, McWilliam H, Mukherjee G, Nardone F, Plaister S, Robinson S, Sobhany S, Vaughan R, Wu D, Zhu W, Apweiler R, Hubbard T, Birney E.
Nucleic Acids Res Volume 36 (2008) p.d5-12
DOI: 10.1093/nar/gkm1018

Arabidopsis reactome: a foundation knowledgebase for plant systems biology.
Tsesmetzis N, Couchman M, Higgins J, Smith A, Doonan JH, Seifert GJ, Schmidt EE, Vastrik I, Birney E, Wu G, D'Eustachio P, Stein LD, Morris RJ, Bevan MW, Walsh SV.
Plant Cell Volume 20 (2008) p.1426-1436
DOI: 10.1105/tpc.108.057976

Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes.
Margulies EH, Birney E.
Nat Rev Genet Volume 9 (2008) p.303-313
DOI: 10.1038/nrg2185

Levers and fulcrums: progress in cis-regulatory motif models.
Birney E.
Nat Methods Volume 5 (2008) p.297-298
DOI: 10.1038/nmeth0408-297

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.
Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavaré S, Beck S.
Nat Biotechnol Volume 26 (2008) p.779-785
DOI: 10.1038/nbt1414

Genome-wide nucleotide-level mammalian ancestor reconstruction.
Paten B, Herrero J, Fitzgerald S, Beal K, Flicek P, Holmes I, Birney E.
Genome Res Volume 18 (2008) p.1829-1843
DOI: 10.1101/gr.076521.108

Integrating biological data--the Distributed Annotation System.
Jenkinson AM, Albrecht M, Birney E, Blankenburg H, Down T, Finn RD, Hermjakob H, Hubbard TJ, Jimenez RC, Jones P, Kähäri A, Kulesha E, Macías JR, Reeves GA, Prlić A.
BMC Bioinformatics Volume 9 Suppl 8 (2008) p.s3
DOI: 10.1186/1471-2105-9-s8-s3

Confounding between recombination and selection, and the Ped/Pop method for detecting selection.
O'Reilly PF, Birney E, Balding DJ.
Genome Res Volume 18 (2008) p.1304-1313
DOI: 10.1101/gr.067181.107

Advanced genomic data mining.
Fernández-Suárez XM, Birney E.
PLoS Comput Biol Volume 4 (2008) p.e1000121
DOI: 10.1371/journal.pcbi.1000121

SNP and haplotype mapping for genetic analysis in the rat.
STAR Consortium, Saar K, Beck A, Bihoreau MT, Birney E, Brocklebank D, Chen Y, Cuppen E, Demonchy S, Dopazo J, Flicek P, Foglio M, Fujiyama A, Gut IG, Gauguier D, Guigo R, Guryev V, Heinig M, Hummel O, Jahn N, Klages S, Kren V, Kube M, Kuhl H, Kuramoto T, Kuroki Y, Lechner D, Lee YA, Lopez-Bigas N, Lathrop GM, Mashimo T, Medina I, Mott R, Patone G, Perrier-Cornet JA, Platzer M, Pravenec M, Reinhardt R, Sakaki Y, Schilhabel M, Schulz H, Serikawa T, Shikhagaie M, Tatsumoto S, Taudien S, Toyoda A, Voigt B, Zelenika D, Zimdahl H, Hubner N.
Nat Genet Volume 40 (2008) p.560-566
DOI: 10.1038/ng.124

Ensembl 2008.
Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Eyre T, Fitzgerald S, Fernandez-Banet J, Gräf S, Haider S, Hammond M, Holland R, Howe KL, Howe K, Johnson N, Jenkinson A, Kähäri A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Slater G, Smedley D, Spudich G, Trevanion S, Vilella AJ, Vogel J, White S, Wood M, Birney E, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Hubbard TJ, Kasprzyk A, Proctor G, Smith J, Ureta-Vidal A, Searle S.
Nucleic Acids Res Volume 36 (2008) p.d707-14
DOI: 10.1093/nar/gkm988

The HGNC Database in 2008: a resource for the human genome.
Bruford EA, Lush MJ, Wright MW, Sneddon TP, Povey S, Birney E.
Nucleic Acids Res Volume 36 (2008) p.d445-8
DOI: 10.1093/nar/gkm881

What everybody should know about the rat genome and its online resources.
Twigger SN, Pruitt KD, Fernández-Suárez XM, Karolchik D, Worley KC, Maglott DR, Brown G, Weinstock G, Gibbs RA, Kent J, Birney E, Jacob HJ.
Nat Genet Volume 40 (2008) p.523-527
DOI: 10.1038/ng0508-523

Genome analysis of the platypus reveals unique signatures of evolution.
Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, López-Otín C, Ordóñez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Alsop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AF, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ES, Gemmell NJ, Buschiazzo E, Vargas Jentzsch IM, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison EP, Sachidanandam R, Smith C, Hannon GJ, Tsend-Ayush E, McMillan D, Attenborough R, Rens W, Ferguson-Smith M, Lefèvre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhardt R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux JL, Niwa H, Sekita Y, Huang X, Stark A, Kheradpour P, Kellis M, Flicek P, Chen Y, Webber C, Hardison R, Nelson J, Hallsworth-Pepin K, Delehaunty K, Markovic C, Minx P, Feng Y, Kremitzki C, Mitreva M, Glasscock J, Wylie T, Wohldmann P, Thiru P, Nhan MN, Pohl CS, Smith SM, Hou S, Nefedov M, de Jong PJ, Renfree MB, Mardis ER, Wilson RK.
Nature Volume 453 (2008) p.175-183
DOI: 10.1038/nature06936

Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
Zerbino DR, Birney E.
Genome Res Volume 18 (2008) p.821-829
DOI: 10.1101/gr.074492.107

Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs.
Paten B, Herrero J, Beal K, Fitzgerald S, Birney E.
Genome Res Volume 18 (2008) p.1814-1828
DOI: 10.1101/gr.076554.108

ENFIN - An Integrative Structure for Systems Biology
Reisinger F, Corpas M, Hancock J, Hermjakob H, Birney E, Kahlem P.
Volume (2008) p.132-143
DOI: 10.1007/978-3-540-69828-9_13

An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs).
Rakyan VK, Down TA, Thorne NP, Flicek P, Kulesha E, Gräf S, Tomazou EM, Bäckdahl L, Johnson N, Herberth M, Howe KL, Jackson DK, Miretti MM, Fiegler H, Marioni JC, Birney E, Hubbard TJ, Carter NP, Tavaré S, Beck S.
Genome Res Volume 18 (2008) p.1518-1529
DOI: 10.1101/gr.077479.108

2007

Evolutionary and biomedical insights from the rhesus macaque genome.
Rhesus Macaque Genome Sequencing and Analysis Consortium, Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, Hardison RC, Makova KD, Miller W, Milosavljevic A, Palermo RE, Siepel A, Sikela JM, Attaway T, Bell S, Bernard KE, Buhay CJ, Chandrabose MN, Dao M, Davis C, Delehaunty KD, Ding Y, Dinh HH, Dugan-Rocha S, Fulton LA, Gabisi RA, Garner TT, Godfrey J, Hawes AC, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Kirkness EF, Cree A, Fowler RG, Lee S, Lewis LR, Li Z, Liu YS, Moore SM, Muzny D, Nazareth LV, Ngo DN, Okwuonu GO, Pai G, Parker D, Paul HA, Pfannkoch C, Pohl CS, Rogers YH, Ruiz SJ, Sabo A, Santibanez J, Schneider BW, Smith SM, Sodergren E, Svatek AF, Utterback TR, Vattathil S, Warren W, White CS, Chinwalla AT, Feng Y, Halpern AL, Hillier LW, Huang X, Minx P, Nelson JO, Pepin KH, Qin X, Sutton GG, Venter E, Walenz BP, Wallis JW, Worley KC, Yang SP, Jones SM, Marra MA, Rocchi M, Schein JE, Baertsch R, Clarke L, Csürös M, Glasscock J, Harris RA, Havlak P, Jackson AR, Jiang H, Liu Y, Messina DN, Shen Y, Song HX, Wylie T, Zhang L, Birney E, Han K, Konkel MK, Lee J, Smit AF, Ullmer B, Wang H, Xing J, Burhans R, Cheng Z, Karro JE, Ma J, Raney B, She X, Cox MJ, Demuth JP, Dumas LJ, Han SG, Hopkins J, Karimpour-Fard A, Kim YH, Pollack JR, Vinar T, Addo-Quaye C, Degenhardt J, Denby A, Hubisz MJ, Indap A, Kosiol C, Lahn BT, Lawson HA, Marklein A, Nielsen R, Vallender EJ, Clark AG, Ferguson B, Hernandez RD, Hirani K, Kehrer-Sawatzki H, Kolb J, Patil S, Pu LL, Ren Y, Smith DG, Wheeler DA, Schenck I, Ball EV, Chen R, Cooper DN, Giardine B, Hsu F, Kent WJ, Lesk A, Nelson DL, O'brien WE, Prüfer K, Stenson PD, Wallace JC, Ke H, Liu XM, Wang P, Xiang AP, Yang F, Barber GP, Haussler D, Karolchik D, Kern AD, Kuhn RM, Smith KE, Zwieg AS.
Science Volume 316 (2007) p.222-234
DOI: 10.1126/science.1139247

The implications of alternative splicing in the ENCODE protein complement.
Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Olason PI, Albrecht M, Hegyi H, Giorgetti A, Raimondo D, Lagarde J, Laskowski RA, López G, Sadowski MI, Watson JD, Fariselli P, Rossi I, Nagy A, Kai W, Størling Z, Orsini M, Assenov Y, Blankenburg H, Huthmacher C, Ramírez F, Schlicker A, Denoeud F, Jones P, Kerrien S, Orchard S, Antonarakis SE, Reymond A, Birney E, Brunak S, Casadio R, Guigo R, Harrow J, Hermjakob H, Jones DT, Lengauer T, Orengo CA, Patthy L, Thornton JM, Tramontano A, Valencia A.
Proc Natl Acad Sci U S A Volume 104 (2007) p.5495-5500
DOI: 10.1073/pnas.0700800104

Update of the Anopheles gambiae PEST genome assembly.
Sharakhova MV, Hammond MP, Lobo NF, Krzywinski J, Unger MF, Hillenmeyer ME, Bruggner RV, Birney E, Collins FH.
Genome Biol Volume 8 (2007) p.r5
DOI: 10.1186/gb-2007-8-1-r5

Estimating the neutral rate of nucleotide substitution using introns.
Hoffman MM, Birney E.
Mol Biol Evol Volume 24 (2007) p.522-531
DOI: 10.1093/molbev/msl179

Patterns of somatic mutation in human cancer genomes.
Greenman C, Stephens P, Smith R, Dalgliesh GL, Hunter C, Bignell G, Davies H, Teague J, Butler A, Stevens C, Edkins S, O'Meara S, Vastrik I, Schmidt EE, Avis T, Barthorpe S, Bhamra G, Buck G, Choudhury B, Clements J, Cole J, Dicks E, Forbes S, Gray K, Halliday K, Harrison R, Hills K, Hinton J, Jenkinson A, Jones D, Menzies A, Mironenko T, Perry J, Raine K, Richardson D, Shepherd R, Small A, Tofts C, Varian J, Webb T, West S, Widaa S, Yates A, Cahill DP, Louis DN, Goldstraw P, Nicholson AG, Brasseur F, Looijenga L, Weber BL, Chiew YE, DeFazio A, Greaves MF, Green AR, Campbell P, Birney E, Easton DF, Chenevix-Trench G, Tan MH, Khoo SK, Teh BT, Yuen ST, Leung SY, Wooster R, Futreal PA, Stratton MR.
Nature Volume 446 (2007) p.153-158
DOI: 10.1038/nature05610

Genome browsing with Ensembl: a practical overview.
Spudich G, Fernández-Suárez XM, Birney E.
Brief Funct Genomic Proteomic Volume 6 (2007) p.202-219
DOI: 10.1093/bfgp/elm025

Challenges and standards in integrating surveys of structural variation.
Scherer SW, Lee C, Birney E, Altshuler DM, Eichler EE, Carter NP, Hurles ME, Feuk L.
Nat Genet Volume 39 (2007) p.s7-15
DOI: 10.1038/ng2093

Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation.
Ettwiller L, Paten B, Ramialison M, Birney E, Wittbrodt J.
Nat Methods Volume 4 (2007) p.563-565
DOI: 10.1038/nmeth1061

Double Dutch for duplications.
Birney E.
Nat Genet Volume 39 (2007) p.1303-1304
DOI: 10.1038/ng1107-1303

Identification of novel peptide hormones in the human proteome by hidden Markov model screening.
Mirabeau O, Perlas E, Severini C, Audero E, Gascuel O, Possenti R, Birney E, Rosenthal N, Gross C.
Genome Res Volume 17 (2007) p.320-327
DOI: 10.1101/gr.5755407

Optimized design and assessment of whole genome tiling arrays.
Gräf S, Nielsen FG, Kurtz S, Huynen MA, Birney E, Stunnenberg H, Flicek P.
Bioinformatics Volume 23 (2007) p.i195-204
DOI: 10.1093/bioinformatics/btm200

In vivo validation of a computationally predicted conserved Ath5 target gene set.
Del Bene F, Ettwiller L, Skowronska-Krawczyk D, Baier H, Matter JM, Birney E, Wittbrodt J.
PLoS Genet Volume 3 (2007) p.1661-1671
DOI: 10.1371/journal.pgen.0030159

ENFIN a network to enhance integrative systems biology.
Kahlem P, Birney E.
Ann N Y Acad Sci Volume 1115 (2007) p.23-31
DOI: 10.1196/annals.1407.016

Genome sequence of Aedes aegypti, a major arbovirus vector.
Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, Loftus B, Xi Z, Megy K, Grabherr M, Ren Q, Zdobnov EM, Lobo NF, Campbell KS, Brown SE, Bonaldo MF, Zhu J, Sinkins SP, Hogenkamp DG, Amedeo P, Arensburger P, Atkinson PW, Bidwell S, Biedler J, Birney E, Bruggner RV, Costas J, Coy MR, Crabtree J, Crawford M, Debruyn B, Decaprio D, Eiglmeier K, Eisenstadt E, El-Dorry H, Gelbart WM, Gomes SL, Hammond M, Hannick LI, Hogan JR, Holmes MH, Jaffe D, Johnston JS, Kennedy RC, Koo H, Kravitz S, Kriventseva EV, Kulp D, Labutti K, Lee E, Li S, Lovin DD, Mao C, Mauceli E, Menck CF, Miller JR, Montgomery P, Mori A, Nascimento AL, Naveira HF, Nusbaum C, O'leary S, Orvis J, Pertea M, Quesneville H, Reidenbach KR, Rogers YH, Roth CW, Schneider JR, Schatz M, Shumway M, Stanke M, Stinson EO, Tubio JM, Vanzee JP, Verjovski-Almeida S, Werner D, White O, Wyder S, Zeng Q, Zhao Q, Zhao Y, Hill CA, Raikhel AS, Soares MB, Knudson DL, Lee NH, Galagan J, Salzberg SL, Paulsen IT, Dimopoulos G, Collins FH, Birren B, Fraser-Liggett CM, Severson DW.
Science Volume 316 (2007) p.1718-1723
DOI: 10.1126/science.1138878

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.
Nature Volume 447 (2007) p.799-816
DOI: 10.1038/nature05874

Reactome: a knowledge base of biologic pathways and processes.
Vastrik I, D'Eustachio P, Schmidt E, Gopinath G, Croft D, de Bono B, Gillespie M, Jassal B, Lewis S, Matthews L, Wu G, Birney E, Stein L.
Genome Biol Volume 8 (2007) p.r39
DOI: 10.1186/gb-2007-8-3-r39

VectorBase: a home for invertebrate vectors of human pathogens.
Lawson D, Arensburger P, Atkinson P, Besansky NJ, Bruggner RV, Butler R, Campbell KS, Christophides GK, Christley S, Dialynas E, Emmert D, Hammond M, Hill CA, Kennedy RC, Lobo NF, MacCallum MR, Madey G, Megy K, Redmond S, Russo S, Severson DW, Stinson EO, Topalis P, Zdobnov EM, Birney E, Gelbart WM, Kafatos FC, Louis C, Collins FH.
Nucleic Acids Res Volume 35 (2007) p.d503-5
DOI: 10.1093/nar/gkl960

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.
Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Brown JB, Bickel P, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Stone EA, Rosenbloom KR, Kent WJ, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Hinrichs A, Trumbower H, Clawson H, Zweig A, Kuhn RM, Barber G, Harte R, Karolchik D, Field MA, Moore RA, Matthewson CA, Schein JE, Marra MA, Antonarakis SE, Batzoglou S, Goldman N, Hardison R, Haussler D, Miller W, Pachter L, Green ED, Sidow A.
Genome Res Volume 17 (2007) p.760-774
DOI: 10.1101/gr.6034307

Evolutionary genomics: come fly with us.
Birney E.
Nature Volume 450 (2007) p.184-185
DOI: 10.1038/450184a

The landscape of histone modifications across 1% of the human genome in five human cell lines.
Koch CM, Andrews RM, Flicek P, Dillon SC, Karaöz U, Clelland GK, Wilcox S, Beare DM, Fowler JC, Couttet P, James KD, Lefebvre GC, Bruce AW, Dovey OM, Ellis PD, Dhami P, Langford CF, Weng Z, Birney E, Carter NP, Vetrie D, Dunham I.
Genome Res Volume 17 (2007) p.691-707
DOI: 10.1101/gr.5704207

Ensembl 2007.
Hubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Fitzgerald S, Fernandez-Banet J, Graf S, Haider S, Hammond M, Herrero J, Holland R, Howe K, Howe K, Johnson N, Kahari A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Melsopp C, Megy K, Meidl P, Ouverdin B, Parker A, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Severin J, Slater G, Smedley D, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wood M, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Flicek P, Kasprzyk A, Proctor G, Searle S, Smith J, Ureta-Vidal A, Birney E.
Nucleic Acids Res Volume 35 (2007) p.d610-7
DOI: 10.1093/nar/gkl996

2006

Ensembl 2006.
Birney E, Andrews D, Caccamo M, Chen Y, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, Flicek P, Gräf S, Hammond M, Herrero J, Howe K, Iyer V, Jekosch K, Kähäri A, Kasprzyk A, Keefe D, Kokocinski F, Kulesha E, London D, Longden I, Melsopp C, Meidl P, Overduin B, Parker A, Proctor G, Prlic A, Rae M, Rios D, Redmond S, Schuster M, Sealy I, Searle S, Severin J, Slater G, Smedley D, Smith J, Stabenau A, Stalker J, Trevanion S, Ureta-Vidal A, Vogel J, White S, Woodwark C, Hubbard TJ.
Nucleic Acids Res Volume 34 (2006) p.d556-61
DOI: 10.1093/nar/gkj133

Ensembl’s annotation pipeline and its use in eukaryotic genomes
Fernandez XM, Searle S, Birney E.
Volume (2006) p.109-203

TranscriptSNPView: a genome-wide catalog of mouse coding variation.
Cunningham F, Rios D, Griffiths M, Smith J, Ning Z, Cox T, Flicek P, Marin-Garcin P, Herrero J, Rogers J, van der Weyden L, Bradley A, Birney E, Adams DJ.
Nat Genet Volume 38 (2006) p.853
DOI: 10.1038/ng0806-853a

Dry work in a wet world: computation in systems biology.
Kahlem P, Birney E.
Mol Syst Biol Volume 2 (2006) p.40
DOI: 10.1038/msb4100080

Picking pyknons out of the human genome.
Meynert A, Birney E.
Cell Volume 125 (2006) p.836-838
DOI: 10.1016/j.cell.2006.05.019

EGASP: the human ENCODE Genome Annotation Assessment Project.
Guigó R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E, Castelo R, Eyras E, Ucla C, Gingeras TR, Harrow J, Hubbard T, Lewis SE, Reese MG.
Genome Biol Volume 7 Suppl 1 (2006) p.s2.1-31
DOI: 10.1186/gb-2006-7-s1-s2

2005

Automated generation of heuristics for biological sequence comparison.
Slater GS, Birney E.
BMC Bioinformatics Volume 6 (2005) p.31
DOI: 10.1186/1471-2105-6-31

A survey of homozygous deletions in human cancer genomes.
Cox C, Bignell G, Greenman C, Stabenau A, Warren W, Stephens P, Davies H, Watt S, Teague J, Edkins S, Birney E, Easton DF, Wooster R, Futreal PA, Stratton MR.
Proc Natl Acad Sci U S A Volume 102 (2005) p.4542-4547
DOI: 10.1073/pnas.0408593102

Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags.
Hubbard SJ, Grafham DV, Beattie KJ, Overton IM, McLaren SR, Croning MD, Boardman PE, Bonfield JK, Burnside J, Davies RM, Farrell ER, Francis MD, Griffiths-Jones S, Humphray SJ, Hyland C, Scott CE, Tang H, Taylor RG, Tickle C, Brown WR, Birney E, Rogers J, Wilson SA.
Genome Res Volume 15 (2005) p.174-183
DOI: 10.1101/gr.3011405

Reactome: a knowledgebase of biological pathways.
Joshi-Tope G, Gillespie M, Vastrik I, D'Eustachio P, Schmidt E, de Bono B, Jassal B, Gopinath GR, Wu GR, Matthews L, Lewis S, Birney E, Stein L.
Nucleic Acids Res Volume 33 (2005) p.d428-32
DOI: 10.1093/nar/gki072

Protein Sequence Analysis and Domain Identification
Ponting CP, Birney E.
Volume (2005) p.527-541
DOI: 10.1385/1-59259-890-0:527

Report of an EU projects workshop on systems biology held in Brussels, Belgium on 8 December 2004.
Birney E, Ciliberto A, Colding-Jørgensen M, Goldbeter A, Hohmann S, Kuiper M, Lehrach H, Miczka G, Mosekilde E, Westerhoff H, Wolkenhauer O.
Syst Biol (Stevenage) Volume 152 (2005) p.55-60

The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates.
Ettwiller L, Paten B, Souren M, Loosli F, Wittbrodt J, Birney E.
Genome Biol Volume 6 (2005) p.r104
DOI: 10.1186/gb-2005-6-12-r104

Gene finding in the chicken genome.
Eyras E, Reymond A, Castelo R, Bye JM, Camara F, Flicek P, Huckle EJ, Parra G, Shteynberg DD, Wyss C, Rogers J, Antonarakis SE, Birney E, Guigo R, Brent MR.
BMC Bioinformatics Volume 6 (2005) p.131
DOI: 10.1186/1471-2105-6-131

Ensembl 2005.
Hubbard T, Andrews D, Caccamo M, Cameron G, Chen Y, Clamp M, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, Gilbert J, Hammond M, Herrero J, Hotz H, Howe K, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Keenan S, Kokocinsci F, London D, Longden I, McVicker G, Melsopp C, Meidl P, Potter S, Proctor G, Rae M, Rios D, Schuster M, Searle S, Severin J, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Trevanion S, Ureta-Vidal A, Vogel J, White S, Woodwark C, Birney E.
Nucleic Acids Res Volume 33 (2005) p.d447-53
DOI: 10.1093/nar/gki138

2004

The International Protein Index: an integrated database for proteomics experiments.
Kersey PJ, Duarte J, Williams A, Karavidopoulou Y, Birney E, Apweiler R.
Proteomics Volume 4 (2004) p.1985-1988
DOI: 10.1002/pmic.200300721

Genome information resources - developments at Ensembl.
Hammond MP, Birney E.
Trends Genet Volume 20 (2004) p.268-272
DOI: 10.1016/j.tig.2004.04.002

A SNP map of the rat genome generated from cDNA sequences.
Zimdahl H, Nyakatura G, Brandt P, Schulz H, Hummel O, Fartmann B, Brett D, Droege M, Monti J, Lee YA, Sun Y, Zhao S, Winter EE, Ponting CP, Chen Y, Kasprzyk A, Birney E, Ganten D, Hubner N.
Science Volume 303 (2004) p.807
DOI: 10.1126/science.1092427

Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Egan A, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Albà M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F, Rat Genome Sequencing Project Consortium.
Nature Volume 428 (2004) p.493-521
DOI: 10.1038/nature02426

Biological database design and implementation.
Birney E, Clamp M.
Brief Bioinform Volume 5 (2004) p.31-38
DOI: 10.1093/bib/5.1.31

EnsMart: a generic system for fast and flexible access to biological data.
Kasprzyk A, Keefe D, Smedley D, London D, Spooner W, Melsopp C, Hammond M, Rocca-Serra P, Cox T, Birney E.
Genome Res Volume 14 (2004) p.160-169
DOI: 10.1101/gr.1645104

The Ensembl core software libraries.
Stabenau A, McVicker G, Melsopp C, Proctor G, Clamp M, Birney E.
Genome Res Volume 14 (2004) p.929-933
DOI: 10.1101/gr.1857204

Ensembl 2004.
Birney E, Andrews D, Bevan P, Caccamo M, Cameron G, Chen Y, Clarke L, Coates G, Cox T, Cuff J, Curwen V, Cutts T, Down T, Durbin R, Eyras E, Fernandez-Suarez XM, Gane P, Gibbins B, Gilbert J, Hammond M, Hotz H, Iyer V, Kahari A, Jekosch K, Kasprzyk A, Keefe D, Keenan S, Lehvaslaiho H, McVicker G, Melsopp C, Meidl P, Mongin E, Pettett R, Potter S, Proctor G, Rae M, Searle S, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Ureta-Vidal A, Woodwark C, Clamp M, Hubbard T.
Nucleic Acids Res Volume 32 (2004) p.d468-70
DOI: 10.1093/nar/gkh038

Comparison of human chromosome 21 conserved nongenic sequences (CNGs) with the mouse and dog genomes shows that their selective constraint is independent of their genic environment.
Dermitzakis ET, Kirkness E, Schwarz S, Birney E, Reymond A, Antonarakis SE.
Genome Res Volume 14 (2004) p.852-859
DOI: 10.1101/gr.1934904

GeneWise and Genomewise.
Birney E, Clamp M, Durbin R.
Genome Res Volume 14 (2004) p.988-995
DOI: 10.1101/gr.1865504

Sockeye: a 3D environment for comparative genomics.
Montgomery SB, Astakhova T, Bilenky M, Birney E, Fu T, Hassel M, Melsopp C, Rak M, Robertson AG, Sleumer M, Siddiqui AS, Jones SJ.
Genome Res Volume 14 (2004) p.956-962
DOI: 10.1101/gr.1890304

An overview of Ensembl.
Birney E, Andrews TD, Bevan P, Caccamo M, Chen Y, Clarke L, Coates G, Cuff J, Curwen V, Cutts T, Down T, Eyras E, Fernandez-Suarez XM, Gane P, Gibbins B, Gilbert J, Hammond M, Hotz HR, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Keenan S, Lehvaslaiho H, McVicker G, Melsopp C, Meidl P, Mongin E, Pettett R, Potter S, Proctor G, Rae M, Searle S, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Ureta-Vidal A, Woodwark KC, Cameron G, Durbin R, Cox A, Hubbard T, Clamp M.
Genome Res Volume 14 (2004) p.925-928
DOI: 10.1101/gr.1860604

The Anopheles gambiae genome: an update.
Mongin E, Louis C, Holt RA, Birney E, Collins FH.
Trends Parasitol Volume 20 (2004) p.49-52
DOI: 10.1016/j.pt.2003.11.003

2003

The Genome Knowledgebase: a resource for biologists and bioinformaticists.
Joshi-Tope G, Vastrik I, Gopinath GR, Matthews L, Schmidt E, Gillespie M, D'Eustachio P, Jassal B, Lewis S, Wu G, Birney E, Stein L.
Cold Spring Harb Symp Quant Biol Volume 68 (2003) p.237-243
DOI: 10.1101/sqb.2003.68.237

Unrestricted free access works and must continue.
Salzberg S, Birney E, Eddy S, White O.
Nature Volume 422 (2003) p.801
DOI: 10.1038/422801a

Ensembl 2002: accommodating comparative genomics.
Clamp M, Andrews D, Barker D, Bevan P, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Hubbard T, Kasprzyk A, Keefe D, Lehvaslaiho H, Iyer V, Melsopp C, Mongin E, Pettett R, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, Birney E.
Nucleic Acids Res Volume 31 (2003) p.38-42
DOI: 10.1093/nar/gkg083

The European Bioinformatics Institute's data resources.
Brooksbank C, Camon E, Harris MA, Magrane M, Martin MJ, Mulder N, O'Donovan C, Parkinson H, Tuli MA, Apweiler R, Birney E, Brazma A, Henrick K, Lopez R, Stoesser G, Stoehr P, Cameron G.
Nucleic Acids Res Volume 31 (2003) p.43-50
DOI: 10.1093/nar/gkg066

Ensembl: a genome infrastructure.
Birney E, Ensembl Team.
Cold Spring Harb Symp Quant Biol Volume 68 (2003) p.213-215
DOI: 10.1101/sqb.2003.68.213

Comparative genomics: genome-wide analysis in metazoan eukaryotes.
Ureta-Vidal A, Ettwiller L, Birney E.
Nat Rev Genet Volume 4 (2003) p.251-262
DOI: 10.1038/nrg1043

Discovering novel cis-regulatory motifs using functional networks.
Ettwiller LM, Rung J, Birney E.
Genome Res Volume 13 (2003) p.883-895
DOI: 10.1101/gr.866403

2002

The Bioperl toolkit: Perl modules for the life sciences.
Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehväslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E.
Genome Res Volume 12 (2002) p.1611-1618
DOI: 10.1101/gr.361602

The Pfam protein families database.
Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL.
Nucleic Acids Res Volume 30 (2002) p.276-280
DOI: 10.1093/nar/30.1.276

Genome annotation techniques: new approaches and challenges.
Rust AG, Mongin E, Birney E.
Drug Discov Today Volume 7 (2002) p.s70-6
DOI: 10.1016/s1359-6446(02)02289-4

Databases and tools for browsing genomes.
Birney E, Clamp M, Hubbard T.
Annu Rev Genomics Hum Genet Volume 3 (2002) p.293-310
DOI: 10.1146/annurev.genom.3.030502.101529

Initial sequencing and comparative analysis of the mouse genome.
Mouse Genome Sequencing Consortium, Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigó R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES.
Nature Volume 420 (2002) p.520-562
DOI: 10.1038/nature01262

The Ensembl genome database project.
Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Huminiecki L, Kasprzyk A, Lehvaslaiho H, Lijnzaad P, Melsopp C, Mongin E, Pettett R, Pocock M, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, Clamp M.
Nucleic Acids Res Volume 30 (2002) p.38-41
DOI: 10.1093/nar/30.1.38

A physical map of the mouse genome.
Gregory SG, Sekhon M, Schein J, Zhao S, Osoegawa K, Scott CE, Evans RS, Burridge PW, Cox TV, Fox CA, Hutton RD, Mullenger IR, Phillips KJ, Smith J, Stalker J, Threadgold GJ, Birney E, Wylie K, Chinwalla A, Wallis J, Hillier L, Carter J, Gaige T, Jaeger S, Kremitzki C, Layman D, Maas J, McGrane R, Mead K, Walker R, Jones S, Smith M, Asano J, Bosdet I, Chan S, Chittaranjan S, Chiu R, Fjell C, Fuhrmann D, Girn N, Gray C, Guin R, Hsiao L, Krzywinski M, Kutsche R, Lee SS, Mathewson C, McLeavy C, Messervier S, Ness S, Pandoh P, Prabhu AL, Saeedi P, Smailus D, Spence L, Stott J, Taylor S, Terpstra W, Tsai M, Vardy J, Wye N, Yang G, Shatsman S, Ayodeji B, Geer K, Tsegaye G, Shvartsbeyn A, Gebregeorgis E, Krol M, Russell D, Overton L, Malek JA, Holmes M, Heaney M, Shetty J, Feldblyum T, Nierman WC, Catanese JJ, Hubbard T, Waterston RH, Rogers J, de Jong PJ, Fraser CM, Marra M, McPherson JD, Bentley DR.
Nature Volume 418 (2002) p.743-750
DOI: 10.1038/nature00957

Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster.
Zdobnov EM, von Mering C, Letunic I, Torrents D, Suyama M, Copley RR, Christophides GK, Thomasova D, Holt RA, Subramanian GM, Mueller HM, Dimopoulos G, Law JH, Wells MA, Birney E, Charlab R, Halpern AL, Kokoza E, Kraft CL, Lai Z, Lewis S, Louis C, Barillas-Mury C, Nusskern D, Rubin GM, Salzberg SL, Sutton GG, Topalis P, Wides R, Wincker P, Yandell M, Collins FH, Ribeiro J, Gelbart WM, Kafatos FC, Bork P.
Science Volume 298 (2002) p.149-159
DOI: 10.1126/science.1077061

Immunity-related genes and gene families in Anopheles gambiae.
Christophides GK, Zdobnov E, Barillas-Mury C, Birney E, Blandin S, Blass C, Brey PT, Collins FH, Danielli A, Dimopoulos G, Hetru C, Hoa NT, Hoffmann JA, Kanzok SM, Letunic I, Levashina EA, Loukeris TG, Lycett G, Meister S, Michel K, Moita LF, Müller HM, Osta MA, Paskewitz SM, Reichhart JM, Rzhetsky A, Troxler L, Vernick KD, Vlachou D, Volz J, von Mering C, Xu J, Zheng L, Bork P, Kafatos FC.
Science Volume 298 (2002) p.159-165
DOI: 10.1126/science.1077136

The genome sequence of the malaria mosquito Anopheles gambiae.
Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R, Salzberg SL, Loftus B, Yandell M, Majoros WH, Rusch DB, Lai Z, Kraft CL, Abril JF, Anthouard V, Arensburger P, Atkinson PW, Baden H, de Berardinis V, Baldwin D, Benes V, Biedler J, Blass C, Bolanos R, Boscus D, Barnstead M, Cai S, Center A, Chaturverdi K, Christophides GK, Chrystal MA, Clamp M, Cravchik A, Curwen V, Dana A, Delcher A, Dew I, Evans CA, Flanigan M, Grundschober-Freimoser A, Friedli L, Gu Z, Guan P, Guigo R, Hillenmeyer ME, Hladun SL, Hogan JR, Hong YS, Hoover J, Jaillon O, Ke Z, Kodira C, Kokoza E, Koutsos A, Letunic I, Levitsky A, Liang Y, Lin JJ, Lobo NF, Lopez JR, Malek JA, McIntosh TC, Meister S, Miller J, Mobarry C, Mongin E, Murphy SD, O'Brochta DA, Pfannkoch C, Qi R, Regier MA, Remington K, Shao H, Sharakhova MV, Sitter CD, Shetty J, Smith TJ, Strong R, Sun J, Thomasova D, Ton LQ, Topalis P, Tu Z, Unger MF, Walenz B, Wang A, Wang J, Wang M, Wang X, Woodford KJ, Wortman JR, Wu M, Yao A, Zdobnov EM, Zhang H, Zhao Q, Zhao S, Zhu SC, Zhimulev I, Coluzzi M, della Torre A, Roth CW, Louis C, Kalush F, Mural RJ, Myers EW, Adams MD, Smith HO, Broder S, Gardner MJ, Fraser CM, Birney E, Bork P, Brey PT, Venter JC, Weissenbach J, Kafatos FC, Collins FH, Hoffman SL.
Science Volume 298 (2002) p.129-149
DOI: 10.1126/science.1076181

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.
Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schönbach C, Gojobori T, Baldarelli R, Hill DP, Bult C, Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, Corbani LE, Cousins S, Dalla E, Dragani TA, Fletcher CF, Forrest A, Frazer KS, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson IJ, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y, Lenhard B, Lyons PA, Maglott DR, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed DJ, Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CA, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor MS, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG, Wynshaw-Boris A, Yanagisawa M, Yang I, Yang L, Yuan Z, Zavolan M, Zhu Y, Zimmer A, Carninci P, Hayatsu N, Hirozane-Kishikawa T, Konno H, Nakamura M, Sakazume N, Sato K, Shiraki T, Waki K, Kawai J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Imotani K, Ishii Y, Itoh M, Kagawa I, Miyazaki A, Sakai K, Sasaki D, Shibata K, Shinagawa A, Yasunishi A, Yoshino M, Waterston R, Lander ES, Rogers J, Birney E, Hayashizaki Y, FANTOM Consortium, RIKEN Genome Exploration Research Group Phase I & II Team.
Nature Volume 420 (2002) p.563-573
DOI: 10.1038/nature01266

Apollo: a sequence annotation editor.
Lewis SE, Searle SM, Harris N, Gibson M, Lyer V, Richter J, Wiel C, Bayraktaroglir L, Birney E, Crosby MA, Kaminker JS, Matthews BB, Prochnik SE, Smithy CD, Tupy JL, Rubin GM, Misra S, Mungall CJ, Clamp ME.
Genome Biol Volume 3 (2002) p.research0082
DOI: 10.1186/gb-2002-3-12-research0082

2001

Initial sequencing and analysis of the human genome.
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowski J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, International Human Genome Sequencing Consortium.
Nature Volume 409 (2001) p.860-921
DOI: 10.1038/35057062

Cancer and genomics.
Futreal PA, Kasprzyk A, Birney E, Mullikin JC, Wooster R, Stratton MR.
Nature Volume 409 (2001) p.850-852
DOI: 10.1038/35057046

Integration of cytogenetic landmarks into the draft sequence of the human genome.
Cheung VG, Nowak N, Jang W, Kirsch IR, Zhao S, Chen XN, Furey TS, Kim UJ, Kuo WL, Olivier M, Conroy J, Kasprzyk A, Massa H, Yonescu R, Sait S, Thoreen C, Snijders A, Lemyre E, Bailey JA, Bruzel A, Burrill WD, Clegg SM, Collins S, Dhami P, Friedman C, Han CS, Herrick S, Lee J, Ligon AH, Lowry S, Morley M, Narasimhan S, Osoegawa K, Peng Z, Plajzer-Frick I, Quade BJ, Scott D, Sirotkin K, Thorpe AA, Gray JW, Hudson J, Pinkel D, Ried T, Rowen L, Shen-Ong GL, Strausberg RL, Birney E, Callen DF, Cheng JF, Cox DR, Doggett NA, Carter NP, Eichler EE, Haussler D, Korenberg JR, Morton CC, Albertson D, Schuler G, de Jong PJ, Trask BJ, BAC Resource Consortium.
Nature Volume 409 (2001) p.953-958
DOI: 10.1038/35057192

Hidden Markov models in biological sequence analysis
Birney E.
IBM J. Res. Dev. Volume 45 (2001) p.449-454

Progress in sequencing the mouse genome.
Lindblad-Toh K, Lander ES, McPherson JD, Waterston RH, Rodgers J, Birney E.
Genesis Volume 31 (2001) p.137-141
DOI: 10.1002/gene.10016

The InterPro database, an integrated documentation resource for protein families, domains and functional sites.
Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJ, Zdobnov EM.
Nucleic Acids Res Volume 29 (2001) p.37-40
DOI: 10.1093/nar/29.1.37

Mining the draft human genome.
Birney E, Bateman A, Clamp ME, Hubbard TJ.
Nature Volume 409 (2001) p.827-828
DOI: 10.1038/35057004

2000

The Pfam protein families database.
Bateman A, Birney E, Durbin R, Eddy SR, Howe KL, Sonnhammer EL.
Nucleic Acids Res Volume 28 (2000) p.263-266
DOI: 10.1093/nar/28.1.263

The Bioperl project: motivation and usage
Stajich J, Birney E.
ACM SIGBIO Newsletter Volume 20 (2000) p.13-14
DOI: 10.1145/360262.360267

InterPro--an integrated documentation resource for protein families, domains and functional sites.
Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJ, Zdobnov EM, InterPro Consortium.
Bioinformatics Volume 16 (2000) p.1145-1150
DOI: 10.1093/bioinformatics/16.12.1145

Using GeneWise in the Drosophila annotation experiment.
Birney E, Durbin R.
Genome Res Volume 10 (2000) p.547-548
DOI: 10.1101/gr.10.4.547

Identification of domains from protein sequences.
Ponting CP, Birney E.
Methods Mol Biol Volume 143 (2000) p.53-69

ProtEST: protein multiple sequence alignments from expressed sequence tags.
Cuff JA, Birney E, Clamp ME, Barton GJ.
Bioinformatics Volume 16 (2000) p.111-116
DOI: 10.1093/bioinformatics/16.2.111

Open annotation offers a democratic solution to genome sequencing.
Hubbard T, Birney E.
Nature Volume 403 (2000) p.825
DOI: 10.1038/35002770

Comparative genomics of the eukaryotes.
Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, Fortini ME, Li PW, Apweiler R, Fleischmann W, Cherry JM, Henikoff S, Skupski MP, Misra S, Ashburner M, Birney E, Boguski MS, Brody T, Brokstein P, Celniker SE, Chervitz SA, Coates D, Cravchik A, Gabrielian A, Galle RF, Gelbart WM, George RA, Goldstein LS, Gong F, Guan P, Harris NL, Hay BA, Hoskins RA, Li J, Li Z, Hynes RO, Jones SJ, Kuehl PM, Lemaitre B, Littleton JT, Morrison DK, Mungall C, O'Farrell PH, Pickeral OK, Shue C, Vosshall LB, Zhang J, Zhao Q, Zheng XH, Lewis S.
Science Volume 287 (2000) p.2204-2215
DOI: 10.1126/science.287.5461.2204

Searching databases to find protein domain organization.
Bateman A, Birney E.
Adv Protein Chem Volume 54 (2000) p.137-157
DOI: 10.1016/s0065-3233(00)54005-4

Hidden Markov models for database similarity searches
Birney E.
Volume (2000) p.77

1999

Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs.
Jareborg N, Birney E, Durbin R.
Genome Res Volume 9 (1999) p.815-824
DOI: 10.1101/gr.9.9.815

Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins.
Bateman A, Birney E, Durbin R, Eddy SR, Finn RD, Sonnhammer EL.
Nucleic Acids Res Volume 27 (1999) p.260-262
DOI: 10.1093/nar/27.1.260

1998

Pfam: multiple sequence alignments and HMM-profiles of protein domains.
Sonnhammer EL, Eddy SR, Birney E, Bateman A, Durbin R.
Nucleic Acids Res Volume 26 (1998) p.320-322
DOI: 10.1093/nar/26.1.320

SPEM: a parser for EMBL style flat file database entries.
Pocock MR, Hubbard T, Birney E.
Bioinformatics Volume 14 (1998) p.823-824
DOI: 10.1093/bioinformatics/14.9.823

1997

Dynamite: a flexible code generating language for dynamic programming methods used in sequence comparison.
Birney E, Durbin R.
Proc Int Conf Intell Syst Mol Biol Volume 5 (1997) p.56-64

1996

PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames.
Birney E, Thompson JD, Gibson TJ.
Nucleic Acids Res Volume 24 (1996) p.2730-2739
DOI: 10.1093/nar/24.14.2730

1994

PH domain: the first anniversary.
Gibson TJ, Hyvönen M, Musacchio A, Saraste M, Birney E.
Trends Biochem Sci Volume 19 (1994) p.349-353
DOI: 10.1016/0968-0004(94)90108-2

1993

A putative homology of U2AF65 in S. cerevisiae.
Birney E, Kumar S, Krainer AR.
Nucleic Acids Res Volume 21 (1993) p.1333
DOI: 10.1093/nar/21.5.1333

Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors.
Birney E, Kumar S, Krainer AR.
Nucleic Acids Res Volume 21 (1993) p.5803-5816
DOI: 10.1093/nar/21.25.5803

1992

A putative homolog of U2AF65 in S. cerevisiae.
Birney E, Kumar S, Krainer AR.
Nucleic Acids Res Volume 20 (1992) p.4663
DOI: 10.1093/nar/20.17.4663

Services

Team members

Mary Barlow
Elspeth Bruford
Kristian Gray
Ruth Seal
Bethan  Yates