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Ewan Birney - Publications

Affiliations: 
European Bioinformatics Institute, Hinxton, England, United Kingdom 
Website:
http://www.ebi.ac.uk/~birney/

192 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Breeze CE, Paul DS, van Dongen J, Butcher LM, Ambrose JC, Barrett JE, Lowe R, Rakyan VK, Iotchkova V, Frontini M, Downes K, Ouwehand WH, Laperle J, Jacques PÉ, Bourque G, ... ... Birney E, et al. eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data. Cell Reports. 17: 2137-2150. PMID 27851974 DOI: 10.1016/j.celrep.2016.10.059  0.32
2016 Smid M, Rodríguez-González FG, Sieuwerts AM, Salgado R, Prager-Van der Smissen WJ, Vlugt-Daane MV, van Galen A, Nik-Zainal S, Staaf J, Brinkman AB, van de Vijver MJ, Richardson AL, Fatima A, Berentsen K, Butler A, ... ... Birney E, et al. Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration. Nature Communications. 7: 12910. PMID 27666519 DOI: 10.1038/ncomms12910  0.6
2016 Morganella S, Alexandrov LB, Glodzik D, Zou X, Davies H, Staaf J, Sieuwerts AM, Brinkman AB, Martin S, Ramakrishna M, Butler A, Kim HY, Borg Å, Sotiriou C, Futreal PA, ... ... Birney E, et al. The topography of mutational processes in breast cancer genomes. Nature Communications. 7: 11383. PMID 27136393 DOI: 10.1038/ncomms11383  0.6
2016 Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D, Zou X, Martincorena I, Alexandrov LB, Martin S, Wedge DC, Van Loo P, Ju YS, Smid M, Brinkman AB, Morganella S, ... ... Birney E, et al. Landscape of somatic mutations in 560 breast cancer whole-genome sequences. Nature. PMID 27135926 DOI: 10.1038/nature17676  0.6
2016 Zerbino DR, Johnson N, Juetteman T, Sheppard D, Wilder SP, Lavidas I, Nuhn M, Perry E, Raffaillac-Desfosses Q, Sobral D, Keefe D, Gräf S, Ahmed I, Kinsella R, Pritchard B, ... ... Birney E, et al. Ensembl regulation resources. Database : the Journal of Biological Databases and Curation. 2016. PMID 26888907 DOI: 10.1093/database/bav119  0.56
2015 Ip CL, Loose M, Tyson JR, de Cesare M, Brown BL, Jain M, Leggett RM, Eccles DA, Zalunin V, Urban JM, Piazza P, Bowden RJ, Paten B, Mwaigwisya S, Batty EM, ... ... Birney E, et al. MinION Analysis and Reference Consortium: Phase 1 data release and analysis. F1000research. 4: 1075. PMID 26834992 DOI: 10.12688/f1000research.7201.1  0.6
2015 Beck A, Birney E, Graeber M, Tumwine J, Hay P, Ahn HS, Patel A, du Cros P, von Seidlein L, Wareham N, Low N. Progress in Medicine: Experts Take Stock. Plos Medicine. 12: e1001933. PMID 26713445 DOI: 10.1371/journal.pmed.1001933  0.6
2015 Yates A, Akanni W, Amode MR, Barrell D, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, ... ... Birney E, et al. Ensembl 2016. Nucleic Acids Research. PMID 26687719 DOI: 10.1093/nar/gkv1157  0.6
2015 Birney E, Soranzo N. Human genomics: The end of the start for population sequencing. Nature. 526: 52-3. PMID 26432243 DOI: 10.1038/526052a  0.6
2015 Barrett JC, Dunham I, Birney E. Using human genetics to make new medicines. Nature Reviews. Genetics. 16: 561-2. PMID 26370900 DOI: 10.1038/nrg3998  0.6
2015 Huang J, Howie B, McCarthy S, Memari Y, Walter K, Min JL, Danecek P, Malerba G, Trabetti E, Zheng HF, Gambaro G, Richards JB, Durbin R, Timpson NJ, et al. Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel. Nature Communications. 6: 8111. PMID 26368830 DOI: 10.1038/ncomms9111  0.6
2015 Ding Z, Ni Y, Timmer SW, Lee BK, Battenhouse A, Louzada S, Yang F, Dunham I, Crawford GE, Lieb JD, Durbin R, Iyer VR, Birney E. Correction: Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association. Plos Genetics. 11: e1005177. PMID 25919664 DOI: 10.1371/journal.pgen.1005177  0.6
2015 Taylor PN, Porcu E, Chew S, Campbell PJ, Traglia M, Brown SJ, Mullin BH, Shihab HA, Min J, Walter K, Memari Y, Huang J, Barnes MR, Beilby JP, Charoen P, et al. Whole-genome sequence-based analysis of thyroid function. Nature Communications. 6: 5681. PMID 25743335 DOI: 10.1038/ncomms6681  0.6
2015 Cunningham F, 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 SE, ... ... Birney E, et al. Ensembl 2015. Nucleic Acids Research. 43: D662-9. PMID 25352552 DOI: 10.1093/nar/gku1010  0.6
2015 Walter K, Min JL, Huang J, Crooks L, Memari Y, McCarthy S, Perry JRB, Xu C, Futema M, Lawson D, Iotchkova V, Schiffels S, Hendricks AE, Danecek P, Li R, ... ... Birney E, et al. The UK10K project identifies rare variants in health and disease Nature. 526: 82-89. DOI: 10.1038/nature14962  0.6
2014 Ding Z, Ni Y, Timmer SW, Lee BK, Battenhouse A, Louzada S, Yang F, Dunham I, Crawford GE, Lieb JD, Durbin R, Iyer VR, Birney E. Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association. Plos Genetics. 10: e1004798. PMID 25411781 DOI: 10.1371/journal.pgen.1004798  0.6
2014 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, et al. Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proceedings of the National Academy of Sciences of the United States of America. 111: E3366. PMID 25275169 DOI: 10.1073/pnas.1410434111  0.6
2014 Timpson NJ, Walter K, Min JL, Tachmazidou I, Malerba G, Shin SY, Chen L, Futema M, Southam L, Iotchkova V, Cocca M, Huang J, Memari Y, McCarthy S, Danecek P, et al. A rare variant in APOC3 is associated with plasma triglyceride and VLDL levels in Europeans. Nature Communications. 5: 4871. PMID 25225788 DOI: 10.1038/ncomms5871  0.6
2014 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, et al. Defining functional DNA elements in the human genome. Proceedings of the National Academy of Sciences of the United States of America. 111: 6131-8. PMID 24753594 DOI: 10.1073/pnas.1318948111  0.6
2014 Marti-Solano M, Birney E, Bril A, Della Pasqua O, Kitano H, Mons B, Xenarios I, Sanz F. Integrative knowledge management to enhance pharmaceutical R&D. Nature Reviews. Drug Discovery. 13: 239-40. PMID 24687050 DOI: 10.1038/nrd4290  0.6
2014 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, et al. The EBI RDF platform: linked open data for the life sciences. Bioinformatics (Oxford, England). 30: 1338-9. PMID 24413672 DOI: 10.1093/bioinformatics/btt765  0.6
2014 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. Genomic and phenotypic characterization of a wild medaka population: towards the establishment of an isogenic population genetic resource in fish. G3 (Bethesda, Md.). 4: 433-45. PMID 24408034 DOI: 10.1534/g3.113.008722  0.6
2014 Birney E, Pritchard JK. Archaic humans: Four makes a party. Nature. 505: 32-4. PMID 24352230 DOI: 10.1038/nature12847  1
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, ... ... Birney E, et al. Ensembl 2014. Nucleic Acids Research. 42: D749-55. PMID 24316576 DOI: 10.1093/nar/gkt1196  0.6
2014 Brooksbank C, Bergman MT, Apweiler R, Birney E, Thornton J. The European Bioinformatics Institute's data resources 2014. Nucleic Acids Research. 42: D18-25. PMID 24271396 DOI: 10.1093/nar/gkt1206  0.6
2014 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, ... ... Birney E, et al. The Reactome pathway knowledgebase. Nucleic Acids Research. 42: D472-7. PMID 24243840 DOI: 10.1093/nar/gkt1102  0.6
2013 Wright CF, Middleton A, Burton H, Cunningham F, Humphries SE, Hurst J, Birney E, Firth HV. Policy challenges of clinical genome sequencing. Bmj (Clinical Research Ed.). 347: f6845. PMID 24270507 DOI: 10.1136/bmj.f6845  0.6
2013 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, et al. Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development. Nucleic Acids Research. 41: 3600-18. PMID 23393190 DOI: 10.1093/nar/gkt030  0.6
2013 Goldman N, Bertone P, Chen S, Dessimoz C, LeProust EM, Sipos B, Birney E. Towards practical, high-capacity, low-maintenance information storage in synthesized DNA. Nature. 494: 77-80. PMID 23354052 DOI: 10.1038/nature11875  0.6
2013 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. Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Research. 41: 827-41. PMID 23221638 DOI: 10.1093/nar/gks1284  0.6
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, ... ... Birney E, et al. Ensembl 2013. Nucleic Acids Research. 41: D48-55. PMID 23203987 DOI: 10.1093/nar/gks1236  0.6
2013 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. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Research. 41: D171-6. PMID 23203885 DOI: 10.1093/nar/gks1221  0.6
2012 Cochrane G, Cook CE, Birney E. The future of DNA sequence archiving. Gigascience. 1: 2. PMID 23587147 DOI: 10.1186/2047-217X-1-2  0.6
2012 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, et al. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Research. 22: 1798-812. PMID 22955990 DOI: 10.1101/gr.139105.112  0.6
2012 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, et al. Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Research. 22: 1658-67. PMID 22955978 DOI: 10.1101/gr.136838.111  0.6
2012 . An integrated encyclopedia of DNA elements in the human genome. Nature. 489: 57-74. PMID 22955616 DOI: 10.1038/nature11247  0.6
2012 Birney E. The making of ENCODE: Lessons for big-data projects. Nature. 489: 49-51. PMID 22955613 DOI: 10.1038/489049a  1
2012 Spivakov M, Akhtar J, Kheradpour P, Beal K, Girardot C, Koscielny G, Herrero J, Kellis M, Furlong EE, Birney E. Analysis of variation at transcription factor binding sites in Drosophila and humans. Genome Biology. 13: R49. PMID 22950968 DOI: 10.1186/gb-2012-13-9-r49  1
2012 Yip KY, Cheng C, Bhardwaj N, Brown JB, Leng J, Kundaje A, Rozowsky J, Birney E, Bickel P, Snyder M, Gerstein M. Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biology. 13: R48. PMID 22950945 DOI: 10.1186/gb-2012-13-9-r48  1
2012 Dong X, Greven MC, Kundaje A, Djebali S, Brown JB, Cheng C, Gingeras TR, Gerstein M, Guigó R, Birney E, Weng Z. Modeling gene expression using chromatin features in various cellular contexts. Genome Biology. 13: R53. PMID 22950368 DOI: 10.1186/gb-2012-13-9-r53  1
2012 Ware JS, Walsh R, Cunningham F, Birney E, Cook SA. Paralogous annotation of disease-causing variants in long QT syndrome genes. Human Mutation. 33: 1188-91. PMID 22581653 DOI: 10.1002/humu.22114  0.6
2012 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, et al. The genomic basis of adaptive evolution in threespine sticklebacks. Nature. 484: 55-61. PMID 22481358 DOI: 10.1038/nature10944  0.6
2012 Schulz MH, Zerbino DR, Vingron M, Birney E. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics (Oxford, England). 28: 1086-92. PMID 22368243 DOI: 10.1093/bioinformatics/bts094  1
2012 Junion G, Spivakov M, Girardot C, Braun M, Gustafson EH, Birney E, Furlong EE. A transcription factor collective defines cardiac cell fate and reflects lineage history. Cell. 148: 473-86. PMID 22304916 DOI: 10.1016/j.cell.2012.01.030  1
2012 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: improvements to a bioinformatics resource for invertebrate vector genomics. Nucleic Acids Research. 40: D729-34. PMID 22135296 DOI: 10.1093/nar/gkr1089  0.6
2012 Lee BK, Bhinge AA, Battenhouse A, McDaniell RM, Liu Z, Song L, Ni Y, Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR. Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. Genome Research. 22: 9-24. PMID 22090374 DOI: 10.1101/gr.127597.111  0.6
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, ... ... Birney E, et al. Ensembl 2012. Nucleic Acids Research. 40: D84-90. PMID 22086963 DOI: 10.1093/nar/gkr991  0.6
2012 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, et al. Major submissions tool developments at the European Nucleotide Archive. Nucleic Acids Research. 40: D43-7. PMID 22080548 DOI: 10.1093/nar/gkr946  0.6
2012 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, ... ... Birney E, et al. Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. Nucleic Acids Research. 40: D91-7. PMID 22067447 DOI: 10.1093/nar/gkr895  0.6
2012 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, ... ... Birney E, et al. The BioPAX community standard for pathway data sharing (Nature Biotechnology (2010) 28, (935-942)) Nature Biotechnology. 30: 365. DOI: 10.1038/nbt0412-365c  0.6
2011 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, ... ... Birney E, et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 478: 476-82. PMID 21993624 DOI: 10.1038/nature10530  0.6
2011 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, et al. RNAcentral: A vision for an international database of RNA sequences. Rna (New York, N.Y.). 17: 1941-6. PMID 21940779 DOI: 10.1261/rna.2750811  0.6
2011 Keane TM, Goodstadt L, Danecek P, White MA, Wong K, Yalcin B, Heger A, Agam A, Slater G, Goodson M, Furlotte NA, Eskin E, NellÃ¥ker C, Whitley H, Cleak J, ... ... Birney E, et al. Mouse genomic variation and its effect on phenotypes and gene regulation. Nature. 477: 289-94. PMID 21921910 DOI: 10.1038/nature10413  0.6
2011 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, ... ... Birney E, et al. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Research. 21: 1757-67. PMID 21750106 DOI: 10.1101/gr.121541.111  1
2011 . A user's guide to the encyclopedia of DNA elements (ENCODE). Plos Biology. 9: e1001046. PMID 21526222 DOI: 10.1371/journal.pbio.1001046  1
2011 Birney E. Chromatin and heritability: how epigenetic studies can complement genetic approaches. Trends in Genetics : Tig. 27: 172-6. PMID 21414682 DOI: 10.1016/j.tig.2011.02.005  1
2011 Vilella AJ, Birney E, Flicek P, Herrero J. Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses. Genome Biology. 12: 401. PMID 21320298 DOI: 10.1186/gb-2011-12-2-401  0.6
2011 Hsi-Yang Fritz M, Leinonen R, Cochrane G, Birney E. Efficient storage of high throughput DNA sequencing data using reference-based compression. Genome Research. 21: 734-40. PMID 21245279 DOI: 10.1101/gr.114819.110  1
2011 Birney E. Assemblies: the good, the bad, the ugly. Nature Methods. 8: 59-60. PMID 21191376 DOI: 10.1038/nmeth0111-59  1
2011 Boyle AP, Song L, Lee BK, London D, Keefe D, Birney E, Iyer VR, Crawford GE, Furey TS. High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Research. 21: 456-64. PMID 21106903 DOI: 10.1101/gr.112656.110  0.6
2011 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, ... ... Birney E, et al. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Research. 39: D691-7. PMID 21067998 DOI: 10.1093/nar/gkq1018  0.6
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, ... ... Birney E, et al. Ensembl 2011. Nucleic Acids Research. 39: D800-6. PMID 21045057 DOI: 10.1093/nar/gkq1064  0.6
2011 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, et al. The European Nucleotide Archive. Nucleic Acids Research. 39: D28-31. PMID 20972220 DOI: 10.1093/nar/gkq967  0.6
2010 Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR. Allele-specific and heritable chromatin signatures in humans. Human Molecular Genetics. 19: R204-9. PMID 20846943 DOI: 10.1093/hmg/ddq404  1
2010 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, ... ... Birney E, et al. The BioPAX community standard for pathway data sharing. Nature Biotechnology. 28: 935-42. PMID 20829833 DOI: 10.1038/nbt.1666  0.6
2010 Gnad F, Forner F, Zielinska DF, Birney E, Gunawardena J, Mann M. Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes, and mitochondria. Molecular & Cellular Proteomics : McP. 9: 2642-53. PMID 20688971 DOI: 10.1074/mcp.M110.001594  0.6
2010 Jassal B, Jupe S, Caudy M, Birney E, Stein L, Hermjakob H, D'Eustachio P. The systematic annotation of the three main GPCR families in Reactome. Database : the Journal of Biological Databases and Curation. 2010: baq018. PMID 20671204 DOI: 10.1093/database/baq018  0.6
2010 Parkhill J, Birney E, Kersey P. Genomic information infrastructure after the deluge. Genome Biology. 11: 402. PMID 20670392 DOI: 10.1186/gb-2010-11-7-402  0.6
2010 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, et al. Finding and sharing: new approaches to registries of databases and services for the biomedical sciences. Database : the Journal of Biological Databases and Curation. 2010: baq014. PMID 20627863 DOI: 10.1093/database/baq014  0.6
2010 Rios D, McLaren WM, Chen Y, Birney E, Stabenau A, Flicek P, Cunningham F. A database and API for variation, dense genotyping and resequencing data. Bmc Bioinformatics. 11: 238. PMID 20459810 DOI: 10.1186/1471-2105-11-238  1
2010 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. Ensembl variation resources. Bmc Genomics. 11: 293. PMID 20459805 DOI: 10.1186/1471-2164-11-293  1
2010 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, ... ... Birney E, et al. A draft sequence of the Neandertal genome. Science (New York, N.Y.). 328: 710-22. PMID 20448178 DOI: 10.1126/science.1188021  0.6
2010 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, ... ... Birney E, et al. The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance. Genome Research. 20: 791-803. PMID 20430781 DOI: 10.1101/gr.103499.109  0.6
2010 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, ... ... Birney E, et al. Locus Reference Genomic sequences: an improved basis for describing human DNA variants. Genome Medicine. 2: 24. PMID 20398331 DOI: 10.1186/gm145  1
2010 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, ... ... Birney E, et al. Heritable individual-specific and allele-specific chromatin signatures in humans. Science (New York, N.Y.). 328: 235-9. PMID 20299549 DOI: 10.1126/science.1184655  1
2010 Hoffman MM, Birney E. An effective model for natural selection in promoters. Genome Research. 20: 685-92. PMID 20194951 DOI: 10.1101/gr.096719.109  1
2010 Reuveni E, Birney E, Gross CT. The consequence of natural selection on genetic variation in the mouse. Genomics. 95: 196-202. PMID 20171270 DOI: 10.1016/j.ygeno.2010.02.004  0.6
2010 Young AL, Abaan HO, Zerbino D, Mullikin JC, Birney E, Margulies EH. A new strategy for genome assembly using short sequence reads and reduced representation libraries. Genome Research. 20: 249-56. PMID 20123915 DOI: 10.1101/gr.097956.109  0.6
2010 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, ... ... Birney E, et al. A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature. 463: 184-90. PMID 20016488 DOI: 10.1038/nature08629  0.6
2010 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, et al. Improvements to services at the European Nucleotide Archive. Nucleic Acids Research. 38: D39-45. PMID 19906712 DOI: 10.1093/nar/gkp998  0.6
2010 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, ... ... Birney E, et al. Ensembl's 10th year. Nucleic Acids Research. 38: D557-62. PMID 19906699 DOI: 10.1093/nar/gkp972  0.6
2010 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, et al. Ensembl Genomes: extending Ensembl across the taxonomic space. Nucleic Acids Research. 38: D563-9. PMID 19884133 DOI: 10.1093/nar/gkp871  0.6
2010 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, ... ... Birney E, et al. EMMA--mouse mutant resources for the international scientific community. Nucleic Acids Research. 38: D570-6. PMID 19783817 DOI: 10.1093/nar/gkp799  0.6
2010 Fernández XM, Birney E. Ensembl genome browser Vogel and Motulsky's Human Genetics: Problems and Approaches (Fourth Edition). 923-939. DOI: 10.1007/978-3-540-37654-5_45  0.6
2009 Zerbino DR, McEwen GK, Margulies EH, Birney E. Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler. Plos One. 4: e8407. PMID 20027311 DOI: 10.1371/journal.pone.0008407  1
2009 Kahlem P, Clegg A, Reisinger F, Xenarios I, Hermjakob H, Orengo C, Birney E. ENFIN--A European network for integrative systems biology. Comptes Rendus Biologies. 332: 1050-8. PMID 19909926 DOI: 10.1016/j.crvi.2009.09.003  0.6
2009 Flicek P, Birney E. Sense from sequence reads: methods for alignment and assembly. Nature Methods. 6: S6-S12. PMID 19844229 DOI: 10.1038/nmeth.1376  0.6
2009 Durinck S, Spellman PT, Birney E, Huber W. Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nature Protocols. 4: 1184-91. PMID 19617889 DOI: 10.1038/nprot.2009.97  0.6
2009 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, ... ... Birney E, et al. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Research. 19: 1316-23. PMID 19498102 DOI: 10.1101/gr.080531.108  0.6
2009 Paten B, Herrero J, Beal K, Birney E. Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment. Bioinformatics (Oxford, England). 25: 295-301. PMID 19056777 DOI: 10.1093/bioinformatics/btn630  0.6
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, ... ... Birney E, et al. Ensembl 2009. Nucleic Acids Research. 37: D690-7. PMID 19033362 DOI: 10.1093/nar/gkn828  0.6
2009 Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E. EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Research. 19: 327-35. PMID 19029536 DOI: 10.1101/gr.073585.107  1
2009 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, ... ... Birney E, et al. VectorBase: a data resource for invertebrate vector genomics. Nucleic Acids Research. 37: D583-7. PMID 19028744 DOI: 10.1093/nar/gkn857  0.6
2009 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, ... ... Birney E, et al. Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Research. 37: D619-22. PMID 18981052 DOI: 10.1093/nar/gkn863  0.6
2009 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, ... ... Birney E, et al. Petabyte-scale innovations at the European Nucleotide Archive. Nucleic Acids Research. 37: D19-25. PMID 18978013 DOI: 10.1093/nar/gkn765  0.6
2009 Gnad F, Oroshi M, Birney E, Mann M. MAPU 2.0: high-accuracy proteomes mapped to genomes. Nucleic Acids Research. 37: D902-6. PMID 18948283 DOI: 10.1093/nar/gkn773  0.6
2009 Megy K, Hammond M, Lawson D, Bruggner RV, Birney E, Collins FH. Genomic resources for invertebrate vectors of human pathogens, and the role of VectorBase. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 9: 308-13. PMID 18262474 DOI: 10.1016/j.meegid.2007.12.007  0.6
2009 Flicek P, Birney E. Visualising the epigenome Epigenomics. 55-66. DOI: 10.1007/978-1-4020-9187-2_4  0.6
2009 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, ... ... Birney E, et al. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes (Genome Research (2009) 19, (1316-1323)) Genome Research. 19: 1506.  0.6
2008 Paten B, Herrero J, Fitzgerald S, Beal K, Flicek P, Holmes I, Birney E. Genome-wide nucleotide-level mammalian ancestor reconstruction. Genome Research. 18: 1829-43. PMID 18849525 DOI: 10.1101/gr.076521.108  1
2008 Paten B, Herrero J, Beal K, Fitzgerald S, Birney E. Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Research. 18: 1814-28. PMID 18849524 DOI: 10.1101/gr.076554.108  1
2008 Fernández-Suárez XM, Birney E. Advanced genomic data mining. Plos Computational Biology. 4: e1000121. PMID 18818719 DOI: 10.1371/journal.pcbi.1000121  0.6
2008 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. Integrating biological data--the Distributed Annotation System. Bmc Bioinformatics. 9: S3. PMID 18673527 DOI: 10.1186/1471-2105-9-S8-S3  1
2008 O'Reilly PF, Birney E, Balding DJ. Confounding between recombination and selection, and the Ped/Pop method for detecting selection. Genome Research. 18: 1304-13. PMID 18617692 DOI: 10.1101/gr.067181.107  0.6
2008 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, ... ... Birney E, et al. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nature Biotechnology. 26: 779-85. PMID 18612301 DOI: 10.1038/nbt1414  0.6
2008 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. Arabidopsis reactome: a foundation knowledgebase for plant systems biology. The Plant Cell. 20: 1426-36. PMID 18591350 DOI: 10.1105/tpc.108.057976  0.6
2008 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, et al. An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Research. 18: 1518-29. PMID 18577705 DOI: 10.1101/gr.077479.108  0.6
2008 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, et al. Genome analysis of the platypus reveals unique signatures of evolution. Nature. 453: 175-83. PMID 18464734 DOI: 10.1038/nature06936  0.6
2008 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, et al. SNP and haplotype mapping for genetic analysis in the rat. Nature Genetics. 40: 560-6. PMID 18443594 DOI: 10.1038/ng.124  0.6
2008 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. What everybody should know about the rat genome and its online resources. Nature Genetics. 40: 523-7. PMID 18443589 DOI: 10.1038/ng0508-523  0.6
2008 Birney E. Levers and fulcrums: progress in cis-regulatory motif models. Nature Methods. 5: 297-8. PMID 18376393 DOI: 10.1038/nmeth0408-297  1
2008 Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research. 18: 821-9. PMID 18349386 DOI: 10.1101/gr.074492.107  1
2008 Margulies EH, Birney E. Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes. Nature Reviews. Genetics. 9: 303-13. PMID 18347593 DOI: 10.1038/nrg2185  0.6
2008 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, ... ... Birney E, et al. Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database. Nucleic Acids Research. 36: D5-12. PMID 18039715 DOI: 10.1093/nar/gkm1018  0.6
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, ... ... Birney E, et al. Ensembl 2008. Nucleic Acids Research. 36: D707-14. PMID 18000006 DOI: 10.1093/nar/gkm988  0.6
2008 Bruford EA, Lush MJ, Wright MW, Sneddon TP, Povey S, Birney E. The HGNC Database in 2008: a resource for the human genome. Nucleic Acids Research. 36: D445-8. PMID 17984084 DOI: 10.1093/nar/gkm881  0.6
2008 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, et al. Genome analysis of the platypus reveals unique signatures of evolution (Nature (2008) 453, (175-183)) Nature. 455: 256. DOI: 10.1038/nature07253  0.6
2008 Reisinger F, Corpas M, Hancock J, Hermjakob H, Birney E, Kahlem P. ENFIN - An integrative structure for systems biology Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5109: 132-143. DOI: 10.1007/978-3-540-69828-9_13  1
2007 Birney E. Evolutionary genomics: come fly with us. Nature. 450: 184-5. PMID 17994082 DOI: 10.1038/450184a  1
2007 Birney E. Double Dutch for duplications. Nature Genetics. 39: 1303-4. PMID 17968343 DOI: 10.1038/ng1107-1303  1
2007 Spudich G, Fernández-Suárez XM, Birney E. Genome browsing with Ensembl: a practical overview. Briefings in Functional Genomics & Proteomics. 6: 202-19. PMID 17967807 DOI: 10.1093/bfgp/elm025  0.6
2007 Kahlem P, Birney E. ENFIN a network to enhance integrative systems biology. Annals of the New York Academy of Sciences. 1115: 23-31. PMID 17934049 DOI: 10.1196/annals.1407.016  1
2007 Del Bene F, Ettwiller L, Skowronska-Krawczyk D, Baier H, Matter JM, Birney E, Wittbrodt J. In vivo validation of a computationally predicted conserved Ath5 target gene set. Plos Genetics. 3: 1661-71. PMID 17892326 DOI: 10.1371/journal.pgen.0030159  1
2007 Gräf S, Nielsen FG, Kurtz S, Huynen MA, Birney E, Stunnenberg H, Flicek P. Optimized design and assessment of whole genome tiling arrays. Bioinformatics (Oxford, England). 23: i195-204. PMID 17646297 DOI: 10.1093/bioinformatics/btm200  1
2007 Scherer SW, Lee C, Birney E, Altshuler DM, Eichler EE, Carter NP, Hurles ME, Feuk L. Challenges and standards in integrating surveys of structural variation. Nature Genetics. 39: S7-15. PMID 17597783 DOI: 10.1038/ng2093  0.6
2007 Ettwiller L, Paten B, Ramialison M, Birney E, Wittbrodt J. Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation. Nature Methods. 4: 563-5. PMID 17589518 DOI: 10.1038/nmeth1061  0.6
2007 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, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/nature05874  1
2007 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, et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research. 17: 760-74. PMID 17567995 DOI: 10.1101/gr.6034307  0.6
2007 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, ... ... Birney E, et al. The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Research. 17: 691-707. PMID 17567990 DOI: 10.1101/gr.5704207  0.6
2007 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, ... ... Birney E, et al. Genome sequence of Aedes aegypti, a major arbovirus vector. Science (New York, N.Y.). 316: 1718-23. PMID 17510324 DOI: 10.1126/science.1138878  0.6
2007 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, ... ... Birney E, et al. The implications of alternative splicing in the ENCODE protein complement. Proceedings of the National Academy of Sciences of the United States of America. 104: 5495-500. PMID 17372197 DOI: 10.1073/pnas.0700800104  1
2007 Vastrik I, D'Eustachio P, Schmidt E, Joshi-Tope G, Gopinath G, Croft D, de Bono B, Gillespie M, Jassal B, Lewis S, Matthews L, Wu G, Birney E, Stein L. Reactome: a knowledge base of biologic pathways and processes. Genome Biology. 8: R39. PMID 17367534 DOI: 10.1186/gb-2007-8-3-r39  1
2007 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, ... ... Birney E, et al. Patterns of somatic mutation in human cancer genomes. Nature. 446: 153-8. PMID 17344846 DOI: 10.1038/nature05610  0.6
2007 Mirabeau O, Perlas E, Severini C, Audero E, Gascuel O, Possenti R, Birney E, Rosenthal N, Gross C. Identification of novel peptide hormones in the human proteome by hidden Markov model screening. Genome Research. 17: 320-7. PMID 17284679 DOI: 10.1101/gr.5755407  0.6
2007 Sharakhova MV, Hammond MP, Lobo NF, Krzywinski J, Unger MF, Hillenmeyer ME, Bruggner RV, Birney E, Collins FH. Update of the Anopheles gambiae PEST genome assembly. Genome Biology. 8: R5. PMID 17210077 DOI: 10.1186/gb-2007-8-1-r5  1
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, ... ... Birney E, et al. Ensembl 2007. Nucleic Acids Research. 35: D610-7. PMID 17148474 DOI: 10.1093/nar/gkl996  0.6
2007 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, ... ... Birney E, et al. VectorBase: a home for invertebrate vectors of human pathogens. Nucleic Acids Research. 35: D503-5. PMID 17145709 DOI: 10.1093/nar/gkl960  0.6
2007 Hoffman MM, Birney E. Estimating the neutral rate of nucleotide substitution using introns. Molecular Biology and Evolution. 24: 522-31. PMID 17122369 DOI: 10.1093/molbev/msl179  1
2007 Nielsen F, Graef S, Zhang X, Kurtz S, Denissov S, Green R, Birney E, Flicek P, Huynen M, Stunnenberg H. Optimising oligonucleotide array design for ChIP-on-chip Bmc Bioinformatics. 8. DOI: 10.1186/1471-2105-8-S8-P4  1
2006 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, et al. EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biology. 7: S2.1-31. PMID 16925836 DOI: 10.1186/gb-2006-7-s1-s2  0.6
2006 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. TranscriptSNPView: A genome-wide catalog of mouse coding variation [1] Nature Genetics. 38: 853. PMID 16874317 DOI: 10.1038/ng0806-853a  1
2006 Kahlem P, Birney E. Dry work in a wet world: computation in systems biology Molecular Systems Biology [Electronic Resource].. 2: 40. PMID 16820781 DOI: 10.1038/msb4100080  0.6
2006 Meynert A, Birney E. Picking Pyknons out of the Human Genome Cell. 125: 836-838. PMID 16751093 DOI: 10.1016/j.cell.2006.05.019  1
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, et al. Ensembl 2006. Nucleic Acids Research. 34: D556-61. PMID 16381931 DOI: 10.1093/nar/gkj133  0.6
2006 Prlić A, Birney E, Cox T, Down TA, Finn R, Gräf S, Jackson D, Kähäri A, Kulesha E, Pettett R, Smith J, Stalker J, Hubbard TJP. The distributed annotation system for integration of biological data Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4075: 195-203.  0.6
2006 Schmidt E, Birney E, Croft D, De Bono B, D'Eustachio P, Gillespie M, Gopinath G, Jassal B, Lewis S, Matthews L, Stein L, Vastrik I, Wu G. Reactome - A knowledgebase of biological pathways Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4277: 710-719.  1
2005 Birney E, Ciliberto A, Colding-Jørgensen M, Goldbeter A, Hohmann S, Kuiper M, Lehrach H, Miczka G, Mosekilde E, Westerhoff H, Wolkenhauer O. Report of an EU projects workshop on systems biology held in Brussels, Belgium on 8 December 2004. Systems Biology. 152: 55-60. PMID 17044232  1
2005 Ettwiller L, Paten B, Souren M, Loosli F, Wittbrodt J, Birney E. The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates. Genome Biology. 6: R104. PMID 16356267 DOI: 10.1186/gb-2005-6-12-r104  0.6
2005 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. Gene finding in the chicken genome. Bmc Bioinformatics. 6: 131. PMID 15924626 DOI: 10.1186/1471-2105-6-131  1
2005 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. A survey of homozygous deletions in human cancer genomes. Proceedings of the National Academy of Sciences of the United States of America. 102: 4542-7. PMID 15761058 DOI: 10.1073/pnas.0408593102  0.6
2005 Slater GSC, Birney E. Automated generation of heuristics for biological sequence comparison Bmc Bioinformatics. 6. PMID 15713233 DOI: 10.1186/1471-2105-6-31  1
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, ... ... Birney E, et al. Ensembl 2005. Nucleic Acids Research. 33: D447-53. PMID 15608235 DOI: 10.1093/nar/gki138  1
2005 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. Reactome: a knowledgebase of biological pathways. Nucleic Acids Research. 33: D428-32. PMID 15608231 DOI: 10.1093/nar/gki072  0.6
2005 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, ... ... Birney E, et al. Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags. Genome Research. 15: 174-83. PMID 15590942 DOI: 10.1101/gr.3011405  0.6
2004 . Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 432: 695-716. PMID 15592404 DOI: 10.1038/nature03154  0.6
2004 Feingold EA, Good PJ, Guyer MS, Kamholz S, Liefer L, Wetterstrand K, Collins FS, Gingeras TR, Kampa D, Sekinger EA, Cheng J, Hirsch H, Ghosh S, Zhu Z, Patel S, ... ... Birney E, et al. The ENCODE (ENCyclopedia of DNA Elements) Project Science. 306: 636-640. PMID 15499007 DOI: 10.1126/science.1105136  0.6
2004 Kersey PJ, Duarte J, Williams A, Karavidopoulou Y, Birney E, Apweiler R. The International Protein Index: an integrated database for proteomics experiments. Proteomics. 4: 1985-8. PMID 15221759 DOI: 10.1002/pmic.200300721  0.6
2004 Birney E, Clamp M. Biological database design and implementation Briefings in Bioinformatics. 5: 31-38. PMID 15153304  0.6
2004 Hammond MP, Birney E. Genome information resources - Developments at Ensembl Trends in Genetics. 20: 268-272. PMID 15145580 DOI: 10.1016/j.tig.2004.04.002  1
2004 Birney E, Clamp M, Durbin R. GeneWise and Genomewise Genome Research. 14: 988-995. PMID 15123596 DOI: 10.1101/gr.1865504  1
2004 Montgomery SB, Astakhova T, Bilenky M, Birney E, Fu T, Hassel M, Melsopp C, Rak M, Robertson AG, Sleumer M, Siddiqui AS, Jones SJ. Sockeye: a 3D environment for comparative genomics. Genome Research. 14: 956-62. PMID 15123592 DOI: 10.1101/gr.1890304  0.6
2004 Stabenau A, McVicker G, Melsopp C, Proctor G, Clamp M, Birney E. The Ensembl core software libraries. Genome Research. 14: 929-33. PMID 15123588 DOI: 10.1101/gr.1857204  1
2004 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, et al. An overview of Ensembl. Genome Research. 14: 925-8. PMID 15078858 DOI: 10.1101/gr.1860604  1
2004 Dermitzakis ET, Kirkness E, Schwarz S, Birney E, Reymond A, Antonarakis SE. 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 Genome Research. 14: 852-859. PMID 15078857 DOI: 10.1101/gr.1934904  0.6
2004 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, ... ... Birney E, et al. A SNP map of the rat genome generated from cDNA sequences. Science (New York, N.Y.). 303: 807. PMID 14764869 DOI: 10.1126/science.1092427  0.6
2004 Mongin E, Louis C, Holt RA, Birney E, Collins FH. The Anopheles gambiae genome: an update. Trends in Parasitology. 20: 49-52. PMID 14747013 DOI: 10.1016/j.pt.2003.11.003  0.6
2004 Kasprzyk A, Keefe D, Smedley D, London D, Spooner W, Melsopp C, Hammond M, Rocca-Serra P, Cox T, Birney E. EnsMart: a generic system for fast and flexible access to biological data. Genome Research. 14: 160-9. PMID 14707178 DOI: 10.1101/gr.1645104  0.6
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, et al. Ensembl 2004. Nucleic Acids Research. 32: D468-70. PMID 14681459 DOI: 10.1093/nar/gkh038  0.6
2003 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. The Genome Knowledgebase: a resource for biologists and bioinformaticists. Cold Spring Harbor Symposia On Quantitative Biology. 68: 237-43. PMID 15338623  0.6
2003 Birney E. Ensembl: A genome infrastructure Cold Spring Harbor Symposia On Quantitative Biology. 68: 213-215. PMID 15338620  0.6
2003 Ettwiller LM, Rung J, Birney E. Discovering novel cis-regulatory motifs using functional networks. Genome Research. 13: 883-95. PMID 12727907 DOI: 10.1101/gr.866403  1
2003 Salzberg S, Birney E, Eddy S, White O. Unrestricted free access works and must continue. Nature. 422: 801. PMID 12712164 DOI: 10.1038/422801a  0.6
2003 Ureta-Vidal A, Ettwiller L, Birney E. Comparative genomics: genome-wide analysis in metazoan eukaryotes. Nature Reviews. Genetics. 4: 251-62. PMID 12671656 DOI: 10.1038/nrg1043  1
2003 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, et al. The European Bioinformatics Institute's data resources. Nucleic Acids Research. 31: 43-50. PMID 12519944 DOI: 10.1093/nar/gkg066  0.6
2003 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, ... ... Birney E, et al. Ensembl 2002: accommodating comparative genomics. Nucleic Acids Research. 31: 38-42. PMID 12519943 DOI: 10.1093/nar/gkg083  0.6
2002 Lewis SE, Searle SM, Harris N, Gibson M, Lyer V, Richter J, Wiel C, Bayraktaroglu L, Birney E, Crosby MA, Kaminker JS, Matthews BB, Prochnik SE, Smithy CD, Tupy JL, et al. Apollo: a sequence annotation editor. Genome Biology. 3: RESEARCH0082. PMID 12537571  0.6
2002 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, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 420: 520-62. PMID 12466850 DOI: 10.1038/nature01262  0.6
2002 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, ... ... Birney E, et al. The Bioperl toolkit: Perl modules for the life sciences. Genome Research. 12: 1611-8. PMID 12368254 DOI: 10.1101/gr.361602  0.6
2002 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, et al. Immunity-related genes and gene families in Anopheles gambiae. Science (New York, N.Y.). 298: 159-65. PMID 12364793 DOI: 10.1126/science.1077136  0.6
2002 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, et al. Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science (New York, N.Y.). 298: 149-59. PMID 12364792 DOI: 10.1126/science.1077061  0.6
2002 Birney E, Clamp M, Hubbard T. Databases and tools for browsing genomes Annual Review of Genomics and Human Genetics. 3: 293-310. PMID 12194990 DOI: 10.1146/annurev.genom.3.030502.101529  0.6
2002 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, ... ... Birney E, et al. A physical map of the mouse genome. Nature. 418: 743-50. PMID 12181558 DOI: 10.1038/nature00957  0.6
2002 Rust AG, Mongin E, Birney E. Genome annotation techniques: New approaches and challenges Drug Discovery Today. 7: S70-S76. PMID 12047883 DOI: 10.1016/S1359-6446(02)02289-4  1
2002 Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL. The Pfam protein families database. Nucleic Acids Research. 30: 276-80. PMID 11752314  0.6
2002 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, et al. The Ensembl genome database project. Nucleic Acids Research. 30: 38-41. PMID 11752248  1
2002 Rust AG, Morgin E, Birney E. Genome annotation: Approaches and challenges | Annotation du génome: Approches et défis Biofutur. 23-25.  1
2001 Lindblad-Toh K, Lander ES, McPherson JD, Waterston RH, Rodgers J, Birney E. Progress in sequencing the mouse genome. Genesis (New York, N.Y. : 2000). 31: 137-41. PMID 11783003 DOI: 10.1002/gene.10016  1
2001 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, ... ... Birney E, et al. Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature. 409: 953-8. PMID 11237021 DOI: 10.1038/35057192  0.6
2001 Futreal PA, Kasprzyk A, Birney E, Mullikin JC, Wooster R, Stratton MR. Cancer and genomics Nature. 409: 850-852. PMID 11237008 DOI: 10.1038/35057046  0.6
2001 Birney E, Bateman A, Clamp ME, Hubbard TJ. Mining the draft human genome Nature. 409: 827-828. PMID 11236999 DOI: 10.1038/35057004  0.6
2001 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, et al. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Research. 29: 37-40. PMID 11125043  0.6
2001 Birney E. Hidden Markov models in biological sequence analysis Ibm Journal of Research and Development. 45: 449-454.  0.6
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