| Year |
Citation |
Score |
| 2024 |
Birney E. A society-wide conversation is needed about germline genome editing using CRISPR. Nature Medicine. 30: 30-32. PMID 38177854 DOI: 10.1038/s41591-023-02681-1 |
0.323 |
|
| 2023 |
Weilguny L, De Maio N, Munro R, Manser C, Birney E, Loose M, Goldman N. Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design. Nature Biotechnology. PMID 36593407 DOI: 10.1038/s41587-022-01580-z |
0.31 |
|
| 2022 |
Fitzgerald T, Birney E. CNest: A novel copy number association discovery method uncovers 862 new associations from 200,629 whole-exome sequence datasets in the UK Biobank. Cell Genomics. 2: 100167. PMID 36779085 DOI: 10.1016/j.xgen.2022.100167 |
0.364 |
|
| 2022 |
Morales J, Pujar S, Loveland JE, Astashyn A, Bennett R, Berry A, Cox E, Davidson C, Ermolaeva O, Farrell CM, Fatima R, Gil L, Goldfarb T, Gonzalez JM, Haddad D, ... ... Birney E, et al. A joint NCBI and EMBL-EBI transcript set for clinical genomics and research. Nature. 604: 310-315. PMID 35388217 DOI: 10.1038/s41586-022-04558-8 |
0.347 |
|
| 2022 |
Ugolini C, Mulroney L, Leger A, Castelli M, Criscuolo E, Williamson MK, Davidson AD, Almuqrin A, Giambruno R, Jain M, Frigè G, Olsen H, Tzertzinis G, Schildkraut I, Wulf MG, ... ... Birney E, et al. Nanopore ReCappable sequencing maps SARS-CoV-2 5' capping sites and provides new insights into the structure of sgRNAs. Nucleic Acids Research. PMID 35244721 DOI: 10.1093/nar/gkac144 |
0.688 |
|
| 2021 |
Rehm HL, Page AJH, Smith L, Adams JB, Alterovitz G, Babb LJ, Barkley MP, Baudis M, Beauvais MJS, Beck T, Beckmann JS, Beltran S, Bernick D, Bernier A, Bonfield JK, ... ... Birney E, et al. GA4GH: International policies and standards for data sharing across genomic research and healthcare. Cell Genomics. 1. PMID 35072136 DOI: 10.1016/j.xgen.2021.100029 |
0.697 |
|
| 2021 |
Birney E. The International Human Genome Project. Human Molecular Genetics. PMID 34264324 DOI: 10.1093/hmg/ddab198 |
0.363 |
|
| 2021 |
Birney E. The International Human Genome Project. Human Molecular Genetics. PMID 34264324 DOI: 10.1093/hmg/ddab198 |
0.363 |
|
| 2020 |
Meyer HV, Dawes TJW, Serrani M, Bai W, Tokarczuk P, Cai J, de Marvao A, Henry A, Lumbers RT, Gierten J, Thumberger T, Wittbrodt J, Ware JS, Rueckert D, Matthews PM, ... ... Birney E, et al. Genetic and functional insights into the fractal structure of the heart. Nature. PMID 32814899 DOI: 10.1038/S41586-020-2635-8 |
0.747 |
|
| 2020 |
Mirauta BA, Seaton DD, Bensaddek D, Brenes A, Bonder MJ, Kilpinen H, Agu CA, Alderton A, Danecek P, Denton R, Durbin R, Gaffney DJ, Goncalves A, Halai R, ... ... Birney E, et al. Population-scale proteome variation in human induced pluripotent stem cells. Elife. 9. PMID 32773033 DOI: 10.7554/Elife.57390 |
0.584 |
|
| 2020 |
Mirauta BA, Seaton DD, Bensaddek D, Brenes A, Bonder MJ, Kilpinen H, Agu CA, Alderton A, Danecek P, Denton R, Durbin R, Gaffney DJ, Goncalves A, Halai R, Harper S, ... ... Birney E, et al. Author response: Population-scale proteome variation in human induced pluripotent stem cells Elife. DOI: 10.7554/Elife.57390.Sa2 |
0.482 |
|
| 2019 |
Cook CE, Stroe O, Cochrane G, Birney E, Apweiler R. The European Bioinformatics Institute in 2020: building a global infrastructure of interconnected data resources for the life sciences. Nucleic Acids Research. PMID 31701143 DOI: 10.1093/Nar/Gkz1033 |
0.32 |
|
| 2019 |
Saunders G, Baudis M, Becker R, Beltran S, Béroud C, Birney E, Brooksbank C, Brunak S, Van den Bulcke M, Drysdale R, Capella-Gutierrez S, Flicek P, Florindi F, Goodhand P, Gut I, et al. Author Correction: Leveraging European infrastructures to access 1 million human genomes by 2022. Nature Reviews. Genetics. PMID 31520075 DOI: 10.1038/S41576-019-0178-3 |
0.406 |
|
| 2019 |
Saunders G, Baudis M, Becker R, Beltran S, Béroud C, Birney E, Brooksbank C, Brunak S, Van den Bulcke M, Drysdale R, Capella-Gutierrez S, Flicek P, Florindi F, Goodhand P, Gut I, et al. Leveraging European infrastructures to access 1 million human genomes by 2022. Nature Reviews. Genetics. PMID 31455890 DOI: 10.1038/S41576-019-0156-9 |
0.467 |
|
| 2019 |
Birney E. The Convergence of Research and Clinical Genomics. American Journal of Human Genetics. 104: 781-783. PMID 31051111 DOI: 10.1016/J.Ajhg.2019.04.003 |
0.374 |
|
| 2019 |
Vigilante A, Laddach A, Moens N, Meleckyte R, Leha A, Ghahramani A, Culley OJ, Kathuria A, Hurling C, Vickers A, Wiseman E, Tewary M, Zandstra PW, Durbin R, ... ... Birney E, et al. Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors. Cell Reports. 26: 2078-2087.e3. PMID 30784590 DOI: 10.1016/J.Celrep.2019.01.094 |
0.536 |
|
| 2019 |
Iotchkova V, Ritchie GRS, Geihs M, Morganella S, Min JL, Walter K, Timpson NJ, Dunham I, Birney E, Soranzo N. GARFIELD classifies disease-relevant genomic features through integration of functional annotations with association signals. Nature Genetics. PMID 30692680 DOI: 10.1038/S41588-018-0322-6 |
0.481 |
|
| 2019 |
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. Author Correction: Landscape of somatic mutations in 560 breast cancer whole-genome sequences. Nature. PMID 30659290 DOI: 10.1038/S41586-019-0883-2 |
0.404 |
|
| 2019 |
Stark Z, Dolman L, Manolio TA, Ozenberger B, Hill SL, Caulfied MJ, Levy Y, Glazer D, Wilson J, Lawler M, Boughtwood T, Braithwaite J, Goodhand P, Birney E, North KN. Integrating Genomics into Healthcare: A Global Responsibility. American Journal of Human Genetics. 104: 13-20. PMID 30609404 DOI: 10.1016/J.Ajhg.2018.11.014 |
0.447 |
|
| 2018 |
Cook CE, Lopez R, Stroe O, Cochrane G, Brooksbank C, Birney E, Apweiler R. The European Bioinformatics Institute in 2018: tools, infrastructure and training. Nucleic Acids Research. PMID 30445657 DOI: 10.1093/Nar/Gky1124 |
0.338 |
|
| 2018 |
Ellenberg J, Swedlow JR, Barlow M, Cook CE, Sarkans U, Patwardhan A, Brazma A, Birney E. A call for public archives for biological image data. Nature Methods. 15: 849-854. PMID 30377375 DOI: 10.1038/S41592-018-0195-8 |
0.305 |
|
| 2018 |
Melamed A, Yaguchi H, Miura M, Witkover A, Fitzgerald TW, Birney E, Bangham CR. The human leukemia virus HTLV-1 alters the structure and transcription of host chromatin in cis. Elife. 7. PMID 29941091 DOI: 10.7554/Elife.36245 |
0.409 |
|
| 2018 |
Kelleher J, Lin M, Albach CH, Birney E, Davies R, Gourtovaia M, Glazer D, Gonzalez CY, Jackson DK, Kemp A, Marshall J, Nowak A, Senf A, Tovar-Corona JM, Vikhorev A, et al. htsget: a protocol for securely streaming genomic data. Bioinformatics (Oxford, England). PMID 29931085 DOI: 10.1093/Bioinformatics/Bty492 |
0.442 |
|
| 2018 |
Taylor DL, Knowles DA, Scott LJ, Ramirez AH, Casale FP, Wolford BN, Guan L, Varshney A, Albanus RD, Parker SCJ, Narisu N, Chines PS, Erdos MR, Welch RP, Kinnunen L, ... ... Birney E, et al. Interactions between genetic variation and cellular environment in skeletal muscle gene expression. Plos One. 13: e0195788. PMID 29659628 DOI: 10.1371/Journal.Pone.0195788 |
0.318 |
|
| 2018 |
Meyer HV, Birney E. PhenotypeSimulator: a comprehensive framework for multi-trait, multi-locus phenotype to genotype simulation. Bioinformatics (Oxford, England). PMID 29617944 DOI: 10.1093/Bioinformatics/Bty197 |
0.723 |
|
| 2018 |
Barton C, Morganella S, Ødegård-Fougner Ø, Alexander S, Ries J, Fitzgerald T, Ellenberg J, Birney E. ChromoTrace: Computational reconstruction of 3D chromosome configurations for super-resolution microscopy. Plos Computational Biology. 14: e1006002. PMID 29522506 DOI: 10.1371/Journal.Pcbi.1006002 |
0.428 |
|
| 2017 |
Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell PJ, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, et al. Science Forum: The Human Cell Atlas. Elife. 6. PMID 29206104 DOI: 10.7554/Elife.27041 |
0.322 |
|
| 2017 |
Cook CE, Bergman MT, Cochrane G, Apweiler R, Birney E. The European Bioinformatics Institute in 2017: data coordination and integration. Nucleic Acids Research. PMID 29186510 DOI: 10.1093/Nar/Gkx1154 |
0.385 |
|
| 2017 |
Vamathevan J, Birney E. A Review of Recent Advances in Translational Bioinformatics: Bridges from Biology to Medicine Yearb Med Inform. 26: 178-187. PMID 29063562 DOI: 10.15265/Iy-2017-017 |
0.457 |
|
| 2017 |
Jain M, Tyson JR, Loose M, Ip CLC, Eccles DA, O'Grady J, Malla S, Leggett RM, Wallerman O, Jansen HJ, Zalunin V, Birney E, Brown BL, Snutch TP, Olsen HE, et al. MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry. F1000research. 6: 760. PMID 28794860 DOI: 10.12688/F1000Research.11354.1 |
0.433 |
|
| 2017 |
Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, Bala S, Bensaddek D, Casale FP, Culley OJ, Danecek P, Faulconbridge A, Harrison PW, Kathuria A, McCarthy D, ... ... Birney E, et al. Corrigendum: Common genetic variation drives molecular heterogeneity in human iPSCs. Nature. PMID 28614302 DOI: 10.1038/Nature23012 |
0.509 |
|
| 2017 |
Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, Bala S, Bensaddek D, Casale FP, Culley OJ, Danecek P, Faulconbridge A, Harrison PW, Kathuria A, McCarthy D, ... ... Birney E, et al. Common genetic variation drives molecular heterogeneity in human iPSCs. Nature. PMID 28489815 DOI: 10.1038/Nature22403 |
0.569 |
|
| 2017 |
Schor IE, Degner JF, Harnett D, Cannavò E, Casale FP, Shim H, Garfield DA, Birney E, Stephens M, Stegle O, Furlong EE. Promoter shape varies across populations and affects promoter evolution and expression noise. Nature Genetics. PMID 28191888 DOI: 10.1038/Ng.3791 |
0.307 |
|
| 2017 |
Glodzik D, Morganella S, Davies H, Simpson PT, Li Y, Zou X, Diez-Perez J, Staaf J, Alexandrov LB, Smid M, Brinkman AB, Rye IH, Russnes H, Raine K, Purdie CA, ... ... Birney E, et al. A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers. Nature Genetics. PMID 28112740 DOI: 10.1038/Ng.3771 |
0.319 |
|
| 2016 |
Cannavò E, Koelling N, Harnett D, Garfield D, Casale FP, Ciglar L, Gustafson HE, Viales RR, Marco-Ferreres R, Degner JF, Zhao B, Stegle O, Birney E, Furlong EE. Genetic variants regulating expression levels and isoform diversity during embryogenesis. Nature. PMID 28024300 DOI: 10.1038/Nature20802 |
0.324 |
|
| 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 |
0.342 |
|
| 2016 |
Birney E, Smith GD, Greally JM. Epigenome-wide Association Studies and the Interpretation of Disease -Omics. Plos Genetics. 12: e1006105. PMID 27336614 DOI: 10.1371/Journal.Pgen.1006105 |
0.351 |
|
| 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 |
0.371 |
|
| 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 |
0.316 |
|
| 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 |
0.73 |
|
| 2016 |
Marvao Ad, Meyer HV, Dawes TJ, Shi W, Bai W, Rueckert D, Birney E, O'Regan DP, Cook S. Genome wide association analysis of the heart using high-resolution 3D cardiac MRI identifies new genetic loci underlying cardiac structure and function. Journal of Cardiovascular Magnetic Resonance. 18: 1-2. DOI: 10.1186/1532-429X-18-S1-Q63 |
0.33 |
|
| 2016 |
Marvao Ad, Meyer H, Dawes T, Francis C, Shi W, Bai W, Rueckert D, Birney E, O'Regan DP, Cook S. Development of integrated high-resolution three-dimensional MRI and computational modelling techniques to identify novel genetic and anthropometric determinants of cardiac form and function The Lancet. 387. DOI: 10.1016/S0140-6736(16)00423-2 |
0.302 |
|
| 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 |
0.624 |
|
| 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 |
0.723 |
|
| 2015 |
Cook CE, Bergman MT, Finn RD, Cochrane G, Birney E, Apweiler R. The European Bioinformatics Institute in 2016: Data growth and integration. Nucleic Acids Research. PMID 26673705 DOI: 10.1093/Nar/Gkv1352 |
0.322 |
|
| 2015 |
Gaulton KJ, Ferreira T, Lee Y, Raimondo A, Mägi R, Reschen ME, Mahajan A, Locke A, William Rayner N, Robertson N, Scott RA, Prokopenko I, Scott LJ, Green T, Sparso T, ... ... Birney E, et al. Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci. Nature Genetics. PMID 26551672 DOI: 10.1038/Ng.3437 |
0.364 |
|
| 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 |
0.447 |
|
| 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 |
0.714 |
|
| 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 |
0.712 |
|
| 2015 |
Dunham I, Kulesha E, Iotchkova V, Morganella S, Birney E. FORGE: A tool to discover cell specific enrichments of GWAS associated SNPs in regulatory regions F1000research. 4: 18. DOI: 10.12688/F1000Research.6032.1 |
0.395 |
|
| 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 |
0.426 |
|
| 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 |
0.714 |
|
| 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 |
0.355 |
|
| 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 |
0.51 |
|
| 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 |
0.315 |
|
| 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 |
0.359 |
|
| 2014 |
Birney E, Pritchard JK. Archaic humans: Four makes a party. Nature. 505: 32-4. PMID 24352230 DOI: 10.1038/Nature12847 |
0.446 |
|
| 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 |
0.709 |
|
| 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 |
0.335 |
|
| 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 |
0.459 |
|
| 2013 |
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, ... ... Birney E, et al. Genome-wide meta-analysis identifies new susceptibility loci for migraine. Nature Genetics. 45: 912-7. PMID 23793025 DOI: 10.1038/Ng.2676 |
0.349 |
|
| 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 |
0.399 |
|
| 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 |
0.753 |
|
| 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, GarcÃa-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 |
0.414 |
|
| 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 |
0.419 |
|
| 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 |
0.397 |
|
| 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 |
0.594 |
|
| 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 |
0.317 |
|
| 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 |
0.432 |
|
| 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 |
0.389 |
|
| 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 |
0.304 |
|
| 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 |
0.435 |
|
| 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 |
0.463 |
|
| 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 |
0.711 |
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| 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 |
0.365 |
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| 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 |
0.565 |
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| 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 |
0.467 |
|
| 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 |
0.527 |
|
| 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 |
0.479 |
|
| 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 |
0.569 |
|
| 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, Nellåker 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 |
0.656 |
|
| 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 |
0.366 |
|
| 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 |
0.324 |
|
| 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 |
0.379 |
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| 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 |
0.434 |
|
| 2011 |
Birney E. Assemblies: the good, the bad, the ugly. Nature Methods. 8: 59-60. PMID 21191376 DOI: 10.1038/Nmeth0111-59 |
0.383 |
|
| 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 |
0.372 |
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| 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 |
0.35 |
|
| 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 |
0.593 |
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| 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 |
0.409 |
|
| 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 |
0.396 |
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| 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 |
0.318 |
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| 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 |
0.338 |
|
| 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 |
0.467 |
|
| 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 |
0.351 |
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| 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 |
0.491 |
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| 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 |
0.517 |
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| 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 |
0.733 |
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| 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 |
0.472 |
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| 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 |
0.509 |
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| 2010 |
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, ... ... Birney E, et al. International network of cancer genome projects. Nature. 464: 993-8. PMID 20393554 DOI: 10.1038/Nature08987 |
0.383 |
|
| 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 |
0.341 |
|
| 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 |
0.655 |
|
| 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 |
0.752 |
|
| 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 |
0.699 |
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| 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 |
0.71 |
|
| 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 |
0.673 |
|
| 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 |
0.528 |
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| 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 |
0.345 |
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| 2010 |
Flicek P, Birney E. Erratum: Sense from sequence reads: methods for alignment and assembly Nature Methods. 7: 479-479. DOI: 10.1038/Nmeth0610-479B |
0.335 |
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| 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 |
0.351 |
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| 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 |
0.696 |
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| 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 |
0.308 |
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| 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 |
0.406 |
|
| 2009 |
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, et al. Prepublication data sharing. Nature. 461: 168-70. PMID 19741685 DOI: 10.1038/461168A |
0.573 |
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| 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 |
0.41 |
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| 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 |
0.648 |
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| 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 |
0.684 |
|
| 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 |
0.614 |
|
| 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 |
0.571 |
|
| 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 |
0.446 |
|
| 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 |
0.341 |
|
| 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 |
0.418 |
|
| 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 |
0.393 |
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| 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 |
0.471 |
|
| 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. |
0.364 |
|
| 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 |
0.755 |
|
| 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 |
0.681 |
|
| 2008 |
Fernández-Suárez XM, Birney E. Advanced genomic data mining. Plos Computational Biology. 4: e1000121. PMID 18818719 DOI: 10.1371/Journal.Pcbi.1000121 |
0.43 |
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| 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, MacÃas 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 |
0.317 |
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| 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 |
0.367 |
|
| 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 |
0.578 |
|
| 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 |
0.416 |
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| 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 |
0.479 |
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| 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 |
0.435 |
|
| 2008 |
Birney E. Levers and fulcrums: progress in cis-regulatory motif models. Nature Methods. 5: 297-8. PMID 18376393 DOI: 10.1038/Nmeth0408-297 |
0.31 |
|
| 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 |
0.684 |
|
| 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 |
0.497 |
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| 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 |
0.424 |
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| 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 |
0.617 |
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| 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 |
0.399 |
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| 2007 |
Birney E. Evolutionary genomics: come fly with us. Nature. 450: 184-5. PMID 17994082 DOI: 10.1038/450184A |
0.446 |
|
| 2007 |
Birney E. Double Dutch for duplications. Nature Genetics. 39: 1303-4. PMID 17968343 DOI: 10.1038/Ng1107-1303 |
0.406 |
|
| 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 |
0.47 |
|
| 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 |
0.702 |
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| 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 |
0.336 |
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| 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 |
0.425 |
|
| 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 |
0.755 |
|
| 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 |
0.806 |
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| 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 |
0.762 |
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| 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 |
0.332 |
|
| 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 |
0.47 |
|
| 2007 |
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, ... ... Birney E, et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science (New York, N.Y.). 316: 222-34. PMID 17431167 DOI: 10.1126/Science.1139247 |
0.491 |
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| 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 |
0.33 |
|
| 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 |
0.308 |
|
| 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 |
0.357 |
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| 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 |
0.415 |
|
| 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 |
0.629 |
|
| 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 |
0.382 |
|
| 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 |
0.625 |
|
| 2007 |
Bono Bd, Vastrik I, D’Eustachio P, Schmidt E, Gopinath G, Croft D, Gillespie M, Jassal B, Lewis S, Matthews L, Wu G, Birney E, Stein L. Reactome: An integrated expert model of human molecular processes and access toolkit Journal of Integrative Bioinformatics. 4: 286-296. DOI: 10.1515/Jib-2007-84 |
0.392 |
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| 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 |
0.448 |
|
| 2007 |
Jassal B, Schmidt EE, Wu G, Vastrik I, Croft D, Bono Bd, Gopinath G, Gillespie M, Jupe S, O'Kelly G, Matthews L, Garapati PV, Caudy M, Kanapin A, May B, ... ... Birney E, et al. Reactome – a knowledgebase of human biological pathways Nature Precedings. 2: 1-1. DOI: 10.1038/Npre.2009.3200.1 |
0.363 |
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| 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 |
0.475 |
|
| 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 |
0.49 |
|
| 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 |
0.307 |
|
| 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 |
0.737 |
|
| 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 |
0.63 |
|
| 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 |
0.737 |
|
| 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 |
0.495 |
|
| 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 |
0.409 |
|
| 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 |
0.418 |
|
| 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 |
0.625 |
|
| 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 |
0.345 |
|
| 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 |
0.42 |
|
| 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 |
0.618 |
|
| 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 |
0.429 |
|
| 2004 |
Birney E, Clamp M. Biological database design and implementation Briefings in Bioinformatics. 5: 31-38. PMID 15153304 DOI: 10.1093/Bib/5.1.31 |
0.303 |
|
| 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 |
0.514 |
|
| 2004 |
Birney E, Clamp M, Durbin R. GeneWise and Genomewise Genome Research. 14: 988-995. PMID 15123596 DOI: 10.1101/Gr.1865504 |
0.526 |
|
| 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 |
0.492 |
|
| 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 |
0.364 |
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| 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 |
0.675 |
|
| 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 |
0.476 |
|
| 2004 |
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, ... ... Birney E, et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 428: 493-521. PMID 15057822 DOI: 10.1038/Nature02426 |
0.722 |
|
| 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 |
0.402 |
|
| 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 |
0.503 |
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| 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 |
0.44 |
|
| 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 |
0.633 |
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| 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 DOI: 10.1101/Sqb.2003.68.237 |
0.45 |
|
| 2003 |
Birney E. Ensembl: A genome infrastructure Cold Spring Harbor Symposia On Quantitative Biology. 68: 213-215. PMID 15338620 DOI: 10.1101/Sqb.2003.68.213 |
0.455 |
|
| 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 |
0.686 |
|
| 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 |
0.745 |
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| 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 |
0.31 |
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| 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 |
0.684 |
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| 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 DOI: 10.1186/Gb-2002-3-12-Research0082 |
0.517 |
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| 2002 |
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, ... ... Birney E, et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 420: 563-73. PMID 12466851 DOI: 10.1038/Nature01266 |
0.417 |
|
| 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 |
0.534 |
|
| 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 |
0.347 |
|
| 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 |
0.457 |
|
| 2002 |
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, ... ... Birney E, et al. The genome sequence of the malaria mosquito Anopheles gambiae. Science (New York, N.Y.). 298: 129-49. PMID 12364791 DOI: 10.1126/Science.1076181 |
0.483 |
|
| 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 |
0.512 |
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| 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 |
0.472 |
|
| 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 |
0.51 |
|
| 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 |
0.675 |
|
| 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 DOI: 10.1093/Nar/30.1.38 |
0.675 |
|
| 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 |
0.49 |
|
| 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 |
0.495 |
|
| 2001 |
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, ... ... Birney E, et al. Initial sequencing and analysis of the human genome. Nature. 409: 860-921. PMID 11237011 DOI: 10.1038/35057062 |
0.665 |
|
| 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 |
0.474 |
|
| 2001 |
Birney E, Bateman A, Clamp ME, Hubbard TJ. Mining the draft human genome Nature. 409: 827-828. PMID 11236999 DOI: 10.1038/35057004 |
0.512 |
|
| 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 DOI: 10.1093/Nar/29.1.37 |
0.584 |
|
| 2001 |
Ponting CP, Birney E. Identification of domains from protein sequences. Methods in Molecular Biology (Clifton, N.J.). 143: 53-69. PMID 11084902 DOI: 10.1385/1-59259-368-2:53 |
0.34 |
|
| 2001 |
Birney E. Hidden Markov models in biological sequence analysis Ibm Journal of Research and Development. 45: 449-454. DOI: 10.1147/Rd.453.0449 |
0.338 |
|
| 2001 |
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, ... ... Birney E, et al. Erratum: Initial sequencing and analysis of the human genome: International Human Genome Sequencing Consortium (Nature (2001) 409 (860-921)) Nature. 412: 565-566. DOI: 10.1038/35087627 |
0.657 |
|
| 2000 |
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. InterPro--an integrated documentation resource for protein families, domains and functional sites. Bioinformatics (Oxford, England). 16: 1145-50. PMID 11159333 DOI: 10.1093/Bioinformatics/16.12.1145 |
0.545 |
|
| 2000 |
Cuff JA, Birney E, Clamp ME, Barton GJ. ProtEST: protein multiple sequence alignments from expressed sequence tags Bioinformatics. 16: 111-116. PMID 10842731 DOI: 10.1093/Bioinformatics/16.2.111 |
0.435 |
|
| 2000 |
Birney E, Durbin R. Using GeneWise in the Drosophila Annotation Experiment Genome Research. 10: 547-548. PMID 10779496 DOI: 10.1101/Gr.10.4.547 |
0.58 |
|
| 2000 |
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, et al. Comparative genomics of the eukaryotes. Science (New York, N.Y.). 287: 2204-15. PMID 10731134 DOI: 10.1126/Science.287.5461.2204 |
0.458 |
|
| 2000 |
Hubbard T, Birney E. Open annotation offers a democratic solution to genome sequencing. Nature. 403: 825-825. PMID 10706254 DOI: 10.1038/35002770 |
0.455 |
|
| 1999 |
Jareborg N, Birney E, Durbin R. Comparative Analysis of Noncoding Regions of 77 Orthologous Mouse and Human Gene Pairs Genome Research. 9: 815-824. PMID 10508839 DOI: 10.1101/Gr.9.9.815 |
0.649 |
|
| 1999 |
Bateman A, Birney E, Durbin R, Eddy SR, Finn RD, Sonnhammer ELL. Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins Nucleic Acids Research. 27: 260-262. PMID 9847196 DOI: 10.1093/Nar/27.1.260 |
0.664 |
|
| 1998 |
Pocock MR, Hubbard TJP, Birney E. SPEM: a parser for EMBL style flat file database entries. Bioinformatics. 14: 823-824. PMID 9918956 DOI: 10.1093/Bioinformatics/14.9.823 |
0.317 |
|
| 1998 |
Sonnhammer ELL, Eddy SR, Birney E, Bateman A, Durbin R. Pfam: Multiple sequence alignments and HMM-profiles of protein domains Nucleic Acids Research. 26: 320-322. PMID 9399864 DOI: 10.1093/Nar/26.1.320 |
0.716 |
|
| 1996 |
Birney E, Thompson JD, Gibson TJ. PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames. Nucleic Acids Research. 24: 2730-9. PMID 8759004 DOI: 10.1093/Nar/24.14.2730 |
0.392 |
|
| 1993 |
Birney E, Kumar S, Krainer AR. Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors. Nucleic Acids Research. 21: 5803-16. PMID 8290338 DOI: 10.1093/Nar/21.25.5803 |
0.371 |
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