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Ewan Birney

Wikidata Item | Scholia Profile [curation] | Reasonator | SQID

Listed Publications

272 publications found

TitleAuthors (identified)Published InIdentifier(s)TopicPublished Date
GREENER principles for environmentally sustainable computational science[1]Loïc Lannelongue, [2]Hans-Erik G. Aronson, [3]Alex Bateman, [4]Ewan Birney, [5]Talia Caplan, [6]Martin Juckes, [7]Johanna McEntyre, [8]Andrew D. Morris, [9]Gerry Reilly, [10]Michael Inouye [Full author list]DOI: 10.1038/S43588-023-00461-Y
computational science [curation]2023-06-26
COVID-19 trajectories among 57 million adults in England: a cohort study using electronic health records[1]Johan Hilge Thygesen, [2]Christopher Tomlinson, [3]Sam Hollings, [4]Mehrdad A Mizani, [5]Alex Handy, [6]Ashley Akbari, [7]Amitava Banerjee, [8]Jennifer Cooper, [9]Alvina G Lai, [10]Kezhi Li, ..., [40]Colin Berry, [41]Jennifer Beveridge, [42]Ewan Birney, [43]Lana Bojanić, [44]Thomas Bolton, ... [Full author list]Digital Health [curation]DOI: 10.1016/S2589-7500(22)00091-7
electronic health records [curation]; COVID-19 [curation]2022-07-01
Selective clonal persistence of human retroviruses in vivo: Radial chromatin organization, integration site, and host transcription[1]Anat Melamed, [2]Tomas W Fitzgerald, [3]Yuchuan Wang, [4]Jian Ma, [5]Ewan Birney, [6]Charles Bangham [Full author list]Science Advances [curation]DOI: 10.1126/SCIADV.ABM6210
PubMed: 35486737		2022-04-29
Nanopore ReCappable sequencing maps SARS-CoV-2 5' capping sites and provides new insights into the structure of sgRNAs[1]Camilla Ugolini, [2]Logan Mulroney, [3]Adrien Leger, [4]Matteo Castelli, [5]Elena Criscuolo, [6]Maia Kavanagh Williamson, [7]Andrew D Davidson, [8]Abdulaziz Almuqrin, [9]Roberto Giambruno, [10]Miten Jain, ..., [19]Massimo Clementi, [20]Nicasio Mancini, [21]Ewan Birney, [22]Mark Akeson, [23]Francesco Nicassio, ... [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKAC144
PubMed: 35244721		SARS-CoV-2 [curation]2022-04-01
A joint NCBI and EMBL-EBI transcript set for clinical genomics and research[1]Joannella Morales, [2]Shashikant Pujar, [3]Jane E Loveland, [4]Alex Astashyn, [5]Ruth Bennett, [6]Andrew Berry, [7]Eric Cox, [8]Claire Davidson, [9]Olga Ermolaeva, [10]Catherine M Farrell, ..., [34]David Webb, [35]Paul Flicek, [36]Ewan Birney, [37]Kim D. Pruitt, [38]Adam Frankish, ... [Full author list]Nature [curation]DOI: 10.1038/S41586-022-04558-8
PubMed: 35388217		2022-04-01
Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel[1]Adrien Leger, [2]Ian Brettell, [3]Jack Monahan, [4]Carl Barton, [5]Nadeshda Wolf, [6]Natalja Kusminski, [7]Cathrin Herder, [8]Narendar Aadepu, [9]Clara Becker, [10]Jakob Gierten, ..., [23]Felix Loosli, [24]Joachim Wittbrodt, [25]Ewan Birney, [26]Tomas W Fitzgerald [Full author list]Genome Biology [curation]DOI: 10.1186/S13059-022-02602-4
2022-02-21
RNA modifications detection by comparative Nanopore direct RNA sequencing[1]Adrien Leger, [2]Paulo P. Amaral, [3]Luca Pandolfini, [4]Charlotte Capitanchik, [5]Federica Capraro, [6]Valentina Miano, [7]Valentina Migliori, [8]Patrick Toolan-Kerr, [9]Theodora Sideri, [10]Anton J. Enright, [11]Konstantinos Tzelepis, [12]Folkert J van Werven, [13]Nicholas M Luscombe, [14]Isaia Barbieri, [15]Jernej Ule, [16]Tomas W Fitzgerald, [17]Ewan Birney, [18]Tommaso Leonardi, [19]Tony Kouzarides [Full author list]Nature Communications [curation]DOI: 10.1038/S41467-021-27393-3
2021-12-10
Genomic reconstruction of the SARS-CoV-2 epidemic in England[1]Harald S Vöhringer, [2]Theo Sanderson, [3]Matthew Sinnott, [4]Nicola De Maio, [5]Thuy Nguyen, [6]Richard Goater, [7]Frank Schwach, [8]Ian Harrison, [9]Joel Hellewell, [10]Cristina V. Ariani, ..., [22]Ewan Birney, [23]Erik M. Volz, [24]Sebastian Funk, ... [Full author list]Nature [curation]DOI: 10.1038/S41586-021-04069-Y
PubMed: 34649268		SARS-CoV-2 [curation]2021-12-01
GA4GH: International policies and standards for data sharing across genomic research and healthcare[1]Heidi L. Rehm, [2]Angela Page, [3]Lindsay Smith, [4]Jeremy B. Adams, [5]Gil Alterovitz, [6]Lawrence J. Babb, [7]Maxmillian P. Barkley, [8]Michael Baudis, [9]Michael Beauvais, [10]Tim N Beck, ..., [200]Peter Goodhand, [201]Kathryn North, [202]Ewan Birney [Full author list]DOI: 10.1016/J.XGEN.2021.100029
data sharing [curation]2021-11-10
Highly accurate protein structure prediction for the human proteome[1]Kathryn Tunyasuvunakool, [2]Jonas Adler, [3]Zachary Wu, [4]Tim Green, [5]Michał Zieliński, [6]Augustin Žídek, [7]Alex Bridgland, [8]Andrew Cowie, [9]Clemens Meyer, [10]Agata Laydon, ..., [28]Andrew W Senior, [29]Koray Kavukcuoglu, [30]Ewan Birney, [31]Pushmeet Kohli, [32]John M. Jumper, ... [Full author list]Nature [curation]DOI: 10.1038/S41586-021-03828-1
human [curation]; proteome [curation]; AlphaFold2 [curation]2021-07-22
The International Human Genome Project[1]Ewan Birney [Full author list]Human Molecular Genetics [curation]DOI: 10.1093/HMG/DDAB198
2021-07-14
REMBI: Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology[1]Ugis Sarkans, [2]Wah Chiu, [3]Lucy Collinson, [4]Michele C. Darrow, [5]Jan Ellenberg, [6]David Grunwald, [7]Jean-Karim Hériché, [8]Andrii Iudin, [9]Gabriel G. Martins, [10]Terry Meehan, ..., [20]Mary Barlow, [21]Omer Ali Bayraktar, [22]Ewan Birney, [23]Cesare Catavitello, [24]Christopher Cawthorne, ... [Full author list]Nature Methods [curation]DOI: 10.1038/S41592-021-01166-8
metadata [curation]2021-05-21
Genetic variation affects morphological retinal phenotypes extracted from UK Biobank optical coherence tomography images[1]Hannah Currant, [2]Pirro G Hysi, [3]Tomas W Fitzgerald, [4]Puya Gharahkhani, [5]Pieter W M Bonnemaijer, [6]Anne Senabouth, [7]Alex W. Hewitt, [10]Denize Atan, ..., [33]Paul J Foster, [34]Praveen J Patel, [35]Ewan Birney, [36]Anthony P Khawaja [Full author list]PLOS Genetics [curation]DOI: 10.1371/JOURNAL.PGEN.1009497
PubMed: 33979322		molecular biology [curation]; genetic variation [curation]2021-05-01
Genome-wide meta-analysis identifies 127 open-angle glaucoma loci with consistent effect across ancestries[1]Puya Gharahkhani, [2]Eric Jorgenson, [3]Pirro G Hysi, [4]Anthony Khawaja, [5]Sarah Pendergrass, [6]Xikun Han, [7]Jue Sheng Ong, [8]Alex W. Hewitt, [9]Ayellet V Segrè, [10]John M Rouhana, ..., [47]Toru Nakazawa, [48]Hannah Currant, [49]Ewan Birney, [50]Xin Wang, [51]Adam Auton, ... [Full author list]Nature Communications [curation]DOI: 10.1038/S41467-020-20851-4
PubMed: 33627673		open-angle glaucoma [curation]2021-02-24
The European Bioinformatics Institute: empowering cooperation in response to a global health crisis[1]Gaia Cantelli, [2]Guy R. Cochrane, [3]Cath Brooksbank, [4]Ellen McDonagh, [5]Paul Flicek, [6]Johanna McEntyre, [7]Ewan Birney, [8]Rolf Apweiler, [9]Catherine Brooksbank [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKAA1077
PubMed: 33245775		bioinformatics [curation]; cooperation [curation]2020-11-27
Genetic and functional insights into the fractal structure of the heart[1]Meyer Verena Hannah, [2]Timothy J W Dawes, [3]Marta Serrani, [4]Wenjia Bai, [5]Paweł F Tokarczuk, [6]Jiashen Cai, [7]Antonio de Marvao, [8]Albert Henry, [9]R Thomas Lumbers, [10]Jakob Gierten, [11]Thomas Thumberger, [12]Joachim Wittbrodt, [13]James Ware, [14]Daniel Rueckert, [15]Paul M. Matthews, [16]Sanjay Prasad Gupta, [17]Maria L Costantino, [18]Stuart A Cook, [19]Ewan Birney, [20]Declan P O'Regan [Full author list]Nature [curation]DOI: 10.1038/S41586-020-2635-8
PubMed: 32814899		2020-08-19
The European Bioinformatics Institute in 2020: building a global infrastructure of interconnected data resources for the life sciences[1]Charles E Cook, [2]Oana Stroe, [3]Guy R. Cochrane, [4]Ewan Birney, [5]Rolf Apweiler [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKZ1033
PubMed: 31701143		bioinformatics [curation]; life sciences [curation]2020-01-01
RNA modifications detection by comparative Nanopore direct RNA sequencing[0]Paulo P Amaral, [1]Adrien Leger, [2]Paulo P. Amaral, [3]Luca Pandolfini, [4]Charlotte Capitanchik, [5]Federica Capraro, [6]Isaia Barbieri, [7]Valentina Migliori, [8]Nicholas M. Luscombe, [9]Anton J Enright, [10]Konstantinos Tzelepis, [11]Jernej Ule, [12]Tomas Fitzgerald, [13]Ewan Birney, [14]Tommaso Leonardi, [15]Tony Kouzarides [Full author list]DOI: 10.1101/843136
2019-11-15
Author Correction: Leveraging European infrastructures to access 1 million human genomes by 2022[1]Gary Saunders, [2]Michael Baudis, [3]Regina Becker, [4]Sergi Beltran, [5]Christophe Béroud, [6]Ewan Birney, [7]Catherine Brooksbank, [8]Søren Brunak, [9]Marc Van den Bulcke, [10]Rachel A Drysdale, ... [Full author list]Nature Reviews Genetics [curation]DOI: 10.1038/S41576-019-0178-3
PubMed: 31520075		2019-11-01
Leveraging European infrastructures to access 1 million human genomes by 2022[1]Gary Saunders, [2]Michael Baudis, [3]Regina Becker, [4]Sergi Beltran, [5]Christophe Béroud, [6]Ewan Birney, [7]Catherine Brooksbank, [8]Søren Brunak, [9]Marc Van den Bulcke, [10]Rachel A Drysdale, ... [Full author list]Nature Reviews Genetics [curation]DOI: 10.1038/S41576-019-0156-9
PubMed: 31455890		2019-08-27
Comparison of Associations with Different Macular Inner Retinal Thickness Parameters in a Large Cohort: The UK Biobank[1]Anthony P Khawaja, [2]Sharon Chua, [3]Pirro G Hysi, [4]Stelios Georgoulas, [5]Hannah Currant, [6]Tomas W Fitzgerald, [7]Ewan Birney, [8]Fang Ko, [9]Qi Yang, [10]Charles Reisman, [11]David F Garway-Heath, [12]Chris J Hammond, [13]Peng T Khaw, [14]Paul J Foster, [15]Praveen J Patel, [16]Nicholas Strouthidis, [17]UK Biobank Eye and Vision Consortium [Full author list]Ophthalmology [curation]DOI: 10.1016/J.OPHTHA.2019.08.015
PubMed: 31585827		biobank [curation]2019-08-21
Biomolecular Data Resources: Bioinformatics Infrastructure for Biomedical Data Science[1]Jessica Vamathevan, [2]Rolf Apweiler, [3]Ewan Birney [Full author list]Annual Review of Biomedical Data Science [curation]DOI: 10.1146/ANNUREV-BIODATASCI-072018-021321
data science [curation]2019-05-15
Integrative analysis of gene expression, DNA methylation, physiological traits, and genetic variation in human skeletal muscle[1]D Leland Taylor, [2]Anne U Jackson, [3]Narisu Narisu, [4]Gibran Hemani, [5]Michael R Erdos, [6]Peter S Chines, [7]Amy Swift, [8]Jackie Idol, [9]John P Didion, [10]Ryan P Welch, ..., [19]Michael Boehnke, [20]Laura J Scott, [21]Ewan Birney, [22]Francis Collins [Full author list]Proceedings of the National Academy of Sciences of the United States of America [curation]DOI: 10.1073/PNAS.1814263116
PubMed: 31076557		genetic variation [curation]; physiological trait [curation]2019-05-10
The Convergence of Research and Clinical Genomics[1]Ewan Birney [Full author list]American Journal of Human Genetics [curation]DOI: 10.1016/J.AJHG.2019.04.003
PubMed: 31051111		genomics [curation]2019-05-01
Genomic analysis reveals a functional role for myocardial trabeculae in adults[1]Hannah V Meyer, [2]Timothy J W Dawes, [3]Marta Serrani, [4]Wenjia Bai, [5]Pawel Tokarczuk, [6]Jiashen Cai, [7]Antonio de Marvao, [8]Daniel Rueckert, [9]Paul M. Matthews, [10]Maria L Costantino, [11]Ewan Birney, [12]Stuart A Cook, [13]Declan P O'Regan [Full author list]DOI: 10.1101/553651
2019-02-22
Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors[1]Alessandra Vigilante, [2]Anna Laddach, [3]Nathalie Moens, [4]Ruta Meleckyte, [5]Andreas Leha, [6]Arsham Ghahramani, [7]Oliver J Culley, [8]Annie Kathuria, [9]Chloe Hurling, [10]Alice Vickers, [11]Erika Wiseman, [12]Mukul Tewary, [13]Peter W Zandstra, [15]Richard M. Durbin, [16]Franca Fraternali, [17]Oliver Stegle, [18]Ewan Birney, [19]Nicholas M Luscombe, [20]Davide Danovi, [21]Fiona Watt [Full author list]Cell Reports [curation]DOI: 10.1016/J.CELREP.2019.01.094
PubMed: 30784590		cell adhesion [curation]; Fibronectin 1 [curation]; SNV [curation]; Ipsc [curation]2019-02-19
Author Correction: Landscape of somatic mutations in 560 breast cancer whole-genome sequences[1]Serena Nik-Zainal, [2]Helen Davies, [3]Johan Staaf, [4]Manasa Ramakrishna, [5]Dominik Glodzik, [6]Xueqing Zou, [7]Iñigo Martincorena, [8]Ludmil B. Alexandrov, [9]Sancha Martin, [10]David C. Wedge, ..., [78]Jórunn Erla Eyfjörd, [79]Alastair M Thompson, [80]Ewan Birney, [81]Hendrik Gerard Stunnenberg, [82]Marc J van de Vijver, ... [Full author list]Nature [curation]DOI: 10.1038/S41586-019-0883-2
PubMed: 30659290		whole genome sequencing [curation]2019-02-01
GARFIELD classifies disease-relevant genomic features through integration of functional annotations with association signals[1]Valentina Iotchkova, [2]Graham R S Ritchie, [3]Matthias Geihs, [4]Sandro Morganella, [5]Josine L Min, [6]Klaudia Walter, [7]Nicholas J. Timpson, [8]UK10K Consortium, [9]Ian Dunham, [10]Ewan Birney, [11]Nicole Soranzo [Full author list]Nature Genetics [curation]DOI: 10.1038/S41588-018-0322-6
PubMed: 30692680		2019-01-28
htsget: a protocol for securely streaming genomic data[1]Jerome Kelleher, [2]Mike Lin, [3]C H Albach, [4]Ewan Birney, [5]Robert Davies, [6]Marina Gourtovaia, [7]David Glazer, [8]Cristina Y Gonzalez, [9]David K Jackson, [10]Aaron Kemp, [11]John Marshall, [12]Andrew Nowak, [13]Alexander Senf, [14]Jaime M Tovar-Corona, [15]Alexander Vikhorev, [16]Thomas M. Keane, [17]GA4GH Streaming Task Team [Full author list]Bioinformatics [curation]DOI: 10.1093/BIOINFORMATICS/BTY492
PubMed: 29931085		2019-01-01
The European Bioinformatics Institute in 2018: tools, infrastructure and training[1]Charles E Cook, [2]Rodrigo López, [3]Oana Stroe, [4]Guy R. Cochrane, [5]Cath Brooksbank, [5-Q47502911]Catherine Brooksbank, [6]Ewan Birney, [7]Rolf Apweiler [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKY1124
PubMed: 30445657		infrastructure [curation]; bioinformatics [curation]2019-01-01
Integrating Genomics into Healthcare: A Global Responsibility[1]Zornitza Stark, [2]Lena Dolman, [3]Teri A Manolio, [4]Brad Ozenberger, [5]Sue L Hill, [6]Mark J Caulfied, [7]Yves Levy, [8]David Glazer, [9]Julia Wilson, [10]Mark Lawler, [11]Tiffany Boughtwood, [12]Jeffrey Braithwaite, [13]Peter Goodhand, [14]Ewan Birney, [15]Kathryn North [Full author list]American Journal of Human Genetics [curation]DOI: 10.1016/J.AJHG.2018.11.014
PubMed: 30609404		genomics [curation]2019-01-01
A call for public archives for biological image data[1]Jan Ellenberg, [2]Jason Swedlow, [3]Mary Barlow, [4]Charles E Cook, [5]Ugis Sarkans, [6]Ardan Patwardhan, [7]Alvis Brazma, [8]Ewan Birney [Full author list]Nature Methods [curation]DOI: 10.1038/S41592-018-0195-8
PubMed: 30377375		2018-11-01
A roadmap for restoring trust in Big Data[1]Mark Lawler, [2]Andrew D Morris, [3]Richard Sullivan, [3-Q42337438]Richard Sullivan, [4]Ewan Birney, [5]Anna Middleton, [6]Lydia Makaroff, [7]Bartha Knoppers, [8]Denis Horgan, [9]Alexander Eggermont [Full author list]Lancet Oncology Commission [curation]DOI: 10.1016/S1470-2045(18)30425-X
PubMed: 30102210		big data [curation]2018-08-01
The human leukemia virus HTLV-1 alters the structure and transcription of host chromatin in cis.[1]Anat Melamed, [2]Hiroko Yaguchi, [3]Michi Miura, [4]Aviva Witkover, [5]Tomas W Fitzgerald, [6]Ewan Birney, [7]Charles Bangham [Full author list]eLife [curation]DOI: 10.7554/ELIFE.36245
PubMed: 29941091		Human T-lymphotropic virus 1 [curation]2018-06-26
Interactions between genetic variation and cellular environment in skeletal muscle gene expression.[1]D Leland Taylor, [2]David A Knowles, [3]Laura J Scott, [4]Andrea H Ramirez, [5]Francesco Paolo Casale, [6]Brooke N Wolford, [7]Li Guan, [8]Arushi Varshney, [9]Ricardo D'Oliveira Albanus, [10]Stephen C J Parker, ..., [22]Oliver Stegle, [23]Michael Boehnke, [24]Ewan Birney, [25]Francis Collins [Full author list]PLOS One [curation]DOI: 10.1371/JOURNAL.PONE.0195788
PubMed: 29659628		genetic variation [curation]2018-04-16
PhenotypeSimulator: a comprehensive framework for multi-trait, multi-locus phenotype to genotype simulation.[1]Hannah Verena Meyer, [2]Ewan Birney [Full author list]Bioinformatics [curation]DOI: 10.1093/BIOINFORMATICS/BTY197
PubMed: 29617944		2018-03-29
Identifying extrinsic versus intrinsic drivers of variation in cell behaviour in human iPS cell lines from healthy donors[1]Alessandra Vigilante, [2]Anna Laddach, [3]Nathalie Moens, [4]Ruta Meleckyte, [5]Andreas Leha, [6]Arsham Ghahramani, [7]Oliver J. Culley, [8]Annie Kathuria, [9]Chloe Hurling, [10]Alice Vickers, [11]Mukul Tewary, [12]Peter Zandstra, [13]Richard Durbin, [14]Franca Fraternali, [15]Oliver Stegle, [16]Ewan Birney, [17]Nicholas M Luscombe, [18]Davide Danovi, [19]Fiona Watt [Full author list]DOI: 10.1101/285627
2018-03-20
ChromoTrace: Computational reconstruction of 3D chromosome configurations for super-resolution microscopy.[1]Carl Barton, [2]Sandro Morganella, [3]Øyvind Ødegård-Fougner, [4]Stephanie Alexander, [5]Jonas Ries, [6]Tomas W Fitzgerald, [7]Jan Ellenberg, [8]Ewan Birney [Full author list]PLOS Computational Biology [curation]DOI: 10.1371/JOURNAL.PCBI.1006002
PubMed: 29522506		2018-03-09
The human leukemia virus HTLV-1 alters the structure and transcription of host chromatin in cis[1]Anat Melamed, [2]Hiroko Yaguchi, [3]Michi Miura, [4]Aviva Witkover, [5]Tomas W Fitzgerald, [6]Ewan Birney, [7]Charles R. M. Bangham, [7-Q45428812]Charles Bangham [Full author list]DOI: 10.1101/277335
leukemia [curation]; Human T-lymphotropic virus 1 [curation]2018-03-07
LiMMBo: a simple, scalable approach for linear mixed models in high-dimensional genetic association studies[1]Meyer Verena Hannah, [2]Francesco Paolo Casale, [3]Oliver Stegle, [4]Ewan Birney [Full author list]DOI: 10.1101/255497
2018-01-30
The Human Cell Atlas.[1]Aviv Regev, [2]Sarah Teichmann, [3]Eric Lander, [4]Amir Giladi, [5]Christophe Benoist, [6]Ewan Birney, [7]Bernd Bodenmiller, [8]Peter J Campbell, [9]Piero Carninci, [10]Menna R Clatworthy, ... [Full author list]eLife [curation]DOI: 10.7554/ELIFE.27041
PubMed: 29206104		cell [curation]; atlas [curation]; Homo sapiens [curation]2017-12-05
The European Bioinformatics Institute in 2017: data coordination and integration[1]Charles E Cook, [2]Mary T Bergman, [3]Guy R. Cochrane, [4]Rolf Apweiler, [5]Ewan Birney [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKX1154
PubMed: 29186510		bioinformatics [curation]2017-11-25
Genomics in healthcare: GA4GH looks to 2022[1]Ewan Birney, [2]Jessica Vamathevan, [3]Peter Goodhand [Full author list]DOI: 10.1101/203554
genomics [curation]2017-10-15
Corrigendum: A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers.[1]Dominik Glodzik, [2]Sandro Morganella, [3]Helen Davies, [4]Peter T Simpson, [5]Yilong Li, [6]Xueqing Zou, [7]Javier Diez-Perez, [8]Johan Staaf, [9]Ludmil B Alexandrov, [10]Marcel Smid, ..., [16]Sunil R Lakhani, [17]Alastair M Thompson, [18]Ewan Birney, [19]Hendrik Gerard Stunnenberg, [20]Marc van de Vijver, ... [Full author list]Nature Genetics [curation]DOI: 10.1038/NG1117-1661A
PubMed: 29074948		A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers [curation]; susceptibility locus [curation]2017-10-01
A Review of Recent Advances in Translational Bioinformatics: Bridges from Biology to Medicine[1]Jessica Vamathevan, [2]Ewan Birney [Full author list]Yearbook of medical informatics : Advances in an interdisciplinary science [curation]DOI: 10.15265/IY-2017-017
PubMed: 29063562		bioinformatics [curation]; data sharing [curation]2017-08-01
Corrigendum: Common genetic variation drives molecular heterogeneity in human iPSCs[1]Leena Helena Kilpinen-Barrett, [2]Angela Goncalves, [3]Andreas Leha, [4]Vackar Afzal, [5]Kaur Alasoo, [6]Sofie Ashford, [7]Sendu Bala, [8]Dalila Bensaddek, [9]Francesco Paolo Casale, [10]Oliver J Culley, ..., [33]Anja Kolb-Kokocinski, [34]Philip Beales, [35]Ewan Birney, [36]Davide Danovi, [37]Angus Lamond, ... [Full author list]Nature [curation]DOI: 10.1038/NATURE23012
PubMed: 28614302		genetic variation [curation]; heterogeneity [curation]; Common genetic variation drives molecular heterogeneity in human iPSCs [curation]; Common genetic variation drives molecular heterogeneity in human iPSCs [curation]2017-06-14
MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry[1]Miten Jain, [2]John R Tyson, [3]Matthew Loose, [4]Camilla L C Ip, [5]David Eccles, [6]Justin O'Grady, [7]Sunir Malla, [8]Richard Leggett, [9]Ola Wallerman, [10]Hans J Jansen, [11]Vadim Zalunin, [12]Ewan Birney, [13]Bonnie L Brown, [14]Terrance P Snutch, [15]Hugh E Olsen, [16]MinION Analysis and Reference Consortium [Full author list]F1000Research [curation]DOI: 10.12688/F1000RESEARCH.11354.1
PubMed: 28794860		2017-05-31
The Human Cell Atlas[1]Aviv Regev, [2]Sarah Teichmann, [3]Eric Lander, [4]Amir Giladi, [5]Christophe Benoist, [6]Ewan Birney, [7]Bernd Bodenmiller, [8]Peter J Campbell, [9]Piero Carninci, [10]Menna R Clatworthy, ... [Full author list]DOI: 10.1101/121202
2017-05-08
ChromoTrace: Reconstruction of 3D Chromosome Configurations by Super-Resolution Microscopy[1]Carl Barton, [2]Sandro Morganella, [3]Øyvind Ødegård-Fougner, [4]Stephanie Alexander, [5]Jonas Ries, [6]Tomas W Fitzgerald, [7]Jan Ellenberg, [8]Ewan Birney [Full author list]DOI: 10.1101/115436
2017-03-09
Promoter shape varies across populations and affects promoter evolution and expression noise.[1]Ignacio E Schor, [2]Jacob F Degner, [3]Dermot Harnett, [4]Enrico Cannavò, [5]Francesco P Casale, [6]Heejung Shim, [7]David A Garfield, [8]Ewan Birney, [9]Matthew Stephens, [10]Oliver Stegle, [11]Eileen E. M. Furlong [Full author list]Nature Genetics [curation]DOI: 10.1038/NG.3791
PubMed: 28191888		2017-02-13
Interactions between genetic variation and cellular environment in skeletal muscle gene expression[1]D Leland Taylor, [2]David A Knowles, [3]Laura J Scott, [4]Andrea H Ramirez, [5]Francesco Paolo Casale, [6]Brooke N Wolford, [7]Li Guan, [8]Arushi Varshney, [9]Ricardo D'Oliveira Albanus, [10]Stephen C.J. Parker, ..., [22]Oliver Stegle, [23]Michael Boehnke, [24]Ewan Birney, [25]Francis Collins [Full author list]DOI: 10.1101/105429
2017-02-03
Genetic variants regulating expression levels and isoform diversity during embryogenesis.[1]Enrico Cannavò, [2]Nils Koelling, [3]Dermot Harnett, [4]David Garfield, [5]Francesco P Casale, [6]Lucia Ciglar, [7]Hilary E Gustafson, [8]Rebecca R Viales, [9]Raquel Marco-Ferreres, [10]Jacob F Degner, [11]Bingqing Zhao, [12]Oliver Stegle, [13]Ewan Birney, [14]Eileen E. M. Furlong [Full author list]Nature [curation]DOI: 10.1038/NATURE20802
PubMed: 28024300		embryogenesis [curation]2016-12-26
Open Targets: a platform for therapeutic target identification and validation[1]Gautier Koscielny, [2]Peter An, [3]Denise Carvalho Silva, [4]Jennifer A Cham, [5]Luca Fumis, [6]Rippa Gasparyan, [7]Samiul Hasan, [8]Nikiforos Karamanis, [9]Michael Maguire, [10]Eliseo Papa, ..., [52]Philippe Sanseau, [53]Jessica Vamathevan, [54]Ewan Birney, [55]Jeffrey C Barrett, [56]Ian Dunham [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKW1055
PubMed: 27899665		2016-11-29
GARFIELD - GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction[1]Valentina Iotchkova, [2]Graham R.S. Ritchie, [3]Matthias Geihs, [4]Sandro Morganella, [5]Josine L. Min, [6]Klaudia Walter, [7]Nicholas J. Timpson, [8]Ian Dunham, [9]Ewan Birney, [10]Nicole Soranzo [Full author list]DOI: 10.1101/085738
genome-wide association study [curation]2016-11-07
The Mighty Fruit Fly Moves into Outbred Genetics[1]Ewan Birney [Full author list]PLOS Genetics [curation]DOI: 10.1371/JOURNAL.PGEN.1006388
PubMed: 27812108		2016-11-03
eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data[1]Charles E Breeze, [2]Dirk S Paul, [3]Jenny van Dongen, [4]Lee M Butcher, [5]John C Ambrose, [6]James E Barrett, [7]Robert Lowe, [8]Vardhman K Rakyan, [9]Valentina Iotchkova, [10]Mattia Frontini, ..., [23]Andrew E Teschendorff, [24]Javier Herrero, [25]Ewan Birney, [26]Ian Dunham, [27]Stephan Beck [Full author list]Cell Reports [curation]DOI: 10.1016/J.CELREP.2016.10.059
PubMed: 27851974		2016-11-01
Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration[1]Marcel Smid, [2]F Germán Rodríguez-González, [3]Anieta M Sieuwerts, [4]Roberto Salgado, [5]Wendy J C Prager-Van der Smissen, [6]Michelle van der Vlugt-Daane, [7]Anne van Galen, [8]Serena Nik-Zainal, [9]Johan Staaf, [10]Arie B Brinkman, ..., [41]Anita Langerød, [42]Anne-Lise Børresen-Dale, [43]Ewan Birney, [44]Hendrik Gerard Stunnenberg, [45]Mike Stratton, ... [Full author list]Nature Communications [curation]DOI: 10.1038/NCOMMS12910
PubMed: 27666519		transcriptome [curation]; immune cell infiltration [curation]2016-09-26
Epigenome-wide Association Studies and the Interpretation of Disease -Omics[1]Ewan Birney, [2]George Davey Smith, [3]John Greally [Full author list]PLOS Genetics [curation]DOI: 10.1371/JOURNAL.PGEN.1006105
PubMed: 27336614		regulation of gene expression [curation]; genome-wide association study [curation]; genetic epigenesis [curation]; genetic predisposition to disease [curation]2016-06-01
Common genetic variation drives molecular heterogeneity in human iPSCs[1]Leena Helena Kilpinen-Barrett, [2]Angela Goncalves, [3]Andreas Leha, [4]Vackar Afzal, [5]Sofie Ashford, [6]Sendu Bala, [7]Dalila Bensaddek, [8]Francesco Paolo Casale, [9]Oliver Culley, [10]Petr Danacek, ..., [28]Anja Kolb-Kokocinski, [29]Philip Beales, [30]Ewan Birney, [31]Davide Danovi, [32]Angus Lamond, ... [Full author list]DOI: 10.1101/055160
heterogeneity [curation]2016-05-25
Landscape of somatic mutations in 560 breast cancer whole-genome sequences[1]Serena Nik-Zainal, [2]Helen Davies, [3]Johan Staaf, [4]Manasa Ramakrishna, [5]Dominik Glodzik, [6]Xueqing Zou, [7]Iñigo Martincorena, [8]Ludmil B. Alexandrov, [9]Sancha Martin, [10]David C. Wedge, ..., [78]Jórunn Erla Eyfjörd, [79]Alastair M Thompson, [80]Ewan Birney, [81]Hendrik Gerard Stunnenberg, [82]Marc van de Vijver, ... [Full author list]Nature [curation]DOI: 10.1038/NATURE17676
PubMed: 27135926		whole genome sequencing [curation]2016-05-02
The topography of mutational processes in breast cancer genomes[1]Sandro Morganella, [2]Ludmil B. Alexandrov, [3]Dominik Glodzik, [4]Xueqing Zou, [5]Helen Davies, [6]Johan Staaf, [7]Anieta M Sieuwerts, [8]Arie B Brinkman, [9]Sancha Martin, [10]Manasa Ramakrishna, ..., [30]Cristina Rada, [31]Michael Stratton, [32]Ewan Birney, [33]Serena Nik-Zainal [Full author list]Nature Communications [curation]DOI: 10.1038/NCOMMS11383
PubMed: 27136393		breast cancer [curation]2016-05-02
Ensembl regulation resources[1]Daniel R Zerbino, [2]Nathan Johnson, [3]Thomas Juetteman, [4]Dan Sheppard, [5]Steven P Wilder, [6]Ilias Lavidas, [7]Michael Nuhn, [8]Emily Pritchard, [9]Quentin Raffaillac-Desfosses, [10]Daniel Sobral, ..., [18]Anne Parker, [19]Steven Trevanion, [20]Ewan Birney, [21]Ian Dunham, [22]Paul Flicek [Full author list]Database [curation]DOI: 10.1093/DATABASE/BAV119
PubMed: 26888907		2016-02-17
Genome wide association analysis of the heart using high-resolution 3D cardiac MRI identifies new genetic loci underlying cardiac structure and function[1]Antonio de Marvao, [2]Hannah V Meyer, [3]Timothy J Dawes, [4]Wenzhe Shi, [5]Wenjia Bai, [6]Daniel Rueckert, [7]Ewan Birney, [8]Declan P O'Regan, [9]Stuart Cook [Full author list]Journal of Cardiovascular Magnetic Resonance [curation]DOI: 10.1186/1532-429X-18-S1-Q63
genome-wide association study [curation]2016-01-27
The European Bioinformatics Institute in 2016: Data growth and integration[1]Charles E Cook, [2]Mary Todd Bergman, [3]Robert D. Finn, [4]Guy R. Cochrane, [5]Ewan Birney, [6]Rolf Apweiler [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKV1352
PubMed: 26673705		bioinformatics [curation]2016-01-04
The EMBL-EBI channel[1]Johanna McEntyre, [2]Ewan Birney [Full author list]F1000Research [curation]DOI: 10.12688/F1000RESEARCH.7764.1
PubMed: 26913196		2016-01-01
Progress in Medicine: Experts Take Stock[1]PLOS Medicine Editors, [2]Andrew Beck, [3]Ewan Birney, [4]Manuel Graeber, [5]James K. Tumwine, [6]Phillipa J. Hay, [7]Hyeong Sik Ahn, [8]Anushka Patel, [9]Philipp du Cros, [10]Lorenz von Seidlein, [11]Nick Wareham, [12]Nicola Low, [12-Q28152053]Nicola Low [Full author list]PLOS MEDICINE [curation]DOI: 10.1371/JOURNAL.PMED.1001933
PubMed: 26713445		2015-12-29
Ensembl 2016[1]Andrew D Yates, [2]Wasiu Akanni, [3]M Ridwan Amode, [4]Daniel Barrell, [5]Konstantinos Billis, [6]Denise Carvalho Silva, [7]Carla A Cummins, [8]Peter Clapham, [9]Stephen Fitzgerald, [10]Laurent Gil, ..., [35]Steven P Wilder, [36]Amonida Zadissa, [37]Ewan Birney, [38]Jennifer Harrow, [39]Matthieu Muffato, ... [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKV1157
PubMed: 26687719		2015-12-19
Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci[1]Kyle J Gaulton, [2]Teresa Ferreira, [3]Yeji Lee, [4]Anne Raimondo, [5]Reedik Mägi, [6]Michael E Reschen, [7]Anubha Mahajan, [8]Adam E Locke, [9]N William Rayner, [10]Neil Robertson, ..., [148]Eleftheria Zeggini, [149]Ian Dunham, [150]Ewan Birney, [151]Lorenzo Pasquali, [152]Jorge Ferrer, ... [Full author list]Nature Genetics [curation]DOI: 10.1038/NG.3437
PubMed: 26551672		type 2 diabetes [curation]; susceptibility locus [curation]2015-11-09
MinION Analysis and Reference Consortium: Phase 1 data release and analysis[1]Camilla L C Ip, [2]Matthew Loose, [3]John R Tyson, [4]Mariateresa de Cesare, [5]Bonnie L Brown, [6]Miten Jain, [7]Richard Leggett, [8]David Eccles, [9]Vadim Zalunin, [10]John M Urban, ..., [16]Jared T Simpson, [17]Terrance P Snutch, [18]Ewan Birney, [19]David Buck, [20]Sara Goodwin, ... [Full author list]F1000Research [curation]DOI: 10.12688/F1000RESEARCH.7201.1
PubMed: 26834992		2015-10-15
The end of the start for population sequencing[1]Ewan Birney, [2]Nicole Soranzo [Full author list]Nature [curation]DOI: 10.1038/526052A
PubMed: 26432243		2015-10-01
Using human genetics to make new medicines.[1]Jeffrey C Barrett, [2]Ian Dunham, [3]Ewan Birney [Full author list]Nature Reviews Genetics [curation]DOI: 10.1038/NRG3998
PubMed: 26370900		human genetics [curation]2015-09-15
Correction: Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association[1]Zhihao Ding, [2]Yunyun Ni, [3]Sander W Timmer, [4]Bum-Kyu Lee, [5]Anna Battenhouse, [6]Sandra Louzada, [7]Fengtang Yang, [8]Ian Dunham, [9]Gregory E. Crawford, [10]Jason D Lieb, [11]Richard M. Durbin, [12]Vishwanath R Iyer, [13]Ewan Birney [Full author list]PLOS Genetics [curation]DOI: 10.1371/JOURNAL.PGEN.1005177
PubMed: 25919664		2015-04-28
FORGE: A tool to discover cell specific enrichments of GWAS associated SNPs in regulatory regions[1]Ian Dunham, [2]Eugene Kulesha, [3]Valentina Iotchkova, [4]Sandro Morganella, [5]Ewan Birney [Full author list]F1000Research [curation]DOI: 10.12688/F1000RESEARCH.6032.1
genome-wide association study [curation]2015-01-22
FORGE : A tool to discover cell specific enrichments of GWAS associated SNPs in regulatory regions[1]Ian Dunham, [2]Eugene Kulesha, [3]Valentina Iotchkova, [4]Sandro Morganella, [5]Ewan Birney [Full author list]DOI: 10.1101/013045
genome-wide association study [curation]2014-12-20
Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association[1]Zhihao Ding, [2]Yunyun Ni, [3]Sander W Timmer, [4]Bum-Kyu Lee, [5]Anna Battenhouse, [6]Sandra Louzada, [7]Fengtang Yang, [8]Ian Dunham, [9]Gregory E. Crawford, [10]Jason D Lieb, [11]Richard M. Durbin, [12]Vishwanath R Iyer, [13]Ewan Birney [Full author list]PLOS Genetics [curation]DOI: 10.1371/JOURNAL.PGEN.1004798
PubMed: 25411781		2014-11-01
Ensembl 2015[1]Fiona Cunningham, [2]M Ridwan Amode, [3]Daniel Barrell, [4]Kathryn Beal, [5]Konstantinos Billis, [6]Simon Brent, [7]Denise Carvalho Silva, [8]Peter Clapham, [9]Guy Coates, [10]Stephen Fitzgerald, ..., [37]Amonida Zadissa, [38]Bronwen Aken, [39]Ewan Birney, [40]Jennifer Harrow, [41]Rhoda Kinsella, ... [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKU1010
PubMed: 25352552		2014-10-28
Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease[1]Manolis Kellis, [2]Barbara J. Wold, [3]Michael P. Snyder, [4]Bradley Bernstein, [5]Anshul Kundaje, [6]Georgi K Marinov, [7]Lucas D Ward, [8]Ewan Birney, [9]Gregory E. Crawford, [10]Job Dekker, ... [Full author list]Proceedings of the National Academy of Sciences of the United States of America [curation]DOI: 10.1073/PNAS.1410434111
PubMed: 25275169		human biology [curation]2014-08-01
The EBI RDF platform: linked open data for the life sciences[1]Simon Jupp, [2]James Malone, [3]Jerven Bolleman, [4]Marco Brandizi, [4-Q47502895]Marco Brandizi, [5]Mark Davies, [6]Leyla Garcia, [7]Anna Gaulton, [8]Sebastien Gehant, [9]Camille Laibe, [10]Nicole Redaschi, [11]Sarala Wimalaratne, [12]Maria-Jesus Martin, [13]Nicolas Le Novère, [14]Helen Parkinson, [15]Ewan Birney, [16]Andy Jenkinson [Full author list]Bioinformatics [curation]DOI: 10.1093/BIOINFORMATICS/BTT765
PubMed: 24413672		Resource Description Framework [curation]; open data [curation]; linked data [curation]; life sciences [curation]; computational mathematics [curation]; linked open data [curation]2014-05-01
Defining functional DNA elements in the human genome[1]Manolis Kellis, [2]Barbara J. Wold, [3]Michael P. Snyder, [4]Bradley Bernstein, [5]Anshul Kundaje, [6]Georgi K Marinov, [7]Lucas D Ward, [8]Ewan Birney, [9]Gregory E. Crawford, [10]Job Dekker, ... [Full author list]Proceedings of the National Academy of Sciences of the United States of America [curation]DOI: 10.1073/PNAS.1318948111
PubMed: 24753594		2014-04-29
Integrative knowledge management to enhance pharmaceutical R&D[1]Maria Marti-Solano, [2]Ewan Birney, [3]Antoine Bril, [4]Oscar Della Pasqua, [5]Hiroaki Kitano, [6]Barend Mons, [7]Ioannis Xenarios, [8]Ferran Sanz [Full author list]Nature Reviews Drug Discovery [curation]DOI: 10.1038/NRD4290
PubMed: 24687050		knowledge management [curation]2014-04-01
Genomic and phenotypic characterization of a wild medaka population: towards the establishment of an isogenic population genetic resource in fish[1]Mikhail Spivakov, [2]Thomas O Auer, [3]Ravindra Peravali, [4]Ian Dunham, [5]Dirk Dolle, [6]Asao Fujiyama, [7]Atsushi Toyoda, [8]Tomoyuki Aizu, [9]Yohei Minakuchi, [10]Felix Loosli, [11]Kiyoshi Naruse, [12]Ewan Birney, [13]Joachim Wittbrodt [Full author list]G3 [curation]DOI: 10.1534/G3.113.008722
PubMed: 24408034		fish [curation]; population genetics [curation]2014-03-20
The Reactome pathway knowledgebase[1]David Croft, [2]Antonio Fabregat, [3]Robin Haw, [4]Marija Orlic-Milacic, [5]Joel Weiser, [6]Guanming Wu, [7]Michael Caudy, [8]Phani Garapati, [9]Marc Gillespie, [10]Maulik R. Kamdar, ..., [18]Heeyeon Song, [19]Mark Williams, [20]Ewan Birney, [21]Henning Hermjakob, [22]Lincoln Stein, ... [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKT1102
PubMed: 24243840		knowledge base [curation]; Reactome [curation]2014-01-01
Ensembl 2014[1]Paul Flicek, [2]M Ridwan Amode, [3]Daniel Barrell, [4]Kathryn Beal, [5]Konstantinos Billis, [6]Simon Brent, [7]Denise Carvalho-Silva, [8]Peter Clapham, [9]Guy Coates, [10]Stephen Fitzgerald, ..., [39]Amonida Zadissa, [40]Bronwen Aken, [41]Ewan Birney, [42]Fiona Cunningham, [43]Rhoda Kinsella, ... [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKT1196
PubMed: 24316576		2014-01-01
Archaic humans: Four makes a party.[1]Ewan Birney, [2]Jonathan K Pritchard [Full author list]Nature [curation]DOI: 10.1038/NATURE12847
PubMed: 24352230		2013-12-18
The European Bioinformatics Institute's data resources 2014[1]Catherine Brooksbank, [2]Mary Todd Bergman, [2-Q86836478]Mary Todd Bergman, [3]Rolf Apweiler, [4]Ewan Birney, [5]Janet Thornton [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKT1206
PubMed: 24271396		bioinformatics [curation]2013-11-23
Policy challenges of clinical genome sequencing[1]Caroline F Wright, [2]Anna Middleton, [2-Q56395820]Anna Middleton, [3]Hilary Burton, [4]Fiona Cunningham, [4-Q30347508]Fiona Cunningham, [5]S. E. Humphries, [6]Jane Hurst, [7]Ewan Birney, [7-Q4869199]Ewan Birney, [8]H. V. Firth, [8-Q92271212]Helen V. Firth [Full author list]The BMJ [curation]DOI: 10.1136/BMJ.F6845
PubMed: 24270507		whole genome sequencing [curation]2013-11-22
Genome-wide meta-analysis identifies new susceptibility loci for migraine[1]Verneri Anttila, [2]Bendik S. Winsvold, [3]Padhraig Gormley, [4]Tobias Kurth, [5]Francesco Bettella, [6]George McMahon, [7]Mikko Kallela, [8]Rainer Malik, [9]Boukje de Vries, [10]Gisela M Terwindt, ..., [73]Suzanne B R Jacobs, [74]J Raphael Gibbs, [75]Ewan Birney, [76]Jaakko Kaprio, [77]Brenda Penninx, ... [Full author list]Nature Genetics [curation]DOI: 10.1038/NG.2676
PubMed: 23793025		migraine [curation]; meta-analysis [curation]; susceptibility locus [curation]2013-06-23
Towards practical, high-capacity, low-maintenance information storage in synthesized DNA[1]Nick Goldman, [2]Paul Bertone, [3]Siyuan Chen, [4]Christophe Dessimoz, [5]Emily M LeProust, [6]Botond Sipos, [7]Ewan Birney [Full author list]Nature [curation]DOI: 10.1038/NATURE11875
PubMed: 23354052		2013-02-07
Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development[1]Remo Sanges, [2]Yavor Hadzhiev, [3]Marion Gueroult-Bellone, [4]Agnes Roure, [5]Marco Ferg, [6]Nicola Meola, [7]Gabriele Amore, [8]Swaraj Basu, [9]Euan R. Brown, [10]Marco De Simone, [11]Francesca Petrera, [12]Danilo Licastro, [13]Uwe Strähle, [14]Sandro Banfi, [15]Patrick Lemaire, [16]Ewan Birney, [17]Ferenc Müller, [18]Elia Stupka [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKT030
PubMed: 23393190		2013-02-07
Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium[1]Jie Wang, [2]Jiali Zhuang, [3]Sowmya Iyer, [4]Xin-Ying Lin, [5]Melissa C Greven, [6]Bong-Hyun Kim, [7]Jill Moore, [8]Brian G Pierce, [9]Xianjun Dong, [10]Daniel Virgil, [11]Ewan Birney, [12]Jui-Hung Hung, [13]Zhiping Weng [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKS1221
PubMed: 23203885		database [curation]2013-01-01
Ensembl 2013[1]Paul Flicek, [2]Ikhlak Ahmed, [3]M Ridwan Amode, [4]Daniel Barrell, [5]Kathryn Beal, [6]Simon Brent, [7]Denise Carvalho-Silva, [8]Peter Clapham, [9]Guy Coates, [10]Susan Fairley, ..., [41]Steven P Wilder, [42]Bronwen Aken, [43]Ewan Birney, [44]Fiona Cunningham, [45]Ian Dunham, ... [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKS1236
PubMed: 23203987		2013-01-01
Integrative annotation of chromatin elements from ENCODE data[1]Michael M. Hoffman, [2]Jason Ernst, [3]Steven P Wilder, [4]Anshul Kundaje, [5]Robert S Harris, [6]Max Libbrecht, [7]Belinda Giardine, [8]Paul M Ellenbogen, [9]Jeffrey A Bilmes, [10]Ewan Birney, [11]Ross Hardison, [12]Ian Dunham, [13]Manolis Kellis, [14]William S. Noble [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKS1284
PubMed: 23221638		2012-12-05
Journey to the genetic interior. Interview by Stephen S Hall[1]Ewan Birney [Full author list]Scientific American [curation]PubMed: 230298962012-10-01
The making of ENCODE: Lessons for big-data projects[1]Ewan Birney [Full author list]Nature [curation]DOI: 10.1038/489049A
PubMed: 22955613		big data [curation]; data ethics [curation]2012-09-06
Understanding transcriptional regulation by integrative analysis of transcription factor binding data[1]Chao Cheng, [2]Roger Alexander, [3]Renqiang Min, [4]Jing Leng, [5]Kevin Y Yip, [6]Joel Rozowsky, [7]Koon-Kiu Yan, [8]Xianjun Dong, [9]Sarah Djebali, [10]Yijun Ruan, [11]Carrie Chase Davis, [12]Piero Carninci, [13]Timo Lassmann, [14]Thomas R. Gingeras, [15]Roderic Guigó i Serra, [16]Ewan Birney, [17]Zhiping Weng, [18]Michael P. Snyder, [19]Mark Bender Gerstein [Full author list]Genome Research [curation]DOI: 10.1101/GR.136838.111
PubMed: 22955978		2012-09-01
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors[1]Jie Wang, [2]Jiali Zhuang, [3]Sowmya Iyer, [4]XinYing Lin, [5]Troy W Whitfield, [6]Melissa C Greven, [7]Brian G Pierce, [8]Xianjun Dong, [9]Anshul Kundaje, [10]Yong Cheng, [11]Oliver J Rando, [12]Ewan Birney, [13]Richard M Myers, [14]William S Noble, [15]Michael P. Snyder, [16]Zhiping Weng [Full author list]Genome Research [curation]DOI: 10.1101/GR.139105.112
PubMed: 22955990		2012-09-01
Modeling gene expression using chromatin features in various cellular contexts[1]Xianjun Dong, [2]Melissa C Greven, [3]Anshul Kundaje, [4]Sarah Djebali, [5]James B Brown, [6]Chao Cheng, [7]Thomas R. Gingeras, [8]Mark Bender Gerstein, [9]Roderic Guigó i Serra, [10]Ewan Birney, [11]Zhiping Weng [Full author list]Genome Biology [curation]DOI: 10.1186/GB-2012-13-9-R53
PubMed: 22950368		RNA sequencing [curation]2012-06-13
Paralogous annotation of disease-causing variants in long QT syndrome genes[1]James Ware, [2]Roddy Walsh, [3]Fiona Cunningham, [4]Ewan Birney, [5]Stuart A Cook [Full author list]Human Mutation [curation]DOI: 10.1002/HUMU.22114
PubMed: 22581653		long QT syndrome [curation]2012-06-07
The genomic basis of adaptive evolution in threespine sticklebacks[1]Felicity Jones, [2]Manfred Grabherr, [3]Yingguang Frank Chan, [4]Pamela Russell, [5]Evan Mauceli, [6]Jeremy Johnson, [7]Ross Swofford, [8]Mono Pirun, [9]Michael C. Zody, [10]Simon White, [11]Ewan Birney, [12]Stephen Searle, [13]Jeremy Schmutz, ... [Full author list]Nature [curation]DOI: 10.1038/NATURE10944
PubMed: 22481358		pollen [curation]; adaptive evolution [curation]2012-04-05
Erratum: Corrigendum: The BioPAX community standard for pathway data sharing[1]Emek Demir, [2]Michael P Cary, [3]Suzanne Paley, [4]Ken Fukuda, [5]Christian Lemer, [6]Imre Vastrik, [7]Guanming Wu, [8]Peter D'Eustachio, [9]Carl Schaefer, [10]Joanne Luciano, ..., [77]Shannon K. McWeeney, [78]Mirit I. Aladjem, [79]Ewan Birney, [80]Julio Collado-Vides, [81]Susumu Goto, ... [Full author list]Nature Biotechnology [curation]DOI: 10.1038/NBT0412-365C
data sharing [curation]; The BioPAX community standard for pathway data sharing [curation]2012-04-01
A transcription factor collective defines cardiac cell fate and reflects lineage history[1]Guillaume Junion, [2]Mikhail Spivakov, [3]Charles Girardot, [4]Martina Braun, [5]E Hilary Gustafson, [6]Ewan Birney, [7]Eileen E. M. Furlong [Full author list]Cell [curation]DOI: 10.1016/J.CELL.2012.01.030
PubMed: 22304916		2012-02-03
Analysis of variation at transcription factor binding sites in Drosophila and humans[1]Mikhail Spivakov, [2]Junaid Akhtar, [3]Pouya Kheradpour, [4]Kathryn Beal, [5]Charles Girardot, [6]Gautier Koscielny, [7]Javier Herrero, [8]Manolis Kellis, [9]Eileen E. M. Furlong, [10]Ewan Birney [Full author list]Genome Biology [curation]DOI: 10.1186/GB-2012-13-9-R49
PubMed: 22950968		Drosophila [curation]2012-01-01
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors[1]Kevin Y Yip, [2]Chao Cheng, [3]Nitin Bhardwaj, [4]James B Brown, [5]Jing Leng, [6]Anshul Kundaje, [7]Joel Rozowsky, [8]Ewan Birney, [9]Peter J. Bickel, [10]Michael P. Snyder, [11]Mark Bender Gerstein [Full author list]Genome Biology [curation]DOI: 10.1186/GB-2012-13-9-R48
PubMed: 22950945		2012-01-01
The future of DNA sequence archiving[1]Guy R. Cochrane, [2]Charles E Cook, [3]Ewan Birney [Full author list]GigaScience [curation]DOI: 10.1186/2047-217X-1-2
PubMed: 23587147		2012-01-01
Ensembl 2012[1]Paul Flicek, [2]M Ridwan Amode, [3]Daniel Barrell, [4]Kathryn Beal, [5]Simon Brent, [7]Peter Clapham, [8]Guy Coates, [9]Susan Fairley, [10]Stephen Fitzgerald, ..., [41]Steven P Wilder, [42]Bronwen Aken, [43]Ewan Birney, [44]Fiona Cunningham, [45]Ian Dunham, ... [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKR991
PubMed: 22086963		2012-01-01
Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells[1]Bum-Kyu Lee, [2]Akshay A Bhinge, [3]Anna Battenhouse, [4]Ryan M McDaniell, [5]Zheng Liu, [6]Lingyun Song, [7]Yunyun Ni, [8]Ewan Birney, [9]Jason D Lieb, [10]Terrence S. Furey, [11]Gregory E. Crawford, [12]Vishwanath R Iyer [Full author list]Genome Research [curation]DOI: 10.1101/GR.127597.111
PubMed: 22090374		2011-11-16
Major submissions tool developments at the European Nucleotide Archive[1]Clara Amid, [2]Ewan Birney, [3]Lawrence Bower, [4]Ana M. Cerdeño-Tárraga, [5]Ying Cheng, [6]Iain Cleland, [7]Nadeem Faruque, [8]Richard Gibson, [9]Neil Goodgame, [10]Christopher I. Hunter, ... [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKR946
PubMed: 22080548		2011-11-12
Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species[1]Paul J. Kersey, [2]Daniel M Staines, [3]Daniel Lawson, [4]Eugene Kulesha, [5]Paul F. Derwent, [6]Jay D Humphrey, [7]Daniel S T Hughes, [8]Stephen Keenan, [9]Arnaud Kerhornou, [10]Gautier Koscielny, ..., [19]Derek Wilson, [20]Andrew D Yates, [21]Ewan Birney [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKR895
PubMed: 22067447		2011-11-08
RNAcentral: A vision for an international database of RNA sequences[1]Alex Bateman, [2]Shipra Agrawal, [3]Ewan Birney, [4]Elspeth A Bruford, [5]Janusz Bujnicki, [6]Guy R. Cochrane, [7]James R Cole, [8]Marcel E. Dinger, [9]Anton J. Enright, [10]Paul P. Gardner, ... [Full author list]RNA [curation]DOI: 10.1261/RNA.2750811
PubMed: 21940779		database [curation]; RNACentral [curation]2011-11-01
A high-resolution map of human evolutionary constraint using 29 mammals[1]Kerstin Lindblad-Toh, [2]Manuel Garber, [3]Or zuk, [4]Michael F Lin, [5]Brian J Parker, [6]Stefan Washietl, [7]Pouya Kheradpour, [8]Jason Ernst, [9]Gregory Jordan, [10]Evan Mauceli, ..., [77]Patrick Minx, [78]Erica Sodergren, [79]Ewan Birney, [80]Elliott H. Margulies, [81]Javier Herrero, ... [Full author list]Nature [curation]DOI: 10.1038/NATURE10530
PubMed: 21993624		2011-10-27
Mouse genomic variation and its effect on phenotypes and gene regulation[1]Thomas M. Keane, [2]Leo Goodstadt, [3]Petr Danecek, [4]Michael A White, [5]Kim Wong, [6]Binnaz Yalçın, [7]Andreas Heger, [8]Avigail Agam, [9]Guy Slater, [10]Martin Goodson, ..., [37]Bret A Payseur, [38]Chris Ponting, [39]Ewan Birney, [40]Jonathan Flint, [41]David J Adams [Full author list]Nature [curation]DOI: 10.1038/NATURE10413
PubMed: 21921910		2011-09-14
Strengths and Weaknesses of Selected Modeling Methods Used in Systems Biology[1]Pascal Kahlem, [2]Alessandro DiCara, [3]Maxime Durot, [4]John M., [5]Edda Klipp, [6]Vincent Schachter, [7]Eran Segal, [8]Ioannis Xenarios, [9]Ewan Birney, [10]Luis Mendoz [Full author list]DOI: 10.5772/22126
2011-09-12
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity[1]Lingyun Song, [2]Zhancheng Zhang, [3]Linda L Grasfeder, [4]Alan P. Boyle, [5]Paul G Giresi, [6]Bum-Kyu Lee, [7]Nathan C. Sheffield, [8]Stefan Gräf, [9]Mikael Huss, [10]Damian Keefe, ..., [20]Zhuzhu Zhang, [21]Neil D Clarke, [22]Ewan Birney, [23]Vishwanath R Iyer, [24]Gregory E. Crawford, ... [Full author list]Genome Research [curation]DOI: 10.1101/GR.121541.111
PubMed: 21750106		2011-07-12
Efficient storage of high throughput DNA sequencing data using reference-based compression[1]Markus Hsi-Yang Fritz, [2]Rasko Leinonen, [3]Guy R. Cochrane, [4]Ewan Birney [Full author list]Genome Research [curation]DOI: 10.1101/GR.114819.110
PubMed: 21245279		DNA sequencing [curation]2011-05-01
Chromatin and heritability: how epigenetic studies can complement genetic approaches[1]Ewan Birney [Full author list]Trends in Genetics [curation]DOI: 10.1016/J.TIG.2011.02.005
PubMed: 21414682		heritability [curation]2011-03-16
High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells[1]Alan P. Boyle, [2]Lingyun Song, [3]Bum-Kyu Lee, [4]Darin London, [5]Damian Keefe, [6]Ewan Birney, [7]Vishwanath R Iyer, [8]Gregory E. Crawford, [9]Terrence S. Furey [Full author list]Genome Research [curation]DOI: 10.1101/GR.112656.110
PubMed: 21106903		2011-03-01
Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses[1]Albert J. Vilella, [2]Ewan Birney, [3]Paul Flicek, [4]Javier Herrero [Full author list]Genome Biology [curation]DOI: 10.1186/GB-2011-12-2-401
PubMed: 21320298		phylogenetics [curation]2011-02-21
The European Nucleotide Archive[1]Rasko Leinonen, [2]Ruth Akhtar, [3]Ewan Birney, [4]Lawrence Bower, [5]Ana M. Cerdeño-Tárraga, [6]Ying Cheng, [7]Iain Cleland, [8]Nadeem Faruque, [9]Neil Goodgame, [10]Richard Gibson, ... [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKQ967
PubMed: 20972220		2011-01-01
Ensembl 2011[1]Paul Flicek, [2]M Ridwan Amode, [3]Daniel Barrell, [4]Kathryn Beal, [5]Simon Brent, [6]Yuan Chen, [7]Peter Clapham, [8]Guy Coates, [9]Susan Fairley, [10]Stephen Fitzgerald, ..., [40]Jorge Zamora, [41]Bronwen Aken, [42]Ewan Birney, [43]Fiona Cunningham, [44]Ian Dunham, ... [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKQ1064
PubMed: 21045057		2011-01-01
Reactome: a database of reactions, pathways and biological processes[1]David Croft, [2]Gavin O'Kelly, [3]Guanming Wu, [4]Robin Haw, [5]Marc Gillespie, [6]Lisa Matthews, [7]Michael Caudy, [8]Phani Garapati, [9]Gopal Gopinath, [10]Bijay Jassal, ..., [17]Veronica Shamovsky, [18]Christina K. Yung, [19]Ewan Birney, [20]Henning Hermjakob, [21]Peter D'Eustachio, ... [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKQ1018
PubMed: 21067998		database [curation]2011-01-01
Assemblies: the good, the bad, the ugly.[1]Ewan Birney [Full author list]Nature Methods [curation]DOI: 10.1038/NMETH0111-59
PubMed: 21191376		2011-01-01
Erratum: Corrigendum: The BioPAX community standard for pathway data sharing[1]Emek Demir, [2]Michael P Cary, [3]Suzanne Paley, [4]Ken Fukuda, [5]Christian Lemer, [6]Imre Vastrik, [7]Guanming Wu, [8]Peter D'Eustachio, [9]Carl Schaefer, [10]Joanne Luciano, ..., [77]Shannon K. McWeeney, [78]Mirit I. Aladjem, [79]Ewan Birney, [80]Julio Collado-Vides, [81]Susumu Goto, ... [Full author list]Nature Biotechnology [curation]DOI: 10.1038/NBT1210-1308C
data sharing [curation]; The BioPAX community standard for pathway data sharing [curation]2010-12-07
Allele-specific and heritable chromatin signatures in humans[1]Ewan Birney, [2]Jason D Lieb, [3]Terrence S. Furey, [4]Gregory E. Crawford, [5]Vishwanath R Iyer [Full author list]Human Molecular Genetics [curation]DOI: 10.1093/HMG/DDQ404
PubMed: 20846943		nucleoprotein [curation]; human genome [curation]2010-10-15
The BioPAX community standard for pathway data sharing[1]Emek Demir, [2]Michael P Cary, [3]Suzanne Paley, [4]Ken Fukuda, [5]Christian Lemer, [6]Imre Vastrik, [7]Guanming Wu, [8]Peter D'Eustachio, [9]Carl Schaefer, [10]Joanne Luciano, ..., [78]Shannon K. McWeeney, [79]Mirit I. Aladjem, [80]Ewan Birney, [81]Julio Collado-Vides, [82]Susumu Goto, ... [Full author list]Nature Biotechnology [curation]DOI: 10.1038/NBT.1666
PubMed: 20829833		biotechnology [curation]; microbiology [curation]; BioPAX [curation]; data sharing [curation]2010-09-01
Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes, and mitochondria[1]Florian Gnad, [2]Francesca Forner, [3]Dorota F Zielinska, [4]Ewan Birney, [5]Jeremy Gunawardena, [6]Matthias Mann [Full author list]Molecular & Cellular Proteomics [curation]DOI: 10.1074/MCP.M110.001594
PubMed: 20688971		prokaryotes [curation]; mitochondrion [curation]; phosphorylation [curation]2010-08-05
The systematic annotation of the three main GPCR families in Reactome[1]Bijay Jassal, [2]Steven Jupe, [3]Michael Caudy, [4]Ewan Birney, [5]Lincoln Stein, [6]Henning Hermjakob, [7]Peter D'Eustachio [Full author list]Database [curation]DOI: 10.1093/DATABASE/BAQ018
PubMed: 20671204		G protein-coupled receptor [curation]2010-07-29
Finding and sharing: new approaches to registries of databases and services for the biomedical sciences[1]Damian Smedley, [2]Paul N. Schofield, [3]Chao-Kung Chen, [4]Vassilis Aidinis, [5]Chrysanthi Ainali, [6]Jonathan Bard, [7]Rudi Balling, [8]Ewan Birney, [9]Andrew Blake, [10]Erik Bongcam-Rudloff, ... [Full author list]Database [curation]DOI: 10.1093/DATABASE/BAQ014
PubMed: 20627863		database [curation]2010-07-06
A database and API for variation, dense genotyping and resequencing data[1]Daniel Rios, [2]William M McLaren, [3]Yuan Chen, [4]Ewan Birney, [5]Arne Stabenau, [6]Paul Flicek, [7]Fiona Cunningham [Full author list]BMC Bioinformatics [curation]DOI: 10.1186/1471-2105-11-238
PubMed: 20459810		database [curation]2010-05-11
A Draft Sequence of the Neandertal Genome[1]R. E. Green, [2]J. Krause, [3]A. W. Briggs, [4]T. Maricic, [5]U. Stenzel, [6]Martin Kircher, [7]Nick Patterson, [8]Heng Li, [9]Weiwei Zhai, [10]M. H. Y. Fritz, ..., [47]Evan E. Eichler, [48]D. Falush, [49]Ewan Birney, [50]J. C. Mullikin, [51]M. Slatkin, ... [Full author list]Science [curation]DOI: 10.1126/SCIENCE.1188021
PubMed: 20448178		cell line [curation]; Neanderthal genome [curation]2010-05-06
The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance[1]Santosh S Atanur, [2]Inanc Birol, [3]Victor Guryev, [4]Martin Hirst, [5]Oliver Hummel, [6]Catherine Morrissey, [7]Jacques Behmoaras, [8]Xose Fernandez, [9]Michelle D Johnson, [10]William M McLaren, ..., [23]Norbert Hubner, [24]Steven Jones, [25]Ewan Birney, [26]Timothy J Aitman [Full author list]Genome Research [curation]DOI: 10.1101/GR.103499.109
PubMed: 20430781		2010-04-29
Locus Reference Genomic sequences: an improved basis for describing human DNA variants[1]Raymond Dalgleish, [2]Paul Flicek, [3]Fiona Cunningham, [4]Alex Astashyn, [5]Raymond E Tully, [6]Glenn Proctor, [7]Yuan Chen, [8]William M McLaren, [9]Pontus Larsson, [10]Brendan Vaughan, [11]Christophe Beroud, [12]Glen Dobson, [13]Heikki Lehväslaiho, [14]Peter E Taschner, [15]Johan T den Dunnen, [16]Andrew Devereau, [17]Ewan Birney, [18]Anthony J Brookes, [19]Donna R. Maglott [Full author list]Genome Medicine [curation]DOI: 10.1186/GM145
PubMed: 20398331		2010-04-15
International network of cancer genome projects[1]International Cancer Genome Consortium, [2]Thomas J. Hudson, [3]Warwick Anderson, [4]Axel Artez, [5]Anna D Barker, [6]Cindy Bell, [7]Rosa R Bernabé, [8]M K Bhan, [9]Fabien Calvo, [10]Iiro Eerola, ..., [241]Michael R Stratton, [242]P. Andrew Futreal, [243]Ewan Birney, [244]Ake Borg, [245]Anne-Lise Børresen-Dale, ... [Full author list]Nature [curation]DOI: 10.1038/NATURE08987
PubMed: 20393554		data ethics [curation]2010-04-01
Heritable individual-specific and allele-specific chromatin signatures in humans[1]Ryan McDaniell, [2]Bum-Kyu Lee, [3]Lingyun Song, [4]Zheng Liu, [5]Alan P. Boyle, [6]Michael R Erdos, [7]Laura J Scott, [8]Mario A Morken, [9]Katerina S Kucera, [10]Anna Battenhouse, [11]Damian Keefe, [12]Francis Collins, [13]Huntington F Willard, [14]Jason D Lieb, [15]Terrence S. Furey, [16]Gregory E. Crawford, [17]Vishwanath R Iyer, [18]Ewan Birney [Full author list]Science [curation]DOI: 10.1126/SCIENCE.1184655
PubMed: 20299549		2010-03-18
An effective model for natural selection in promoters[1]Michael M. Hoffman, [2]Ewan Birney [Full author list]Genome Research [curation]DOI: 10.1101/GR.096719.109
PubMed: 20194951		2010-03-01
The consequence of natural selection on genetic variation in the mouse[1]Eli Reuveni, [2]Ewan Birney, [3]Cornelius T Gross [Full author list]Genomics [curation]DOI: 10.1016/J.YGENO.2010.02.004
PubMed: 20171270		genetic variation [curation]2010-02-18
A new strategy for genome assembly using short sequence reads and reduced representation libraries[1]Andrew L Young, [2]Hatice Ozel Abaan, [3]Daniel R Zerbino, [4]James C Mullikin, [5]Ewan Birney, [6]Elliott H. Margulies [Full author list]Genome Research [curation]DOI: 10.1101/GR.097956.109
PubMed: 20123915		2010-02-01
A small-cell lung cancer genome with complex signatures of tobacco exposure[1]Erin D Pleasance, [2]Philip J Stephens, [3]Sarah O'Meara, [4]David J McBride, [5]Alison Meynert, [6]David R. Jones, [7]Meng-Lay Lin, [8]David Beare, [9]King Wai Lau, [10]Chris Greenman, ..., [33]John D Minna, [34]Adi Gazdar, [35]Ewan Birney, [36]Michael D Rhodes, [37]Kevin McKernan, ... [Full author list]Nature [curation]DOI: 10.1038/NATURE08629
PubMed: 20016488		lung cancer [curation]; cell line [curation]2010-01-14
Ensembl variation resources[1]Yuan Chen, [2]Fiona Cunningham, [3]Daniel Rios, [4]William M McLaren, [5]James Smith, [6]Bethan Pritchard, [7]Giulietta Spudich, [8]Simon Brent, [9]Eugene Kulesha, [10]Pablo Marin-Garcia, [11]Damian Smedley, [12]Ewan Birney, [13]Paul Flicek [Full author list]BMC Genomics [curation]DOI: 10.1186/1471-2164-11-293
PubMed: 20459805		2010-01-01
Genomic information infrastructure after the deluge[1]Julian Parkhill, [2]Ewan Birney, [3]Paul J. Kersey [Full author list]Genome Biology [curation]DOI: 10.1186/GB-2010-11-7-402
PubMed: 20670392		infrastructure [curation]2010-01-01
Improvements to services at the European Nucleotide Archive[1]Rasko Leinonen, [2]Ruth Akhtar, [3]Ewan Birney, [4]James K. Bonfield, [5]Lawrence Bower, [6]Matt Corbett, [7]Ying Cheng, [8]Fehmi Demiralp, [9]Nadeem Faruque, [10]Neil Goodgame, ... [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKP998
PubMed: 19906712		2010-01-01
Ensembl's 10th year[1]Paul Flicek, [2]Bronwen Aken, [3]Benoit Ballester, [4]Kathryn Beal, [5]Eugene Bragin, [6]Simon Brent, [7]Yuan Chen, [8]Peter Clapham, [9]Guy Coates, [10]Susan Fairley, ..., [45]Steven P Wilder, [46]Amonida Zadissa, [47]Ewan Birney, [48]Fiona Cunningham, [49]Ian Dunham, ... [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKP972
PubMed: 19906699		2010-01-01
Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler[1]Daniel R Zerbino, [2]Gayle K McEwen, [3]Elliott H. Margulies, [4]Ewan Birney [Full author list]PLOS One [curation]DOI: 10.1371/JOURNAL.PONE.0008407
PubMed: 20027311		2009-12-22
Ensembl Genomes: extending Ensembl across the taxonomic space[1]Paul J. Kersey, [2]D Lawson, [3]Ewan Birney, [4]P S Derwent, [5]Matthias Haimel, [6]Javier Herrero, [7]Stephen Keenan, [8]Arnaud Kerhornou, [9]G Koscielny, [10]Andreas K Kähäri, [11]R J Kinsella, [12]Eugene Kulesha, [13]U Maheswari, [14]Karyn Megy, [15]Michael Nuhn, [16]G Proctor, [17]Daniel M Staines, [18]F Valentin, [19]Albert J. Vilella, [20]Andrew D Yates [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKP871
PubMed: 19884133		2009-11-01
Sense from sequence reads: methods for alignment and assembly[1]Paul Flicek, [2]Ewan Birney [Full author list]Nature Methods [curation]DOI: 10.1038/NMETH.1376
PubMed: 19844229		sequence alignment [curation]2009-11-01
ENFIN--A European network for integrative systems biology[1]Pascal Kahlem, [2]Andrew Clegg, [3]Florian Reisinger, [4]Ioannis Xenarios, [5]Henning Hermjakob, [6]Christine Orengo, [7]Ewan Birney [Full author list]Comptes Rendus. Biologies [curation]DOI: 10.1016/J.CRVI.2009.09.003
PubMed: 19909926		2009-11-01
EMMA--mouse mutant resources for the international scientific community[1]Phil Wilkinson, [2]Jitka Sengerova, [3]Raffaele Matteoni, [4]Chao-Kung Chen, [5]Gaetan Soulat, [6]Abel Ureta-Vidal, [7]Sabine Fessele, [8]Michael Hagn, [9]Marzia Massimi, [10]Karen Pickford, ..., [18]Vanessa Larrigaldie, [19]Johan Leyritz, [20]Ewan Birney, [21]Glauco P Tocchini-Valentini, [22]Steve Brown, ... [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKP799
PubMed: 19783817		2009-09-26
Prepublication data sharing[2]Ewan Birney, [3]Thomas J. Hudson, [4]Eric D. Green, [5]Chris Gunter, [6]Sean Eddy, [7]Jane Rogers, [8]Jennifer R Harris, [9]S Dusko Ehrlich, [10]Rolf Apweiler, ... [Full author list]Nature [curation]DOI: 10.1038/461168A
PubMed: 19741685		data sharing [curation]; academic publishing [curation]; data ethics [curation]2009-09-10
Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt[1]Steffen Durinck, [2]Paul Spellman, [3]Ewan Birney, [4]Wolfgang Huber [Full author list]Nature Protocols [curation]DOI: 10.1038/NPROT.2009.97
PubMed: 19617889		data set [curation]; R package [curation]2009-07-23
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes[1]Kim D. Pruitt, [2]Jennifer Harrow, [3]Rachel A. Harte, [4]Craig Wallin, [5]Mark Diekhans, [6]Donna R. Maglott, [7]Steve Searle, [8]Catherine M Farrell, [9]Jane E Loveland, [10]Barbara J. Ruef, ..., [42]Laurens G Wilming, [43]Wenyu Wu, [44]Ewan Birney, [45]David Haussler, [46]Tim Hubbard, ... [Full author list]Genome Research [curation]DOI: 10.1101/GR.080531.108
PubMed: 19498102		2009-07-01
Reactome – a knowledgebase of human biological pathways[1]Bijay Jassal, [2]Phani Garapati, [3]Gopal Gopinath, [4]Michael Caudy, [5]Marc Gillespie, [6]Alexander Kanapin, [7]Steven Jupe, [8]Bruce May, [9]Gavin O'Kelly, [10]Shahana Mahajan, [11]Ewan Birney, [12]Peter D'Eustachio, [13]Esther Schmidt, [14]Lincoln Stein, [15]Guanming Wu, [16]Imre Vastrik, [17]Lisa Matthews, [18]David Croft, [19]Bernard de Bono [Full author list]Nature Precedings [curation]DOI: 10.1038/NPRE.2009.3200.1
knowledge base [curation]2009-05-03
Reactome – a knowledgebase of human biological pathways[1]Bijay Jassal, [2]Bijay Jassal, [3]Esther Schmidt, [4]Guanming Wu, [5]Imre Vastrik, [6]David Croft, [7]Bernard de Bono, [8]Gopal Gopinath, [9]Marc Gillespie, [10]Steven Jupe, [11]Gavin O'Kelly, [12]Lisa Matthews, [13]Phani Garapati, [14]Michael Caudy, [15]Alexander Kanapin, [16]Bruce May, [17]Shahana Mahajan, [18]Ewan Birney, [19]Peter D'Eustachio, [20]Lincoln Stein [Full author list]Nature Precedings [curation]DOI: 10.1038/NPRE.2009.3200
knowledge base [curation]2009-05-03
Genomic resources for invertebrate vectors of human pathogens, and the role of VectorBase[1]Karyn Megy, [2]M Hammond, [3]D Lawson, [4]R V Bruggner, [5]Ewan Birney, [6]F H Collins [Full author list]Infection, Genetics and Evolution [curation]DOI: 10.1016/J.MEEGID.2007.12.007
PubMed: 18262474		2009-05-01
Correction: Reactome: a knowledge base of biologic pathways and processes[1]Imre Vastrik, [2]Peter D'Eustachio, [3]Esther Schmidt, [4]Gopal Gopinath, [5]David Croft, [6]Bernard de Bono, [7]Marc Gillespie, [8]Bijay Jassal, [9]Suzanna Lewis, [10]Lisa Matthews, [11]Guanming Wu, [12]Ewan Birney, [13]Lincoln Stein [Full author list]Genome Biology [curation]DOI: 10.1186/GB-2009-10-2-402
knowledge base [curation]2009-02-04
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates[1]Albert J. Vilella, [2]Jessica Severin, [3]Abel Ureta-Vidal, [4]Li Heng, [5]Richard M. Durbin, [6]Ewan Birney [Full author list]Genome Research [curation]DOI: 10.1101/GR.073585.107
PubMed: 19029536		phylogenetics [curation]2009-02-01
VectorBase: a data resource for invertebrate vector genomics[1]Daniel Lawson, [2]Peter Arensburger, [3]Peter Atkinson, [4]Nora Besansky, [5]Robert V Bruggner, [6]Ryan Butler, [7]Kathryn S Campbell, [8]George K Christophides, [9]Scott Christley, [10]Emmanuel Dialynas, ..., [21]Eric O Stinson, [22]Pantelis Topalis, [23]Ewan Birney, [24]William M Gelbart, [25]Fotis Kafatos, ... [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKN857
PubMed: 19028744		genomics [curation]2009-01-01
Ensembl 2009[1]Tim Hubbard, [2]Aken BL, [3]Ayling S, [4]Ballester B, [5]Beal K, [6]Bragin E, [7]Brent S, [8]Chen Y, [9]Clapham P, [10]Laura Clarke, ..., [46]Wilder S, [47]Zadissa A, [48]Ewan Birney, [49]Fiona Cunningham, [50]Curwen V, ... [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKN828
PubMed: 19033362		2009-01-01
Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment.[1]Benedict Paten, [2]Javier Herrero, [3]Kathryn Beal, [4]Ewan Birney [Full author list]Bioinformatics [curation]DOI: 10.1093/BIOINFORMATICS/BTN630
PubMed: 19056777		sequence alignment [curation]2008-12-04
Reactome knowledgebase of human biological pathways and processes[1]Lisa Matthews, [2]Gopal Gopinath, [3]Marc Gillespie, [4]Michael Caudy, [5]David Croft, [6]Bernard de Bono, [7]Phani Garapati, [8]Jill Hemish, [9]Henning Hermjakob, [10]Bijay Jassal, [11]Alexander Kanapin, [12]Suzanna Lewis, [13]Shahana Mahajan, [14]Bruce May, [15]Esther Schmidt, [16]Imre Vastrik, [17]Guanming Wu, [18]Ewan Birney, [19]Lincoln Stein, [20]Peter D'Eustachio [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKN863
PubMed: 18981052		knowledge base [curation]; Reactome [curation]2008-11-03
Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs[1]Benedict Paten, [2]Javier Herrero, [3]Kathryn Beal, [4]Stephen Fitzgerald, [5]Ewan Birney [Full author list]Genome Research [curation]DOI: 10.1101/GR.076554.108
PubMed: 18849524		2008-11-01
Genome-wide nucleotide-level mammalian ancestor reconstruction[1]Benedict Paten, [2]Javier Herrero, [3]Stephen Fitzgerald, [4]Kathryn Beal, [5]Paul Flicek, [6]Ian Holmes, [7]Ewan Birney [Full author list]Genome Research [curation]DOI: 10.1101/GR.076521.108
PubMed: 18849525		2008-11-01
Petabyte-scale innovations at the European Nucleotide Archive[1]Guy R. Cochrane, [2]Ruth Akhtar, [3]James K. Bonfield, [4]Lawrence Bower, [5]Fehmi Demiralp, [6]Nadeem Faruque, [7]Richard Gibson, [8]Gemma Hoad, [9]Tim Hubbard, [10]Christopher I. Hunter, ..., [25]Robert Vaughan, [26]Vadim Zalunin, [27]Ewan Birney [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKN765
PubMed: 18978013		2008-10-31
MAPU 2.0: high-accuracy proteomes mapped to genomes[1]Florian Gnad, [2]Mario Oroshi, [3]Ewan Birney, [4]Matthias Mann [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKN773
PubMed: 18948283		2008-10-23
Advanced genomic data mining[1]Xosé M Fernández-Suárez, [2]Ewan Birney [Full author list]PLOS Computational Biology [curation]DOI: 10.1371/JOURNAL.PCBI.1000121
PubMed: 18818719		data mining [curation]2008-09-26
Genome analysis of the platypus reveals unique signatures of evolution[1]Wesley C Warren, [2]Ladeana Hillier, [3]Jenny Graves, [4]Ewan Birney, [5]Chris P. Ponting, [6]Frank Grutzner, [7]Katherine Belov, [8]Webb Miller, [9]Laura Clarke, [10]Asif T. Chinwalla, ... [Full author list]Nature [curation]DOI: 10.1038/NATURE07253
2008-09-11
An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)[1]Vardhman K Rakyan, [2]Thomas A Down, [3]Natalie P Thorne, [4]Paul Flicek, [5]Eugene Kulesha, [6]Stefan Gräf, [7]Eleni M Tomazou, [8]Liselotte Bäckdahl, [9]Nathan Johnson, [10]Marlis Herberth, [11]Kevin L Howe, [12]David K Jackson, [13]Marcos M Miretti, [14]Heike Fiegler, [15]John Marioni, [16]Ewan Birney, [17]Tim Hubbard, [18]Nigel P Carter, [19]Simon Tavaré, [20]Stephan Beck [Full author list]Genome Research [curation]DOI: 10.1101/GR.077479.108
PubMed: 18577705		2008-09-01
Confounding between recombination and selection, and the Ped/Pop method for detecting selection[1]Paul F. O'Reilly, [2]Ewan Birney, [3]David J. Balding [Full author list]Genome Research [curation]DOI: 10.1101/GR.067181.107
PubMed: 18617692		2008-07-10
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis[1]Thomas A Down, [2]Vardhman K Rakyan, [3]Daniel J Turner, [4]Paul Flicek, [5]Heng Li, [6]Eugene Kulesha, [7]Stefan Gräf, [8]Nathan Johnson, [9]Javier Herrero, [10]Eleni M Tomazou, ..., [16]Marcos M Miretti, [17]John Marioni, [18]Ewan Birney, [19]Tim Hubbard, [20]Richard M. Durbin, ... [Full author list]Nature Biotechnology [curation]DOI: 10.1038/NBT1414
PubMed: 18612301		biomedical engineering [curation]; bioengineering [curation]; deconvolution [curation]2008-07-01
Arabidopsis reactome: a foundation knowledgebase for plant systems biology[1]Nicolas Tsesmetzis, [2]Matthew Couchman, [3]Janet Higgins, [4]Alison Smith, [5]John H Doonan, [6]Georg J Seifert, [7]Esther E Schmidt, [8]Imre Vastrik, [9]Ewan Birney, [10]Guanming Wu, [11]Peter D'Eustachio, [12]Lincoln Stein, [13]Richard J Morris, [14]Michael Bevan, [15]Sean V Walsh [Full author list]The Plant Cell [curation]DOI: 10.1105/TPC.108.057976
PubMed: 18591350		knowledge base [curation]2008-06-01
Genome analysis of the platypus reveals unique signatures of evolution[1]Wesley C Warren, [2]Ladeana Hillier, [3]Jenny Graves, [4]Ewan Birney, [5]Chris Ponting, [6]Frank Grutzner, [7]Katherine Belov, [8]Webb Miller, [9]Laura Clarke, [10]Asif T. Chinwalla, ... [Full author list]Nature [curation]DOI: 10.1038/NATURE06936
PubMed: 18464734		2008-05-08
Velvet: algorithms for de novo short read assembly using de Bruijn graphs[1]Daniel R Zerbino, [2]Ewan Birney [Full author list]Genome Research [curation]DOI: 10.1101/GR.074492.107
PubMed: 18349386		algorithm [curation]2008-05-01
What everybody should know about the rat genome and its online resources[1]Simon N Twigger, [2]Kim D. Pruitt, [3]Xose Fernandez, [4]Donna Karolchik, [5]Kim C Worley, [6]Donna R. Maglott, [7]Garth Brown, [8]George Weinstock, [9]Richard A Gibbs, [10]Jim Kent, [11]Ewan Birney, [12]Howard J Jacob [Full author list]Nature Genetics [curation]DOI: 10.1038/NG0508-523
PubMed: 18443589		2008-05-01
SNP and haplotype mapping for genetic analysis in the rat[1]STAR Consortium, [2]Kathrin Saar, [3]Alfred Beck, [4]Marie-Thérèse Bihoreau, [5]Ewan Birney, [6]Denise Brocklebank, [7]Yuan Chen, [8]Edwin Cuppen, [9]Stephanie Demonchy, [10]Joaquín Dopazo, ... [Full author list]Nature Genetics [curation]DOI: 10.1038/NG.124
PubMed: 18443594		2008-05-01
Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes[1]Elliott H. Margulies, [2]Ewan Birney [Full author list]Nature Reviews Genetics [curation]DOI: 10.1038/NRG2185
PubMed: 18347593		2008-04-01
Levers and fulcrums: progress in cis-regulatory motif models.[1]Ewan Birney [Full author list]Nature Methods [curation]DOI: 10.1038/NMETH0408-297
PubMed: 18376393		2008-04-01
Ensembl 2008[1]Paul Flicek, [2]B L Aken, [3]K Beal, [4]Benoit Ballester, [5]M Caccamo, [6]Y Chen, [7]Lara Clarke, [8]Guy Coates, [9]Fiona Cunningham, [10]T Cutts, ..., [46]S White, [47]M Wood, [48]Ewan Birney, [49]T Cox, [50]V Curwen, ... [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKM988
PubMed: 18000006		2008-01-01
Integrating biological data--the Distributed Annotation System[1]Andy Jenkinson, [2]Mario Albrecht, [3]Ewan Birney, [4]Hagen Blankenburg, [5]Thomas Down, [6]Robert D. Finn, [7]Henning Hermjakob, [8]Tim JP Hubbard, [10]Philip Jones, [14]Gabrielle A Reeves, [8-Q15990056]Tim Hubbard, [9]Rafael C. Jimenez, [11]Andreas K Kähäri, [12]Eugene Kulesha, [13]Jose Ramon Macias, [15]Andreas Prlić [Full author list]BMC Bioinformatics [curation]DOI: 10.1186/1471-2105-9-S8-S3
PubMed: 18673527		2008-01-01
Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database[1]Guy R. Cochrane, [2]Ruth Akhtar, [3]Philippe Aldebert, [4]Nicola Althorpe, [5]Alastair Baldwin, [6]Kirsty Bates, [7]Sumit Bhattacharyya, [8]James K. Bonfield, [9]Lawrence Bower, [10]Paul Browne, ..., [34]Rolf Apweiler, [35]Tim Hubbard, [36]Ewan Birney [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKM1018
PubMed: 18039715		database [curation]2008-01-01
Optimising oligonucleotide array design for ChIP-on-chip[1]Fiona G.G. Nielsen, [2]Stefan Graef, [3]Xinmin Zhang, [4]Stefan Kurtz, [5]Sergei Denissov, [6]Roland Green, [7]Ewan Birney, [8]Paul Flicek, [9]Martijn Huynen, [10]Henk Stunnenberg [Full author list]BMC Bioinformatics [curation]DOI: 10.1186/1471-2105-8-S8-P4
2007-11-20
The HGNC Database in 2008: a resource for the human genome[1]Elspeth A Bruford, [2]Michael J Lush, [3]Mathew W Wright, [4]Tam P Sneddon, [5]Sue Povey, [6]Ewan Birney [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKM881
PubMed: 17984084		database [curation]2007-11-04
Evolutionary genomics: come fly with us.[1]Ewan Birney [Full author list]Nature [curation]DOI: 10.1038/450184A
PubMed: 17994082		genomics [curation]2007-11-01
Double Dutch for duplications[1]Ewan Birney [Full author list]Nature Genetics [curation]DOI: 10.1038/NG1107-1303
PubMed: 17968343		2007-11-01
ENFIN a network to enhance integrative systems biology[1]Pascal Kahlem, [2]Ewan Birney [Full author list]Annals of the New York Academy of Sciences [curation]DOI: 10.1196/ANNALS.1407.016
PubMed: 17934049		2007-10-12
Genome browsing with Ensembl: a practical overview[1]Giulietta Spudich, [2]Xose Fernandez, [3]Ewan Birney [Full author list]Briefings in functional genomics & proteomics [curation]DOI: 10.1093/BFGP/ELM025
PubMed: 17967807		2007-09-01
In vivo validation of a computationally predicted conserved Ath5 target gene set[1]Filippo Del Bene, [2]Laurence M Ettwiller, [3]Dorota Skowronska-Krawczyk, [4]Herwig Baier, [5]Jean-Marc Matter, [6]Ewan Birney, [7]Joachim Wittbrodt [Full author list]PLOS Genetics [curation]DOI: 10.1371/JOURNAL.PGEN.0030159
PubMed: 17892326		2007-08-01
Challenges and standards in integrating surveys of structural variation[1]Stephen W. Scherer, [2]Charles Lee, [3]Ewan Birney, [4]David Altshuler, [5]Evan E. Eichler, [6]Nigel P Carter, [7]Matthew E Hurles, [8]Lars Feuk [Full author list]Nature Genetics [curation]DOI: 10.1038/NG2093
PubMed: 17597783		2007-07-01
Optimized design and assessment of whole genome tiling arrays[1]Stefan Gräf, [2]Fiona G.G. Nielsen, [3]Stefan Kurtz, [4]Martijn A Huynen, [5]Ewan Birney, [6]Henk Stunnenberg, [7]Paul Flicek [Full author list]Bioinformatics [curation]DOI: 10.1093/BIOINFORMATICS/BTM200
PubMed: 17646297		whole genome sequencing [curation]2007-07-01
Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation.[1]Laurence Ettwiller, [2]Benedict Paten, [3]Mirana Ramialison, [4]Ewan Birney, [5]Joachim Wittbrodt [Full author list]Nature Methods [curation]DOI: 10.1038/NMETH1061
PubMed: 17589518		2007-06-24
Genome sequence of Aedes aegypti, a major arbovirus vector[1]Vishvanath Nene, [2]Jennifer R Wortman, [3]Daniel Lawson, [4]Brian J Haas, [5]Chinnappa D Kodira, [6]Zhijian Jake Tu, [7]Brendan Loftus, [8]Zhiyong Xi, [9]Karyn Megy, [10]Manfred Grabherr, ..., [23]Shelby L. Bidwell, [24]Jim Biedler, [25]Ewan Birney, [26]Robert V Bruggner, [27]Javier Costas, ... [Full author list]Science [curation]DOI: 10.1126/SCIENCE.1138878
PubMed: 17510324		Aedes [curation]; arbovirus [curation]; Aedes aegypti [curation]; insect vector [curation]; insect genome [curation]2007-06-22
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project[1]ENCODE Project Consortium, [2]Ewan Birney, [3]John Stamatoyannopoulos, [4]Anindya Dutta, [5]Roderic Guigó i Serra, [6]Thomas R. Gingeras, [7]Elliott H. Margulies, [8]Zhiping Weng, [9]Michael P. Snyder, [10]Emmanouil Dermitzakis, ..., [203-Q114294290]Atif Shahab, ..., [246-Q90016751]Yijun Ruan, ... [Full author list]Nature [curation]DOI: 10.1038/NATURE05874
PubMed: 17571346		human genome [curation]2007-06-01
The landscape of histone modifications across 1% of the human genome in five human cell lines[1]Christof Koch, [2]Robert M Andrews, [3]Paul Flicek, [4]Shane C Dillon, [5]Ulaş Karaöz, [6]Gayle K Clelland, [7]Sarah Wilcox, [8]David M Beare, [9]Joanna C Fowler, [10]Phillippe Couttet, ..., [17]Cordelia F Langford, [18]Zhiping Weng, [19]Ewan Birney, [20]Nigel P Carter, [21]David Vetrie, ... [Full author list]Genome Research [curation]DOI: 10.1101/GR.5704207
PubMed: 17567990		2007-06-01
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome[1]Elliott H. Margulies, [2]Gregory M Cooper, [3]George Asimenos, [4]Daryl J Thomas, [5]Colin N Dewey, [6]Adam C. Siepel, [7]Ewan Birney, [8]Damian Keefe, [9]Ariel S Schwartz, [10]Minmei Hou, ... [Full author list]Genome Research [curation]DOI: 10.1101/GR.6034307
PubMed: 17567995		sequence alignment [curation]2007-06-01
Evolutionary and biomedical insights from the rhesus macaque genome[1]Rhesus Macaque Genome Sequencing and Analysis Consortium, [2]Richard A Gibbs, [3]Jeffrey Rogers, [4]Michael Katze, [5]Roger E Bumgarner, [6]George Weinstock, [7]Elaine Mardis, [8]Karin A. Remington, [9]Robert L. Strausberg, [10]Craig Venter, ..., [106]Todd Wylie, [107]Lan Zhang, [108]Ewan Birney, [109]Kyudong Han, [110]Miriam K Konkel, ... [Full author list]Science [curation]DOI: 10.1126/SCIENCE.1139247
PubMed: 17431167		Macaca [curation]2007-04-01
The implications of alternative splicing in the ENCODE protein complement[1]Michael L Tress, [2]Pier Luigi Martelli, [3]Adam Frankish, [4]Gabrielle A Reeves, [5]Jan Jaap Wesselink, [6]Corin Yeats, [7]Páll Isólfur Olason, [8]Mario Albrecht, [9]Hedi Hegyi, [10]Alejandro Giorgetti, ..., [32]Stilianos Antonarakis, [33]Alexandre Reymond, [34]Ewan Birney, [35]Søren Brunak, [36]Rita Casadio, ... [Full author list]Proceedings of the National Academy of Sciences of the United States of America [curation]DOI: 10.1073/PNAS.0700800104
PubMed: 17372197		alternative mRNA splicing, via spliceosome [curation]2007-03-27
Identification of novel peptide hormones in the human proteome by hidden Markov model screening[1]Olivier Mirabeau, [2]Emerald Perlas, [3]Cinzia Severini, [4]Enrica Audero, [5]Olivier Gascuel, [6]Roberta Possenti, [7]Ewan Birney, [8]Nadia Rosenthal, [9]Cornelius Gross [Full author list]Genome Research [curation]DOI: 10.1101/GR.5755407
PubMed: 17284679		hidden Markov model [curation]; Markov model [curation]; Spexin hormone [curation]; ECRG4 augurin precursor [curation]; Spexin hormone [curation]; positive regulation of gastro-intestinal system smooth muscle contraction [curation]; Spexin hormone [curation]2007-02-06
Estimating the neutral rate of nucleotide substitution using introns[1]Michael M. Hoffman, [2]Ewan Birney [Full author list]Molecular Biology and Evolution [curation]DOI: 10.1093/MOLBEV/MSL179
PubMed: 17122369		2007-02-01
Ensembl 2007[1]Tim Hubbard, [2]B L Aken, [10]T Cutts, ..., [3]K Beal, [4]Benoit Ballester, [5]M Caccamo, [6]Y Chen, [7]Lara Clarke, [8]Guy Coates, [9]Fiona Cunningham, ..., [56]James Smith, [57]Abel Ureta-Vidal, [58]Ewan Birney [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKL996
PubMed: 17148474		2007-01-01
VectorBase: a home for invertebrate vectors of human pathogens[1]Daniel Lawson, [2]Peter Arensburger, [3]Peter Atkinson, [4]Nora Besansky, [5]Robert V Bruggner, [6]Ryan Butler, [7]Kathryn S Campbell, [8]George K Christophides, [9]Scott Christley, [10]Emmanuel Dialynas, ..., [23]Pantelis Topalis, [24]Evgeny M Zdobnov, [25]Ewan Birney, [26]William M Gelbart, [27]Fotis Kafatos, ... [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKL960
PubMed: 17145709		2007-01-01
Reactome: a knowledge base of biologic pathways and processes[1]Imre Vastrik, [2]Peter D'Eustachio, [3]Esther Schmidt, [4]Gopal Gopinath, [5]David Croft, [6]Bernard de Bono, [7]Marc Gillespie, [8]Bijay Jassal, [9]Suzanna Lewis, [10]Lisa Matthews, [11]Guanming Wu, [12]Ewan Birney, [13]Lincoln Stein [Full author list]Genome Biology [curation]DOI: 10.1186/GB-2007-8-3-R39
PubMed: 17367534		knowledge base [curation]2007-01-01
Update of the Anopheles gambiae PEST genome assembly[1]Maria V Sharakhova, [2]Martin P Hammond, [3]Neil F Lobo, [4]Jaroslaw Krzywinski, [5]Maria F Unger, [6]Maureen E Hillenmeyer, [7]Robert V Bruggner, [8]Ewan Birney, [9]Frank H Collins [Full author list]Genome Biology [curation]DOI: 10.1186/GB-2007-8-1-R5
PubMed: 17210077		Anopheles gambiae [curation]2007-01-01
EGASP: the human ENCODE Genome Annotation Assessment Project[1]Roderic Guigó i Serra, [2]Paul Flicek, [3]Josep F. Abril, [4]Alexandre Reymond, [5]Julien Lagarde, [6]France Denoeud, [7]Stilianos Antonarakis, [8]Michael Ashburner, [9]Vladimir B. Bajic, [10]Ewan Birney, [11]Robert Castelo, [12]Eduardo Eyras, [13]Catherine Ucla, [14]Thomas R. Gingeras, [15]Jennifer Harrow, [16]Tim Hubbard, [17]Suzanna Lewis, [18]Martin G Reese [Full author list]Genome Biology [curation]DOI: 10.1186/GB-2006-7-S1-S2
PubMed: 16925836		genomics [curation]; human genome [curation]; genome annotation [curation]2006-08-07
TranscriptSNPView: a genome-wide catalog of mouse coding variation[1]Fiona Cunningham, [2]Daniel Rios, [3]Mark Griffiths, [4]James Smith, [5]Zemin Ning, [6]Tony Cox, [7]Paul Flicek, [8]Pablo Marin-Garcin, [9]Javier Herrero, [10]Jane Rogers, [11]Louise van der Weyden, [12]Allan Bradley, [13]Ewan Birney, [14]David J Adams [Full author list]Nature Genetics [curation]DOI: 10.1038/NG0806-853A
PubMed: 16874317		2006-08-01
Dry work in a wet world: computation in systems biology[1]Pascal Kahlem, [2]Ewan Birney [Full author list]Molecular Systems Biology [curation]DOI: 10.1038/MSB4100080
PubMed: 16820781		2006-07-04
Picking pyknons out of the human genome[1]Alison Meynert, [2]Ewan Birney [Full author list]Cell [curation]DOI: 10.1016/J.CELL.2006.05.019
PubMed: 16751093		2006-06-02
Ensembl 2006[1]Ewan Birney, [2]D Andrews, [3]M Caccamo, [4]Y Chen, [5]Laura Clarke, [6]Guy Coates, [7]T Cox, [8]Fiona Cunningham, [9]V Curwen, [10]T Cutts, ... [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKJ133
PubMed: 16381931		2006-01-01
The Distributed Annotation System for Integration of Biological Data[1]Andreas Prlić, [2]Ewan Birney, [3]Tony Cox, [4]Thomas A. Down, [5]Rob Finn, [6]Stefan Gräf, [7]David Jackson, [8]Andreas Kähäri, [9]Eugene Kulesha, [10]Roger Pettett, [11]James Smith, [12]Jim Stalker, [13]Tim J. P. Hubbard [Full author list]Lecture Notes in Computer Science [curation]DOI: 10.1007/11799511_17
2006-01-01
The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates[1]Laurence Ettwiller, [2]Benedict Paten, [3]Marcel Souren, [4]Felix Loosli, [5]Joachim Wittbrodt, [6]Ewan Birney [Full author list]Genome Biology [curation]DOI: 10.1186/GB-2005-6-12-R104
PubMed: 16356267		2005-12-02
Report of an EU projects workshop on systems biology held in Brussels, Belgium on 8 December 2004[1]Ewan Birney, [2]Andrea Ciliberto, [3]Morten Colding-Jørgensen, [4]Albert Goldbeter, [5]Stefan Hohmann, [6]Martin Kuiper, [7]Hans Lehrach, [8]Gisela Miczka, [9]Erik Mosekilde, [10]Hans Westerhoff, [11]Olaf Wolkenhauer [Full author list]IET Systems Biology [curation]PubMed: 17044232Belgium [curation]; workshop [curation]2005-06-01
A survey of homozygous deletions in human cancer genomes[1]Charles Cox, [2]Graham Bignell, [3]Chris Greenman, [4]Arne Stabenau, [5]William Warren, [6]Philip Stephens, [7]Helen Davies, [8]Stephen Watt, [9]Jon Teague, [10]Sara Edkins, [11]Ewan Birney, [12]Douglas F. Easton, [13]Richard Wooster, [14]P. Andrew Futreal, [15]Michael Stratton [Full author list]Proceedings of the National Academy of Sciences of the United States of America [curation]DOI: 10.1073/PNAS.0408593102
PubMed: 15761058		homozygosity [curation]2005-03-10
Automated generation of heuristics for biological sequence comparison[1]Guy St C Slater, [2]Ewan Birney [Full author list]BMC Bioinformatics [curation]DOI: 10.1186/1471-2105-6-31
PubMed: 15713233		automation [curation]2005-01-01
Reactome: a knowledgebase of biological pathways[1]G Joshi-Tope, [2]M Gillespie, [3]I Vastrik, [4]Peter D'Eustachio, [5]E Schmidt, [6]B de Bono, [7]Bijay Jassal, [8]G R Gopinath, [9]G R Wu, [10]Lisa Matthews, [11]S Lewis, [12]Ewan Birney, [13]L Stein [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKI072
PubMed: 15608231		knowledge base [curation]; Reactome [curation]2005-01-01
Ensembl 2005[1]Tim Hubbard, [2]D Andrews, [3]M Caccamo, [4]G Cameron, [5]Y Chen, [6]M Clamp, [7]Laura Clarke, [8]Guy Coates, [9]T Cox, [10]Fiona Cunningham, ..., [51]S White, [52]C Woodwark, [53]Ewan Birney [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKI138
PubMed: 15608235		2005-01-01
Gene finding in the chicken genome[1]Eduardo Eyras, [2]Alexandre Reymond, [3]Robert Castelo, [4]Jacqueline M Bye, [5]Francisco Camara, [6]Paul Flicek, [7]Elizabeth J. Huckle, [8]Genís Parra, [9]David Shteynberg, [10]Carine Wyss, [11]Jane Rogers, [12]Stilianos Antonarakis, [13]Ewan Birney, [14]Roderic Guigó i Serra, [15]Michael R Brent [Full author list]BMC Bioinformatics [curation]DOI: 10.1186/1471-2105-6-131
PubMed: 15924626		2005-01-01
Protein Sequence Analysis and Domain Identification[1]Chris P. Ponting, [2]Ewan Birney [Full author list]DOI: 10.1385/1-59259-890-0:527
2005-01-01
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution[1]Ladeana Hillier, [2]Webb Miller, [3]Ewan Birney, [4]Wesley C Warren, [5]Ross Hardison, [6]Chris Ponting, [7]Peer Bork, [8]David W Burt, [9]Martien Groenen, [10]Mary E. Delany, ... [Full author list]Nature [curation]DOI: 10.1038/NATURE03154
PubMed: 15592404		chicken genome project [curation]2004-12-09
Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags[1]Simon J. Hubbard, [2]Darren V. Grafham, [3]Kevin J Beattie, [4]Ian M Overton, [5]Stuart R McLaren, [6]Michael D R Croning, [7]Paul E Boardman, [8]James K. Bonfield, [9]Joan Burnside, [10]Robert M Davies, ..., [19]Cheryll Tickle, [20]William R A Brown, [21]Ewan Birney, [22]Jane Rogers, [23]Stuart A Wilson [Full author list]Genome Research [curation]DOI: 10.1101/GR.3011405
PubMed: 15590942		transcriptome [curation]2004-12-08
Genome information resources - developments at Ensembl[1]Martin P Hammond, [2]Ewan Birney [Full author list]Trends in Genetics [curation]DOI: 10.1016/J.TIG.2004.04.002
PubMed: 15145580		2004-06-01
GeneWise and Genomewise[1]Ewan Birney, [2]Michele Clamp, [3]Richard M. Durbin [Full author list]Genome Research [curation]DOI: 10.1101/GR.1865504
PubMed: 15123596		2004-05-01
The Ensembl core software libraries[1]Arne Stabenau, [2]Graham McVicker, [3]Craig Melsopp, [4]Glenn Proctor, [5]Michele Clamp, [6]Ewan Birney [Full author list]Genome Research [curation]DOI: 10.1101/GR.1857204
PubMed: 15123588		software [curation]2004-05-01
Sockeye: a 3D environment for comparative genomics[1]Stephen B Montgomery, [2]Tamara Astakhova, [3]Mikhail Bilenky, [4]Ewan Birney, [5]Tony Fu, [6]Maik Hassel, [7]Craig Melsopp, [8]Marcin Rak, [9]A Gordon Robertson, [10]Monica Sleumer, [11]Asim S Siddiqui, [12]Steven J M Jones [Full author list]Genome Research [curation]DOI: 10.1101/GR.1890304
PubMed: 15123592		comparative genomics [curation]2004-05-01
An overview of Ensembl[1]Ewan Birney, [2]Dan Andrews, [3]Andrew P Bevan, [4]Mario Caccamo, [5]Yuan Chen, [6]Laura Clarke, [7]Guy Coates, [8]James Cuff, [9]Val Curwen, [10]Tim Cutts, ... [Full author list]Genome Research [curation]DOI: 10.1101/GR.1860604
PubMed: 15078858		2004-04-12
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[1]Emmanouil Dermitzakis, [2]Ewen F. Kirkness, [3]Scott Schwarz, [4]Ewan Birney, [5]Alexandre Reymond, [6]Stilianos Antonarakis [Full author list]Genome Research [curation]DOI: 10.1101/GR.1934904
PubMed: 15078857		2004-04-12
Genome sequence of the Brown Norway rat yields insights into mammalian evolution[1]Richard A Gibbs, [2]George Weinstock, [3]Michael L Metzker, [4]Donna Muzny, [5]Erica Sodergren, [6]Steven S. Scherer, [7]Graham Scott, [8]David Steffen, [9]Kim C Worley, [10]Paula E. Burch, ..., [104]Evan E. Eichler, [105]Eray Tuzun, [106]Ewan Birney, [107]Emmanuel Mongin, [108]Abel Ureta-Vidal, ... [Full author list]Nature [curation]DOI: 10.1038/NATURE02426
PubMed: 15057822		Norway [curation]2004-04-01
Biological database design and implementation[1]Ewan Birney, [2]Michele Clamp [Full author list]Briefings in Bioinformatics [curation]DOI: 10.1093/BIB/5.1.31
PubMed: 15153304		database [curation]; biocuration [curation]2004-03-01
A SNP map of the rat genome generated from cDNA sequences[1]Heike Zimdahl, [2]Gerald Nyakatura, [3]Petra Brandt, [4]Herbert Schulz, [5]Oliver Hummel, [6]Berthold Fartmann, [7]David Brett, [8]Marcus Droege, [9]Jan Monti, [10]Young-Ae Lee, [11]Yinyan Sun, [12]Shaying Zhao, [13]Eitan E Winter, [14]Chris Ponting, [15]Yuan Chen, [16]Arek Kasprzyk, [17]Ewan Birney, [18]Detlev Ganten, [19]Norbert Hubner [Full author list]Science [curation]DOI: 10.1126/SCIENCE.1092427
PubMed: 14764869		2004-02-01
The Anopheles gambiae genome: an update[1]Emmanuel Mongin, [2]Christos Louis, [3]Robert A. Holt, [4]Ewan Birney, [5]Frank H Collins [Full author list]Trends in Parasitology [curation]DOI: 10.1016/J.PT.2003.11.003
PubMed: 14747013		Anopheles gambiae [curation]2004-02-01
EnsMart: a generic system for fast and flexible access to biological data[1]Arek Kasprzyk, [2]Damian Keefe, [3]Damian Smedley, [4]Darin London, [5]William Spooner, [6]Craig Melsopp, [7]Martin Hammond, [8]Philippe Rocca-Serra, [9]Tony Cox, [10]Ewan Birney [Full author list]Genome Research [curation]DOI: 10.1101/GR.1645104
PubMed: 14707178		data sharing [curation]2004-01-01
Ensembl 2004[1]Ewan Birney, [2]D Andrews, [3]Andrew P Bevan, [4]M Caccamo, [5]G Cameron, [6]Y Chen, [7]Laura Clarke, [8]Guy Coates, [9]T Cox, [10]J Cuff, ... [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKH038
PubMed: 14681459		2004-01-01
Discovering novel cis-regulatory motifs using functional networks[1]Laurence M Ettwiller, [2]Johan Rung, [3]Ewan Birney [Full author list]Genome Research [curation]DOI: 10.1101/GR.866403
PubMed: 12727907		2003-05-01
Comparative genomics: genome-wide analysis in metazoan eukaryotes[1]Abel Ureta-Vidal, [2]Laurence Ettwiller, [3]Ewan Birney [Full author list]Nature Reviews Genetics [curation]DOI: 10.1038/NRG1043
PubMed: 12671656		comparative genomics [curation]2003-04-01
Unrestricted free access works and must continue[1]Steven Salzberg, [2]Ewan Birney, [3]Sean Eddy, [4]Owen White [Full author list]Nature [curation]DOI: 10.1038/422801A
PubMed: 12712164		2003-04-01
The European Bioinformatics Institute's data resources[1]Catherine Brooksbank, [2]Evelyn Camon, [3]Midori A Harris, [4]Michele Magrane, [5]Maria-Jesus Martin, [6]Nicola Mulder, [7]Claire O'Donovan, [8]Helen Parkinson, [9]Mary Ann Tuli, [10]Rolf Apweiler, [11]Ewan Birney, [12]Alvis Brazma, [13]Kim Henrick, [14]Rodrigo López, [15]Guenter Stoesser, [16]Peter Stoehr, [17]Graham Cameron [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKG066
PubMed: 12519944		bioinformatics [curation]2003-01-01
Ensembl: a genome infrastructure[1]Ewan Birney, [2]Ensembl Team [Full author list]Cold Spring Harbor Symposia on Quantitative Biology [curation]DOI: 10.1101/SQB.2003.68.213
PubMed: 15338620		infrastructure [curation]2003-01-01
Ensembl 2002: accommodating comparative genomics[1]M Clamp, [2]D Andrews, [3]D Barker, [4]Andrew P Bevan, [5]G Cameron, [6]Y Chen, [7]L Clark, [8]T Cox, [9]J Cuff, [10]V Curwen, ..., [34]A Ureta-Vidal, [35]I Vastrik, [36]Ewan Birney [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/GKG083
PubMed: 12519943		comparative genomics [curation]2003-01-01
The Genome Knowledgebase: a resource for biologists and bioinformaticists.[1]G Joshi-Tope, [2]I Vastrik, [3]G R Gopinath, [4]L Matthews, [5]E Schmidt, [6]M Gillespie, [7]Peter D'Eustachio, [8]Bijay Jassal, [9]S Lewis, [10]G Wu, [11]Ewan Birney, [12]L Stein [Full author list]Cold Spring Harbor Symposia on Quantitative Biology [curation]DOI: 10.1101/SQB.2003.68.237
PubMed: 15338623		knowledge base [curation]2003-01-01
Initial sequencing and comparative analysis of the mouse genome[1]Asif T. Chinwalla, [2]Lisa L. Cook, [3]Kim Delehaunty, [4]Ginger A. Fewell, [5]Lucinda A. Fulton, [6]Robert S. Fulton, [7]Tina A. Graves, [8]LaDeana W. Hillier, [9]Elaine Mardis, [10]John D. McPherson, ..., [68]Dudley Wyman, [69]Michael C. Zody, [70]Ewan Birney, [71]Nick Goldman, [72]Arkadiusz Kasprzyk, ..., [230]Robert Baertsch, [231]Eric Berry, [232]Ewan Birney, [233]Peer Bork, [234]Nicolas Bray, ... [Full author list]Nature [curation]DOI: 10.1038/NATURE01262
PubMed: 12466850		2002-12-05
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs[1]Yasushi Okazaki, [2]M Furuno, [3]Takeya Kasukawa, [4]J Adachi, [5]Hidemasa U. Bono, [6]S Kondo, [7]Itoshi Nikaido, [8]N Osato, [9]R Saito, [10]H Suzuki, ..., [135]Eric Lander, [136]J Rogers, [137]Ewan Birney, [138]Y Hayashizaki, [139]FANTOM Consortium, ... [Full author list]Nature [curation]DOI: 10.1038/NATURE01266
PubMed: 12466851		transcriptome [curation]2002-12-01
The genome sequence of the malaria mosquito Anopheles gambiae[1]Robert A. Holt, [2]G Mani Subramanian, [3]Aaron Halpern, [4]Granger G Sutton, [5]Rosane Charlab, [6]Deborah R Nusskern, [7]Patrick Wincker, [8]Andrew G. Clark, [9]José M. Ribeiro, [10]Ron Wides, ..., [114]Malcolm J Gardner, [115]Claire M. Fraser, [116]Ewan Birney, [117]Peer Bork, [118]Paul T Brey, ... [Full author list]Science [curation]DOI: 10.1126/SCIENCE.1076181
PubMed: 12364791		malaria [curation]; Anopheles gambiae [curation]2002-10-01
The Bioperl toolkit: Perl modules for the life sciences[1]Jason E. Stajich, [2]David Block, [3]Kris Boulez, [4]Steven E. Brenner, [5]Stephen A Chervitz, [6]Chris Dagdigian, [7]Georg Fuellen, [8]James G R Gilbert, [9]Ian Korf, [10]Hilmar Lapp, ..., [19]Elia Stupka, [20]Mark D. Wilkinson, [21]Ewan Birney [Full author list]Genome Research [curation]DOI: 10.1101/GR.361602
PubMed: 12368254		Perl [curation]; life sciences [curation]; BioPerl [curation]2002-10-01
Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster[1]Evgeny M. Zdobnov, [2]Christian von Mering, [3]Ivica Letunic, [4]David Torrents, [5]Mikita Suyama, [6]Richard R Copley, [7]George K Christophides, [8]Dana Thomasova, [9]Robert A. Holt, [10]G Mani Subramanian, ..., [13]John H Law, [14]Michael A Wells, [15]Ewan Birney, [16]Rosane Charlab, [17]Aaron L Halpern, ... [Full author list]Science [curation]DOI: 10.1126/SCIENCE.1077061
PubMed: 12364792		Drosophila melanogaster [curation]; Anopheles gambiae [curation]2002-10-01
Immunity-related genes and gene families in Anopheles gambiae[1]George K Christophides, [2]Evgeny M. Zdobnov, [3]Carolina Barillas-Mury, [4]Ewan Birney, [5]Stephanie Blandin, [6]Claudia Blass, [7]Paul T Brey, [8]Frank H Collins, [9]Alberto Danielli, [10]George Dimopoulos, ... [Full author list]Science [curation]DOI: 10.1126/SCIENCE.1077136
PubMed: 12364793		Anopheles gambiae [curation]2002-10-01
A physical map of the mouse genome[1]Simon G Gregory, [2]Mandeep Sekhon, [3]Jacqueline Schein, [4]Shaying Zhao, [5]Kazutoyo Osoegawa, [6]Carol E Scott, [7]Richard S Evans, [8]Paul W Burridge, [9]Tony V Cox, [10]Christopher A Fox, ..., [15]Jim Stalker, [16]Glen J Threadgold, [17]Ewan Birney, [18]Kristine M Wylie, [19]Asif T. Chinwalla, ... [Full author list]Nature [curation]DOI: 10.1038/NATURE00957
PubMed: 12181558		2002-08-04
Genome annotation techniques: new approaches and challenges[1]Alistair G Rust, [2]Emmanuel Mongin, [3]Ewan Birney [Full author list]Drug Discovery Today [curation]DOI: 10.1016/S1359-6446(02)02289-4
PubMed: 12047883		genome annotation [curation]2002-06-01
Databases and tools for browsing genomes[1]Ewan Birney, [2]Michele Clamp, [3]Tim Hubbard [Full author list]Annual Review of Genomics and Human Genetics [curation]DOI: 10.1146/ANNUREV.GENOM.3.030502.101529
PubMed: 12194990		2002-04-15
The Ensembl genome database project[1]Tim Hubbard, [2]D Barker, [3]Ewan Birney, [4]G Cameron, [5]Y Chen, [6]L Clark, [7]T Cox, [8]J Cuff, [9]V Curwen, [10]T Down, ... [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/30.1.38
PubMed: 11752248		database [curation]2002-01-01
Apollo: a sequence annotation editor[1]S E Lewis, [2]S M J Searle, [3]N Harris, [4]M Gibson, [5]V Lyer, [6]J Richter, [7]C Wiel, [8]L Bayraktaroglu, [9]Ewan Birney, [10]M A Crosby, [11]J S Kaminker, [12]B B Matthews, [13]S E Prochnik, [14]C D Smithy, [15]J L Tupy, [16]G M Rubin, [17]S Misra, [18]Christopher J. Mungall, [19]M E Clamp [Full author list]Genome Biology [curation]DOI: 10.1186/GB-2002-3-12-RESEARCH0082
PubMed: 12537571		2002-01-01
The Pfam protein families database[1]Alex Bateman, [2]Ewan Birney, [3]Lorenzo Cerruti, [4]Richard M. Durbin, [5]Laurence Etwiller, [6]Sean Eddy, [7]Sam Griffiths-Jones, [8]Kevin L Howe, [9]Mhairi Marshall, [10]Erik Sonnhammer [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/30.1.276
PubMed: 11752314		database [curation]; Pfam [curation]2002-01-01
Progress in sequencing the mouse genome[1]Kerstin Lindblad-Toh, [2]Eric Lander, [3]John D. McPherson, [4]Robert H. Waterston, [5]Jane Rodgers, [6]Ewan Birney [Full author list]Genesis [curation]DOI: 10.1002/GENE.10016
PubMed: 11783003		cell biology [curation]; endocrinology [curation]2001-12-01
Initial sequencing and analysis of the human genome[1]Eric Lander, [2]Lauren M. Linton, [3]Bruce Birren, [4]Chad Nusbaum, [5]Michael C. Zody, [6]Jennifer Baldwin, [7]Keri Devon, [8]Ken Dewar, [9]Michael Doyle, [10]William FitzHugh, ..., [172]Alex Bateman, [173]Serafim Batzoglou, [174]Ewan Birney, [175]Peer Bork, [176]Daniel G. Brown, ... [Full author list]Nature [curation]DOI: 10.1038/35057062
PubMed: 11237011		Human Genome Project [curation]; data ethics [curation]2001-02-15
Cancer and genomics[1]P. Andrew Futreal, [2]Kasprzyk A, [3]Ewan Birney, [4]Mullikin JC, [5]Richard Wooster, [6]Michael Stratton [Full author list]Nature [curation]DOI: 10.1038/35057046
PubMed: 11237008		genomics [curation]2001-02-01
Mining the draft human genome[1]Ewan Birney, [2]Alex Bateman, [3]Clamp ME, [4]Tim Hubbard [Full author list]Nature [curation]DOI: 10.1038/35057004
PubMed: 11236999		2001-02-01
Integration of cytogenetic landmarks into the draft sequence of the human genome[1]V G Cheung, [2]N Nowak, [3]W Jang, [4]I R Kirsch, [5]S Zhao, [6]X N Chen, [7]Terrence S. Furey, [8]U J Kim, [9]W L Kuo, [10]M Olivier, ..., [45]G L Shen-Ong, [46]R L Strausberg, [47]Ewan Birney, [48]David F. Callen, [49]J F Cheng, ... [Full author list]Nature [curation]DOI: 10.1038/35057192
PubMed: 11237021		draft sequence of the human genome [curation]2001-02-01
The InterPro database, an integrated documentation resource for protein families, domains and functional sites[1]Rolf Apweiler, [2]Terri Attwood, [3]Amos Bairoch, [4]Alex Bateman, [5]Ewan Birney, [6]M Biswas, [7]P Bucher, [8]L Cerutti, [9]F Corpet, [10]M D Croning, ... [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/29.1.37
PubMed: 11125043		InterPro [curation]2001-01-01
InterPro--an integrated documentation resource for protein families, domains and functional sites[1]Rolf Apweiler, [2]Terri Attwood, [3]Amos Bairoch, [4]Alex Bateman, [5]Ewan Birney, [6]M Biswas, [7]P Bucher, [8]L Cerutti, [9]F Corpet, [10]M D Croning, ... [Full author list]Bioinformatics [curation]DOI: 10.1093/BIOINFORMATICS/16.12.1145
PubMed: 11159333		2000-12-01
The Bioperl project[1]Jason Stajich, [2]Ewan Birney [Full author list]DOI: 10.1145/360262.360267
2000-08-01
Using GeneWise in the Drosophila annotation experiment[1]Ewan Birney, [2]Richard M. Durbin [Full author list]Genome Research [curation]DOI: 10.1101/GR.10.4.547
PubMed: 10779496		Drosophila [curation]2000-04-01
ProtEST: protein multiple sequence alignments from expressed sequence tags[1]Cuff JA, [2]Ewan Birney, [3]Clamp ME, [4]Geoffrey J. Barton [Full author list]Bioinformatics [curation]DOI: 10.1093/BIOINFORMATICS/16.2.111
PubMed: 10842731		sequence alignment [curation]2000-02-01
Open annotation offers a democratic solution to genome sequencing[1]Tim Hubbard, [2]Ewan Birney [Full author list]Nature [curation]DOI: 10.1038/35002770
PubMed: 10706254		whole genome sequencing [curation]2000-02-01
The Pfam protein families database.[1]Alex Bateman, [2]Ewan Birney, [3]Richard M. Durbin, [4]Sean Eddy, [5]Kevin L Howe, [6]Sonnhammer EL [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/28.1.263
PubMed: 10592242		database [curation]; Pfam [curation]2000-01-01
Searching databases to find protein domain organization[1]Alex Bateman, [2]Ewan Birney [Full author list]Advances in Protein Chemistry [curation]DOI: 10.1016/S0065-3233(00)54005-4
PubMed: 10829227		2000-01-01
Identification of domains from protein sequences[1]C P Ponting, [1-Q5107785]Chris Ponting, [2]E Birney, [2-Q4869199]Ewan Birney [Full author list]Methods in Molecular Biology [curation]DOI: 10.1385/1-59259-368-2:53
PubMed: 11084902		2000-01-01
Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs[1]Niclas Jareborg, [2]Ewan Birney, [3]Richard M. Durbin [Full author list]Genome Research [curation]DOI: 10.1101/GR.9.9.815
PubMed: 10508839		1999-09-01
Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins[1]Alex Bateman, [2]Ewan Birney, [3]Richard M. Durbin, [4]S R Eddy, [5]R D Finn, [6]E L Sonnhammer [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/27.1.260
PubMed: 9847196		1999-01-01
Pfam: multiple sequence alignments and HMM-profiles of protein domains[1]E L Sonnhammer, [1-Q30303525]Erik Sonnhammer, [2]S R Eddy, [2-Q7440970]Sean Eddy, [3]Ewan Birney, [4]Alex Bateman, [5]Richard M. Durbin [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/26.1.320
PubMed: 9399864		sequence alignment [curation]1998-01-01
SPEM: a parser for EMBL style flat file database entries[1]M R Pocock, [2]Tim Hubbard, [3]Ewan Birney [Full author list]Bioinformatics [curation]DOI: 10.1093/BIOINFORMATICS/14.9.823
PubMed: 9918956		1998-01-01
Dynamite: a flexible code generating language for dynamic programming methods used in sequence comparison[1]Ewan Birney, [2]Richard M. Durbin [Full author list]Proceedings. International Conference on Intelligent Systems for Molecular Biology [curation]PubMed: 93220161997-01-01
PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames[1]Ewan Birney, [2]J D Thompson, [3]T J Gibson [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/24.14.2730
PubMed: 8759004		1996-07-15
PH domain: the first anniversary[1]Toby J. Gibson, [2]M Hyvönen, [3]Andrea Musacchio, [4]M Saraste, [5]Ewan Birney [Full author list]Trends in Biochemical Sciences [curation]DOI: 10.1016/0968-0004(94)90108-2
PubMed: 7985225		1994-09-01
Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors[1]A R Krainer, [1-Q4869199]Ewan Birney, [2]S Kumar, [3]A R Krainer [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/21.25.5803
PubMed: 8290338		RNA recognition motif domain [curation]; RNA analysis [curation]1993-12-25
A putative homology of U2AF65 in S. cerevisiae[1]Ewan Birney, [2]Kumar S, [3]Krainer AR [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/21.5.1333
PubMed: 8464721		1993-03-01
A putative homolog of U2AF65 in S. cerevisiae[1]Ewan Birney, [2]S Kumar, [3]A R Krainer [Full author list]Nucleic Acids Research [curation]DOI: 10.1093/NAR/20.17.4663
PubMed: 1408772		1992-09-11
ENFIN - An Integrative Structure for Systems Biology[1]Florian Reisinger, [2]Manuel Corpas, [3]John M. Hancock, [4]Henning Hermjakob, [5]Ewan Birney, [6]Pascal Kahlem [Full author list]Lecture Notes in Computer Science [curation]DOI: 10.1007/978-3-540-69828-9_13
Visualising the Epigenome[1]Paul Flicek, [2]Ewan Birney [Full author list]DOI: 10.1007/978-1-4020-9187-2_4
Correct Q number of author item for selected works.
NO replacement author: revert to author name strings

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