Dynamite: A Flexible Code Generating Language for Dynamic Programming Methods Used in Sequence Comparison. - Ewan Birney; Richard Durbin (ISMB, 1997)

SPEM: a parser for EMBL style flat file database entries. - Matthew R. Pocock; Tim J. P. Hubbard; Ewan Birney (Bioinform., 1998)

Pfam: multiple sequence alignments and HMM-profiles of protein domains. - Erik L. L. Sonnhammer; Sean R. Eddy; Ewan Birney; Alex Bateman; Richard Durbin (Nucleic Acids Res., 1998)

Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. - Alex Bateman; Ewan Birney; Richard Durbin; Sean R. Eddy; Robert D. Finn; Erik L. L. Sonnhammer (Nucleic Acids Res., 1999)

InterPro-an integrated documentation resource for protein families, domains and functional sites. - Rolf Apweiler; Terri K. Attwood; Amos Bairoch; Alex Bateman; Ewan Birney; Margaret Biswas; Philipp Bucher; Lorenzo Cerutti; Florence Corpet; Michael D. R. Croning; Richard Durbin; Laurent Falquet; et al. (Bioinform., 2000)

ProtEST: protein multiple sequence alignments from expressed sequence tags. - James A. Cuff; Ewan Birney; Michele E. Clamp; Geoffrey J. Barton (Bioinform., 2000)

The Pfam Protein Families Database. - Alex Bateman; Ewan Birney; Richard Durbin; Sean R. Eddy; Kevin L. Howe; Erik L. L. Sonnhammer (Nucleic Acids Res., 2000)

Ensembl: Annotating metazoan genomes. - Ewan Birney (German Conference on Bioinformatics, 2001)

Hidden Markov models in biological sequence analysis. - Ewan Birney (IBM J. Res. Dev., 2001)

The InterPro database, an integrated documentation resource for protein families, domains and functional sites. - Rolf Apweiler; Terri K. Attwood; Amos Bairoch; Alex Bateman; Ewan Birney; Margaret Biswas; Philipp Bucher; Lorenzo Cerutti; Florence Corpet; Michael D. R. Croning; Richard Durbin; Laurent Falquet; et al. (Nucleic Acids Res., 2001)

The Pfam Protein Families Database. - Alex Bateman; Ewan Birney; Lorenzo Cerutti; Richard Durbin; Laurence Ettwiller; Sean R. Eddy; Sam Griffiths-Jones; Kevin L. Howe; Mhairi Marshall; Erik L. L. Sonnhammer (Nucleic Acids Res., 2002)

The Ensembl genome database project. - Tim J. P. Hubbard; Daniel Barker; Ewan Birney; Graham Cameron; Yuan Chen 007; Laura Clarke; Tony Cox 001; James A. Cuff; Val Curwen; Thomas A. Down; Richard Durbin; Eduardo Eyras; et al. (Nucleic Acids Res., 2002)

The European Bioinformatics Institute's data resources. - Catherine Brooksbank; Evelyn Camon; Midori A. Harris; Michele Magrane; Maria Jesus Martin; Nicola J. Mulder; Claire O'Donovan; Helen E. Parkinson; Mary Ann Tuli; Rolf Apweiler; Ewan Birney; Alvis Brazma; et al. (Nucleic Acids Res., 2003)

Ensembl 2002: accommodating comparative genomics. - Michele E. Clamp; T. Daniel Andrews; Daniel Barker; Paul Bevan 001; Graham Cameron; Yuan Chen 007; Laura Clarke; Tony Cox 001; James A. Cuff; Val Curwen; Thomas A. Down; Richard Durbin; et al. (Nucleic Acids Res., 2003)

Biological database design and implementation. - Ewan Birney; Michele E. Clamp (Briefings Bioinform., 2004)

Ensembl 2004. - Ewan Birney; T. Daniel Andrews; Paul Bevan 001; Mario Cáccamo; Graham Cameron; Yuan Chen 007; Laura Clarke; Guy Coates; Tony Cox 001; James A. Cuff; Val Curwen; Tim Cutts; et al. (Nucleic Acids Res., 2004)

Gene finding in the chicken genome. - Eduardo Eyras; Alexandre Reymond; Robert Castelo; Jacqueline M. Bye; Francisco Camara; Paul Flicek; Elizabeth J. Huckle; Genis Parra; David D. Shteynberg; Carine Wyss; Jane Rogers; Stylianos E. Antonarakis; et al. (BMC Bioinform., 2005)

Automated generation of heuristics for biological sequence comparison. - Guy St. C. Slater; Ewan Birney (BMC Bioinform., 2005)

Ensembl 2005. - Tim J. P. Hubbard; D. Andrews; Mario Cáccamo; Graham Cameron; Yuan Chen 007; Michele E. Clamp; Laura Clarke; Guy Coates; Tony Cox 001; Fiona Cunningham; Val Curwen; Tim Cutts; et al. (Nucleic Acids Res., 2005)

Reactome: a knowledgebase of biological pathways. - G. Joshi-Tope; Marc Gillespie; Imre Vastrik; Peter D'Eustachio; Esther Schmidt; Bernard de Bono; Bijay Jassal; Gopal R. Gopinath; G. R. Wu; Lisa Matthews; Suzanna Lewis; Ewan Birney; et al. (Nucleic Acids Res., 2005)

The Distributed Annotation System for Integration of Biological Data. - Andreas Prlic; Ewan Birney; Tony Cox 001; Thomas A. Down; Robert D. Finn; Stefan Gräf; David K. Jackson; Andreas Kähäri; Eugene Kulesha; Roger Pettett; James A. Smith; Jim Stalker; et al. (DILS, 2006)

Reactome - A Knowledgebase of Biological Pathways. - Esther Schmidt; Ewan Birney; David Croft 001; Bernard de Bono; Peter D'Eustachio; Marc Gillespie; Gopal Gopinath; Bijay Jassal; Suzanna Lewis; Lisa Matthews; Lincoln Stein; Imre Vastrik; et al. (OTM Workshops (1), 2006)

Ensembl 2006. - Ewan Birney; T. Daniel Andrews; Mario Cáccamo; Yuan Chen 007; Laura Clarke; Guy Coates; Tony Cox 001; Fiona Cunningham; Val Curwen; Tim Cutts; Thomas A. Down; Richard Durbin; et al. (Nucleic Acids Res., 2006)

Optimized design and assessment of whole genome tiling arrays. - Stefan Gräf; Fiona G. G. Nielsen; Stefan Kurtz; Martijn A. Huynen; Ewan Birney; Henk Stunnenberg; Paul Flicek (ISMB/ECCB (Supplement of Bioinformatics), 2007)

Optimising oligonucleotide array design for ChIP-on-chip. - Fiona G. G. Nielsen; Stefan Gräf; Xinmin Zhang; Stefan Kurtz; Sergei Denissov; Roland Green; Ewan Birney; Paul Flicek; Martijn A. Huynen; Henk Stunnenberg (BMC Bioinform., 2007)

Reactome: An integrated expert model of human molecular processes and access toolkit. - Bernard de Bono; Imre Vastrik; Peter D'Eustachio; Esther Schmidt; Gopal Gopinath; David Croft 001; Marc Gillespie; Bijay Jassal; Suzanna Lewis; Lisa Matthews; Guanming Wu; Ewan Birney; et al. (J. Integr. Bioinform., 2007)

Ensembl 2007. - Tim J. P. Hubbard; Bronwen L. Aken; Kathryn Beal; Benoît Ballester; Mario Cáccamo; Yuan Chen 007; Laura Clarke; Guy Coates; Fiona Cunningham; Tim Cutts; Thomas A. Down; S. C. Dyer; et al. (Nucleic Acids Res., 2007)

VectorBase: a home for invertebrate vectors of human pathogens. - Daniel Lawson; Peter Arensburger; Peter Atkinson; Nora J. Besansky; Robert V. Bruggner; Ryan Butler; Kathryn S. Campbell; George K. Christophides; Scott Christley; Emmanuel Dialynas; David B. Emmert; Martin Hammond; et al. (Nucleic Acids Res., 2007)

ENFIN - An Integrative Structure for Systems Biology. - Florian Reisinger; Manuel Corpas; John M. Hancock; Henning Hermjakob; Ewan Birney; Pascal Kahlem (DILS, 2008)

Integrating biological data - the Distributed Annotation System. - Andrew M. Jenkinson; Mario Albrecht; Ewan Birney; Hagen Blankenburg; Thomas A. Down; Robert D. Finn; Henning Hermjakob; Tim J. P. Hubbard; Rafael C. Jiménez; Philip Jones; Andreas Kähäri; Eugene Kulesha; et al. (BMC Bioinform., 2008)

The HGNC Database in 2008: a resource for the human genome. - Elspeth A. Bruford; Michael J. Lush; Mathew W. Wright; Tam P. Sneddon; Sue Povey; Ewan Birney (Nucleic Acids Res., 2008)

Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database. - Guy Cochrane; Ruth Akhtar; Philippe Aldebert; Nicola Althorpe; Alastair Baldwin; Kirsty Bates; Sumit Bhattacharyya; James K. Bonfield; Lawrence Bower; Paul Browne; Matias Castro; Tony Cox 001; et al. (Nucleic Acids Res., 2008)

Ensembl 2008. - Paul Flicek; Bronwen L. Aken; Kathryn Beal; Benoît Ballester; Mario Cáccamo; Yuan Chen 007; Laura Clarke; Guy Coates; Fiona Cunningham; Tim Cutts; Thomas A. Down; S. C. Dyer; et al. (Nucleic Acids Res., 2008)

Advanced Genomic Data Mining. - Xosé M. Fernández-Suárez; Ewan Birney (PLoS Comput. Biol., 2008)

Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment. - Benedict Paten; Javier Herrero; Kathryn Beal; Ewan Birney (Bioinform., 2009)

Petabyte-scale innovations at the European Nucleotide Archive. - Guy Cochrane; Ruth Akhtar; James K. Bonfield; Lawrence Bower; Fehmi Demiralp; Nadeem Faruque; Richard Gibson; Gemma Hoad; Tim J. P. Hubbard; Christopher I. Hunter; Mikyung Jang; Szilveszter Juhos; et al. (Nucleic Acids Res., 2009)

MAPU 2.0: high-accuracy proteomes mapped to genomes. - Florian Gnad; Mario Oroshi; Ewan Birney; Matthias Mann 002 (Nucleic Acids Res., 2009)

Ensembl 2009. - Tim J. P. Hubbard; Bronwen L. Aken; Sarah C. Ayling; Benoît Ballester; Kathryn Beal; Eugene Bragin; Simon Brent; Yuan Chen 007; Peter Clapham; Laura Clarke; Guy Coates; Susan Fairley; et al. (Nucleic Acids Res., 2009)

VectorBase: a data resource for invertebrate vector genomics. - Daniel Lawson; Peter Arensburger; Peter Atkinson; Nora J. Besansky; Robert V. Bruggner; Ryan Butler; Kathryn S. Campbell; George K. Christophides; Scott Christley; Emmanuel Dialynas; Martin Hammond; Catherine A. Hill; et al. (Nucleic Acids Res., 2009)

Reactome knowledgebase of human biological pathways and processes. - Lisa Matthews; Gopal Gopinath; Marc Gillespie; Michael Caudy; David Croft 001; Bernard de Bono; Phani V. Garapati; Jill Hemish; Henning Hermjakob; Bijay Jassal; Alexander Kanapin; Suzanna Lewis; et al. (Nucleic Acids Res., 2009)

The systematic annotation of the three main GPCR families in Reactome. - Bijay Jassal; Steven Jupe; Michael Caudy; Ewan Birney; Lincoln Stein; Henning Hermjakob; Peter D'Eustachio (Database J. Biol. Databases Curation, 2010)

Finding and sharing: new approaches to registries of databases and services for the biomedical sciences. - Damian Smedley; Paul N. Schofield; Chao-Kung Chen; Vassilis Aidinis; Crysanthi Ainali; Jonathan B. L. Bard; Rudi Balling; Ewan Birney; Andrew Blake 003; Erik Bongcam-Rudloff; Anthony J. Brookes; Gianni Cesareni; et al. (Database J. Biol. Databases Curation, 2010)

A database and API for variation, dense genotyping and resequencing data. - Daniel Rios; William M. McLaren; Yuan Chen 007; Ewan Birney; Arne Stabenau; Paul Flicek; Fiona Cunningham (BMC Bioinform., 2010)

Ensembl's 10th year. - Paul Flicek; Bronwen L. Aken; Benoît Ballester; Kathryn Beal; Eugene Bragin; Simon Brent; Yuan Chen 007; Peter Clapham; Guy Coates; Susan Fairley; Stephen Fitzgerald; Julio Fernandez-Banet; et al. (Nucleic Acids Res., 2010)

Ensembl Genomes: Extending Ensembl across the taxonomic space. - Paul J. Kersey; Daniel Lawson; Ewan Birney; Paul S. Derwent; Matthias Haimel; Javier Herrero; Stephen Keenan; Arnaud Kerhornou; Gautier Koscielny; Andreas Kähäri; Rhoda Kinsella; Eugene Kulesha; et al. (Nucleic Acids Res., 2010)

Improvements to services at the European Nucleotide Archive. - Rasko Leinonen; Ruth Akhtar; Ewan Birney; James K. Bonfield; Lawrence Bower; Matthew Corbett; Ying Cheng; Fehmi Demiralp; Nadeem Faruque; Neil Goodgame; Richard Gibson; Gemma Hoad; et al. (Nucleic Acids Res., 2010)

EMMA - mouse mutant resources for the international scientific community. - Phil Wilkinson 002; Jitka Sengerova; Raffaele Matteoni; Chao-Kung Chen; Gaetan Soulat; Abel Ureta-Vidal; Sabine Fessele; Michael Hagn 002; Marzia Massimi; Karen Pickford; Richard H. Butler; Susan Marschall; et al. (Nucleic Acids Res., 2010)

Reactome: a database of reactions, pathways and biological processes. - David Croft 001; Gavin O'Kelly; Guanming Wu; Robin Haw; Marc Gillespie; Lisa Matthews; Michael Caudy; Phani V. Garapati; Gopal Gopinath; Bijay Jassal; Steven Jupe; Irina Kalatskaya; et al. (Nucleic Acids Res., 2011)

Ensembl 2011. - Paul Flicek; M. Ridwan Amode; Daniel Barrell; Kathryn Beal; Simon Brent; Yuan Chen 007; Peter Clapham; Guy Coates; Susan Fairley; Stephen Fitzgerald; Leo Gordon; Maurice Hendrix; et al. (Nucleic Acids Res., 2011)

The European Nucleotide Archive. - Rasko Leinonen; Ruth Akhtar; Ewan Birney; Lawrence Bower; Ana Cerdeño-Tárraga; Ying Cheng; Iain Cleland; Nadeem Faruque; Neil Goodgame; Richard Gibson; Gemma Hoad; Mikyung Jang; et al. (Nucleic Acids Res., 2011)

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. - Marcel H. Schulz; Daniel R. Zerbino; Martin Vingron; Ewan Birney (Bioinform., 2012)

Major submissions tool developments at the European nucleotide archive. - Clara Amid; Ewan Birney; Lawrence Bower; Ana Cerdeño-Tárraga; Ying Cheng; Iain Cleland; Nadeem Faruque; Richard Gibson; Neil Goodgame; Christopher I. Hunter; Mikyung Jang; Rasko Leinonen; et al. (Nucleic Acids Res., 2012)

Ensembl 2012. - Paul Flicek; M. Ridwan Amode; Daniel Barrell; Kathryn Beal; Simon Brent; Denise Carvalho-Silva; Peter Clapham; Guy Coates; Susan Fairley; Stephen Fitzgerald; Laurent Gil; Leo Gordon; et al. (Nucleic Acids Res., 2012)

Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. - Paul J. Kersey; Daniel M. Staines; Daniel Lawson; Eugene Kulesha; Paul S. Derwent; Jay C. Humphrey; Daniel S. T. Hughes; Stephen Keenan; Arnaud Kerhornou; Gautier Koscielny; Nicholas Langridge; Mark D. McDowall; et al. (Nucleic Acids Res., 2012)

Ensembl 2013. - Paul Flicek; Ikhlak Ahmed; M. Ridwan Amode; Daniel Barrell; Kathryn Beal; Simon Brent; Denise Carvalho-Silva; Peter Clapham; Guy Coates; Susan Fairley; Stephen Fitzgerald; Laurent Gil; et al. (Nucleic Acids Res., 2013)

Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. - Jie Wang; Jiali Zhuang; Sowmya Iyer; Xin-Ying Lin; Melissa C. Greven; Bong-Hyun Kim; Jill Moore; Brian G. Pierce; Xianjun Dong; Daniel Virgil; Ewan Birney; Jui-Hung Hung; et al. (Nucleic Acids Res., 2013)

Towards practical, high-capacity, low-maintenance information storage in synthesized DNA. - Nick Goldman; Paul Bertone; Siyuan Chen; Christophe Dessimoz; Emily M. LeProust; Botond Sipos; Ewan Birney (Nat., 2013)

The EBI RDF platform: linked open data for the life sciences. - Simon Jupp; James Malone; Jerven T. Bolleman; Marco Brandizi; Mark Davies; Leyla J. García; Anna Gaulton; Sebastien Gehant; Camille Laibe; Nicole Redaschi; Sarala M. Wimalaratne; Maria Jesus Martin; et al. (Bioinform., 2014)

The European Bioinformatics Institute's data resources 2014. - Catherine Brooksbank; Mary Todd Bergman; Rolf Apweiler; Ewan Birney; Janet M. Thornton (Nucleic Acids Res., 2014)

The Reactome pathway knowledgebase. - David Croft 001; Antonio Fabregat Mundo; Robin Haw; Marija Milacic; Joel Weiser; Guanming Wu; Michael Caudy; Phani V. Garapati; Marc Gillespie; Maulik R. Kamdar; Bijay Jassal; Steven Jupe; et al. (Nucleic Acids Res., 2014)

Ensembl 2014. - Paul Flicek; M. Ridwan Amode; Daniel Barrell; Kathryn Beal; Konstantinos Billis; Simon Brent; Denise Carvalho-Silva; Peter Clapham; Guy Coates; Stephen Fitzgerald; Laurent Gil; Carlos García-Girón; et al. (Nucleic Acids Res., 2014)

FORGE: A tool to discover cell specific enrichments of GWAS associated SNPs in regulatory regions. - Ian Dunham; Eugene Kulesha; Valentina Iotchkova; Sandro Morganella; Ewan Birney (F1000Research, 2015)

MinION Analysis and Reference Consortium: Phase 1 data release and analysis. - Camilla L. C. Ip; Matthew Loose; John R. Tyson; Mariateresa de Cesare; Bonnie L. Brown; Miten Jain; Richard M. Leggett; David A. Eccles; Vadim Zalunin; John M. Urban; Paolo Piazza; Rory J. Bowden; et al. (F1000Research, 2015)

Ensembl 2015. - Fiona Cunningham; M. Ridwan Amode; Daniel Barrell; Kathryn Beal; Konstantinos Billis; Simon Brent; Denise Carvalho-Silva; Peter Clapham; Guy Coates; Stephen Fitzgerald; Laurent Gil; Carlos García-Girón; et al. (Nucleic Acids Res., 2015)

Ensembl regulation resources. - Daniel R. Zerbino; Nathan Johnson; Thomas Juettemann; Daniel Sheppard; Steven P. Wilder; Ilias Lavidas; Michael Nuhn; Emily Perry; Quentin Raffaillac-Desfosses; Daniel Sobral; Damian Keefe; Stefan Gräf; et al. (Database J. Biol. Databases Curation, 2016)

The European Bioinformatics Institute in 2016: Data growth and integration. - Charles E. Cook; Mary Todd Bergman; Robert D. Finn; Guy Cochrane; Ewan Birney; Rolf Apweiler (Nucleic Acids Res., 2016)

Ensembl 2016. - Andrew D. Yates; Wasiu A. Akanni; M. Ridwan Amode; Daniel Barrell; Konstantinos Billis; Denise Carvalho-Silva; Carla A. Cummins; Peter Clapham; Stephen Fitzgerald; Laurent Gil; Carlos García-Girón; Leo Gordon; et al. (Nucleic Acids Res., 2016)

Open Targets: a platform for therapeutic target identification and validation. - Gautier Koscielny; Peter An; Denise Carvalho-Silva; Jennifer A. Cham; Luca Fumis; Rippa Gasparyan; Samiul Hasan; Nikiforos Karamanis; Michael Maguire; Eliseo Papa; Andrea Pierleoni; Miguel Pignatelli; et al. (Nucleic Acids Res., 2017)

PhenotypeSimulator: A comprehensive framework for simulating multi-trait, multi-locus genotype to phenotype relationships. - Hannah Verena Meyer; Ewan Birney (Bioinform., 2018)

The European Bioinformatics Institute in 2017: data coordination and integration. - Charles E. Cook; Mary Todd Bergman; Guy Cochrane; Rolf Apweiler; Ewan Birney (Nucleic Acids Res., 2018)

ChromoTrace: Computational reconstruction of 3D chromosome configurations for super-resolution microscopy. - Carl Barton; Sandro Morganella; Øyvind Ødegård-Fougner; Stephanie Alexander; Jonas Ries; Tomas W. Fitzgerald; Jan Ellenberg; Ewan Birney (PLoS Comput. Biol., 2018)

htsget: a protocol for securely streaming genomic data. - Jerome Kelleher; Mike Lin; Carl H. Albach; Ewan Birney; Robert Davies; Marina Gourtovaia; David Glazer; Cristina Y. González; David K. Jackson; Aaron Kemp; John Marshall; Andrew Nowak; et al. (Bioinform., 2019)

The European Bioinformatics Institute in 2018: tools, infrastructure and training. - Charles E. Cook; Rodrigo Lopez; Oana Stroe; Guy Cochrane; Cath Brooksbank; Ewan Birney; Rolf Apweiler (Nucleic Acids Res., 2019)

The European Bioinformatics Institute in 2020: building a global infrastructure of interconnected data resources for the life sciences. - Charles E. Cook; Oana Stroe; Guy Cochrane; Ewan Birney; Rolf Apweiler (Nucleic Acids Res., 2020)

Big Data in Biology: What the Pandemic has Taught us. - Ewan Birney (ITAT, 2021)

The European Bioinformatics Institute: empowering cooperation in response to a global health crisis. - Gaia Cantelli; Guy Cochrane; Cath Brooksbank; Ellen M. McDonagh; Paul Flicek; Johanna R. McEntyre; Ewan Birney; Rolf Apweiler (Nucleic Acids Res., 2021)

The European Bioinformatics Institute (EMBL-EBI) in 2021. - Gaia Cantelli; Alex Bateman; Cath Brooksbank; Anton I. Petrov; Rahuman S. Malik-Sheriff; Michele Ide-Smith; Henning Hermjakob; Paul Flicek; Rolf Apweiler; Ewan Birney; Johanna R. McEntyre (Nucleic Acids Res., 2022)

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. - Mihaly Varadi; Stephen Anyango; Mandar S. Deshpande; Sreenath Nair; Cindy Natassia; Galabina Yordanova; David Yuan; Oana Stroe; Gemma Wood; Agata Laydon; Augustin Zídek; Tim Green; et al. (Nucleic Acids Res., 2022)

GREENER principles for environmentally sustainable computational science. - Loïc Lannelongue; Hans-Erik G. Aronson; Alex Bateman; Ewan Birney; Talia Caplan; Martin Juckes; Johanna R. McEntyre; Andrew D. Morris; Gerry Reilly; Michael Inouye (Nat. Comput. Sci., 2023)

Benchmarking of computational methods for m6A profiling with Nanopore direct RNA sequencing. - Simone Maestri; Mattia Furlan; Logan Mulroney; Lucia Coscujuela Tarrero; Camilla Ugolini; Fabio Dalla Pozza; Tommaso Leonardi; Ewan Birney; Francesco Nicassio; Mattia Pelizzola (Briefings Bioinform., 2024)