Ewan Birney

Ewan Birney

Ewan Birney in 2014, portrait courtesy of the Royal Society
Born John Frederick William Birney[1][2][3]
December 1972 (age 4344)[4][5][6]
Paddington, London[5]
Alma mater
Thesis Sequence alignment in bioinformatics (2000)
Doctoral advisor Richard Durbin[8]
Doctoral students
Other notable students Mikhail Spivakov (postdoc)[24][25][26]
Known for
Notable awards
Spouse Barley Birney (née Laycock) (m. 2003)[5][42]
Children Two[5]


John Frederick William Birney, known as Ewan, (born 1972)[5][6] FRS[39] FMedSci[41] is joint Director with Rolf Apweiler of the European Bioinformatics Institute (EBI),[43][44][45][46] part of the European Molecular Biology Laboratory (EMBL) in Hinxton, Cambridgeshire. He is also an Associate Faculty member at the Wellcome Trust Sanger Institute[47] and an Honorary Professor of Bioinformatics at the University of Cambridge.[48] Birney has made significant contributions to the analysis of genomes. Through his development of innovative bioinformatics and computational biology tools, researchers around the world are able to predict and annotate regions of interest in DNA with speed and confidence.[35]


Birney was educated at Eton College as an Oppidan Scholar where he studied GCE Advanced Levels in Maths, Biology, Chemistry and Art.[5][49] Before going to university, Birney completed a gap year internship at Cold Spring Harbor Laboratory supervised by James Watson[6][34] and Adrian Krainer.[34][50][51] He acted as a bookmaker to the genomics community, taking bets on estimates of the total number of genes (and so-called "junk DNA"[52]) in the human genome.[34][53][54]

Birney completed his Bachelor of Arts degree in Biochemistry at Balliol College, Oxford in 1996[5][6][55] followed by a PhD at the Wellcome Trust Sanger Institute, supervised by Richard Durbin[8] as postgraduate student of St John's College, Cambridge.[56][57] During his university education he completed an internship in financial services in the City of London for the Swiss Bank Corporation.[34][49]


Birney is one of the founders of the Ensembl genome browser and other databases, and has played a key role in many large-scale genomics projects, notably the sequencing of the Human Genome in 2000 and the analysis of genome function in the ENCODE project.[54][58] He has played a role in annotating the genome sequences of the human,[59] mouse,[60] chicken[61] and several other organisms. His research group focuses on genomic algorithms and inter-individual differences in human and other animal species.[42][43][46][52][62][63][64][65][66][67]

Birney is known for his role in the ENCODE consortium.[7][54][68][69][70][71][72] Prior to the ENCODE project, Birney has been involved in the creation of a number of widely used bioinformatics and computational biology tools, either directly (PairWise,[28] GeneWise,[29] GenomeWise,[30]), or in collaboration with students and postdocs, e.g. Exonerate[31] (with Guy Slater), Enredo (Javier Herrero[73]), Pecan (Benedict Paten[18]), the Velvet assembler (Daniel Zerbino[74] ) and CRAM (Markus Hsi-Yang Fritz,[11] Rasko Leinonen[75] and Vadim Zalunin). Birney has also contributed to several other projects including the Pfam[76] database, InterPro,[77] BioPerl,[78][79] and HMMER[80] and Ensembl[81] toolkits.

As of 2015 Birney's research group focuses on genomic algorithms and studying inter individual differences, in both human and other species. He has supervised several PhD students and postdocs that have worked in his laboratory.[9][11][12][16][18][19][20][23][82] This research has been funded by the Biotechnology and Biological Sciences Research Council (BBSRC), Medical Research Council (MRC)[83] the Wellcome Trust and the European Union.[84] Birney is also a consultant to Oxford Nanopore Technologies[85] and on the scientific advisory board of The Genome Analysis Centre (TGAC) in Norwich.[86][87]

Awards and honours

Birney has won several awards: In 2003, he gave the inaugural Francis Crick Lecture at the Royal Society:

The inaugural Francis Crick Lecture was awarded to Birney, for his leading role in establishing international standards for software used in genome informatics, and in making research data and software openly available to the research community. The lecture, entitled 'Being human: what our genome tells us' took place at the Royal Society on 4 December 2003.[35]

In 2005, Birney was awarded the Overton Prize by the International Society for Computational Biology (ISCB):

Dr. Ewan Birney of the European Molecular Biology Laboratory (EMBL) European Bioinformatics Institute (EBI), was awarded the 2005 Overton Prize in honour of his advocacy of open source bioinformatics, and his generous contributions to the BioPerl community. Perhaps even more important to biology is his leadership of the Ensembl genome annotation project, providing rapid and accurate computational annotations for eukaryotic genomes."[36]

In 2005 Birney was awarded the Benjamin Franklin Award in Bioinformatics:

As expressed by his nominators, Birney has been a significant force in Open Source in Bioinformatics and science. He has been a strong advocate for making genome information freely available to all. His work co-leading the Ensembl project has made high-quality genome annotation available freely over the web, preventing a class system of labs which can and cannot afford to pay subscription fees to proprietary data. The project has worked hard to make the data available in a variety of ways to make the data accessible and easily available for mining. The Ensembl project has been open-source from the outset, enabling researchers and corporations alike to reuse and extend the software system. Birney has been an advocate of open science as well. Along with Sean Eddy, he criticised journal decisions to allow papers to be published without releasing the genome sequence data at the same time. He is also the author of the freely available Wise package of tools, which are important parts of genome annotation pipelines. He serves as a co-leader of the open-source bioinformatics toolkit Bioperl and also co-founded and currently serves as president of the Open Bioinformatics foundation, an organisation that support the development of several bioinformatics toolkits.[88]

Birney was elected a Fellow of the Royal Society (FRS) in 2014.[2][35] His certificate of election and candidature reads

Ewan has grown to be a force in genomics due to his innovation in genome analysis, both algorithmic and integrative analyses. He wrote the first error tolerant, splice aware protein alignment program, used in the human and subsequent genome analysis; he co-authored one of the first and most widely used short read assemblers. In terms of data integration, Ewan has led the analysis in many genomic consortia, in particular ENCODE, leading the integration of many genomic assays; for example making robust predictions of enhancers, promoters, and their integration with disease associated regions. He also co-developed many widely used bioinformatics resources.[39]

In 2015, Birney was elected a Fellow of the Academy of Medical Sciences (FMedSci). His citation on election reads:

Associate Director of the European Bioinformatics Institute, Dr Ewan Birney has been a prominent leader in genomics internationally for many years and led the ENCODE project. He is a polymath who has drawn from diverse fields, such as speech recognition, computer science and human genetics, to develop world-leading research programmes in population and comparative genomics.

His influence on genomics has been profound, and he has contributed new tools and concepts that have been far ahead of their time. His central position in genomics/bioinformatics in Europe and indeed the world gives him a deep understanding of the impact of genomics technologies on future healthcare and health economics.[41]

In 2014, Birney was awarded an Honorary Doctor of Science (DSc) degree from Brunel University London in recognition of his service to science.[89] In 2002, Birney was named as one of the MIT Technology Review TR100 top 100 innovators in the world under the age of 35:[90] Birney was also awarded EMBO Membership[37] in 2012.[38]

Personal life

Birney is married to Barley Birney (née Laycock)[42] with two children.[5] He appeared on a special Christmas edition of University Challenge in 2014 representing Balliol College, Oxford with Charlotte Higgins and Alan Beith.[91]


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  12. 1 2 Hoffman, Michael (2008). Quantifying evolution and natural selection in vertebrate noncoding sequence (PhD thesis). University of Cambridge. OCLC 885435476.
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  24. Spivakov, M.; Akhtar, J.; Kheradpour, P.; Beal, K.; Girardot, C.; Koscielny, G.; Herrero, J.; Kellis, M.; Furlong, E. E.; Birney, E. (2012). "Analysis of variation at transcription factor binding sites in Drosophila and humans". Genome Biology. 13 (9): R49. doi:10.1186/gb-2012-13-9-r49. PMC 3491393Freely accessible. PMID 22950968.
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  28. 1 2 Birney, E.; Thompson, J.; Gibson, T. (1996). "PairWise and SearchWise: Finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames". Nucleic Acids Research. 24 (14): 2730–2739. doi:10.1093/nar/24.14.2730. PMC 145991Freely accessible. PMID 8759004.
  29. 1 2 Birney, E.; Durbin, R. (2000). "Using GeneWise in the Drosophila annotation experiment". Genome Research. 10 (4): 547–548. doi:10.1101/gr.10.4.547. PMC 310858Freely accessible. PMID 10779496.
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  31. 1 2 Slater, G.; Birney, E. (2005). "Automated generation of heuristics for biological sequence comparison". BMC Bioinformatics. 6: 31. doi:10.1186/1471-2105-6-31. PMC 553969Freely accessible. PMID 15713233.
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  46. 1 2 Kellis, M; Wold, B; Snyder, M. P.; Bernstein, B. E.; Kundaje, A; Marinov, G. K.; Ward, L. D.; Birney, E; Crawford, G. E.; Dekker, J; Dunham, I; Elnitski, L. L.; Farnham, P. J.; Feingold, E. A.; Gerstein, M; Giddings, M. C.; Gilbert, D. M.; Gingeras, T. R.; Green, E. D.; Guigo, R; Hubbard, T; Kent, J; Lieb, J. D.; Myers, R. M.; Pazin, M. J.; Ren, B; Stamatoyannopoulos, J. A.; Weng, Z; White, K. P.; Hardison, R. C. (2014). "Defining functional DNA elements in the human genome". Proceedings of the National Academy of Sciences. 111 (17): 6131–6138. Bibcode:2014PNAS..111.6131K. doi:10.1073/pnas.1318948111. PMC 4035993Freely accessible. PMID 24753594.
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  52. 1 2 Hall, Stephen S. (2012). "Journey to the genetic interior. What was once known as junk DNA turns out to hold hidden treasures, says computational biologist Ewan Birney". Scientific American. 307 (4): 80–82, 84. doi:10.1038/scientificamerican1012-80. PMID 23029896.
  53. Pertea, M.; Salzberg, S. L. (2010). "Between a chicken and a grape: Estimating the number of human genes". Genome Biology. 11 (5): 206. doi:10.1186/gb-2010-11-5-206. PMC 2898077Freely accessible. PMID 20441615.
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  63. Goldman, N.; Bertone, P.; Chen, S.; Dessimoz, C.; Leproust, E. M.; Sipos, B.; Birney, E. (2013). "Towards practical, high-capacity, low-maintenance information storage in synthesized DNA". Nature. 494 (7435): 77–80. Bibcode:2013Natur.494...77G. doi:10.1038/nature11875. PMC 3672958Freely accessible. PMID 23354052.
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  66. Jupp, S; Malone, J; Bolleman, J; Brandizi, M; Davies, M; Garcia, L; Gaulton, A; Gehant, S; Laibe, C; Redaschi, N; Wimalaratne, S. M.; Martin, M; Le Novère, N; Parkinson, H; Birney, E; Jenkinson, A. M. (2014). "The EBI RDF platform: Linked open data for the life sciences". Bioinformatics. 30 (9): 1338–9. doi:10.1093/bioinformatics/btt765. PMC 3998127Freely accessible. PMID 24413672.
  67. Marti-Solano, M; Birney, E; Bril, A; Della Pasqua, O; Kitano, H; Mons, B; Xenarios, I; Sanz, F (2014). "Integrative knowledge management to enhance pharmaceutical R&D". Nature Reviews Drug Discovery. 13 (4): 239–40. doi:10.1038/nrd4290. PMID 24687050.
  68. Kellis, M.; Wold, B.; Snyder, M. P.; Bernstein, B. E.; Kundaje, A.; Marinov, G. K.; Ward, L. D.; Birney, E.; Crawford, G. E.; Dekker, J.; Dunham, I.; Elnitski, L. L.; Farnham, P. J.; Feingold, E. A.; Gerstein, M.; Giddings, M. C.; Gilbert, D. M.; Gingeras, T. R.; Green, E. D.; Guigo, R.; Hubbard, T.; Kent, J.; Lieb, J. D.; Myers, R. M.; Pazin, M. J.; Ren, B.; Stamatoyannopoulos, J.; Weng, Z.; White, K. P.; Hardison, R. C. (2014). "Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease". Proceedings of the National Academy of Sciences. 111 (33): E3366–E3366. doi:10.1073/pnas.1410434111. ISSN 0027-8424.
  69. Birney, E. (2012). "The making of ENCODE: Lessons for big-data projects". Nature. 489 (7414): 49–51. Bibcode:2012Natur.489...49B. doi:10.1038/489049a. PMID 22955613.
  70. Dunham, I.; Bernstein, A.; Birney, S. F.; Dunham, P. J.; Green, C. A.; Gunter, F.; Snyder, C. B.; Frietze, S.; Harrow, J.; Kaul, R.; Khatun, J.; Lajoie, B. R.; Landt, S. G.; Lee, B. K.; Pauli, F.; Rosenbloom, K. R.; Sabo, P.; Safi, A.; Sanyal, A.; Shoresh, N.; Simon, J. M.; Song, L.; Trinklein, N. D.; Altshuler, R. C.; Birney, E.; Brown, J. B.; Cheng, C.; Djebali, S.; Dong, X.; Dunham, I. (2012). "An integrated encyclopedia of DNA elements in the human genome". Nature. 489 (7414): 57–74. Bibcode:2012Natur.489...57T. doi:10.1038/nature11247. PMC 3439153Freely accessible. PMID 22955616.
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  75. Leinonen, R.; Akhtar, R.; Birney, E.; Bonfield, J.; Bower, L.; Corbett, M.; Cheng, Y.; Demiralp, F.; Faruque, N.; Goodgame, N.; Gibson, R.; Hoad, G.; Hunter, C.; Jang, M.; Leonard, S.; Lin, Q.; Lopez, R.; Maguire, M.; McWilliam, H.; Plaister, S.; Radhakrishnan, R.; Sobhany, S.; Slater, G.; Ten Hoopen, P.; Valentin, F.; Vaughan, R.; Zalunin, V.; Zerbino, D.; Cochrane, G. (2009). "Improvements to services at the European Nucleotide Archive". Nucleic Acids Research. 38 (Database issue): D39–D45. doi:10.1093/nar/gkp998. PMC 2808951Freely accessible. PMID 19906712.
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Academic offices
Preceded by
Janet Thornton
Director of the European Bioinformatics Institute
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