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Ewan Birney
computational biology bioinformatics health

1. Introduction

John Frederick William Birney (known as Ewan) (born 6 December 1972)[1][2][3][4] CBE FRS FMedSci[5][6] is joint director with Rolf Apweiler of the European Bioinformatics Institute (EBI),[7][8][9] part of the European Molecular Biology Laboratory (EMBL) in Hinxton, Cambridgeshire. He also serves as non-executive director of Genomics England, chair of the Global Alliance for Genomics and Health (GA4GH)[10] and honorary professor of Bioinformatics at the University of Cambridge.[11] Birney has made significant contributions to genomics, through his development of innovative bioinformatics and computational biology tools.[12] He was previously an associate faculty member at the Wellcome Trust Sanger Institute.[13].

2. Education

Birney was educated at Eton College as an Oppidan Scholar.[3][14] Before going to university, Birney completed a gap year internship at Cold Spring Harbor Laboratory supervised by James Watson[4][15] and Adrian Krainer.[15][16][17] He managed a sweepstake known as GeneSweep,[18] for the genomics community, taking bets on estimates of the total number of genes (and noncoding or "junk" DNA[19]) in the human genome.[15][20][21]

Birney completed his Bachelor of Arts degree in Biochemistry at Balliol College, Oxford in 1996[3][4][22] followed by a PhD at the Wellcome Trust Sanger Institute, supervised by Richard Durbin[23] at St John's College, Cambridge.[24] His doctoral research used dynamic programming,[25] finite-state machines and probabilistic automatons for sequence alignment.[23]

During his university education he completed internships in financial services and the valuation of options and stock for the Swiss Bank Corporation[14] and the office of the Mayor of Baltimore.[15]

3. Research and Career

Birney is one of the founders of the Ensembl genome browser and other databases, and has played a role in the sequencing of the Human Genome in 2000 and the analysis of genome function in the ENCODE project.[21][26] He has played a role in annotating the genome sequences of the human,[27] mouse,[28] chicken[29] and several other organisms. His research group focuses on genomic algorithms and inter-individual differences in human and other animals.[7][9][19][30][31][32][33][34][35][36]

Birney is known for his role in the ENCODE consortium.[21][37][38][39][40][41] Prior to the ENCODE project, Birney has been involved in creation of a number of widely used bioinformatics and computational biology tools, either directly (PairWise, GeneWise, GenomeWise,), or in collaboration with students and postdocs, e.g. Exonerate (with Guy Slater), Enredo (Javier Herrero[42]), Pecan (Benedict Paten[43]), the Velvet assembler (Daniel Zerbino[44] ) and CRAM (Markus Hsi-Yang Fritz,[45] Rasko Leinonen[46] and Vadim Zalunin). Birney has also contributed to several other projects including the Pfam[47] database, InterPro,[48] BioPerl,[49][50] and HMMER[51] and Ensembl[52] 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[53] and postdoctoral researchers that have worked in his laboratory.[43][45][54][55][56][57][58][59][60][61][62][63] His research has been funded by the Biotechnology and Biological Sciences Research Council (BBSRC), Medical Research Council (MRC)[64] the Wellcome Trust and the European Union.[65]

Birney serves as a consultant to Oxford Nanopore Technologies[66] and on the scientific advisory board of the Earlham Institute (formerly TGAC) in Norwich.[67][68]

2.1. Awards and Honours

In 2002, Birney was named as one of the MIT Technology Review TR100 top 100 innovators in the world under the age of 35.[69]

In 2003, he gave the inaugural Francis Crick Lecture at the Royal Society:[12]

In 2005, he was awarded the Overton Prize by the International Society for Computational Biology (ISCB) for his advocacy of open source bioinformatics, contributions to the BioPerl community and leadership of the Ensembl genome annotation project..

In 2005 Birney was awarded the Benjamin Franklin Award in Bioinformatics:[70]

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.

He was awarded membership of the European Molecular Biology Organization (EMBO) in 2012 and elected a Fellow of the Royal Society (FRS) in 2014.[12][71] His certificate of election and candidature reads:[5]

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.

In 2014, Birney was awarded an Honorary Doctor of Science (DSc) degree from Brunel University London.[72]

In 2015, Birney was elected a Fellow of the Academy of Medical Sciences (FMedSci). [6]

He was appointed Commander of the Order of the British Empire (CBE) in the 2019 New Year Honours.[73][74]

4. Personal Life

Birney is married to Barley Birney (née Laycock)[30] with two children.[3]

Further Reading
In this part, we encourage you to list the link of papers wrote by the character, or published reviews/articles about his/her academic contributions. Edit


  1. NHGRI's Oral History Collection: Interview with Ewan Birney on YouTube
  2. Anon (2017). "So, I am Ewan Birney". National Human Genome Research Institute. Archived from the original on 2017-07-04. 
  3. Anon (2015). "Birney, Dr John Frederick William, (Ewan)". Who's Who (online Oxford University Press ed.). A & C Black, an imprint of Bloomsbury Publishing plc. doi:10.1093/ww/9780199540884.013.U281970.  (subscription or UK public library membership required)
  4. Hopkin, Karen (June 2005). "Bring Me Your Genomes: The Ewan Birney Story". The Scientist 19 (11): 60. Archived from the original on 31 March 2012. Retrieved 2011-06-10. 
  5. "Certificate of election EC/2014/06: Ewan Birney FRS". London: Royal Society. Archived from the original on 9 July 2019. 
  6. Anon (2015). "Dr Ewan Birney FRS FMedSci". London: Academy of Medical Sciences. Archived from the original on 2015-07-06. 
  7. Ewan Birney publications from Europe PubMed Central
  8. Parkhill, J; Birney, E; Kersey, P (2010). "Genomic information infrastructure after the deluge". Genome Biology 11 (7): 402. doi:10.1186/gb-2010-11-7-402. PMID 20670392.
  9. Kellis; Wold, B; Snyder, M. P.; Bernstein, B. E.; Kundaje, A; Marinov, G. K.; Ward, L. D.; Birney, E et al. (2014). "Defining functional DNA elements in the human genome". Proceedings of the National Academy of Sciences 111 (17): 6131–6138. doi:10.1073/pnas.1318948111. PMID 24753594. Bibcode: 2014PNAS..111.6131K.
  10. Birney, Ewan (2017). "About Ewan Birney". 
  11. Anon (2014-12-12). "Honorary Professors". Cambridge University Reporter (University of Cambridge) CXLV (5). Archived from the original on 2015-03-15. 
  12. Anon (2014). "Dr Ewan Birney FMedSci FRS". London: Royal Society. Archived from the original on 2015-11-17.  One or more of the preceding sentences incorporates text from the website where: All text published under the heading 'Biography' on Fellow profile pages is available under Creative Commons Attribution 4.0 International License. --"Royal Society Terms, conditions and policies". Archived from the original on 25 September 2015. Retrieved 2016-03-09. 
  13. "Sanger Faculty". Wellcome Trust Sanger Institute. Archived from the original on 2015-03-16. 
  14. Anon (2015). "Dr Ewan Birney FRS". Archived from the original on 2015-07-06. 
  15. Al-Khalili, Jim (2013). "The Life Scientific, Ewan Birney". BBC. 
  16. Birney, E.; Kumar, S.; Krainer, A. (1992). "A putative homolog of U2AF65 in S. Cerevisiae". Nucleic Acids Research 20 (17): 4663. doi:10.1093/nar/20.17.4663. PMID 1408772.
  17. Birney, Ewan (2013-02-10). "Scientists and their emotions: the highs ... and the lows: A computational biologist describes the elation of making a breakthrough – and the misery of not doing so – while three other scientists tell us how their work plays on their emotions". London: The Observer. 
  18. Pennisi, E. (2003). "Human Genome: A Low Number Wins the GeneSweep Pool". Science 300 (5625): 1484b–1484. doi:10.1126/science.300.5625.1484b. ISSN 0036-8075. PMID 12791949.
  19. 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.
  20. 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. PMID 20441615.
  21. Graur, D.; Zheng, Y.; Price, N.; Azevedo, R. B. R.; Zufall, R. A.; Elhaik, E. (2013). "On the Immortality of Television Sets: "Function" in the Human Genome According to the Evolution-Free Gospel of ENCODE". Genome Biology and Evolution 5 (3): 578–590. doi:10.1093/gbe/evt028. PMID 23431001.
  22. Anon (2012). "The age of the genome, Ewan Birney in Floreat Domus". Archived from the original on 24 February 2012. Balliol College newspaper
  23. Birney, Ewan (2000). Sequence alignment in bioinformatics (PDF) (PhD thesis). University of Cambridge. OCLC 894597337. EThOS Archived (PDF) from the original on 9 July 2019. Retrieved 19 November 2017.
  24. Smaglik, Paul (2012). "Turning point: Ewan Birney". Nature 482 (7383): 123–728. doi:10.1038/nj7383-123a.
  25. E. Birney & R. Durbin (1997). "Dynamite: a flexible code generating language for dynamic programming methods used in sequence comparison". Proceedings. International Conference on Intelligent Systems for Molecular Biology 5: 56–64. PMID 9322016.
  26. "ENCODE: Encyclopedia of DNA Elements" on YouTube
  27. Lander, E. S.; Linton, M.; Birren, B.; Nusbaum, C.; Zody, C.; Baldwin, J.; Devon, K.; Dewar, K. et al. (Feb 2001). "Initial sequencing and analysis of the human genome". Nature 409 (6822): 860–921. doi:10.1038/35057062. ISSN 0028-0836. PMID 11237011. Bibcode: 2001Natur.409..860L. 
  28. Chinwalla, A. T.; Waterston, L. L.; Lindblad-Toh, K. D.; Birney, G. A.; Rogers, L. A.; Abril, R. S.; Agarwal, T. A.; Agarwala, L. W. et al. (2002). "Initial sequencing and comparative analysis of the mouse genome". Nature 420 (6915): 520–562. doi:10.1038/nature01262. PMID 12466850. Bibcode: 2002Natur.420..520W.
  29. Eyras, E.; Reymond, A.; Castelo, R.; Bye, J. M.; Camara, F.; Flicek, P.; Huckle, E. J.; Parra, G. et al. (2005). "Gene finding in the chicken genome". BMC Bioinformatics 6: 131. doi:10.1186/1471-2105-6-131. PMID 15924626.
  30. Pennisi, Elizabeth (2012). "Profile of Ewan Birney: Genomics' Big Talker". Science 337 (6099): 1167–1169. doi:10.1126/science.337.6099.1167. PMID 22955814.
  31. "Churchill College: Biographies: Ewan Birney". Archived from the original on 3 April 2011. 
  32. 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. doi:10.1038/nature11875. PMID 23354052. Bibcode: 2013Natur.494...77G.
  33. "An Interview with Ewan Birney: Keynote Speaker at O'Reilly's Bioinformatics Technology Conference". O'Reilly Media. Archived from the original on 2015-05-27. 
  34. Ewan Birney publications indexed by the Scopus bibliographic database. (Subscription content?)
  35. Jupp, S; Malone, J; Bolleman, J; Brandizi, M; Davies, M; Garcia, L; Gaulton, A; Gehant, S et al. (2014). "The EBI RDF platform: Linked open data for the life sciences". Bioinformatics 30 (9): 1338–9. doi:10.1093/bioinformatics/btt765. PMID 24413672.
  36. 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.
  37. {{Google Scholar id}} template missing ID and not present in Wikidata.
  38. Kellis, M.; Wold, B.; Snyder, M. P.; Bernstein, B. E.; Kundaje, A.; Marinov, G. K.; Ward, L. D.; Birney, E. et al. (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. PMID 25275169. Bibcode: 2014PNAS..111E3366K.
  39. Birney, Ewan (2012). "The making of ENCODE: Lessons for big-data projects". Nature 489 (7414): 49–51. doi:10.1038/489049a. PMID 22955613. Bibcode: 2012Natur.489...49B.
  40. Dunham, I.; Bernstein, A.; Birney, S. F.; Dunham, P. J.; Green, C. A.; Gunter, F.; Snyder, C. B.; Frietze, S. et al. (2012). "An integrated encyclopedia of DNA elements in the human genome". Nature 489 (7414): 57–74. doi:10.1038/nature11247. PMID 22955616. Bibcode: 2012Natur.489...57T.
  41. ENCODE Project Consortium (2011). Becker PB. ed. "A User's Guide to the Encyclopedia of DNA Elements (ENCODE)". PLOS Biology 9 (4): e1001046. doi:10.1371/journal.pbio.1001046. PMID 21526222.
  42. Paten, B.; Herrero, J.; Beal, K.; Fitzgerald, S. (2008). "Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs". Genome Research 18 (11): 1814–1828. doi:10.1101/gr.076554.108. PMID 18849524.
  43. Paten, Benedict John (2006). Large-scale multiple alignment and transcriptionally associated pattern discovery in vertebrate genomes (PhD thesis). University of Cambridge. OCLC 890155216. EThOS
  44. Zerbino, D. R.; Birney, E. (2008). "Velvet: Algorithms for de novo short read assembly using de Bruijn graphs". Genome Research 18 (5): 821–829. doi:10.1101/gr.074492.107. ISSN 1088-9051. PMID 18349386.
  45. Fritz, Markus (2011). Exploiting high throughput DNA sequencing data for genomic analysis (PhD thesis). University of Cambridge. OCLC 890152397. EThOS
  46. Leinonen, R.; Akhtar, R.; Birney, E.; Bonfield, J.; Bower, L.; Corbett, M.; Cheng, Y.; Demiralp, F. et al. (2009). "Improvements to services at the European Nucleotide Archive". Nucleic Acids Research 38 (Database issue): D39–D45. doi:10.1093/nar/gkp998. PMID 19906712.
  47. "The Pfam protein families database". Nucleic Acids Research 30 (1): 276–280. 2002. doi:10.1093/nar/30.1.276. PMID 11752314.
  48. Apweiler, R.; Attwood, T. K.; Bairoch, A.; Bateman, A.; Birney, E.; Biswas, M.; Bucher, P.; Cerutti, L. et al. (2001). "The InterPro database, an integrated documentation resource for protein families, domains and functional sites". Nucleic Acids Research 29 (1): 37–40. doi:10.1093/nar/29.1.37. PMID 11125043.
  49. Stajich, J. E.; Block, D.; Boulez, K.; Brenner, S.; Chervitz, S.; Dagdigian, C.; Fuellen, G.; Gilbert, J. et al. (2002). "The BioPerl Toolkit: Perl Modules for the Life Sciences". Genome Research 12 (10): 1611–1618. doi:10.1101/gr.361602. PMID 12368254.
  50. Anon (2013). "Ewan Birney - BioPerl". Archived from the original on 12 December 2012. 
  51. Bateman, A.; Birney, E.; Durbin, R.; Eddy, S.; Finn, R.; Sonnhammer, E. (1999). "Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins". Nucleic Acids Research 27 (1): 260–262. doi:10.1093/nar/27.1.260. PMID 9847196.
  52. Flicek, P.; Ahmed, I.; Amode, M. R.; Barrell, D.; Beal, K.; Brent, S.; Carvalho-Silva, D.; Clapham, P. et al. (2012). "Ensembl 2013". Nucleic Acids Research 41 (D1): D48–D55. doi:10.1093/nar/gks1236. PMID 23203987.
  53. Birney, Ewan (2018-04-10). "@ewanbirney Best present as a supervisor...". Archived from the original on 10 April 2018. Retrieved 2018-08-30. 
  54. Taylor, Dennis Leland (2018). A genetic analysis of molecular traits in skeletal muscle. (PhD thesis). University of Cambridge. doi:10.17863/CAM.21243. EThOS
  55. O'Reilly, Paul F. (2009). Detecting recent positive selection in humans on a genome-wide scale. (PhD thesis). Imperial College London. OCLC 757093727. EThOS
  56. Ettwiller, Laurence Michele (2004). Computational Investigations into cis-Regulation in Eukaryotes (PhD thesis). University of Cambridge. OCLC 890156758. EThOS
  57. Hoffman, Michael Milner (2008). Quantifying evolution and natural selection in vertebrate noncoding sequence. (PhD thesis). University of Cambridge. doi:10.17863/CAM.13940. OCLC 885435476. EThOS
  58. Meynert, Alison Maria (2009). Function and evolution of regulatory elements in vertebrates (PhD thesis). University of Cambridge. OCLC 890148982. EThOS
  59. Ruklisa, Dace (2015). Large Scale Genomic Association Studies in Fruit Fly and Human (PhD thesis). University of Cambridge. OCLC 890151540. EThOS
  60. Timmer, Sander Willem (2015). Understanding the epigenome using system genetics. (PhD thesis). University of Cambridge. doi:10.17863/CAM.15988. OCLC 903609296. EThOS
  61. Zerbino, Daniel Robert (2009). Genome assembly and comparison using de Bruijn graphs (PhD thesis). University of Cambridge. OCLC 890153795. EThOS
  62. "EMBL International PhD Programme - completed theses | EBI Training". Archived from the original on 22 February 2013. 
  63. "EMBL-EBI PhD Theses - European Bioinformatics Institute". 
  64. "UK Government Research grants awarded to Ewan Birney". Swindon: Research Councils UK. Archived from the original on 2015-06-04. 
  65. "Google Tech Talk 2012-07-12: Human Genetics and Genomics: The Science for the 21st Century by Ewan Birney" on YouTube
  66. Cookson, Clive (2012-02-17). "Oxford Nanopore unveils mini-DNA reader". Financial Times (London). Retrieved 2014-10-20. 
  67. "TGAC new Scientific Advisory Board: a multidisciplinary set of key experts". TGAC Norwich UK. Archived from the original on 23 December 2015. 
  68. "Ewan Birney European Molecular Biology Lab - Big Data 2014 - MediaSpace - Stanford Medicine". 
  69. "2002 Young Innovators Under 35: Ewan Birney, 29". Technology Review. 2002. Archived from the original on 29 March 2011. 
  70. Bioinformatics Press release Ewan Birney wins the 2005 Benjamin Franklin Award in Bioinformatics
  71. Anon (2015). "Fellowship of the Royal Society 1660-2015". London: Royal Society. Archived from the original on 15 October 2015. 
  72. "In recognition of his outstanding service to science, Dr Ewan Birney is awarded the honorary degree of Doctor of Science". Brunel University London. Archived from the original on 2015-04-21. 
  73. "Cambridge in the 2019 New Year honours list". 28 December 2018. 
  74. "John BIRNEY". 
Name: Ewan Birney
Born: Dec 1972
Paddington, London
Title: Unknown
Affiliation: Unknown
Honor: Unknown
Subjects: Others
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