Ewan Birney

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Ewan Birney

CBE FRS FMedSci
Dr Ewan Birney FRS.jpg
Birney in 2014
Born
John Frederick William Birney [1] [2] [3]

(1972-12-06) 6 December 1972 (age 51) [4] [5] [6] [7]
Paddington, London, [6] England
Other namesEwan Birney
John Birney [8]
Education Eton College
Alma mater
Known for
Spouse
Barley Laycock
​
(m. 2003)​
[6] [12]
ChildrenTwo [6]
Awards
Scientific career
Fields
Institutions
Thesis Sequence alignment in bioinformatics  (2000)
Doctoral advisor Richard Durbin [18]
Website ewanbirney.com

John Frederick William Birney (known as Ewan Birney) CBE FRS FMedSci [19] [20] (born 6 December 1972) [21] [4] [6] [7] is joint director of EMBL's European Bioinformatics Institute (EMBL-EBI), [22] [23] [24] in Hinxton, Cambridgeshire and deputy director general of the European Molecular Biology Laboratory (EMBL). [25] He also serves as non-executive director of Genomics England, [26] chair of the Global Alliance for Genomics and Health (GA4GH) [27] [28] and honorary professor of bioinformatics at the University of Cambridge. [29] Birney has made significant contributions to genomics, through his development of innovative bioinformatics and computational biology tools. [13] He previously served as an associate faculty member at the Wellcome Trust Sanger Institute. [30]

Contents

Education

Birney was educated at Eton College as an Oppidan Scholar. [6] [31] Before going to university, Birney completed a gap year internship at Cold Spring Harbor Laboratory supervised by James Watson [7] [32] and Adrian Krainer. [32] [33] [34]

Birney completed his Bachelor of Arts degree in Biochemistry at the University of Oxford in 1996, where he was an undergraduate student at Balliol College, Oxford. [6] [7] [35] He completed his PhD at the Sanger Institute, supervised by Richard Durbin [18] while he was a postgraduate student at St John's College, Cambridge. [36] His doctoral research used dynamic programming, [37] finite-state machines and probabilistic automatons for sequence alignment. [18]

While he was a student he completed internships in the office of the Mayor of Baltimore and also in financial services on valuation of options for the Swiss Bank Corporation. [31] [32] [ when? ]

Research and career

From 2000 to 2003, Birney organised a scientific wager and sweepstake known as GeneSweep, [38] [9] for the genomics community, taking bets on estimates of the total number of genes (and noncoding DNA [39] ) in the human genome. [32] [40] [41]

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. [41] [42] He has played a role in annotating the genome sequences of the human, [43] mouse, [44] chicken [45] and several other organisms. His research group focuses on computational genomics and inter-individual differences in human and other animals. [12] [22] [24] [39] [46] [47] [48] [49] [50] [51]

Birney is known for his role in the ENCODE consortium. [17] [41] [52] [53] [54] [55] [56] 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, [57] GeneWise, [58] GenomeWise, [59] ), or in collaboration with students and postdocs, e.g. Exonerate [60] (with Guy Slater), Enredo (Javier Herrero [61] ), Pecan (Benedict Paten [62] ), the Velvet assembler (Daniel Zerbino [63] ) and CRAM (Markus Hsi-Yang Fritz, [64] Rasko Leinonen [65] and Vadim Zalunin). Birney has also contributed to several other projects including the Pfam [66] database, InterPro, [67] BioPerl, [68] [69] and HMMER [70] and Ensembl genome database project. [71]

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 [72] and postdoctoral researchers that have worked in his laboratory. [73] [74] [75] [76] [64] [77] [78] [62] [79] [80] [81] [82] [83] His research has been funded by the Biotechnology and Biological Sciences Research Council (BBSRC), Medical Research Council (MRC) [84] the National Human Genome Research Institute (NHGRI), [3] the Wellcome Trust and the European Union. [85]

Birney serves as a consultant to Oxford Nanopore Technologies [86] and on the scientific advisory board of the Earlham Institute (formerly TGAC) in Norwich. [87] [88] Since 2022, he has served on the governing board at Eton College. [89]

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. [90] In 2003, he gave the inaugural Francis Crick Lecture at the Royal Society: [13] 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. [14] In 2005 Birney was awarded the Benjamin Franklin Award in Bioinformatics: [91]

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.

Birney was awarded membership of the European Molecular Biology Organization (EMBO) [15] in 2012 [16] and elected a Fellow of the Royal Society (FRS) in 2014. [2] [13] His certificate of election and candidature reads: [19]

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.

Birney has been awarded an Honorary Doctor of Science (DSc) degrees: in 2014 from Brunel University London [92] and in 2021 from University of Tartu, [93] Estonia. In 2015, Birney was elected a Fellow of the Academy of Medical Sciences (FMedSci). [20] Birney was appointed Commander of the Order of the British Empire (CBE) in the 2019 New Year Honours. [94] [8]

Personal life

Birney married in 2003 [12] and has two children. [6]

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References

  1. ↑ Anon (4 November 1993). "John Frederick William Birney". Oxford University Gazette . Oxford University Press. 124 (4305). Archived from the original on 16 June 2015.
  2. 1 2 Anon (2015). "Fellowship of the Royal Society 1660-2015". London: Royal Society. Archived from the original on 15 October 2015.
  3. 1 2 Ewan Birney's ORCID   0000-0001-8314-8497
  4. 1 2 Anon (2017). "So, I am Ewan Birney" (PDF). genome.gov. National Human Genome Research Institute. Archived from the original (PDF) on 4 July 2017.
  5. ↑ Anon (2016). "John Frederick William BIRNEY, Eagle Genomics Limited". London: Companies House. Archived from the original on 25 April 2016.
  6. 1 2 3 4 5 6 7 8 Anon (2015). "Birney, Dr John Frederick William, (Ewan)" . Who's Who (online Oxford University Press  ed.). A & C Black. doi:10.1093/ww/9780199540884.013.U281970.(Subscription or UK public library membership required.)
  7. 1 2 3 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 10 June 2011.
  8. 1 2 Anon (2018). "John BIRNEY: Professor John Frederick William BIRNEY F.R.S." The London Gazette . London. Archived from the original on 28 December 2019.
  9. 1 2 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. S2CID   82493401. Closed Access logo transparent.svg
  10. ↑ ENCODE Project Consortium; Birney E; Stamatoyannopoulos JA; Dutta A; Guigó R; Gingeras TR; Margulies EH; Weng Z; Snyder M; Dermitzakis ET; et al. (2007). "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project". Nature. 447 (7146): 799–816. Bibcode:2007Natur.447..799B. doi:10.1038/nature05874. PMC   2212820 . PMID   17571346.
  11. ↑ Hubbard, T.; Barker, D.; Birney, E.; Cameron, G.; Chen, Y.; Clark, L.; Cox, T.; Cuff, J.; Curwen, V.; Down, T.; Durbin, R.; Eyras, E.; Gilbert, J.; Hammond, M.; Huminiecki, L.; Kasprzyk, A.; Lehvaslaiho, H.; Lijnzaad, P.; Melsopp, C.; Mongin, E.; Pettett, R.; Pocock, M.; Potter, S.; Rust, A.; Schmidt, E.; Searle, S.; Slater, G.; Smith, J.; Spooner, W.; Stabenau, A. (2002). "The Ensembl genome database project". Nucleic Acids Research. 30 (1): 38–41. doi:10.1093/nar/30.1.38. PMC   99161 . PMID   11752248.
  12. 1 2 3 Pennisi, Elizabeth (2012). "Profile of Ewan Birney: Genomics' Big Talker". Science . 337 (6099): 1167–1169. doi:10.1126/science.337.6099.1167. PMID   22955814.
  13. 1 2 3 4 Anon (2014). "Dr Ewan Birney FMedSci FRS". London: Royal Society. Archived from the original on 17 November 2015. One or more of the preceding sentences incorporates text from the royalsociety.org 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 9 March 2016.{{cite web}}: CS1 maint: bot: original URL status unknown (link)
  14. 1 2 "ISCB Newsletter 8-2 Dr. Ewan Birney Named as the 2005 Overton Prize Winner!". Archived from the original on 22 October 2015.
  15. 1 2 "The EMBO Pocket Directory" (PDF). European Molecular Biology Organization. Archived from the original on 16 March 2015.
  16. 1 2 Anon (2012). "EMBO MEMBER: Ewan Birney". people.embo.org. Heidelberg: European Molecular Biology Organization.
  17. 1 2 3 4 Ewan Birney publications indexed by Google Scholar OOjs UI icon edit-ltr-progressive.svg
  18. 1 2 3 Birney, Ewan (2000). Sequence alignment in bioinformatics (PDF) (PhD thesis). University of Cambridge. OCLC   894597337. EThOS   uk.bl.ethos.621653. Archived (PDF) from the original on 9 July 2019. Retrieved 19 November 2017.
  19. 1 2 "Certificate of election EC/2014/06: Ewan Birney FRS". London: Royal Society. Archived from the original on 9 July 2019.
  20. 1 2 Anon (2015). "Dr Ewan Birney FRS FMedSci". acmedsci.ac.uk. London: Academy of Medical Sciences. Archived from the original on 6 July 2015.
  21. ↑ NHGRI's Oral History Collection: Interview with Ewan Birney on YouTube
  22. 1 2 Ewan Birney publications from Europe PubMed Central
  23. ↑ 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 . PMC   2926780 . PMID   20670392.
  24. 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   4035993 . PMID   24753594.
  25. ↑ Heard, Edith (2020). "Restructure of senior management". embl.org. Heidelberg: European Molecular Biology Laboratory.
  26. ↑ Anon (2016). "Professor Ewan Birney appointed to the Genomics England Board". genomicsengland.co.uk. Genomics England. Archived from the original on 11 July 2017.
  27. ↑ Ewan Birney on Twitter OOjs UI icon edit-ltr-progressive.svg
  28. ↑ Birney, Ewan (2017). "About Ewan Birney". ewanbirney.com. Archived from the original on 1 December 2017. Retrieved 19 November 2017.
  29. ↑ Anon (12 December 2014). "Honorary Professors". Cambridge University Reporter . University of Cambridge. CXLV (5). Archived from the original on 15 March 2015.
  30. ↑ Anon (2015). "Sanger Faculty". Wellcome Trust Sanger Institute. Archived from the original on 16 March 2015.
  31. 1 2 Anon (2015). "Dr Ewan Birney FRS". thescientific23.com. Archived from the original on 6 July 2015.
  32. 1 2 3 4 Al-Khalili, Jim (2013). "The Life Scientific, Ewan Birney". bbc.co.uk. BBC.
  33. ↑ 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. PMC   334203 . PMID   1408772.
  34. ↑ Birney, Ewan (10 February 2013). "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". theguardian.com. London: The Observer.
  35. ↑ Anon (2012). "The age of the genome, Ewan Birney in Floreat Domus". balliol.ox.ac.uk. Balliol College newspaper. Archived from the original on 24 February 2012.
  36. ↑ Smaglik, Paul (2012). "Turning point: Ewan Birney". Nature . 482 (7383): 123–728. doi: 10.1038/nj7383-123a . S2CID   144288448.
  37. ↑ Birney, Ewan; Durbin, Richard (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.
  38. ↑ Pearson, Helen (2003). "Geneticists play the numbers game in vain". Nature. 423 (6940): 576. Bibcode:2003Natur.423..576P. doi: 10.1038/423576a . ISSN   0028-0836. PMID   12789304. S2CID   54588944.
  39. 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.
  40. ↑ 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   2898077 . PMID   20441615.
  41. 1 2 3 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. PMC   3622293 . PMID   23431001.
  42. ↑ "ENCODE: Encyclopedia of DNA Elements" on YouTube
  43. ↑ Lander, E. S.; Linton, M.; Birren, B.; Nusbaum, C.; Zody, C.; Baldwin, J.; Devon, K.; Dewar, K.; Doyle, M.; Fitzhugh, W.; Funke, R.; Gage, D.; Harris, K.; Heaford, A.; Howland, J.; Kann, L.; Lehoczky, J.; Levine, R.; McEwan, P.; McKernan, K.; Meldrim, J.; Mesirov, J. P.; Miranda, C.; Morris, W.; Naylor, J.; Raymond, C.; Rosetti, M.; Santos, R.; Sheridan, A.; et al. (February 2001). "Initial sequencing and analysis of the human genome" (PDF). Nature. 409 (6822): 860–921. Bibcode:2001Natur.409..860L. doi:10.1038/35057062. ISSN   0028-0836. PMID   11237011.
  44. ↑ 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.; Ainscough, E. R.; Alexandersson, J. D.; An, T. L.; Antonarakis, W. E.; Attwood, J. O.; Baertsch, M. N.; Bailey, K. H.; Barlow, C. S.; Beck, T. C.; Berry, B.; Birren, J.; Bloom, E.; Bork, R. H.; Botcherby, M. C.; Bray, R. K.; Brent, S. P.; Brown, P.; Brown, E.; Bult, B.; Burton, T.; Butler, D. G.; et al. (2002). "Initial sequencing and comparative analysis of the mouse genome". Nature. 420 (6915): 520–562. Bibcode:2002Natur.420..520W. doi: 10.1038/nature01262 . PMID   12466850.
  45. ↑ Eyras, E.; Reymond, A.; Castelo, R.; Bye, J. M.; Camara, F.; Flicek, P.; Huckle, E. J.; Parra, G.; Shteynberg, D. D.; Wyss, C.; Rogers, J.; Antonarakis, S. E.; Birney, E.; Guigo, R.; Brent, M. R. (2005). "Gene finding in the chicken genome". BMC Bioinformatics. 6: 131. doi: 10.1186/1471-2105-6-131 . PMC   1174864 . PMID   15924626.
  46. ↑ "Churchill College: Biographies: Ewan Birney". chu.cam.ac.uk. Archived from the original on 3 April 2011.
  47. ↑ 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   3672958 . PMID   23354052.
  48. ↑ "An Interview with Ewan Birney: Keynote Speaker at O'Reilly's Bioinformatics Technology Conference". oreilly.com. O'Reilly Media. Archived from the original on 27 May 2015.
  49. ↑ Ewan Birney publications indexed by the Scopus bibliographic database. (subscription required)
  50. ↑ 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   3998127 . PMID   24413672.
  51. ↑ 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. S2CID   20972353.
  52. ↑ 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. Bibcode:2014PNAS..111E3366K. doi: 10.1073/pnas.1410434111 . ISSN   0027-8424. PMC   4143047 . PMID   25275169.
  53. ↑ Birney, Ewan (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. S2CID   32178490.
  54. ↑ 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.; et al. (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   3439153 . PMID   22955616.
  55. ↑ 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 . PMC   3079585 . PMID   21526222. Open Access logo PLoS transparent.svg
  56. ↑ Ewan Birney at DBLP Bibliography Server OOjs UI icon edit-ltr-progressive.svg
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  93. ↑ "The University of Tartu has conferred the degree of Honorary Doctor of Bioinformatics on Professor Ewan Birney for his excellent research work, international cooperation, role as an advocate of open science". www.ut.ee. University of Tartu.
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