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.
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 awareprotein 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 married in 2003[18] and has two children.[13]
Referencesedit
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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)
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^ abPennisi, 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.
^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. PMC2212820. PMID 17571346.
^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. PMC2926780. PMID 20670392.
^ abKellis, 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. PMC4035993. PMID 24753594.
^Heard, Edith (2020). "Restructure of senior management". embl.org. Heidelberg: European Molecular Biology Laboratory.
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^Anon (12 December 2014). "Honorary Professors". Cambridge University Reporter. CXLV (5). University of Cambridge. Archived from the original on 15 March 2015.
^Anon (2015). "Sanger Faculty". Wellcome Trust Sanger Institute. Archived from the original on 16 March 2015.
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^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. PMC334203. PMID 1408772.
^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.
^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.
^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.
^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.
^ abHall, 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.
^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. PMC2898077. PMID 20441615.
^ abcGraur, 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. PMC3622293. PMID 23431001.
^"ENCODE: Encyclopedia of DNA Elements" on YouTube
^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.
^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.
^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. PMC1174864. PMID 15924626.
^"Churchill College: Biographies: Ewan Birney". chu.cam.ac.uk. Archived from the original on 3 April 2011.
^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. PMC3672958. PMID 23354052.
^"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.
^Ewan Birney publications indexed by the Scopus bibliographic database. (subscription required)
^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. PMC3998127. PMID 24413672.
^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.
^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. PMC4143047. PMID 25275169.
^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.
^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. PMC3439153. PMID 22955616.
^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. PMC3079585. PMID 21526222.
^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. PMC145991. PMID 8759004.
^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. PMC310858. PMID 10779496.
^Birney, E.; Clamp, M.; Durbin, R. (2004). "GeneWise and Genomewise". Genome Research. 14 (5): 988–995. doi:10.1101/gr.1865504. PMC479130. PMID 15123596.
^Slater, G.; Birney, E. (2005). "Automated generation of heuristics for biological sequence comparison". BMC Bioinformatics. 6: 31. doi:10.1186/1471-2105-6-31. PMC553969. PMID 15713233.
^Paten, B.; Herrero, J.; Beal, K.; Fitzgerald, S.; Birney, E. (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. PMC2577869. PMID 18849524.
^ abPaten, Benedict John (2006). Large-scale multiple alignment and transcriptionally associated pattern discovery in vertebrate genomes (PhD thesis). University of Cambridge. OCLC 890155216. EThOS uk.bl.ethos.612811.
^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. PMC2336801. PMID 18349386.
^ abFritz, Markus (2011). Exploiting high throughput DNA sequencing data for genomic analysis (PhD thesis). University of Cambridge. OCLC 890152397. EThOS uk.bl.ethos.610819. Archived from the original on 30 August 2018. Retrieved 30 August 2018.
^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. PMC2808951. PMID 19906712.
^Bateman, A.; Birney, E.; Cerruti, L.; Durbin, R.; Etwiller, L.; Eddy, S.; Griffiths-Jones, S.; Howe, K.; Marshall, M.; Sonnhammer, E. L. (2002). "The Pfam protein families database". Nucleic Acids Research. 30 (1): 276–280. doi:10.1093/nar/30.1.276. PMC99071. PMID 11752314.
^Apweiler, R.; Attwood, T. K.; Bairoch, A.; Bateman, A.; Birney, E.; Biswas, M.; Bucher, P.; Cerutti, L.; Corpet, F.; Croning, M. D.; Durbin, R.; Falquet, L.; Fleischmann, W.; Gouzy, J.; Hermjakob, H.; Hulo, N.; Jonassen, I.; Kahn, D.; Kanapin, A.; Karavidopoulou, Y.; Lopez, R.; Marx, B.; Mulder, N. J.; Oinn, T. M.; Pagni, M.; Servant, F.; Sigrist, C. J.; Zdobnov, E. M. (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. PMC29841. PMID 11125043.
^Stajich, J. E.; Block, D.; Boulez, K.; Brenner, S.; Chervitz, S.; Dagdigian, C.; Fuellen, G.; Gilbert, J.; Korf, I.; Lapp, H.; Lehväslaiho, H.; Matsalla, C.; Mungall, C. J.; Osborne, B. I.; Pocock, M. R.; Schattner, P.; Senger, M.; Stein, L. D.; Stupka, E.; Wilkinson, M. D.; Birney, E. (2002). "The BioPerl Toolkit: Perl Modules for the Life Sciences". Genome Research. 12 (10): 1611–1618. doi:10.1101/gr.361602. PMC187536. PMID 12368254.
^Anon (2013). "Ewan Birney - BioPerl". bioperl.org. Archived from the original on 12 December 2012.
^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. PMC148151. PMID 9847196.
^Flicek, P.; Ahmed, I.; Amode, M. R.; Barrell, D.; Beal, K.; Brent, S.; Carvalho-Silva, D.; Clapham, P.; Coates, G.; Fairley, S.; Fitzgerald, S.; Gil, L.; Garcia-Giron, C.; Gordon, L.; Hourlier, T.; Hunt, S.; Juettemann, T.; Kahari, A. K.; Keenan, S.; Komorowska, M.; Kulesha, E.; Longden, I.; Maurel, T.; McLaren, W. M.; Muffato, M.; Nag, R.; Overduin, B.; Pignatelli, M.; Pritchard, B.; Pritchard, E. (2012). "Ensembl 2013". Nucleic Acids Research. 41 (D1): D48–D55. doi:10.1093/nar/gks1236. PMC3531136. PMID 23203987.
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^Meyer, Hannah Verena (2018). Genetic association of high-dimensional traits. cam.ac.uk (PhD thesis). University of Cambridge. doi:10.17863/CAM.26456. OCLC 1064682860. EThOS uk.bl.ethos.753477.
^Taylor, Dennis Leland (2018). A genetic analysis of molecular traits in skeletal muscle. cam.ac.uk (PhD thesis). University of Cambridge. doi:10.17863/CAM.21243. EThOS uk.bl.ethos.744632.
^O'Reilly, Paul F. (2009). Detecting recent positive selection in humans on a genome-wide scale. jisc.ac.uk (PhD thesis). Imperial College London. OCLC 757093727. EThOS uk.bl.ethos.511880. Archived from the original on 30 August 2018.
^Ettwiller, Laurence Michele (2004). Computational Investigations into cis-Regulation in Eukaryotes (PhD thesis). University of Cambridge. OCLC 890156758. EThOS uk.bl.ethos.613876.
^Hoffman, Michael Milner (2008). Quantifying evolution and natural selection in vertebrate noncoding sequence. cam.ac.uk (PhD thesis). University of Cambridge. doi:10.17863/CAM.13940. OCLC 885435476. EThOS uk.bl.ethos.604139.
^Meynert, Alison Maria (2009). Function and evolution of regulatory elements in vertebrates (PhD thesis). University of Cambridge. OCLC 890148982. EThOS uk.bl.ethos.608495.
^Ruklisa, Dace (2015). Large Scale Genomic Association Studies in Fruit Fly and Human (PhD thesis). University of Cambridge. OCLC 890151540. EThOS uk.bl.ethos.610178.
^Timmer, Sander Willem (2015). Understanding the epigenome using system genetics. cam.ac.uk (PhD thesis). University of Cambridge. doi:10.17863/CAM.15988. OCLC 903609296. EThOS uk.bl.ethos.637101.
^Zerbino, Daniel Robert (2009). Genome assembly and comparison using de Bruijn graphs (PhD thesis). University of Cambridge. OCLC 890153795. EThOS uk.bl.ethos.611752. Archived from the original on 30 August 2018.
^"EMBL International PhD Programme - completed theses | EBI Training". Archived from the original on 22 February 2013.
^"EMBL-EBI PhD Theses". ebi.ac.uk. European Bioinformatics Institute.
^"UK Government Research grants awarded to Ewan Birney". Swindon: Research Councils UK. Archived from the original on 4 June 2015.
^"Google Tech Talk 2012-07-12: Human Genetics and Genomics: The Science for the 21st Century by Ewan Birney" on YouTube
^Cookson, Clive (17 February 2012). "Oxford Nanopore unveils mini-DNA reader". Financial Times. London. Archived from the original on 11 December 2022. Retrieved 20 October 2014.
^"TGAC new Scientific Advisory Board: a multidisciplinary set of key experts". tgac.ac.uk. The Genome Analysis Centre, Norwich. Archived from the original on 23 December 2015.
^"Ewan Birney European Molecular Biology Lab - Big Data 2014 - MediaSpace - Stanford Medicine". mediaspace.stanford.edu.
^"2002 Young Innovators Under 35: Ewan Birney, 29". Technology Review. 2002. Archived from the original on 29 March 2011. Retrieved 22 June 2011.
^"Press release: Ewan Birney wins the 2005 Benjamin Franklin Award in Bioinformatics". bioinformatics.org.
^"In recognition of his outstanding service to science, Dr Ewan Birney is awarded the honorary degree of Doctor of Science". brunel.ac.uk. Brunel University London. Archived from the original on 21 April 2015.
^"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.
^"Cambridge in the 2019 New Year honours list". cam.ac.uk. University of Cambridge. 28 December 2018.
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