Ewan Birney

From Wikipedia, the free encyclopedia
Dr. Ewan Birney

Ewan Birney speaking at the World Economic Forum in Davos, 2013
Born 1972 (age 41–42)[1]
Fields Biology
Bioinformatics
Genomics[2]
Institutions University of Oxford
University of Cambridge
EBI
Sanger Institute
Churchill College, Cambridge
Cold Spring Harbor Laboratory
Alma mater Balliol College, Oxford
(undergraduate)
St John's College, Cambridge
(postgraduate)
Thesis Sequence alignment in bioinformatics (2000)
Doctoral advisor Richard Durbin[3]
Doctoral students Laurence Ettwiller[4][5]
Markus Hsi-Yang Fritz[6]
Michael Hoffman[7][8]
Alison Meynert[9][10]
Ben Paten[11]
Dace Ruklisa[12]
Sander Timmer[13]
Daniel Zerbino[14]
Other notable students Mikhail Spivakov (postdoc)[15][16][17]
Known for Ensembl[18]
PairWise[19]
GeneWise[20]
GenomeWise[21]
Exonerate[22]
ENCODE consortium[23]
Influences James Watson
Richard Durbin
Adrian Krainer[24]
Notable awards EMBO member (2012)
Overton Prize (2005)[25]
Ben Franklin Award (2005)
Crick Lecture (2003)[26]
TR100 (2002)[27]
Website
www.ebi.ac.uk/~birney
twitter.com/ewanbirney
genomeinformatician.blogspot.co.uk
www.sanger.ac.uk/research/faculty/ebirney
Dr Ewan Birney (Born 1972)[1] is an English Biologist and Associate Director of the European Bioinformatics Institute (EMBL-EBI) jointly with Rolf Apweiler, sharing strategic oversight of bioinformatics services.

Education

Birney was educated at Eton College,[24] completed his undergraduate degree in biochemistry at Balliol College, Oxford[1][28] and did his PhD at the Wellcome Trust Sanger Institute, under the supervision of Richard Durbin[3] as postgraduate student of St John's College, Cambridge.[29][30]

Before studying at university Birney completed a gap year internship at Cold Spring Harbor Laboratory under the supervision of James Watson[1] and Adrian Krainer.[24][31][32] He has also acted as a bookmaker to the genomics community, taking bets on different estimates of the total number of genes (and so-called "junk DNA"[33]) in the human genome.[24][34][35]

Research

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.[36] He has played a role in annotating the genome sequences of the human,[37] mouse,[38] chicken[39] and several other organisms. His research group currently focuses on genomic algorithms and inter-individual differences in human and other animal species.[40][41][42][33][43][44][45][46]

Birney is known for his role in the ENCODE consortium.[2][47][48][49][50][35][51] 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,[19] GeneWise,[20] GenomeWise,[21]), or in collaboration with students and postdocs, eg Exonerate[22] (with Guy Slater), Enredo (Javier Herrero[52]), Pecan (Benedict Paten[11]), the Velvet assembler (Daniel Zerbino[53]) and CRAM (Markus Hsi-Yang Fritz,[6] Rasko Leinonen[54] and Vadim Zalunin). Birney has also contributed to several other projects including the Pfam[55] database, InterPro,[56] BioPerl,[57][58] and HMMER[59] and Ensembl[60] toolkits.

His research group currently focuses on genomic algorithms and studying inter individual differences, in both human and other species. Birney has supervised several PhD students and postdocs that have worked in his laboratory.[4][6][7][9][11][12][14][61] This research has been funded by the Biotechnology and Biological Sciences Research Council,[62] the Wellcome Trust and the European Union.[63]

Awards

Overton Prize

Birney was awarded the Overton Prize in 2005:

“ 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."[25] ”

Benjamin Franklin Award

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.[64] ”

Royal Society Francis Crick Lecture

The inaugural Francis Crick Lecture was awarded to Dr Ewan 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 inaugural Francis Crick Lecture was awarded to Dr Ewan 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.[26] ”

Technology Review TR100 Award

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

“ Think of the human genome as Tolstoy’s War and Peace in the original Russian—immense, exciting, but for most, indecipherable. British bioinformatician Ewan Birney wants to make the genome’s information accessible to all. His Ensembl software and data allow researchers to find information on the Web on any known or predicted gene and to automatically match pieces of genes they have sequenced with other genes—without tediously combing through endless raw-sequence data. Cofounded by Birney, the Ensembl project has become one of the most popular resources for genome research, and its software is freely available to use and modify. With his related work adapting programming languages such as Perl and Java to biological projects, Birney has become a force in the bioinformatics open-source community. “In bioinformatics” he says, “the software is actually not that important. What’s much more important is the data.” Birney’s ambitious tools will help researchers deliver on the promise of new drugs and treatments derived from the Human Genome Project.[65] ”

References

  1. ↑ 1.0 1.1 1.2 1.3 Hopkin, Karen (06 2005). "Bring Me Your Genomes: The Ewan Birney Story". The Scientist 19 (11): 60. Archived from the original on 10 June 2011. Retrieved 10 June 2011. 
  2. ↑ 2.0 2.1 List of publications from Google Scholar
  3. ↑ 3.0 3.1 Birney, Ewan (2000). Sequence alignment in bioinformatics (PhD thesis). University of Cambridge. 
  4. ↑ 4.0 4.1 Ettwiller, Laurence (2004). Computational Investigations into cis-Regulation in Eukaryotes (PhD thesis). University of Cambridge. 
  5. ↑ Ettwiller, L. M.; Rung, J.; Birney, E. (2003). "Discovering Novel cis-Regulatory Motifs Using Functional Networks". Genome Research 13 (5): 883–895. doi:10.1101/gr.866403. PMC 430934. PMID 12727907. 
  6. ↑ 6.0 6.1 6.2 Fritz, Markus (2011). Exploiting high throughput DNA sequencing data for genomic analysis (PhD thesis). University of Cambridge. 
  7. ↑ 7.0 7.1 Hoffman, Michael (2008). Quantifying evolution and natural selection in vertebrate noncoding sequence (PhD thesis). University of Cambridge. 
  8. ↑ Hoffman, M. M.; Birney, E. (2006). "Estimating the Neutral Rate of Nucleotide Substitution Using Introns". Molecular Biology and Evolution 24 (2): 522–531. doi:10.1093/molbev/msl179. PMID 17122369. 
  9. ↑ 9.0 9.1 Meynert, Alison (2009). Function and evolution of regulatory elements in vertebrates (PhD thesis). University of Cambridge. 
  10. ↑ Meynert, A.; Birney, E. (2006). "Picking Pyknons out of the Human Genome". Cell 125 (5): 836–838. doi:10.1016/j.cell.2006.05.019. PMID 16751093. 
  11. ↑ 11.0 11.1 11.2 Paten, Ben (2006). Large-scale multiple alignment and transcriptionally associated pattern discovery in vertebrate genomes (PhD thesis). University of Cambridge. 
  12. ↑ 12.0 12.1 Ruklisa, Dace (2011). Large Scale Genomic Association Studies in Fruit Fly and Human (PhD thesis). University of Cambridge. 
  13. ↑ "Sander Timmer – PhD candidate in Biological Sciences". Archived from the original on 2013-07-02. 
  14. ↑ 14.0 14.1 Zerbino, Daniel (2009). Genome assembly and comparison (PhD thesis). University of Cambridge. 
  15. ↑ 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 3491393. PMID 22950968. 
  16. ↑ "Ewan's Blog; bioinformatician at large: ENCODE: My own thoughts". Archived from the original on 2013-02-12. 
  17. ↑ Junion, G.; Spivakov, M.; Girardot, C.; Braun, M.; Gustafson, E.  H.; Birney, E.; Furlong, E. E. M. (2012). "A Transcription Factor Collective Defines Cardiac Cell Fate and Reflects Lineage History". Cell 148 (3): 473–486. doi:10.1016/j.cell.2012.01.030. PMID 22304916. 
  18. ↑ 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. 
  19. ↑ 19.0 19.1 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 145991. PMID 8759004. 
  20. ↑ 20.0 20.1 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 310858. PMID 10779496. 
  21. ↑ 21.0 21.1 Birney, E.; Clamp, M.; Durbin, R. (2004). "GeneWise and Genomewise". Genome Research 14 (5): 988–995. doi:10.1101/gr.1865504. PMC 479130. PMID 15123596. 
  22. ↑ 22.0 22.1 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 553969. PMID 15713233. 
  23. ↑ 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. 
  24. ↑ 24.0 24.1 24.2 24.3 "BBC Radio 4 - The Life Scientific, Ewan Birney interviewed by Jim Al-Khalili, 2013-06-11". 
  25. ↑ 25.0 25.1 "ISCB Newsletter 8-2 Dr. Ewan Birney Named as the 2005 Overton Prize Winner!". Archived from the original on 28 February 2012. 
  26. ↑ 26.0 26.1 http://royalsociety.org/Content.aspx?id=3479 Royal Society article Recent Crick lectures
  27. ↑ MIT (2002). 2002 Young Innovators under 35, Ewan Birney, 29, Technology Review.
  28. ↑ "The age of the genome, Ewan Birney in Floreat Domus". Archived from the original on 28 February 2012. Balliol College newspaper
  29. ↑ "EBI's Ewan Birney: Quest for the Genomic Dragons".  Science Watch Newsletter Interview
  30. ↑ Smaglik, P. (2012). "Turning point: Ewan Birney". Nature 482 (7383): 123–728. doi:10.1038/nj7383-123a. 
  31. ↑ 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. 
  32. ↑ "Ewan Birney: 'There is a mistaken view that scientists are unemotional people | Science | The Observer 10th February 2013". 
  33. ↑ 33.0 33.1 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. 
  34. ↑ 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. 
  35. ↑ 35.0 35.1 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. 
  36. ↑ "ENCODE: Encyclopedia of DNA Elements" on YouTube
  37. ↑ 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. (Feb 2001). "Initial sequencing and analysis of the human genome". Nature 409 (6822): 860–921. doi:10.1038/35057062. ISSN 0028-0836. PMID 11237011. 
  38. ↑ 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.; Campbell, J. (2002). "Initial sequencing and comparative analysis of the mouse genome". Nature 420 (6915): 520–562. doi:10.1038/nature01262. PMID 12466850. 
  39. ↑ 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. 
  40. ↑ "Churchill College: Biographies: Ewan Birney". Archived from the original on 28 February 2012. 
  41. ↑ Pennisi, E. (2012). "Profile of Ewan Birney: Genomics' Big Talker". Science 337 (6099): 1167–1169. doi:10.1126/science.337.6099.1167. PMID 22955814. 
  42. ↑ 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. 
  43. ↑ An Interview with Ewan Birney: Keynote Speaker at O'Reilly's Bioinformatics Technology Conference
  44. ↑ Peer reviewed publications by Ewan Birney from PubMed
  45. ↑ Ewan Birney research profile on BiomedExperts
  46. ↑ Ewan Birney from the Scopus bibliographic database
  47. ↑ Birney, E. (2012). "The making of ENCODE: Lessons for big-data projects". Nature 489 (7414): 49–51. doi:10.1038/489049a. PMID 22955613. 
  48. ↑ 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. doi:10.1038/nature11247. PMC 3439153. PMID 22955616. 
  49. ↑ ENCODE Project Consortium (2011). "A User's Guide to the Encyclopedia of DNA Elements (ENCODE)". In Becker PB. PLoS Biology 9 (4): e1001046. doi:10.1371/journal.pbio.1001046. PMC 3079585. PMID 21526222. 
  50. ↑ List of publications from Microsoft Academic Search
  51. ↑ List of publications from the DBLP Bibliography Server
  52. ↑ 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. PMC 2577869. PMID 18849524. 
  53. ↑ 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. PMC 2336801. PMID 18349386. 
  54. ↑ 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 2808951. PMID 19906712. 
  55. ↑ 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. PMC 99071. PMID 11752314. 
  56. ↑ 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. PMC 29841. PMID 11125043. 
  57. ↑ 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. PMC 187536. PMID 12368254. 
  58. ↑ "Ewan Birney - BioPerl". Archived from the original on 2013-02-12. 
  59. ↑ 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. PMC 148151. PMID 9847196. 
  60. ↑ 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. PMC 3531136. PMID 23203987. 
  61. ↑ "EMBL International PhD Programme - completed theses | EBI Training". Archived from the original on 2013-02-12. 
  62. ↑ http://www.bbsrc.ac.uk/PA/grants/PersonDetails.aspx?Personid=-38782 Grants awarded to Ewan Birney by the BBSRC
  63. ↑ "Google Tech Talk 2012-07-12: Human Genetics and Genomics: The Science for the 21st Century by Ewan Birney" on YouTube
  64. ↑ Bioinformatics Press release Ewan Birney wins the 2005 Benjamin Franklin Award in Bioinformatics
  65. ↑ "2002 Young Innovators Under 35: Ewan Birney, 29". Technology Review. 2002. Archived from the original on 28 February 2012. 
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