Ewan Birney

Ewan Birney

Ewan Birney in 2014, portrait via the Royal Society
Born 1972 (age 42–43)[1][2]
Paddington, London[1]
Fields
Institutions
Alma mater
Thesis Sequence alignment in bioinformatics (2000)
Doctoral advisor Richard Durbin[4]
Doctoral students
Other notable students Mikhail Spivakov (postdoc)[17][18][19]
Known for
Influences
Notable awards
Spouse Barley Birney (née Laycock)[32]
Children
  • Rosie Birney
  • Joe Birney[33]

Website

Ewan Birney FRS[30] born 1972[1][2] is a Biologist and Associate Director of the European Bioinformatics Institute (EMBL-EBI) jointly with Rolf Apweiler, sharing strategic oversight of bioinformatics services.[34][35][36][37]

Education

Birney was educated at Eton College.[1] Before studying at university Birney completed a gap year internship at Cold Spring Harbor Laboratory under the supervision of James Watson[2][27] and Adrian Krainer.[27][38][39] He acted as a bookmaker to the genomics community, taking bets on different estimates of the total number of genes (and so-called "junk DNA"[40]) in the human genome.[27][41][42]

Birney completed his Bachelor of Arts degree in Biochemistry at Balliol College, Oxford in 1996[1][2][43] and did his PhD at the Wellcome Trust Sanger Institute, under the supervision of Richard Durbin[4] as postgraduate student of St John's College, Cambridge.[44][45]

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.[42][46] He has played a role in annotating the genome sequences of the human,[47] mouse,[48] chicken[49] and several other organisms. His research group currently focuses on genomic algorithms and inter-individual differences in human and other animal species.[50][32][34][40][51][52][53][54][55][56][57]

Birney is known for his role in the ENCODE consortium.[3][42][58][59][60][61][62][63] 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,[21] GeneWise,[22] GenomeWise,[23]), or in collaboration with students and postdocs, e.g. Exonerate[24] (with Guy Slater), Enredo (Javier Herrero[64]), Pecan (Benedict Paten[12]), the Velvet assembler (Daniel Zerbino[65]) and CRAM (Markus Hsi-Yang Fritz,[7] Rasko Leinonen[66] and Vadim Zalunin). Birney has also contributed to several other projects including the Pfam[67] database, InterPro,[68] BioPerl,[69][70] and HMMER[71] and Ensembl[72] 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.[5][7][8][10][12][13][16][73] This research has been funded by the Biotechnology and Biological Sciences Research Council (BBSRC), Medical Research Council (MRC)[74] the Wellcome Trust and the European Union.[75] Birney is also a consultant to Oxford Nanopore Technologies,[76] on the scientific advisory board of The Genome Analysis Centre (TGAC)[77] and Interim Head of the Centre for Therapeutic Target Validation (CTTV).[78][79]

Awards and honours

Birney has won several awards:

Francis Crick Lecture

In 2003, the Birney gave the inaugural Francis Crick Lecture:

“ 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.[29] ”

Overton Prize

In 2005, Birney was awarded the Overton Prize:

“ 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."[28] ”

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.[80] ”

Fellow of the Royal Society

In 2014, Birney was elected as a Fellow of the Royal Society (FRS). His nomination 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.[30] ”

Other awards

In 2014, Birney was awarded an Honorary Doctor of Science degree from Brunel University London in recognition of his service to science.[81] In 2002, Birney was named as one of the MIT Technology Review TR100 top 100 innovators in the world under the age of 35:[82]

Personal life

Birney is married to Barley Birney (née Laycock)[32] with two children.[1] He appeared on a special Christmas edition of University Challenge in 2014 representing Balliol College, Oxford with Charlotte Higgins and Alan Beith.[83]

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 BIRNEY, Dr Ewan. Who's Who 2015 (online Oxford University Press ed.). A & C Black, an imprint of Bloomsbury Publishing plc. (subscription required)
  2. ↑ 2.0 2.1 2.2 2.3 Hopkin, Karen (June 2005). "Bring Me Your Genomes: The Ewan Birney Story". The Scientist 19 (11): 60. Archived from the original on 10 June 2011. Retrieved 2011-06-10.
  3. ↑ 3.0 3.1 Ewan Birney's publications indexed by Google Scholar, a free service provided by Google
  4. ↑ 4.0 4.1 Birney, Ewan (2000). Sequence alignment in bioinformatics (PhD thesis). University of Cambridge.
  5. ↑ 5.0 5.1 Ettwiller, Laurence (2004). Computational Investigations into cis-Regulation in Eukaryotes (PhD thesis). University of Cambridge.
  6. ↑ 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.
  7. ↑ 7.0 7.1 7.2 Fritz, Markus (2011). Exploiting high throughput DNA sequencing data for genomic analysis (PDF) (PhD thesis). University of Cambridge.
  8. ↑ 8.0 8.1 Hoffman, Michael (2008). Quantifying evolution and natural selection in vertebrate noncoding sequence (PhD thesis). University of Cambridge.
  9. ↑ 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.
  10. ↑ 10.0 10.1 Meynert, Alison (2009). Function and evolution of regulatory elements in vertebrates (PhD thesis). University of Cambridge.
  11. ↑ 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.
  12. ↑ 12.0 12.1 12.2 Paten, Ben (2006). Large-scale multiple alignment and transcriptionally associated pattern discovery in vertebrate genomes (PhD thesis). University of Cambridge.
  13. ↑ 13.0 13.1 Ruklisa, Dace (2011). Large Scale Genomic Association Studies in Fruit Fly and Human (PhD thesis). University of Cambridge.
  14. ↑ "Sander Timmer – PhD candidate in Biological Sciences". Archived from the original on 2013-07-02.
  15. ↑ Ding, Z.; Ni, Y.; Timmer, S. W.; Lee, B. K.; Battenhouse, A.; Louzada, S.; Yang, F.; Dunham, I.; Crawford, G. E.; Lieb, J. D.; Durbin, R.; Iyer, V. R.; Birney, E. (2014). "Quantitative Genetics of CTCF Binding Reveal Local Sequence Effects and Different Modes of X-Chromosome Association". PLoS Genetics 10 (11): e1004798. doi:10.1371/journal.pgen.1004798.
  16. ↑ 16.0 16.1 Zerbino, Daniel (2009). Genome assembly and comparison (PhD thesis). University of Cambridge.
  17. ↑ 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.
  18. ↑ "Ewan's Blog; bioinformatician at large: ENCODE: My own thoughts". Archived from the original on 2013-02-12.
  19. ↑ 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.
  20. ↑ 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.
  21. ↑ 21.0 21.1 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.
  22. ↑ 22.0 22.1 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.
  23. ↑ 23.0 23.1 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.
  24. ↑ 24.0 24.1 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.
  25. ↑ 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.
  26. ↑ 26.0 26.1 Birney, Ewan (2014). "Ewan Birney's homepage". European Bioinformatics Institute. Archived from the original on 2014-12-27.
  27. ↑ 27.0 27.1 27.2 27.3 "The Life Scientific, Ewan Birney interviewed by Jim Al-Khalili". 2013-06-11., BBC Radio 4
  28. ↑ 28.0 28.1 "ISCB Newsletter 8-2 Dr. Ewan Birney Named as the 2005 Overton Prize Winner!". Archived from the original on 28 February 2012.
  29. ↑ 29.0 29.1 http://royalsociety.org/Content.aspx?id=3479 Royal Society article Recent Crick lectures
  30. ↑ 30.0 30.1 30.2 "Dr Ewan Birney FRS".
  31. ↑ https://www.ebi.ac.uk/about/news/press-releases/ewan-birney-FRS
  32. ↑ 32.0 32.1 32.2 Pennisi, Elizabeth (2012). "Profile of Ewan Birney: Genomics' Big Talker". Science 337 (6099): 1167–1169. doi:10.1126/science.337.6099.1167. PMID 22955814.
  33. ↑ Birney, Ewan. "Ewan Birney's Flickr Photostream". flickr.com. Archived from the original on 2014-05-29.[ Ewan Birney's Flickr Photostream], flickr.com
  34. ↑ 34.0 34.1 Ewan Birney publications from Europe PubMed Central
  35. ↑ Ewan Birney on Twitter
  36. ↑ 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.
  37. ↑ 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. doi:10.1073/pnas.1318948111. PMC 4035993. PMID 24753594.
  38. ↑ 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.
  39. ↑ "Ewan Birney: 'There is a mistaken view that scientists are unemotional people | Science | The Observer 10th February 2013". The Guardian (London). 2013-02-10.
  40. ↑ 40.0 40.1 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.
  41. ↑ 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.
  42. ↑ 42.0 42.1 42.2 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.
  43. ↑ "The age of the genome, Ewan Birney in Floreat Domus". Archived from the original on 28 February 2012.Balliol College newspaper
  44. ↑ "EBI's Ewan Birney: Quest for the Genomic Dragons". Science Watch Newsletter Interview
  45. ↑ Smaglik, Paul (2012). "Turning point: Ewan Birney". Nature 482 (7383): 123–728. doi:10.1038/nj7383-123a.
  46. ↑ "ENCODE: Encyclopedia of DNA Elements" on YouTube
  47. ↑ 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.
  48. ↑ 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.
  49. ↑ 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.
  50. ↑ "Churchill College: Biographies: Ewan Birney". Archived from the original on 28 February 2012.
  51. ↑ 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. PMC 3672958. PMID 23354052.
  52. ↑ An Interview with Ewan Birney: Keynote Speaker at O'Reilly's Bioinformatics Technology Conference, O'Reilly Media
  53. ↑ Ewan Birney research profile on BiomedExperts
  54. ↑ Ewan Birney's publications indexed by the Scopus bibliographic database, a service provided by Elsevier.
  55. ↑ 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.
  56. ↑ 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. doi:10.1073/pnas.1318948111. PMC 4035993. PMID 24753594.
  57. ↑ 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.
  58. ↑ 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 of the United States of America 111 (33): E3366. doi:10.1073/pnas.1410434111. PMC 4143047. PMID 25275169.
  59. ↑ Birney, E. (2012). "The making of ENCODE: Lessons for big-data projects". Nature 489 (7414): 49–51. doi:10.1038/489049a. PMID 22955613.
  60. ↑ 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.
  61. ↑ 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.
  62. ↑ List of publications from Microsoft Academic Search
  63. ↑ Ewan Birney's publications indexed by the DBLP Bibliography Server at the University of Trier
  64. ↑ 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.
  65. ↑ 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.
  66. ↑ 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.
  67. ↑ 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.
  68. ↑ 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.
  69. ↑ 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.
  70. ↑ "Ewan Birney - BioPerl". Archived from the original on 2013-02-12.
  71. ↑ 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.
  72. ↑ 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.
  73. ↑ "EMBL International PhD Programme - completed theses | EBI Training". Archived from the original on 2013-02-12.
  74. ↑ UK Government Research grants awarded to Ewan Birney, via Research Councils UK
  75. ↑ "Google Tech Talk 2012-07-12: Human Genetics and Genomics: The Science for the 21st Century by Ewan Birney" on YouTube
  76. ↑ Cookson, Clive (2012-02-17). "Oxford Nanopore unveils mini-DNA reader". Financial Times (London). Retrieved 2014-10-20.
  77. ↑ GAC new Scientific Advisory Board: a multidisciplinary set of key experts, TGAC Norwich UK
  78. ↑ Ewan Birney CTTV, targetvalidation.org
  79. ↑ Big Data of Pharma – Ewan Birney, Big Data in Biomedicine conference, Stanford University School of Medicine
  80. ↑ Bioinformatics Press release Ewan Birney wins the 2005 Benjamin Franklin Award in Bioinformatics
  81. ↑ In recognition of his outstanding service to science, Dr Ewan Birney is awarded the honorary degree of Doctor of Science , Brunel University London
  82. ↑ "2002 Young Innovators Under 35: Ewan Birney, 29". Technology Review. 2002. Archived from the original on 2012-02-28.
  83. ↑ anon (2014). "University Challenge, Christmas 2014 Episode 5 of 10". BBC.