Ewan Birney

Last updated

Ewan Birney
Dr Ewan Birney FRS.jpg
Ewan 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 www.ebi.ac.uk/people/person/ewan-birney OOjs UI icon edit-ltr-progressive.svg

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 privately 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] He has also served on the boards of the Biotechnology and Biological Sciences Research Council (BBSRC), German Cancer Research Center (DKFZ), The Institute of Cancer Research (ICR), Ontario Institute for Cancer Research (OICR), Institute Pasteur and Riken institute. [90]

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. [91] 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: [92]

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 [93] and in 2021 from University of Tartu, [94] 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. [95] [8]

Personal life

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

Related Research Articles

<span class="mw-page-title-main">Michael Ashburner</span> English biologist (1942–2023)

Michael Ashburner was an English biologist and Professor in the Department of Genetics at University of Cambridge. He was also the former joint-head and co-founder of the European Bioinformatics Institute (EBI) of the European Molecular Biology Laboratory (EMBL) and a Fellow of Churchill College, Cambridge.

The European Bioinformatics Institute (EMBL-EBI) is an intergovernmental organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Wellcome Genome Campus in Hinxton near Cambridge, and employs over 600 full-time equivalent (FTE) staff. Institute leaders such as Rolf Apweiler, Alex Bateman, Ewan Birney, and Guy Cochrane, an adviser on the National Genomics Data Center Scientific Advisory Board, serve as part of the international research network of the BIG Data Center at the Beijing Institute of Genomics.

<span class="mw-page-title-main">Robert Stevens (scientist)</span>

Robert David Stevens is a professor of bio-health informatics. and former Head of Department of Computer Science at The University of Manchester

<span class="mw-page-title-main">Janet Thornton</span> British bioinformatician and academic

Dame Janet Maureen Thornton, is a senior scientist and director emeritus at the European Bioinformatics Institute (EBI), part of the European Molecular Biology Laboratory (EMBL). She is one of the world's leading researchers in structural bioinformatics, using computational methods to understand protein structure and function. She served as director of the EBI from October 2001 to June 2015, and played a key role in ELIXIR.

Gerald Mayer Rubin is an American biologist, notable for pioneering the use of transposable P elements in genetics, and for leading the public project to sequence the Drosophila melanogaster genome. Related to his genomics work, Rubin's lab is notable for development of genetic and genomics tools and studies of signal transduction and gene regulation. Rubin also served as a vice president of the Howard Hughes Medical Institute (2003-2020) and founding executive director of its Janelia Research Campus.

<span class="mw-page-title-main">Richard M. Durbin</span> British computational biologist

Richard Michael Durbin is a British computational biologist and Al-Kindi Professor of Genetics at the University of Cambridge. He also serves as an associate faculty member at the Wellcome Sanger Institute where he was previously a senior group leader.

<span class="mw-page-title-main">Lincoln Stein</span> American scientist and academic

Lincoln David Stein is a scientist and Professor in bioinformatics and computational biology at the Ontario Institute for Cancer Research.

<span class="mw-page-title-main">Steven E. Brenner</span> American biologist and academic

Steven Elliot Brenner is a professor at the Department of Plant and Microbial Biology at the University of California Berkeley, adjunct professor at the Department of Bioengineering and Therapeutic Sciences at the University of California, and San Francisco Faculty scientist, Physical Biosciences at the Lawrence Berkeley National Laboratory.

<span class="mw-page-title-main">Cyrus Chothia</span> English biochemist (1942–2019)

Cyrus Homi Chothia was an English biochemist who was an emeritus scientist at the Medical Research Council (MRC) Laboratory of Molecular Biology (LMB) at the University of Cambridge and emeritus fellow of Wolfson College, Cambridge.

<span class="mw-page-title-main">Rolf Apweiler</span> German bioinformatician

Rolf Apweiler is a director of European Bioinformatics Institute (EBI) part of the European Molecular Biology Laboratory (EMBL) with Ewan Birney.

<span class="mw-page-title-main">European Nucleotide Archive</span> Online database from the EBI on Nucleotides

The European Nucleotide Archive (ENA) is a repository providing free and unrestricted access to annotated DNA and RNA sequences. It also stores complementary information such as experimental procedures, details of sequence assembly and other metadata related to sequencing projects. The archive is composed of three main databases: the Sequence Read Archive, the Trace Archive and the EMBL Nucleotide Sequence Database. The ENA is produced and maintained by the European Bioinformatics Institute and is a member of the International Nucleotide Sequence Database Collaboration (INSDC) along with the DNA Data Bank of Japan and GenBank.

<span class="mw-page-title-main">Terri Attwood</span> British bioinformatics researcher

Teresa K. Attwood is a professor of Bioinformatics in the Department of Computer Science and School of Biological Sciences at the University of Manchester and a visiting fellow at the European Bioinformatics Institute (EMBL-EBI). She held a Royal Society University Research Fellowship at University College London (UCL) from 1993 to 1999 and at the University of Manchester from 1999 to 2002.

<span class="mw-page-title-main">Tim Hubbard</span> Professor of Bioinformatics at Kings College London

Timothy John Phillip Hubbard is a Professor of Bioinformatics at King's College London, Head of Genome Analysis at Genomics England and Honorary Faculty at the Wellcome Trust Sanger Institute in Cambridge, UK. From 1 March 2024, Hubbard became the director of Europe's Life Science Data Infrastructure ELIXIR.

<span class="mw-page-title-main">Julian Parkhill</span> Geneticist, working with pathogens

Julian Parkhill is Professor of Bacterial Evolution in the Department of Veterinary Medicine at the University of Cambridge. He previously served as head of pathogen genomics at the Wellcome Sanger Institute.

<span class="mw-page-title-main">Alex Bateman</span> British bioinformatician

Alexander George Bateman is a computational biologist and Head of Protein Sequence Resources at the European Bioinformatics Institute (EBI), part of the European Molecular Biology Laboratory (EMBL) in Cambridge, UK. He has led the development of the Pfam biological database and introduced the Rfam database of RNA families. He has also been involved in the use of Wikipedia for community-based annotation of biological databases.

<span class="mw-page-title-main">Sarah Teichmann</span> German bioinformatician

Sarah Amalia Teichmann is a German scientist who is head of cellular genetics at the Wellcome Sanger Institute and a visiting research group leader at the European Bioinformatics Institute (EMBL-EBI). She serves as director of research in the Cavendish Laboratory, at the University of Cambridge and a senior research fellow at Churchill College, Cambridge.

<span class="mw-page-title-main">Stephen D. M. Brown</span>

Steve David Macleod Brown is director of the Medical Research Council (MRC) Mammalian Genetics Unit, MRC Harwell at Harwell Science and Innovation Campus, Oxfordshire, a research centre on mouse genetics. In addition, he leads the Genetics and Pathobiology of Deafness research group.

<span class="mw-page-title-main">Christine Orengo</span> Professor of Bioinformatics

Christine Anne Orengo is a Professor of Bioinformatics at University College London (UCL) known for her work on protein structure, particularly the CATH database. Orengo serves as president of the International Society for Computational Biology (ISCB), the first woman to do so in the history of the society.

Toby James Gibson is a group leader and biochemist at the European Molecular Biology Laboratory (EMBL) in Heidelberg known for his work on Clustal. According to Nature, Gibson's co-authored papers describing Clustal are among the top ten most highly cited scientific papers of all time.

Christos A. Ouzounis is a computational biologist, a director of research at the CERTH, and Professor of Bioinformatics at Aristotle University in Thessaloniki.

References

  1. Anon (4 November 1993). "John Frederick William Birney". Oxford University Gazette . 124 (4305). Oxford University Press. 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. cam.ac.uk (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 X 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 . CXLV (5). University of Cambridge. 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
  57. 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.
  58. 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.
  59. 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.
  60. 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.
  61. 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. Open Access logo PLoS transparent.svg
  62. 1 2 Paten, 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.
  63. 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. PMC   2336801 . PMID   18349386.
  64. 1 2 Fritz, 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.
  65. 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.
  66. 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.
  67. 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.
  68. 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.
  69. Anon (2013). "Ewan Birney - BioPerl". bioperl.org. Archived from the original on 12 December 2012.
  70. 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.
  71. 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.
  72. Birney, Ewan (10 April 2018). "Best present as a supervisor..." twitter.com. Archived from the original on 10 April 2018. Retrieved 30 August 2018.
  73. 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.
  74. 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. Lock-green.svg
  75. 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.
  76. Ettwiller, Laurence Michele (2004). Computational Investigations into cis-Regulation in Eukaryotes (PhD thesis). University of Cambridge. OCLC   890156758. EThOS   uk.bl.ethos.613876.
  77. 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. Open Access logo PLoS transparent.svg
  78. Meynert, Alison Maria (2009). Function and evolution of regulatory elements in vertebrates (PhD thesis). University of Cambridge. OCLC   890148982. EThOS   uk.bl.ethos.608495.
  79. 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.
  80. 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. Open Access logo PLoS transparent.svg
  81. 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.
  82. "EMBL International PhD Programme - completed theses | EBI Training". Archived from the original on 22 February 2013.
  83. "EMBL-EBI PhD Theses". ebi.ac.uk. European Bioinformatics Institute.
  84. "UK Government Research grants awarded to Ewan Birney". Swindon: Research Councils UK. Archived from the original on 4 June 2015.
  85. "Google Tech Talk 2012-07-12: Human Genetics and Genomics: The Science for the 21st Century by Ewan Birney" on YouTube
  86. 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.
  87. "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.
  88. "Ewan Birney European Molecular Biology Lab - Big Data 2014 - MediaSpace - Stanford Medicine". mediaspace.stanford.edu.
  89. Waldegrave, William (2022). "Eton's Governing Body". etoncollege.com. Archived from the original on 16 July 2023.
  90. Anon (2024). "Ewan Birney: Deputy Director General of EMBL & Joint Director of EMBL". ebi.ac.uk. Archived from the original on 12 February 2024.
  91. "2002 Young Innovators Under 35: Ewan Birney, 29". Technology Review. 2002. Archived from the original on 29 March 2011. Retrieved 22 June 2011.
  92. "Press release: Ewan Birney wins the 2005 Benjamin Franklin Award in Bioinformatics". bioinformatics.org.
  93. "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.
  94. "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.
  95. "Cambridge in the 2019 New Year honours list". cam.ac.uk. University of Cambridge. 28 December 2018.

Creative Commons by small.svg  This article incorporates text available under the CC BY 4.0 license.

Academic offices
Preceded by Director of the European Bioinformatics Institute
2015present
Incumbent