Ewan Birney

Ewan Birney
Born 1972 (age 39–40)[1]
Institutions European Bioinformatics Institute,
Wellcome Trust Sanger Institute,
Churchill College, Cambridge,
Cold Spring Harbor Laboratory
Alma mater Balliol College, Oxford,
St John's College, Cambridge
Doctoral advisor Richard M. Durbin
Doctoral students Alison Meynert (2009)[2][3]
Daniel Zerbino (2009)[4][5]
Michael M. Hoffman (2008)[6][7]
Ben Paten (2006)[8]
Laurence Ettwiller (2004)[9][10]
Known for Ensembl,[11] PairWise,[12] GeneWise,[13] GenomeWise[14] and the ENCODE consortium[15]
Notable awards Overton Prize 2005,[16]
Benjamin Franklin Award (Bioinformatics) 2005,
Royal Society Francis Crick Lecture 2003[17]
Technology Review TR100 Young Innovators 2002[18]

Ewan Birney is a senior scientist at the European Bioinformatics Institute (EBI) and joint head of the Protein And Nucleic Acids (PANDA) group[19] with Rolf Apweiler. The PANDA group is responsible for the widely used Ensembl genome browser, and highly-cited[20] research on, for example, sequence analysis tools.[21] Birney is also a Fellow of Churchill College, Cambridge.[22]

He was educated at Eton College, completed his undergraduate degree in biochemistry at Balliol College, Oxford[1][23] and did his PhD at the Wellcome Trust Sanger Institute, under the supervision of Richard M. Durbin while registered at St John's College, Cambridge.[24]

Before studying at university he completed an internship at Cold Spring Harbor Laboratory under the supervision of James D. Watson[1] and Adrian Krainer.[25] He has contributed to several bioinformatics and computational biology projects including the Pfam[26] database, InterPro,[27] BioPerl[28][29] and HMMER[30] toolkits. Most recently Birney is known for his role in the ENCODE consortium.

Contents

Awards

2005 Overton Prize

"Dr. Ewan Birney of the European Molecular Biology Laboratory (EMBL) European Bioinformatics Institute (EBI), was awarded the 2005 Overton Prize in honor 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."[16]

2005 Benjamin Franklin Award

The 2005 Benjamin Franklin Award in Bioinformatics was awarded to Ewan Birney of the European Bioinformatics Institute. "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 criticized 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 organization that support the development of several bioinformatics toolkits."[31]

2003 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 lecture, entitled 'Being human: what our genome tells us' took place at the Royal Society on 4 December 2003."[17]

Other

In 2002, he was named to the MIT Technology Review TR100 as one of the top 100 innovators in the world under the age of 35.[32]

References

  1. ^ a b c Hopkin, Karen (06 2005). "Bring Me Your Genomes: The Ewan Birney Story". The Scientist 19 (11): 60. Archived from the original on 2011-06-10. http://www.webcitation.org/5zKuWaA4I. Retrieved 2011-06-10. 
  2. ^ Meynert, Alison (2009). Function and evolution of regulatory elements in vertebrates (Ph.D. thesis). University of Cambridge. http://www.ebi.ac.uk/training/ftp/PhDtheses/AlisonMeynertThesis.pdf. 
  3. ^ 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.  edit
  4. ^ Zerbino, Daniel (2009). Genome assembly and comparison (Ph.D. thesis). University of Cambridge. http://www.ebi.ac.uk/training/ftp/PhDtheses/Daniel_Zerbino.pdf. 
  5. ^ 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. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2336801.  edit see Velvet assembler
  6. ^ Hoffman, Michael (2008). Quantifying evolution and natural selection in vertebrate noncoding sequence (Ph.D. thesis). University of Cambridge. http://www.ebi.ac.uk/training/ftp/PhDtheses/Hoffman_thesis.pdf. 
  7. ^ 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.  edit
  8. ^ Paten, Ben (2006). Large-scale multiple alignment and transcriptionally-associated pattern discovery in vertebrate genomes (Ph.D. thesis). University of Cambridge. 
  9. ^ Ettwiller, Laurence (2004). Computational Investigations into cis-Regulation in Eukaryotes (Ph.D. thesis). University of Cambridge. http://www.ebi.ac.uk/training/ftp/PhDtheses/LaurenceEttwillerThesis.pdf. 
  10. ^ 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. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=430934.  edit
  11. ^ Hubbard, T.; Barker, D.; Birney, E.; Cameron, G.; Chen, Y.; Clark, L.; Cox, T.; Cuff, J. et al. (2002). "The Ensembl genome database project". Nucleic Acids Research 30 (1): 38–41. doi:10.1093/nar/30.1.38. PMC 99161. PMID 11752248. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=99161.  edit
  12. ^ 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. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=145991.  edit
  13. ^ 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. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=310858.  edit
  14. ^ 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. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=479130.  edit
  15. ^ Birney, E.; Stamatoyannopoulos, J. A.; Dutta, A.; Guigó, R.; Gingeras, T. R.; Margulies, E. H.; Weng, Z.; Snyder, M. 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. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2212820.  edit
  16. ^ a b http://www.iscb.org/images/stories/newsletter/newsletter8-2/birney.html ISCB Newsletter 8-2 Dr. Ewan Birney Named as the 2005 Overton Prize Winner!
  17. ^ a b http://royalsociety.org/Content.aspx?id=3479 Royal Society article Recent Crick lectures
  18. ^ MIT (2002). 2002 Young Innovators under 35, Ewan Birney, 29, Technology Review.
  19. ^ "The Protein and Nucleotide Database Group (PANDA) Group Home Page at EBI". http://www.ebi.ac.uk/panda/. Retrieved 27 June 2011. 
  20. ^ http://scholar.google.com/scholar?q=ewan+birney Ewan Birney publications in Google Scholar
  21. ^ Ewan Birney's Homepage at the European Bioinformatics Institute
  22. ^ http://www.chu.cam.ac.uk/about/fellows/fellow_details.php?id=22 Churchill College Fellows, Ewan Birney
  23. ^ "The age of the genome, Ewan Birney in Floreat Domus". http://www.balliol.ox.ac.uk/alumni-and-friends/floreat-domus/2008/the-age-of-the-genome. Balliol College newspaper
  24. ^ "EBI's Ewan Birney: Quest for the Genomic Dragons". http://sciencewatch.com/inter/aut/2009/09-jan/09JanFebBirneySW/.  Science Watch Newsletter Interview
  25. ^ 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. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=334203.  edit
  26. ^ Bateman, A.; Birney, E.; Cerruti, L.; Durbin, R.; Etwiller, L.; Eddy, S.; Griffiths-Jones, S.; Howe, K. et al. (2002). "The Pfam protein families database". Nucleic Acids Research 30 (1): 276–280. doi:10.1093/nar/30.1.276. PMC 99071. PMID 11752314. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=99071.  edit
  27. ^ Apweiler, R.; Attwood, T. K.; Bairoch, A.; Bateman, A.; Birney, E.; Biswas, M.; Bucher, P.; Cerutti, L. et al. (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. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=29841.  edit
  28. ^ Stajich, J. E.; Block, D.; Boulez, K.; Brenner, S.; Chervitz, S.; Dagdigian, C.; Fuellen, G.; Gilbert, J. et al. (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. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=187536.  edit
  29. ^ http://bioperl.org/wiki/Ewan_Birney Ewan Birney's BioPERL page
  30. ^ 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. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=148151.  edit
  31. ^ Bioinformatics Press release Ewan Birney wins the 2005 Benjamin Franklin Award in Bioinformatics
  32. ^ "2002 Young Innovators Under 35: Ewan Birney, 29". Technology Review. 2002. http://www.technologyreview.com/TR35/Profile.aspx?TRID=233. Retrieved August 14, 2011. 

External links