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Richard M. Durbin

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For other people with the same name, see Richard Durbin.
Richard Durbin
Richard Durbin in his office at WTSI
Born
Richard Michael Durbin

(1960-12-30) 30 December 1960 (age 63)[18]
NationalityBritish
Alma materUniversity Cambridge (BA, PhD)
Known for
  • Biological Sequence Analysis[19]
Spouse
​
(m. 1996)​
[18]
ParentJames Durbin
Awards
Scientific career
Fields
Institutions
ThesisStudies on the development and organisation of the nervous system of Caenorhabditis elegans (1987)
Doctoral advisorJohn G. White[4]
Doctoral students
Other notable students
Websitesanger.ac.uk/people/directory/durbin-richard

Richard Michael Durbin, FRS,[2] born (1960-12-30) 30 December 1960 (age 63),[18] is a British computational biologist, Senior Group Leader at the Wellcome Trust Sanger Institute[20][21][22][23][3][24] and an Honorary Professor of Computational Genomics at the University of Cambridge.[25]

Education

Durbin was educated at The Hall School Hampstead[citation needed] and Highgate School in London.[18] After competing in the 1978/9 International Mathematical Olympiad,[26] he went on to study at the University of Cambridge graduating in 1982[27] with a first class honours degree on the Cambridge Mathematical Tripos. After graduating, he continued to study for a PhD[4] at St John's College, Cambridge[18] studying the development and organisation of the nervous system of Caenorhabditis elegans[28] whilst working at the Laboratory of Molecular Biology (LMB) in Cambridge, supervised by John Graham White.

Research

Durbin's early work included developing the primary instrument software for one of the first X-ray crystallography area detectors [29] and the MRC Biorad confocal microscope, alongside contributions to neural modelling.[30][31]

He then led the informatics for the Caenorhabditis elegans genome project,[32] and alongside Jean Thierry-Mieg developed the genome database AceDB, which evolved into the WormBase web resource. Following this he played an important role in data collection for and interpretation of the human genome sequence.[33]

He has developed numerous methods for computational sequence analysis.[34][35] These include gene finding (e.g. GeneWise) with Ewan Birney[36] and Hidden Markov models for protein and nucleic acid alignment and matching (e.g. HMMER) with Sean Eddy and Graeme Mitchison. A standard textbook Biological Sequence analysis coauthored with Sean Eddy, Anders Krogh and Graeme Mitchison[19] describes some of this work. Using these methods Durbin worked with colleagues to build a series of important genomic data resources, including the protein family database Pfam,[37] the genome database Ensembl,[38] and the gene family database TreeFam.[12]

More recently Durbin has returned to sequencing and has developed low coverage approaches to population genome sequencing, applied first to yeast,[39][40] and has been one of the leaders in the application of new sequencing technology to study human genome variation.[41][42] Durbin currently co-leads the international 1000 Genomes Project to characterise variation down to 1% allele frequency as a foundation for human genetics.

Awards and honours

Durbin was a joint winner of the Mullard Award of the Royal Society in 1994 (for work on the confocal microscope), won the Lord Lloyd of Kilgerran Award of the Foundation for Science and Technology in 2004, and was elected a Fellow of the Royal Society (FRS) in 2004[2] and a member of the European Molecular Biology Organization (EMBO) in 2009. Durbin's certificate of election for the Royal Society reads:

Durbin is distinguished for his powerful contribution to computational biology. In particular, he played a leading role in establishing the new field of bioinformatics. This allows the handling of biological data on an unprecedented scale, enabling genomics to prosper. He led the analysis of the C. elegans genome, and with Thierry-Mieg developed the database software AceDB. In the international genome project he led the analysis of protein coding genes. He introduced key computational tools in software and data handling. His Pfam database allowed the identification of domains in new protein sequences; it used hidden Markov models to which approach generally he brought rigour and which led to covariance models for RNA sequence.[43]

Personal life

Durbin is the son of James Durbin and is married to Julie Ahringer, a scientist at the Gurdon Institute. They have two children.[18]

References

  1. ^ http://www.biochemist.org/society/page.htm?item=37150 EMBO welcomes 66 leading life scientists as members
  2. ^ a b c "Professor Richard Durbin FRS Fellow". London: Royal Society. Archived from the original on 2015-11-19.
  3. ^ a b Richard Durbin publications indexed by Google Scholar Edit this at Wikidata
  4. ^ a b Durbin, Richard (1987). Studies on the development and organisation of the nervous system of Caenorhabditis elegans (PhD thesis). University of Cambridge. OCLC 499178924.
  5. ^ Birney, Ewan (2000). Sequence alignment in bioinformatics (PhD thesis). University of Cambridge.
  6. ^ Holmes, Ian (1999). Studies in probabilistic sequence alignment and evolution (PhD thesis). University of Cambridge. OCLC 885435671.
  7. ^ Holmes, Ian; Durbin, Richard (1998). "Dynamic Programming Alignment Accuracy". Journal of Computational Biology. 5 (3): 493–504. doi:10.1089/cmb.1998.5.493. PMID 9773345.
  8. ^ Eddy, S. R.; Mitchison, G; Durbin, R (1995). "Maximum discrimination hidden Markov models of sequence consensus". Journal of computational biology : a journal of computational molecular cell biology. 2 (1): 9–23. doi:10.1089/cmb.1995.2.9. PMID 7497123.
  9. ^ Eddy, S. R.; Durbin, R (1994). "RNA sequence analysis using covariance models". Nucleic Acids Research. 22 (11): 2079–88. doi:10.1093/nar/22.11.2079. PMC 308124. PMID 8029015.
  10. ^ Li, H.; Durbin, R. (2009). "Fast and accurate short read alignment with Burrows-Wheeler transform". Bioinformatics. 25 (14): 1754–1760. doi:10.1093/bioinformatics/btp324. PMC 2705234. PMID 19451168.
  11. ^ Li, H.; Ruan, J.; Durbin, R. (2008). "Mapping short DNA sequencing reads and calling variants using mapping quality scores". Genome Research. 18 (11): 1851–1858. doi:10.1101/gr.078212.108. PMC 2577856. PMID 18714091.
  12. ^ a b Li, H.; Coghlan, A.; Ruan, J.; Coin, L. J.; Hériché, J. K.; Osmotherly, L.; Li, R.; Liu, T.; Zhang, Z.; Bolund, L.; Wong, G. K.; Zheng, W.; Dehal, P.; Wang, J.; Durbin, R. (2006). "TreeFam: A curated database of phylogenetic trees of animal gene families". Nucleic Acids Research. 34 (90001): D572–D580. doi:10.1093/nar/gkj118. PMC 1347480. PMID 16381935.
  13. ^ "Heng Li Credits Durbin Pedigree in Accepting Franklin Award". bio-itworld.com. Archived from the original on 2013-02-27.
  14. ^ Bateman, A.; Coin, L.; Durbin, R.; Finn, R. D.; Hollich, V.; Griffiths-Jones, S.; Khanna, A.; Marshall, M.; Moxon, S.; Sonnhammer, E. L.; Studholme, D. J.; Yeats, C.; Eddy, S. R. (2004). "The Pfam protein families database". Nucleic Acids Research. 32 (Database issue): 138D–1141. doi:10.1093/nar/gkh121. ISSN 0305-1048. PMC 308855. PMID 14681378. Open access icon
  15. ^ 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.
  16. ^ Bateman, A; Birney, E; Durbin, R; Eddy, S. R.; Howe, K. L.; Sonnhammer, E. L. (2000). "The Pfam protein families database". Nucleic Acids Research. 28 (1): 263–6. doi:10.1093/nar/28.1.263. PMC 102420. PMID 10592242.
  17. ^ 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.
  18. ^ a b c d e f DURBIN. "DURBIN, Richard Michael". Who's Who. Vol. 2016 (online edition via Oxford University Press ed.). A & C Black. {{cite encyclopedia}}: Unknown parameter |othernames= ignored (help) (Subscription or UK public library membership required.) (subscription required)
  19. ^ a b Durbin, Richard M.; Eddy, Sean R.; Krogh, Anders; Mitchison, Graeme (1998), Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids (1st ed.), Cambridge, New York: Cambridge University Press, ISBN 0-521-62971-3, OCLC 593254083
  20. ^ "Dr Richard Durbin - Wellcome Trust Sanger Institute". Archived from the original on 2012-03-05.
  21. ^ Durbin, Richard M.'s publications indexed by the Scopus bibliographic database. (subscription required)
  22. ^ Richard Durbin archive collection Richard Durbin entry in the Wellcome Library archive.
  23. ^ Richard Durbin on Twitter Edit this at Wikidata
  24. ^ Richard Durbin at DBLP Bibliography Server Edit this at Wikidata
  25. ^ "Honorary Professors". Cambridge University Reporter. CXLV (5). University of Cambridge. 2014-12-12. Archived from the original on 2015-03-15.
  26. ^ Richard M. Durbin's results at International Mathematical Olympiad
  27. ^ "The BioInformer nr. 1, 1997 -- Interview with Dr. Richard Durbin". Archived from the original on 2011-07-30. Retrieved 2011-07-30.
  28. ^ Durbin, Richard (1987). Studies on the development and organisation of the nervous system of Caenorhabditis elegans (Ph.D. thesis). University of Cambridge.
  29. ^ Durbin, R. M.; Burns, R.; Moulai, J.; Metcalf, P.; Freymann, D.; Blum, M.; Anderson, J. E.; Harrison, S. C.; Wiley, D. C. (1986). "Protein, DNA, and virus crystallography with a focused imaging proportional counter". Science. 232 (4754): 1127–1132. doi:10.1126/science.3704639. PMID 3704639.
  30. ^ Durbin, R.; Willshaw, D. (1987). "An analogue approach to the travelling salesman problem using an elastic net method". Nature. 326 (6114): 689–691. doi:10.1038/326689a0. PMID 3561510.
  31. ^ Durbin, R.; Mitchison, G. (1990). "A dimension reduction framework for understanding cortical maps". Nature. 343 (6259): 644–647. doi:10.1038/343644a0. PMID 2304536.
  32. ^ c. Elegans Sequencing, C. (1998). "Genome sequence of the nematode C. Elegans: A platform for investigating biology". Science. 282 (5396): 2012–2018. doi:10.1126/science.282.5396.2012. PMID 9851916.
  33. ^ 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.; Sougnez, C. (Feb 2001). "Initial sequencing and analysis of the human genome". Nature. 409 (6822): 860–921. doi:10.1038/35057062. ISSN 0028-0836. PMID 11237011. {{cite journal}}: Unknown parameter |displayauthors= ignored (|display-authors= suggested) (help)
  34. ^ Simpson, J. T.; Durbin, R. (2011). "Efficient de novo assembly of large genomes using compressed data structures". Genome Research. 22 (3): 549–556. doi:10.1101/gr.126953.111. PMC 3290790. PMID 22156294.
  35. ^ Eilbeck, K.; Lewis, S. E.; Mungall, C. J.; Yandell, M.; Stein, L.; Durbin, R.; Ashburner, M. (2005). "The Sequence Ontology: A tool for the unification of genome annotations". Genome Biology. 6 (5): R44. doi:10.1186/gb-2005-6-5-r44. PMC 1175956. PMID 15892872.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  36. ^ 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.
  37. ^ Sonnhammer, E. L. L.; Eddy, S. R.; Durbin, R. (1997). "Pfam: A comprehensive database of protein domain families based on seed alignments". Proteins: Structure, Function, and Genetics. 28 (3): 405–420. doi:10.1002/(SICI)1097-0134(199707)28:3<405::AID-PROT10>3.0.CO;2-L. PMID 9223186.
  38. ^ 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.
  39. ^ Liti, G.; Carter, D. M.; Moses, A. M.; Warringer, J.; Parts, L.; James, S. A.; Davey, R. P.; Roberts, I. N.; Burt, A.; Koufopanou, V.; Tsai, I. J.; Bergman, C. M.; Bensasson, D.; O'Kelly, M. J. T.; Van Oudenaarden, A.; Barton, D. B. H.; Bailes, E.; Nguyen, A. N.; Jones, M.; Quail, M. A.; Goodhead, I.; Sims, S.; Smith, F.; Blomberg, A.; Durbin, R.; Louis, E. J. (2009). "Population genomics of domestic and wild yeasts". Nature. 458 (7236): 337–341. doi:10.1038/nature07743. PMC 2659681. PMID 19212322.
  40. ^ Warringer, J.; Zörgö, E.; Cubillos, F. A.; Zia, A.; Gjuvsland, A.; Simpson, J. T.; Forsmark, A.; Durbin, R.; Omholt, S. W.; Louis, E. J.; Liti, G.; Moses, A.; Blomberg, A. (2011). Kruglyak, Leonid (ed.). "Trait variation in yeast is defined by population history". PLOS Genetics. 7 (6): e1002111. doi:10.1371/journal.pgen.1002111. PMC 3116910. PMID 21698134.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  41. ^ Bentley, D. R.; Balasubramanian, S.; Swerdlow, H. P.; Smith, G. P.; Milton, J.; Brown, C. G.; Hall, K. P.; Evers, D. J.; Barnes, C. L.; Bignell, H. R.; Boutell, J. M.; Bryant, J.; Carter, R. J.; Keira Cheetham, R.; Cox, A. J.; Ellis, D. J.; Flatbush, M. R.; Gormley, N. A.; Humphray, S. J.; Irving, L. J.; Karbelashvili, M. S.; Kirk, S. M.; Li, H.; Liu, X.; Maisinger, K. S.; Murray, L. J.; Obradovic, B.; Ost, T.; Parkinson, M. L.; Pratt, M. R. (2008). "Accurate whole human genome sequencing using reversible terminator chemistry". Nature. 456 (7218): 53–59. doi:10.1038/nature07517. PMC 2581791. PMID 18987734.
  42. ^ Li, H.; Durbin, R. (2011). "Inference of human population history from individual whole-genome sequences". Nature. 475 (7357): 493–496. doi:10.1038/nature10231. PMC 3154645. PMID 21753753.
  43. ^ "Library and Archive Catalogue". London: The Royal Society. Retrieved 2013-11-14.
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