Richard M. Durbin

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Richard Durbin
Richard Durbin, Wellcome-Sanger, Cambridge, UK (2698443141).jpg
Richard Durbin in his office at WTSI
Born Richard Michael Durbin
(1960-12-30) 30 December 1960 (age 55)[1]
Nationality British
Fields
Institutions
Alma mater University Cambridge (BA, PhD)
Thesis Studies on the development and organisation of the nervous system of Caenorhabditis elegans (1987)
Doctoral advisor John G. White[3]
Doctoral students
Other notable students
Known for
  • Biological Sequence Analysis[17]
Notable awards
Spouse Julie Ahringer (m. 1996)[1]
Website
sanger.ac.uk/people/directory/durbin-richard

Richard Michael Durbin, FRS,[19] born (1960-12-30) 30 December 1960 (age 55),[1] is a British computational biologist, Senior Group Leader at the Wellcome Trust Sanger Institute[20][21][22][23][2][24] and an Honorary Professor of Computational Genomics at the University of Cambridge.[25]

Education[edit]

Durbin was educated at The Hall School Hampstead[citation needed] and Highgate School in London.[1] 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[3] at St John's College, Cambridge[1] 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[edit]

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[17] 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.[11]

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[edit]

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[19] and a member of the European Molecular Biology Organization (EMBO) in 2009. Durbin's certificate of election for the Royal Society reads:

Personal life[edit]

Durbin is the son of James Durbin and is married to Julie Ahringer, a scientist at the Gurdon Institute. They have two children.[1]

References[edit]

  1. ^ a b c d e f DURBIN, Richard Michael. Who's Who. 2016 (online edition via Oxford University Press ed.). A & C Black, an imprint of Bloomsbury Publishing plc.  (subscription required)
  2. ^ a b Richard M. Durbin's publications indexed by Google Scholar, a service provided by Google
  3. ^ 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. 
  4. ^ Birney, Ewan (2000). Sequence alignment in bioinformatics (PhD thesis). University of Cambridge. 
  5. ^ Holmes, Ian (1999). Studies in probabilistic sequence alignment and evolution (PhD thesis). University of Cambridge. OCLC 885435671. 
  6. ^ 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. 
  7. ^ 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. 
  8. ^ 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 308124free to read. PMID 8029015. 
  9. ^ 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 2705234free to read. PMID 19451168. 
  10. ^ 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 2577856free to read. PMID 18714091. 
  11. ^ 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 1347480free to read. PMID 16381935. 
  12. ^ "Heng Li Credits Durbin Pedigree in Accepting Franklin Award". bio-itworld.com. Archived from the original on 2013-02-27. 
  13. ^ 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 308855free to read. PMID 14681378.  open access publication - free to read
  14. ^ 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 99071free to read. PMID 11752314. 
  15. ^ 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 102420free to read. PMID 10592242. 
  16. ^ 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 148151free to read. PMID 9847196. 
  17. ^ 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: Cambridge University Press, doi:10.2277/0521629713, ISBN 0-521-62971-3 
  18. ^ http://www.biochemist.org/society/page.htm?item=37150 EMBO welcomes 66 leading life scientists as members
  19. ^ a b c "Professor Richard Durbin FRS Fellow". London: Royal Society. Archived from the original on 2015-11-19. 
  20. ^ "Dr Richard Durbin - Wellcome Trust Sanger Institute". Archived from the original on 2012-03-05. 
  21. ^ Richard M. Durbin's publications indexed by the Scopus bibliographic database, a service provided by Elsevier. (subscription required)
  22. ^ Richard Durbin archive collection Richard Durbin entry in the Wellcome Library archive.
  23. ^ Richard M. Durbin on Twitter
  24. ^ Richard M. Durbin at DBLP Bibliography Server
  25. ^ "Honorary Professors". Cambridge University Reporter. University of Cambridge. CXLV (5). 2014-12-12. Archived from the original on 2015-03-15. 
  26. ^ Richard M. Durbin's results at the 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.; 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. 
  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 3290790free to read. 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 1175956free to read. PMID 15892872. 
  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 310858free to read. 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 99161free to read. 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 2659681free to read. 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 3116910free to read. PMID 21698134. 
  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 2581791free to read. 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 3154645free to read. PMID 21753753. 
  43. ^ "Library and Archive Catalogue". London: The Royal Society. Retrieved 2013-11-14.