Richard M. Durbin

Richard Michael Durbin, FRS,[3] born (1960-12-30) 30 December 1960,[1] is a British computational biologist. He is currently an Associate Faculty member at the Wellcome Trust Sanger Institute [18] and Professor of Genetics at the University of Cambridge.[19][20] Previously, he was Senior Group Leader at the Wellcome Trust Sanger Institute for over 20 years [21][22][23][24][5][25] and an Honorary Professor of Computational genomics at the University of Cambridge.[26]

For the politician, see Dick Durbin.

Richard Durbin
Richard Durbin in his office at WTSI
Born
Richard Michael Durbin

(1960-12-30) 30 December 1960[1]
NationalityBritish
Alma materUniversity Cambridge (BA, PhD)
Known for
  • Biological Sequence Analysis[2]
Spouse(s)
​
(m. 1996)​
[1]
Awards
Scientific career
Fields
Institutions
ThesisStudies on the development and organisation of the nervous system of Caenorhabditis elegans (1987)
Doctoral advisorJohn G. White[6]
Doctoral studentsEwan Birney[7]
Other notable students
Websitesanger.ac.uk/people/directory/durbin-richard

Education

Durbin was educated at The Hall School Hampstead and Highgate School in London.[1] After competing in the 1978/9 International Mathematical Olympiad,[27] he went on to study at the University of Cambridge graduating in 1982[28] with a second class honours degree in the Cambridge Mathematical Tripos. After graduating, he continued to study for a PhD[6] at St John's College, Cambridge[1] studying the development and organisation of the nervous system of Caenorhabditis elegans[29] 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[30] and the MRC Biorad confocal microscope, alongside contributions to neural modelling.[31][32]

He then led the informatics for the Caenorhabditis elegans genome project,[33] 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.[34]

He has developed numerous methods for computational sequence analysis.[35][36] These include gene finding (e.g. GeneWise) with Ewan Birney[37] 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[2] 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,[38] the genome database Ensembl,[39] 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,[40][41] and has been one of the leaders in the application of new sequencing technology to study human genome variation.[42][43] 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[3] and a member of the European Molecular Biology Organization (EMBO) in 2009. The Royal Society awarded its Gabor Medal to Durbin in 2017 for his contributions to computational biology.[44]

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.[45]

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, Benjamin and Zoe.[1]

References
  1. "DURBIN, Richard Michael". Who's Who. ukwhoswho.com. 2016 (online edition via Oxford University Press ed.). A & C Black, an imprint of Bloomsbury Publishing plc. (subscription or UK public library membership required) (subscription required)
  2. 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, doi:10.2277/0521629713, ISBN 0-521-62971-3, OCLC 593254083
  3. "Professor Richard Durbin FRS Fellow". London: Royal Society. Archived from the original on 19 November 2015.
  4. http://www.biochemist.org/society/page.htm?item=37150 EMBO welcomes 66 leading life scientists as members
  5. Richard Durbin publications indexed by Google Scholar
  6. Durbin, Richard (1987). Studies on the development and organisation of the nervous system of Caenorhabditis elegans (PhD thesis). University of Cambridge. OCLC 499178924.
  7. Birney, Ewan (2000). Sequence alignment in bioinformatics (PhD thesis). University of Cambridge.
  8. Eddy, S. R.; Mitchison, G; Durbin, R (1995). "Maximum discrimination hidden Markov models of sequence consensus". Journal of Computational 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. 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 27 February 2013.
  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.
  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. www-core (webteam). "Durbin, Richard". www.sanger.ac.uk. Retrieved 2 January 2019.
  19. caa30@cam.ac.uk. "Durbin Group — Department of Genetics". www.gen.cam.ac.uk. Retrieved 2 January 2019.
  20. caa30@cam.ac.uk. "Professor Richard Durbin — Department of Genetics". www.gen.cam.ac.uk. Retrieved 2 January 2019.
  21. "Dr Richard Durbin – Wellcome Trust Sanger Institute". Archived from the original on 5 March 2012.
  22. Durbin, Richard M.'s publications indexed by the Scopus bibliographic database. (subscription required)
  23. Richard Durbin archive collection Richard Durbin entry in the Wellcome Library archive.
  24. Richard Durbin on Twitter
  25. Richard Durbin at DBLP Bibliography Server
  26. "Honorary Professors". Cambridge University Reporter. University of Cambridge. CXLV (5). 12 December 2014. Archived from the original on 15 March 2015.
  27. Richard M. Durbin's results at International Mathematical Olympiad
  28. "The BioInformer nr. 1, 1997 – Interview with Dr. Richard Durbin". Archived from the original on 29 July 2011. Retrieved 30 July 2011.
  29. Durbin, Richard (1987). Studies on the development and organisation of the nervous system of Caenorhabditis elegans (PhD thesis). University of Cambridge.
  30. 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. Bibcode:1986Sci...232.1127D. doi:10.1126/science.3704639. PMID 3704639.
  31. Durbin, R.; Willshaw, D. (1987). "An analogue approach to the travelling salesman problem using an elastic net method". Nature. 326 (6114): 689–691. Bibcode:1987Natur.326..689D. doi:10.1038/326689a0. PMID 3561510. S2CID 4321691.
  32. Durbin, R.; Mitchison, G. (1990). "A dimension reduction framework for understanding cortical maps". Nature. 343 (6259): 644–647. Bibcode:1990Natur.343..644D. doi:10.1038/343644a0. PMID 2304536. S2CID 4352870.
  33. c. Elegans Sequencing, C. (1998). "Genome sequence of the nematode C. Elegans: A platform for investigating biology". Science. 282 (5396): 2012–2018. Bibcode:1998Sci...282.2012.. doi:10.1126/science.282.5396.2012. PMID 9851916.
  34. 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. doi:10.1038/35057062. ISSN 0028-0836. PMID 11237011.
  35. 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.
  36. 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.
  37. 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.
  38. 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.
  39. 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.
  40. 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. Bibcode:2009Natur.458..337L. doi:10.1038/nature07743. PMC 2659681. PMID 19212322.
  41. 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.
  42. 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.; et al. (2008). "Accurate whole human genome sequencing using reversible terminator chemistry". Nature. 456 (7218): 53–59. Bibcode:2008Natur.456...53B. doi:10.1038/nature07517. PMC 2581791. PMID 18987734.
  43. 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.
  44. "Gabor Medal - Gabor Medallist 2017". The Royal Society. 2017. Retrieved 10 October 2017.
  45. "Library and Archive Catalogue". London: The Royal Society. Retrieved 14 November 2013.
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