Richard M. Durbin

Richard Durbin

Richard Durbin in his office at WTSI
Born Richard Michael Durbin
30 December 1960[1]
Nationality British
Fields
Institutions
Alma mater St John's College, Cambridge
Thesis Studies on the development and organisation of the nervous system of Caenorhabditis elegans (1987)
Doctoral advisor John G. White[3]
Doctoral students Ewan Birney[4]
Other notable students
Known for
  • Biological Sequence Analysis[15]
Notable awards
Spouse Julie Ahringer (m. 1996)[1]
Website
sanger.ac.uk/research/faculty/rdurbin

Richard Michael Durbin, FRS, born 30 December 1960,[1] is a British computational biologist. He is head of Computational Genomics at the Wellcome Trust Sanger Institute and leader of the Genome Informatics group.[17][18][19][20]

Education

Durbin was educated at The Hall School Hampstead and Highgate School in London.[1] After competing in the 1978/9 International Mathematical Olympiad,[21] he went on to study at the University of Cambridge graduating in 1982[22] 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[23] whilst working at the Laboratory of Molecular Biology (LMB) in Cambridge.

Research

Durbin's early work included developing the primary instrument software for one of the first X-ray crystallography area detectors [24] and the MRC Biorad confocal microscope, alongside contributions to neural modelling.[25][26]

He then led the informatics for the C. elegans genome project,[27] 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.[28]

He has developed numerous methods for computational sequence analysis.[29][30] These include gene finding (e.g. GeneWise) with Ewan Birney[31] 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[15] 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,[32] the genome database Ensembl,[33] and the gene family database TreeFam.[34]

More recently Durbin has returned to sequencing and has developed low coverage approaches to population genome sequencing, applied first to yeast,[35][36] and has been one of the leaders in the application of new sequencing technology to study human genome variation.[37][38] 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 in 2004[2][39][40] and a member of the European Molecular Biology Organization (EMBO) in 2009.

Durbin's candidacy 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."[41]

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.[1]

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 DURBIN, Richard Michael. Who's Who 2014 (online edition via Oxford University Press ed.). A & C Black, an imprint of Bloomsbury Publishing plc. (subscription required)
  2. ↑ 2.0 2.1 Richard M. Durbin's publications indexed by Google Scholar, a free service provided by Google
  3. ↑ 3.0 3.1 Durbin, Richard (1987). Studies on the development and organisation of the nervous system of Caenorhabditis elegans (PhD thesis). University of Cambridge.
  4. ↑ Birney, Ewan (2000). Sequence alignment in bioinformatics (PhD thesis). University of Cambridge.
  5. ↑ 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. PMID 7497123.
  6. ↑ Eddy, S. R.; Durbin, R (1994). "RNA sequence analysis using covariance models". Nucleic acids research 22 (11): 2079–88. PMC 308124. PMID 8029015.
  7. ↑ 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.
  8. ↑ 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.
  9. ↑ 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.
  10. ↑ "Heng Li Credits Durbin Pedigree in Accepting Franklin Award". http://www.bio-itworld.com''. Archived from the original on 2013-02-27.
  11. ↑ 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.
  12. ↑ 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.
  13. ↑ 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. PMC 102420. PMID 10592242.
  14. ↑ 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.
  15. ↑ 15.0 15.1 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
  16. ↑ http://www.biochemist.org/society/page.htm?item=37150 EMBO welcomes 66 leading life scientists as members
  17. ↑ "Dr Richard Durbin - Wellcome Trust Sanger Institute". Archived from the original on 2012-03-05.
  18. ↑ Richard M. Durbin's publications indexed by the Scopus bibliographic database, a service provided by Elsevier.
  19. ↑ Dr Richard Durbin at Debrett's People of Today
  20. ↑ Richard Durbin archive collection Richard Durbin entry in the Wellcome Library archive.
  21. ↑ Richard M. Durbin's results at the International Mathematical Olympiad
  22. ↑ "The BioInformer nr. 1, 1997 -- Interview with Dr. Richard Durbin". Archived from the original on 2011-07-30. Retrieved 2011-07-30.
  23. ↑ Durbin, Richard (1987). Studies on the development and organisation of the nervous system of Caenorhabditis elegans (Ph.D. thesis). University of Cambridge.
  24. ↑ 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.
  25. ↑ 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.
  26. ↑ Durbin, R.; Mitchison, G. (1990). "A dimension reduction framework for understanding cortical maps". Nature 343 (6259): 644–647. doi:10.1038/343644a0. PMID 2304536.
  27. ↑ 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.
  28. ↑ 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.
  29. ↑ 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.
  30. ↑ 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.
  31. ↑ 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.
  32. ↑ 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.
  33. ↑ 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.
  34. ↑ 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.
  35. ↑ 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.
  36. ↑ 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.
  37. ↑ 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.
  38. ↑ 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.
  39. ↑ List of publications from Microsoft Academic Search
  40. ↑ Richard M. Durbin's publications indexed by the DBLP Bibliography Server at the University of Trier
  41. ↑ "Library and Archive Catalogue". London: The Royal Society. Retrieved 2013-11-14.