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David Sankoff

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David Sankoff
David Sankoff at "Models and Algorithms for Genome Evolution" in 2013, Bromont, Quebec.
Born (1942-12-31) December 31, 1942 (age 81)
Montreal, Quebec, Canada
Nationality Canadian
Alma materMcGill University B.Sc. (1963), M.Sc. (1965), Ph.D. (1969)
Known forVariable rules analysis, Code switching, Sequence alignment, Nucleic acid secondary structure, Computational genomics
AwardsFellow, Royal Society of Canada, 1995; Canada Research Chair 2002-2016; Fellow, International Society for Computational Biology, ISCB Senior Scientist Accomplishment Award, 2003; Weldon Memorial Prize, 2004
Scientific career
InstitutionsUniversity of Ottawa, Université de Montréal; Centre de Recherches Mathématiques, Canadian Institute for Advanced Research, Bureau of Statistics of Papua and New Guinea [1]
Thesis Historical Linguistics as a Stochastic Process[2]  (1969)
Doctoral advisorDonald Andrew Dawson[2]
Websitealbuquerque.bioinformatics.uottawa.ca

David Sankoff (born December 31, 1942) is a Canadian mathematician, bioinformatician, computer scientist and linguist. He holds the Canada Research Chair in Mathematical Genomics in the Mathematics and Statistics Department at the University of Ottawa, and is cross-appointed to the Biology Department and the School of Information Technology and Engineering. He was founding editor of the journal Language Variation and Change (Cambridge) and serves on the editorial boards of a number of bioinformatics, computational biology and linguistics journals. Sankoff is best known for his pioneering contributions in computational linguistics and computational genomics. He is considered to be one of the founders of bioinformatics. In particular, he had a key role in introducing dynamic programming[3] for sequence alignment and other problems in computational biology. In Pavel Pevzner's words,[4] "[ Michael Waterman ] and David Sankoff are responsible for transforming bioinformatics from a ‘stamp collection' of ill-defined problems into a rigorous discipline with important biological applications."

Career

Sankoff published his first paper in 1963[5] while he was an undergraduate student in Mathematics at McGill University. Starting with his doctoral research, he developed mathematical formulations to a number of pivotal concepts in socio- and historical linguistics, including glottochronology,[6] variable rules analysis,[7] the linguistic marketplace[8] and code switching.[9]

After completing his Ph.D. in Mathematics, Sankoff began his academic career at the University of Montreal in 1969. In 1971, Sankoff became interested in molecular sequence comparison[3] and devised the first quadratic-time variant of the Needleman-Wunsch algorithm for pairwise sequence alignment.[10] In 1973, Sankoff and Robert Cedergren developed a joint estimation method for phylogeny and multiple sequence alignment of 5S ribosomal RNA,[11] laying the algorithmic foundations of comparative genomics. In 1975, Sankoff and Václav Chvátal studied the behavior of the longest common subsequence problem on random inputs;[12] the constants of proportionality arising in this study have come to be known as the Chvátal–Sankoff constants. In 1980, Robert Cedergen and David Sankoff created the first research group in bioinformatics at the University of Montreal.[13] Sankoff's work in bioinformatics addresses RNA secondary structure, genome rearrangements, sequence alignment, genome evolution and phylogenetics.[14]

Awards

References

  1. ^ :Sankoff, David (2008). "How to Predict the Evolution of a Bilingual Community". In Meyerhoff, Miriam and Naomi Nagy (eds.), Social Lives in Language – Sociolinguistics and multilingual speech communities: Celebrating the work of Gillian Sankoff (pp. 179–194). Amsterdam: John Benjamins. {{cite book}}: External link in |chapterurl= (help); Unknown parameter |chapterurl= ignored (|chapter-url= suggested) (help)
  2. ^ a b David Sankoff at the Mathematics Genealogy Project
  3. ^ a b Sankoff, D. (2000). "The early introduction of dynamic programming into computational biology". Bioinformatics. 16 (1): 41–47. doi:10.1093/bioinformatics/16.1.41. PMID 10812476.
  4. ^ Maisel, M. (2006). "ISCB Honors Michael S. Waterman and Mathieu Blanchette". PLoS Computational Biology. 2 (8): e105. Bibcode:2006PLSCB...2..105M. doi:10.1371/journal.pcbi.0020105. PMC 1526462.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  5. ^ Friesen, J. D.; Sankoff, D.; Siminovitch, L. (1963). "Radiobiological Studies of Vaccinia Virus". Virology. 21 (3): 411–424. doi:10.1016/0042-6822(63)90203-4. PMID 14081366.
  6. ^ Sankoff, David (1970). "On the rate of replacement of word-meaning relationships". Language. 46 (3): 564–569. doi:10.2307/412307. JSTOR 412307.
  7. ^ Cedergren, H. J.; D. Sankoff (1974). "Variable rules: performance as a statistical reflection of competence". Language. 50: 333–355. doi:10.2307/412441. JSTOR 412441.
  8. ^ :Sankoff, D.; S. Laberge (1978). "The linguistic market and the statistical explanation of variability". In D. Sankoff (ed.), Linguistic Variation: Models and Methods (pp. 239-250). New York: Academic Press.
  9. ^ Sankoff, David; Shana Poplack (1981). "A formal grammar for code switching". Papers in Linguistics. 14 (1): 3–46. doi:10.1080/08351818109370523.
  10. ^ Sankoff, D. (1972). "Matching sequences under deletion-insertion constraints". Proceedings of the National Academy of Sciences of the United States of America. 69 (1): 4–6. Bibcode:1972PNAS...69....4S. doi:10.1073/pnas.69.1.4. PMC 427531. PMID 4500555.
  11. ^ Sankoff, D; C. Morel; R. J. Cedergren (1973). "Evolution of 5S RNA and the non-randomness of base replacement". Nature New Biology. 245: 232–234. doi:10.1038/newbio245232a0. PMID 4201431.
  12. ^ Chvatal, Václáv; Sankoff, David (1975), "Longest common subsequences of two random sequences", Journal of Applied Probability, 12: 306–315, doi:10.2307/3212444, MR 0405531.
  13. ^ "History of the Robert Cedergren Centre". Retrieved 25 August 2013.
  14. ^ "ISCB Senior Scientist Award to Sankoff". Retrieved 24 August 2013.
  15. ^ "David Sankoff - Excellence in Research Award". Retrieved 25 August 2013.
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