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David Sankoff

{{Short description|Canadian scientist}}

{{Infobox scientist

| name = David Sankoff

| image = David Sankoff.JPG

| alt =

| caption = David Sankoff at "Models and Algorithms for Genome Evolution" in 2013, Bromont, Quebec.

| birth_date = {{Birth date and age|1942|12|31}}

| birth_place = Montreal, Quebec, Canada

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| nationality = {{flag|CAN|name=Canadian}}

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| alma_mater = McGill University (BSc, MSc, PhD)

| thesis_title = Historical Linguistics as a Stochastic Process

| thesis_url = http://www.worldcat.org/oclc/316118309

| thesis_year = 1969

| doctoral_advisor = Donald Andrew Dawson{{MathGenealogy |id=37220 }}

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| website = {{URL|albuquerque.bioinformatics.uottawa.ca}}

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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 scientific journal Language Variation and Change (Cambridge){{Cite book|title=Making waves : the story of variationist sociolinguistics|last=Sali|first=Tagliamonte|isbn=9781118455166|location=Chichester, West Sussex, United Kingdom|oclc=921307274|date = 2015-11-02}} and serves on the editorial boards of a number of bioinformatics, computational biology and linguistics journals.{{cite web|title=BMC Bioinformatics|url=https://bmcbioinformatics.biomedcentral.com/about/editorial-board|access-date=8 June 2019}}{{cite web|title=Journal of Bioinformatics and Computational Biology|url=https://www.worldscientific.com/page/jbcb/editorial-board|access-date=8 June 2019}}{{cite web|title=Journal of Computational Biology|url=https://home.liebertpub.com/publications/journal-of-computational-biology/31/editorial-board|access-date=8 June 2019}}{{cite web|title=Molecular Phylogenetics and Evolution, Volume 43|url=https://www.deepdyve.com/lp/elsevier/editorial-board-v1uKbN34Xd|access-date=8 June 2019}} 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{{Cite journal | last1 = Sankoff | first1 = D. | title = The early introduction of dynamic programming into computational biology | doi = 10.1093/bioinformatics/16.1.41 | journal = Bioinformatics | volume = 16 | issue = 1 | pages = 41–47 | year = 2000 | pmid = 10812476| doi-access = free }} for sequence alignment and other problems in computational biology. In Pavel Pevzner's words,{{Cite journal | last1 = Maisel | first1 = M. | title = ISCB Honors Michael S. Waterman and Mathieu Blanchette | doi = 10.1371/journal.pcbi.0020105 | journal = PLOS Computational Biology | volume = 2 | issue = 8 | pages = e105 | year = 2006 | pmc = 1526462|bibcode = 2006PLSCB...2..105M | doi-access = free }}

"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."

Education

Sankoff published his first paper in 1963{{Cite journal

| doi = 10.1016/0042-6822(63)90203-4

| last1 = Friesen | first1 = J. D.

| last2 = Sankoff | first2 = D.

| last3 = Siminovitch | first3 = L.

| title = Radiobiological Studies of Vaccinia Virus

| journal = Virology

| volume = 21

| issue = 3

| pages = 411–424

| year = 1963

| pmid = 14081366

}} 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,{{cite journal|last=Sankoff|first=David|title=On the rate of replacement of word-meaning relationships|journal=Language|year=1970|volume=46|issue=3|pages=564–569|jstor=412307|doi=10.2307/412307|citeseerx=10.1.1.667.3279}} variable rules analysis (with Henrietta Cedergren),{{cite journal|last=Cedergren|first=H. J.|author2=D. Sankoff|title=Variable rules: performance as a statistical reflection of competence|journal=Language|year=1974|volume=50|issue=2|pages=333–355|jstor=412441|doi=10.2307/412441|citeseerx=10.1.1.665.3156}} the linguistic marketplace:{{Cite book|last=Sankoff|first=D.|author2=S. Laberge|year=1978|chapter=The linguistic market and the statistical explanation of variability|title=In D. Sankoff (ed.), Linguistic Variation: Models and Methods (pp. 239-250)|location=New York|publisher=Academic Press}} and code switching.{{cite journal|last=Sankoff|first=David|author2=Shana Poplack|author2-link=Shana Poplack|title=A formal grammar for code switching|journal=Papers in Linguistics|year=1981|volume=14|issue=1|pages=3–46|doi=10.1080/08351818109370523|citeseerx=10.1.1.667.3175}}

Career and research

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 and devised the first quadratic-time variant of the Needleman–Wunsch algorithm for pairwise sequence alignment.{{Cite journal

| last1 = Sankoff | first1 = D.

| title = Matching sequences under deletion-insertion constraints

| journal = Proceedings of the National Academy of Sciences of the United States of America

| volume = 69

| issue = 1

| pages = 4–6

| year = 1972

| pmid = 4500555

| pmc = 427531

| doi=10.1073/pnas.69.1.4

|bibcode = 1972PNAS...69....4S | doi-access = free

}}

In 1973, Sankoff and Robert Cedergren developed a joint estimation method for phylogeny and multiple sequence alignment of 5S ribosomal RNA,{{cite journal|last=Sankoff|first=D |author2=C. Morel |author3=R. J. Cedergren|title=Evolution of 5S RNA and the non-randomness of base replacement|journal=Nature New Biology|year=1973|volume=245|issue=147 |pages=232–234|pmid=4201431|doi=10.1038/newbio245232a0}} 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;{{citation

| last1 = Chvatal | first1 = Václáv | author1-link = Václav Chvátal

| last2 = Sankoff | first2 = David | author2-link = David Sankoff

| journal = Journal of Applied Probability

| mr = 0405531

| pages = 306–315

| title = Longest common subsequences of two random sequences

| volume = 12

| issue = 2 | year = 1975 | doi=10.2307/3212444| jstor = 3212444 | s2cid = 250345191 }}. 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.{{cite web|title=History of the Robert Cedergren Centre|url=http://www.centrerc.umontreal.ca/historiquea.html|access-date=25 August 2013}} Sankoff's work in bioinformatics addresses RNA secondary structure, genome rearrangements, sequence alignment, genome evolution and phylogenetics.{{cite web|title=ISCB Senior Scientist Award to Sankoff|url=http://www.iscb.org/iscb-awards/1135|archive-url=https://web.archive.org/web/20160303233531/https://www.iscb.org/iscb-awards/1135|archive-date=2016-03-03|website=iscb.org/iscb-awards|author=Anon|year=2003|url-status=dead}}

=Awards and honors=

  • Inaugural recipient of the International Society for Computational Biology's Senior Scientist Award in 2003.
  • Elected a Fellow of the Royal Society of Canada (1995){{Cite web|title=David Sankoff|url=https://research.uottawa.ca/people/sankoff-david|access-date=2020-11-03|website=Research|language=en}}
  • Elected an ISCB Fellow by the International Society for Computational Biology in 2009{{cite web|archive-url=https://web.archive.org/web/20170320114530/https://www.iscb.org/iscb-fellows|archive-date=2017-03-20|url=https://www.iscb.org/iscb-fellows|website=iscb.org|title=ISCB Fellows|publisher=International Society for Computational Biology|author=Anon|year=2017|url-status=dead}}
  • Marcel-Vincent Prize (1977){{cite web |title=Prix Acfas Thérèse Gouin-Décarie (Prix Marcel-Vincent before 2013) |url=https://www.acfas.ca/prix-concours/prix-acfas/therese-gouin-decarie |website=Acfas PRIX |access-date=19 September 2020 |language=fr |date=2019}}
  • Ontario Distinguished Researcher Award (2002)
  • Weldon Memorial Prize (2004){{Cite book|url=https://www.zoo.ox.ac.uk/article/professor-angela-mclean-awarded-weldon-medal|title=Professor Angela McLean awarded the Weldon Medal|date=2018-05-17}}
  • University of Ottawa Excellence in Research Award{{cite web|title=David Sankoff - Excellence in Research Award|url=http://www.research.uottawa.ca/excellence-awards-recipient_515.html|access-date=25 August 2013|archive-date=24 September 2014|archive-url=https://web.archive.org/web/20140924053312/http://www.research.uottawa.ca/excellence-awards-recipient_515.html|url-status=dead}} (2013)
  • Honorary doctorate, Tel Aviv University (2014){{Cite web|date=2019-06-11|title=Co-founder of bioinformatics to receive an honorary doctorate|url=https://uwaterloo.ca/math/news/co-founder-bioinformatics-receive-honorary-doctorate|access-date=2020-11-03|website=Mathematics|language=en}}

References

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{{ISCB Fellows}}

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Category:1942 births

Category:Living people

Category:Anglophone Quebec people

Category:Canada Research Chairs

Category:Fellows of the International Society for Computational Biology

Category:Fellows of the Royal Society of Canada

Category:Academics from Montreal

Category:McGill University alumni

Category:2023 fellows of the Association for Computing Machinery