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{{Infobox scientist
David Sankoff is a Canadian mathematician, born Dec 31, 1942 in Montreal, and the holder of the Canada Research Chair in Mathematical Genomics in the Mathematics and Statistics Department at the University of Ottawa<ref name="biography of David Sankoff">{{cite web|title=MAGE Conference|url=http://www-etud.iro.umontreal.ca/~lafonman/MAGE2013/bio-david-sankoff.php|accessdate=24 August 2013}}</ref>. Sankoff is a Fellow of the Royal Society of Canada and of the International Society for Computational Biology<ref name="biography of David Sankoff">{{cite web|title=MAGE Conference|url=http://www-etud.iro.umontreal.ca/~lafonman/MAGE2013/bio-david-sankoff.php|accessdate=24 August 2013}}</ref>.
| name = David Sankoff
| image =
| alt =
| caption =
| birth_date = {{Birth date|1942|12|31}}
| birth_place = [[Montreal, Quebec]], [[Canada]]
| relatives =
|religion =
| education =
| residence =
| citizenship =
| nationality = {{flag|CAN|name=Canadian}}
| fields =
| workplaces = [[University of Ottawa]], [[Université de Montréal]]; [[Centre de Recherches Mathématiques]], [[National Statistical Office of Papua New Guinea|Bureau of Statistics of Papua and New Guinea]] <ref name="bilingual">:{{Cite book|last=Sankoff|first=David|year=2008|chapter=How to Predict the Evolution of a Bilingual Community|chapterurl=http://benjamins.com/#catalog/books/impact.24.13san/details|title=''In Meyerhoff, Miriam and Naomi Nagy (eds.),'' Social Lives in Language – Sociolinguistics and multilingual speech communities: Celebrating the work of Gillian Sankoff ''(pp.&nbsp;179–194)''|location=Amsterdam|publisher=[[John Benjamins]]}}</ref>
| alma_mater = [[McGill University]] B.Sc. (1963), M.Sc. (1965), Ph.D. (1969)
| thesis_title = Historical Linguistics as a Stochastic Process<ref name="mathgene">{{MathGenealogy |id=37220 }}</ref>
| thesis_url =
| thesis_year = 1969
| doctoral_advisor = David Andrew Dawson<ref name="mathgene" />
| academic_advisors =
| doctoral_students =
| notable_students =
| known_for = [[Variable rules analysis]], [[Code switching]], [[Sequence alignment]], [[Nucleic acid secondary structure]], [[Computational genomics]]
| influences = <!--only listing ones also referenced in text-->
| influenced = <!--only listing ones also referenced in text-->
| awards = Fellow, [[Royal Society of Canada]], 1995; [[Canada Research Chair]] 2002-2016; [[:fr:Prix Marcel-Vincent|Marcel-Vincent Prize]], 1977; Ontario Distinguished Researcher Award, 2002; Fellow, [[International Society for Computational Biology]], [[ISCB Senior Scientist Awards| ISCB Senior Scientist Accomplishment Award]], 2003; [[Weldon Memorial Prize]], 2004; [[University of Ottawa]] Excellence in Research Award, 2013<ref>{{cite web|title=Royal Society of Canada Fellowship to Sankoff|url=http://www.research.uottawa.ca/excellence-awards-recipient_53.html|accessdate=24 August 2013}}</ref>
| website = {{URL|albuquerque.bioinformatics.uottawa.ca}}
| footnotes =
| spouse =
| children =
}}


'''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]]<ref name="dphist">{{cite doi|10.1093/bioinformatics/16.1.41}}</ref> for [[sequence alignment]] and other problems in [[computational biology]]. In [[Pavel Pevzner]]'s words<ref name="iscb assp 2006">{{cite doi|10.1371/journal.pcbi.0020105}}</ref>,
Sankoff published his first paper in 1963 while he was an undergraduate student in Mathematics at McGill University. In 1969, Sankoff received his PhD in Mathematics from McGill University (PhD advisor Donald Dawson) with a dissertation in historical linguistics<ref>{{cite web|title=Mathematics Genealogy Project|url=http://genealogy.math.ndsu.nodak.edu/id.php?id=37220|accessdate=24 August 2013}}</ref>. Sankoff began his academic career at the Université de Montréal in 1969<ref name="biography of David Sankoff">{{cite web|title=MAGE Conference|url=http://www-etud.iro.umontreal.ca/~lafonman/MAGE2013/bio-david-sankoff.php|accessdate=24 August 2013}}</ref>. He was founding editor of Language Variation and Change (Cambridge) and serves on the editorial boards of a number of bioinformatics, computational biology and linguistics journals.
"[ [[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 is one of the founding pioneers of computational biology and bioinformatics (along with Michael Waterman<ref name="Michael Waterman wikipedia page">{{cite web|title=Michael Waterman Wikipedia Page|url=http://en.wikipedia.org/wiki/Michael_Waterman|accessdate=24 August 2013}}</ref>, Webb Miller<ref name="Webb Miller wikipedia page">{{cite web|title = Webb Miller Wikipedia Page|url=http://en.wikipedia.org/wiki/Webb_Miller|accessdate=24 August 2013}}</ref>, Eric Lander<ref name="Eric Lander wikipedia page">{{cite web|title=Eric Lander Wikipedia Page|url=http://en.wikipedia.org/wiki/Eric_lander|accessdate=24 August 2013}}</ref>, and a few others). His early work in computational biology inlcuded the introduction of dynamic programming<ref name="Dynamic Programming wikipedia page">{{cite web|title=Dynamic Programming Wikipedia Page|url=http://en.wikipedia.org/wiki/Dynamic_programming|accessdate=24 August 2013}}</ref> for sequences alignment and other problems<ref name="The early introduction of dynamic programming into computational biology>{{cite web|title=The early introduction of dynamic programming into computational biology Page|url=http://bioinformatics.oxfordjournals.org/content/16/1/41.abstract|accessdate=24 August 2013}}</ref>. He has also made important contributions to a number of different fields, most notably linguistics and comparative genomics. His work in comparative genomics has focused on genome rearrangements, and addressed the question of how to infer the evolutionary history of a set of species given the gene orders within the chromosomes.
Sankoff published his first paper in 1963<ref name="vaccinia">{{cite pmid| 14081366}}</ref> 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]]<ref name="word-meaning">{{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|url=http://www.jstor.org/stable/412307}}</ref>, [[variable rules analysis]]<ref name="via">{{cite journal|last=Cedergren|first=H. J.|coauthors=D. Sankoff|title=Variable rules: performance as a statistical reflection of competence|journal=Language|year=1974|volume=50|pages=333-355|url=http://www.jstor.org/stable/412441}}</ref>, the [[linguistic marketplace]]<ref name="marketplace">:{{Cite book|last=Sankoff|first=D.|coauthors=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.&nbsp;239-250)''|location=New York|publisher=Academic Press}}</ref> and [[code switching]]<ref>{{cite journal|last=Sankoff|first=David|coauthors=[[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}}</ref>.


After completing his Ph.D. in Mathematics, Sankoff began his academic career at the [[University of Montreal]] in 1969. In 1971, Sankoff got interested in molecular sequence comparison<ref name="dphist" /> and devised the first [[Time complexity|quadratic-time]] variant of the [[Needleman-Wunsch algorithm]] for pairwise [[sequence alignment]]<ref name="gaps">{{cite pmid| 4500555}}</ref>.
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'''Awards:'''
Sankoff is a Fellow of the Royal Society of Canada<ref>{{cite web|title=Royal Society of Canada Fellowship to Sankoff|url=http://www.research.uottawa.ca/excellence-awards-recipient_53.html|accessdate=24 August 2013}}</ref>. He received the Weldon Memorial Prize from Oxford University and the Award for Excellence in Research from the University of Ottawa. Sankoff is a medalist of the ``Association francophone pour le savoir". Sankoff has also been recognized by the International Society for Computational Biology (ISCB) in two ways: he is a Fellow of the ISCB and was the first recipient of their Senior Scientist Accomplishment Award<ref name="Sankoff ISCB Senior Scientist award page">{{cite web|title = ISCB Senior Scientist Award to Sankoff|url=http://www.iscb.org/iscb-awards/1135|accessdate=24 August 2013}}</ref>.
In 1973, Sankoff and Robert Cedergren developed a [[Computational_phylogenetics#Sankoff-Morel-Cedergren_algorithm|joint estimation method]] for [[phylogeny]] and [[multiple sequence alignment]] of [[5S ribosomal RNA]]<ref name="5S">{{cite journal|last=Sankoff|first=D|coauthors=C. Morel and R. J. Cedergren|title=Evolution of 5S RNA and the non-randomness of base replacement|journal=Nature New Biology|year=1973|volume=245|pages=232-234|pmid=4201431}}</ref> , laying the algorithmic foundations of [[comparative genomics]]. In 1980, Robert Cedergen and David Sankoff created the first research group in bioinformatics at the [[University of Montreal]]<ref>{{cite web|title=History of the Robert Cedergren Centre|url=http://www.centrerc.umontreal.ca/historiquea.html|accessdate=25 August 2013}}</ref> . Sankoff's work in bioinformatics addresses [[Nucleic acid secondary structure|RNA secondary structure]], [[chromosome rearrangement|genome rearrangements]], [[sequence alignment]], genome evolution and [[phylogenetics]].<ref name="Sankoff ISCB Senior Scientist award page">{{cite web|title=ISCB Senior Scientist Award to Sankoff|url=http://www.iscb.org/iscb-awards/1135|accessdate=24 August 2013}}</ref>.
<!--His work in comparative genomics has focused on genome rearrangements, and addressed the question of how to infer the evolutionary history of a set of species given the gene orders within the chromosomes. -->


==References==
==References==
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==Awards==

* Sankoff was the first recipient of the [[International Society for Computational Biology]]'s Senior Scientist Award in 2003.

* Fellow of the [[Royal Society of Canada]] (1995)
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* Fellow of the [[International Society for Computational Biology]]
* [[Weldon Memorial Prize]] (2004)

Revision as of 13:07, 25 August 2013

Template:Unreviewed

David Sankoff
Born(1942-12-31)December 31, 1942
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; Marcel-Vincent Prize, 1977; Ontario Distinguished Researcher Award, 2002; Fellow, International Society for Computational Biology, ISCB Senior Scientist Accomplishment Award, 2003; Weldon Memorial Prize, 2004; University of Ottawa Excellence in Research Award, 2013[1]
Scientific career
InstitutionsUniversity of Ottawa, Université de Montréal; Centre de Recherches Mathématiques, Bureau of Statistics of Papua and New Guinea [2]
Thesis Historical Linguistics as a Stochastic Process[3]  (1969)
Doctoral advisorDavid Andrew Dawson[3]
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[4] for sequence alignment and other problems in computational biology. In Pavel Pevzner's words[5], "[ 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[6] 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[7], variable rules analysis[8], the linguistic marketplace[9] and code switching[10].

After completing his Ph.D. in Mathematics, Sankoff began his academic career at the University of Montreal in 1969. In 1971, Sankoff got interested in molecular sequence comparison[4] and devised the first quadratic-time variant of the Needleman-Wunsch algorithm for pairwise sequence alignment[11]. In 1973, Sankoff and Robert Cedergren developed a joint estimation method for phylogeny and multiple sequence alignment of 5S ribosomal RNA[12] , laying the algorithmic foundations of comparative genomics. 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].

References

  1. ^ "Royal Society of Canada Fellowship to Sankoff". Retrieved 24 August 2013.
  2. ^ :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)
  3. ^ a b David Sankoff at the Mathematics Genealogy Project
  4. ^ a b Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1093/bioinformatics/16.1.41, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1093/bioinformatics/16.1.41 instead.
  5. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1371/journal.pcbi.0020105, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1371/journal.pcbi.0020105 instead.
  6. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 14081366, please use {{cite journal}} with |pmid= 14081366 instead.
  7. ^ Sankoff, David (1970). "On the rate of replacement of word-meaning relationships". Language. 46 (3): 564–569.
  8. ^ Cedergren, H. J. (1974). "Variable rules: performance as a statistical reflection of competence". Language. 50: 333–355. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
  9. ^ :Sankoff, D. (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. {{cite book}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
  10. ^ Sankoff, David (1981). "A formal grammar for code switching". Papers in Linguistics. 14 (1): 3–46. doi:10.1080/08351818109370523. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
  11. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 4500555, please use {{cite journal}} with |pmid= 4500555 instead.
  12. ^ Sankoff, D (1973). "Evolution of 5S RNA and the non-randomness of base replacement". Nature New Biology. 245: 232–234. PMID 4201431. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
  13. ^ "History of the Robert Cedergren Centre". Retrieved 25 August 2013.
  14. ^ "ISCB Senior Scientist Award to Sankoff". Retrieved 24 August 2013.

Awards

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