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Tandy Warnow

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Tandy Warnow
Tandy Warnow
Tandy Warnow speaking at the Intelligent Systems for Molecular Biology (ISMB) conference in 2018
Born
Tandy Jo Warnow
Alma materUniversity of California, Berkeley (BS, PhD)
SpouseGeorge Chacko [4]
Awards
Scientific career
FieldsComputer Science
Computational Biology
Phylogenetics
Metagenomics
Multiple Sequence Alignment[1]
InstitutionsUniversity of Illinois at Urbana–Champaign
University of Pennsylvania
University of Texas
ThesisCombinatorial algorithms for constructing phylogenetic trees (1991)
Doctoral advisorEugene Lawler[2]
Other academic advisorsMichael Waterman
Simon Tavare[citation needed]
Doctoral studentsLuay Nakhleh[3]
Websitetandy.cs.illinois.edu

Tandy Warnow is an American computer scientist and Founder Professor of Engineering and Computer Science at the University of Illinois at Urbana–Champaign.[5][6] She is known for her work on the reconstruction of evolutionary trees, both in biology and in historical linguistics, and also for multiple sequence alignment methods.[7]

Biography

Warnow did both her undergraduate and graduate studies in mathematics at the University of California, Berkeley, earning a bachelor's degree in 1984 and a PhD[2] in 1991 under the supervision of Eugene Lawler. The other members of her dissertation committee were Richard Karp, Manuel Blum, Dan Gusfield, and David Gale.[2]

Research and career

After postdoctoral research at the University of Southern California from 1991-1992 (postdoctoral supervisors Michael Waterman and Simon Tavare) and at Sandia National Laboratories in Albuquerque from 1992-1993, she took a faculty position at the University of Pennsylvania, where she remained until moving in 1999 to the University of Texas. In 2014, Warnow joined the faculty of the University of Illinois in Urbana-Champaign, where she is the Founder Professor of Engineering and Associate Head of the Department of Computer Science. Warnow has courtesy appointments in the Departments of Animal Biology, Bioengineering, Electrical and Computer Engineering, Entomology, Mathematics, Plant Biology, and Statistics.[6][8]

In 1995, research by Warnow, Donald Ringe, and Ann Taylor at the University of Pennsylvania based on perfect phylogeny computations provided a comprehensive theory for the timing of the early subdivisions in the Indo-European languages. Their computations lent support to the Indo-Hittite hypothesis according to which the first of these subdivisions to separate from the rest of the Indo-European languages were the Anatolian languages. Their results also support the Graeco-Armenian hypothesis, according to which the Armenian language and Greek language form a subfamily of Indo-European. They fit the Germanic languages into the evolutionary tree of Indo-European languages, previously considered problematic, by hypothesizing that the Proto-Germanic language was closely related to the Balto-Slavic languages but then became modified by westward migrations of the Germanic tribes which led them into contact with Italic and Celtic speakers.[9] This perfect phylogeny approach was later extended by Warnow and colleagues to allow for undetected borrowing between languages, so that language evolution is modelled with a network rather than a tree.[10]

In 2009, Warnow and her colleagues released their SATé software for co-estimating biological multiple sequence alignments and evolutionary trees.[11] Their software is based less strongly on firm mathematical principles than some previous co-estimation methods (such as BAli-Phy[12]), but is significantly faster, allowing the fast construction of highly accurate trees and alignments for thousands of species. In comparison, the slow performance of previous methods limited them to only comparing dozens of species at a time.[13][14]

Her work from 2014-2018 has focused on three topics: scaling multiple sequence alignments to ultra-large datasets, species tree estimation using multiple genes (and addressing gene tree heterogeneity due to incomplete lineage sorting), and metagenomics. Her major contributions in these topics include the PASTA method for co-estimation of alignments and trees, which improves on SATé, and can produce highly accurate alignments with up to 1,000,000 sequences.[15] She has also developed the ASTRAL method for species tree estimation, which is a statistically consistent method for constructing species trees in the presence of incomplete lineage sorting.[16]

Awards and honors

Warnow was named a Founder Professor of Engineering at the University of Illinois at Urbana-Champaign in 2014, and the David Bruton Jr. Centennial Professorship in Computer Science at the University of Texas at Austin in 2010.[6] Warnow also received a John Simon Guggenheim Foundation Fellowship in 2011, a Radcliffe Institute Fellowship in 2003, a David and Lucile Packard Foundation Fellowship in 1996, and the NSF Young Investigator Award in 1994.[6] In 2015, she was named a Fellow of Association for Computing Machinery (ACM) "For contributions to mathematical theory, algorithms, and software for large-scale molecular phylogenetics and historical linguistics".[17] In 2017, she was elected as a Fellow of the International Society for Computational Biology (ISCB).[18]

Personal life

Warnow's mother was noted archivist Joan Warnow-Blewett, and her father was Morton Warnow, the son of the band leader Mark Warnow and nephew of the composer Raymond Scott. Her twin sister is Kimmen Sjolander, a bioinformatics researcher and faculty member at the University of California. She is married to George Chacko.[4]

References

  1. ^ Tandy Warnow publications indexed by Google Scholar Edit this at Wikidata
  2. ^ a b c Warnow, Tandy Jo (1991). Combinatorial algorithms for constructing phylogenetic trees (PhD thesis). University of California, Berkeley. OCLC 25765772. ProQuest 303937362.
  3. ^ Nakhleh, Luay (2004). Phylogenetic networks (PhD thesis). University of Texas at Austin. hdl.handle.net/2152/2126.
  4. ^ a b http://tandy.cs.illinois.edu/family.html
  5. ^ Tandy Warnow's Official website
  6. ^ a b c d "Tandy Warnow Curriculum vitae" (PDF)., retrieved 2018-01-29.
  7. ^ Warnow, Tandy (2017), Computational Phylogenetics: An Introduction to Designing Methods for Phylogeny Estimation, Cambridge University Press, ISBN 9781107184718
  8. ^ Tandy Jo Warnow at the Mathematics Genealogy Project
  9. ^ Johnson, George (January 2, 1996), "New Family Tree Is Constructed For Indo-European", New York Times.
  10. ^ Nakhleh, Luay; Ringe, Donald A.; Warnow, Tandy (2005). "Perfect Phylogenetic Networks: A New Methodology for Reconstructing the Evolutionary History of Natural Languages". Language. 81 (2): 382–420. doi:10.1353/lan.2005.0078.
  11. ^ Liu, K.; Raghavan, S.; Nelesen, S.; Linder, C. R.; Warnow, T. (18 June 2009). "Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees". Science. 324 (5934): 1561–1564. Bibcode:2009Sci...324.1561L. doi:10.1126/science.1171243. PMID 19541996.
  12. ^ Suchard, Marc; Redelings, Ben (2006). "BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny". Bioinformatics. 22 (16): 2047–2048. doi:10.1093/bioinformatics/btl175. PMID 16679334.
  13. ^ "Method For Computing Evolutionary Trees Could Revolutionize Evolutionary Biology", ScienceDaily, June 18, 2009.
  14. ^ Kloc, Joe (July 1, 2009), "How to build a better tree of life: An unconventional approach to analyzing molecular sequences allows researchers to construct larger evolutionary trees", Seed.
  15. ^ Mirarab, S.; Nguyen, N.; Guo, S.; Wang, L.-S.; Kim, J.; Warnow, T. (2014). "PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences". Journal of Computational Biology. 22 (5): 377–386. doi:10.1089/cmb.2014.0156. PMC 4424971. PMID 25549288.
  16. ^ Mirarab, S.; Warnow, T. (2015). "ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes". Bioinformatics. 31 (12): i44–i52. doi:10.1093/bioinformatics/btv234. PMC 4765870. PMID 26072508.
  17. ^ "ACM Fellows Named for Computing Innovations that Are Advancing Technology in the Digital Age". ACM. 8 December 2015. Archived from the original on 9 December 2015. Retrieved 9 December 2015.
  18. ^ "February 13, 2017: The International Society for Computational Biology Names Seven Members as the ISCB Fellows Class of 2017". www.iscb.org. Retrieved 13 February 2017.
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