[Colloquium] 2/12 TTIC Distinguished Lecture Series: Tandy Warnow

[Mary Marre]

*Distinguished Lecture Series: Tandy Warnow, University of Illinois at
Urbana-Champaign*




*[image: Inline image 4]*
*Friday, February 12, 2016 at 11:00 am*
*Toyota Technological Institute at Chicago*
*6045 S. Kenwood Avenue*
*Room #526**​*



*Tandy Warnow*
Founder Professor of Engineering

Professor of Computer Science

Professor of Bioengineering

Member of the Carl R. Woese Institute for Genomic Biology

Affiliate of Electrical and Computer Engineering, Mathematics, Statistics,
Entomology, Plant Biology, Animal Biology, and PEEC (Program in Ecology,
Evolution, and Conservation Biology)

Adjunct Professor of Computer Science at the University of Texas at Austin

University of Illinois at Urbana-Champaign



*Title:* New HMM-Based Methods in Sequence Alignment, Phylogenetics, and
Metagenomics


*Abstract:*

Multiple sequence alignment of datasets containing many thousands of
sequences is a

challenging problem with applications in phylogeny estimation, protein
structure and function

prediction, taxon identification of metagenomic data, etc. However, few
methods can analyze

large datasets, and none have been shown to have good accuracy on datasets
with more than

about 10,000 sequences, especially if the sequence datasets have evolved
with high rates of

evolution.



In this talk, I will present a new method to obtain highly accurate
estimations of large-scale

multiple sequence alignments and phylogenies. The basic idea is to use an
ensemble of Hidden

Markov Models (HMMs) to represent a "seed alignment", and then align all
the remaining

sequences to the seed alignment. Our method, UPP, returns very accurate
alignments, and trees

on these alignments are also very accurate - even on datasets with as many
as 1,000,000

sequences, or datasets that contain many fragmentary sequences.
Furthermore, UPP is both fast

and very scalable, so that the analysis of the 1-million taxon dataset took
only 24 hours using 12

cores and small amounts of memory.  Finally, this Ensemble of HMMs
technique improves the

accuracy of methods for other bioinformatics problems, including
phylogenetic placement and

taxon identification of metagenomic data.



This is joint work with Nam-phuon Nguyen and Siavash Mirarab.





*Bio:* Tandy Warnow is the Founder Professor of Bioengineering and Computer
Science at

the University of Illinois at Urbana-Champaign, a member of the Carl Woese
Institute for

Genomic Biology, and an affiliate in the departments of Electrical and
Computer

Engineering, Statistics, Mathematics, Animal Biology, Plant Biology, and
Entomology.

Warnow received her PhD in Mathematics in 1991 at the University of
California at Berkeley

under the direction of Eugene Lawler, and she did postdoctoral training
with Simon Tavaré

and Michael Waterman at the University of Southern California from
1991-1992. Tandy was

on the faculty at the University of Pennsylvania from 1994-1999, and then
joined the

University of Texas, before joining the faculty at the University of
Illinois in 2014. Warnow

received the National Science Foundation Young Investigator Award in 1994,
the David and

Lucile Packard Foundation Award in Science and Engineering in 1996, a
Radcliffe Institute

Fellowship in 2006, and a John Simon Guggenheim Foundation Fellowship for
2011.

Warnow’s international service includes being the NSF program director in
charge of the Big

Data program, and serving as the chair of the NIH BDMA (Biodata Management
and

Analysis) study section.  Warnow has published more than 130 papers, and
her research

combines mathematics, computer science, and statistics to develop improved
models and

algorithms for reconstructing complex and large-scale evolutionary
histories in both biology

and historical linguistics.   Her current research focuses on phylogeny and
alignment

estimation for very large datasets (10,000 to 1,000,000 sequences),
estimating species trees

and phylogenetic networks from collections of gene trees, and taxon
identification in

metagenomics.





*Host:* Jinbo Xu, j3xu at ttic.edu


Mary C. Marre
Administrative Assistant
*Toyota Technological Institute*
*6045 S. Kenwood Avenue*
*Room 504*
*Chicago, IL  60637*
*p:(773) 834-1757*
*f: (773) 357-6970*
*mmarre at ttic.edu <mmarre at ttic.edu>*
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