Workshop on Advances in Multiple Sequence Alignment and Phylogeny Estimation
May 20 and 21, 2012
Smithsonian National Museum of Natural History
Washington, DC

The workshop is funded by the National Science Foundation through grant DEB 0733029 to the University of Texas. Registration is required, and attendance is limited to 40 participants. The workshop will include presentations of new methods for multiple sequence alignment and phylogeny estimation, also training in the use of these methods, and personal assistance in analyzing datasets using the SATé software (see this page). Applications for the workshop (and for travel support) are due by February 15, 2012, and will be responded to by March 1. We expect to be able to provide support to all attendees. Please click here for the application form. For more information, please send an email to Tandy Warnow.

Estimating Phylogenetic Trees in Linguistics and Biology
June 18-22, 2012
North American Summer School of Logic, Language, and Information (NASSLI) 2012
Tandy Warnow

Office hours Spring 2012: Tuesdays (starting Jan 24) 3:00-5, or by appointment.

My research focuses on the development of mathematical models and algorithms for estimating evolutionary history in Biology and Historical Linguistics. The main objective is to develop methods that produce much more accurate estimations of evolutionary history than can be obtained using existing tools. Our group is distinguished from many other groups in computational biology due to our focus on ultra-large datasets, with up to 500,000 sequences. We use real data and perform simulations to evaluate the performance of methods that we develop. This research area inolves mathematics, probability, statistics, computer science, and intensive collaborations with domain specialists. My current research is funded by the National Science Foundation (DEB 0733029 and DBI-1062335) and by the John P. Simon Guggenheim Foundation.

Click here for Google Scholar Citations (i10-index 81, and h-index 39).

The CIPRES Project is finally over, but the CIPRES Portal is still available through the TeraGrid. For an abridged version of our final report, see this.

"Plus de détails, plus de détails, disait-il à son fils, il n'y a d'originalité et de vérité que dans les détails..." -- Stendhal, Lucien Leuwen (a quote much loved by my stepfather, Martin J. Klein, and an essential guide for all scholarship).

Collaborations

My students and I are actively working on developing new methods for estimating alignments and trees (both gene trees and species trees), as well as for taxon identification of metagenomic data. We are currently working with three international research projects, two involved with estimating the Avian phylogeny, and also the Thousand Transcriptome Project (1KP), using our methods to estimate alignments and trees on individual genes, and to estimate species trees from these multi-marker datasets. We welcome collaborations with biologists who have data that are difficult to analyze, either because the datasets are too large for current methods, or because current methods fail to have sufficiently high accuracy.

Spring 2012 Courses

  • 394C: Algorithms for Computational Biology. The course topic is algorithm design in computational molecular biology. This year we will focus our study on genome assembly, multiple sequence alignment, phylogeny (evolutionary history) reconstruction, and metagenomics. These problems are individually enormously computationally intensive - computational approaches generally involve attempts to solve NP-hard optimization problems. Algorithmic development, firmly grounded in mathematical theory, is needed by the biological research community. The goal of the course is to enable the students to do high quality research (both mathematical and algorithmic) for these problems. If you are an undergraduate and interested in taking the course, please see me.

  • 336: Analysis of Programs. This is a required course for CS majors. I will draw examples from computational biology to illustrate the ideas in the course. Opportunities for research in algorithm development are possible; see me if you are interested. 

    
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