March 11, 2004: Seminar, Speaker Tiffani L. Williams
Speaker: Tiffani L. Williams (University of New Mexico)
Title: Phylogeny Reconstruction and Experimental Algorithmics

Date: Thursday March 11, 2004
Time: 11:00 AM
Location: Room 1000 SEO

Abstract:
Phylogenetic trees, also known as evolutionary trees, model the evolution of biological species or genes from a common ancestor. Heuristics for the NP-hard maximum parsimony (MP) problem constitute the principle mechanism for estimating phylogenies on large datasets. Traditional MP heuristics spend an enormous amount of computational time searching for the optimal solution; on large datasets, MP searches may require months or even years to solve optimally. My work centers on using experimental algorithmics to design and test algorithms for large-scale phylogeny reconstruction.

In this talk, she will discuss Disk-Covering Methods (DCMs), a suite of techniques for reconstructing phylogenetic trees quickly and accurately. DCMs reduce the time to optimal by an order of magnitude on many datasets. Yet, is it necessary to solve MP optimally? Her work shows that near-optimal solutions to MP give highly accurate estimations of optimal tree topologies. Moreover, they can be obtained in a fraction of the time needed to solve to optimality. Thus, the talk will conclude with a discussion of a stopping criterion for phylogenetic searches.

Bio:
Tiffani L. Williams is an Alfred P. Sloan Postdoctoral Fellow in the Department of Computer Science at the University of New Mexico. She received her Ph.D. in Computer Science from the University of Central Florida in 2000. Her research interests are in the areas of computational biology and high-performance computing, with particular emphasis n applying high-performance techniques to large-scale phylogeny econstruction.













































 
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