[Colloquium] TODAY: Xia/MS Presentation/Nov. 4, 2005
Margaret Jaffey
margaret at cs.uchicago.edu
Fri Nov 4 14:20:54 CST 2005
This is a reminder about Fangfang Xia's MS Presentation.
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Date: Friday, November 4, 2005
Time: 2:30 p.m.
Place: Ryerson 277
M.S. Candidate: Fangfang Xia
M.S. Paper Title: Inferring Species Tree from Gene Trees: A Genetic
Algorithm Approach
Abstract:
We consider the problem of constructing a species tree given a number
of gene trees in an extended /duplication-loss/ model that allows
Horizontal Gene Transfer (HGT). In the frameworks introduced by
various authors [7, 8, 9] this is formulated as an optimization
problem and proved NP-Complete [2]. In this paper, we first present a
polynomial time algorithm for reconciling a gene tree with a species
tree. This solves an open problem in [6]. We then propose a genetic
algorithm approach “/Hytree/” to finding the optimal species tree
from a reference set of gene trees. Our experiments with tryptophan
biosynthesis gene sequence data show this method could help infer
subsystem/organism phylogeny in the presence of HGT and
computationally detect HGT events. Lastly, we discuss various
practical issues in using gene trees to eventually derive the
universal Tree of Life.
Advisor: Prof. Rick Stevens
A draft copy of Fangfang Xia's MS Paper is available in Ry 161A.
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Margaret P. Jaffey margaret at cs.uchicago.edu
Department of Computer Science
Student Support Rep (Ry 161A) (773) 702-6011
The University of Chicago http://www.cs.uchicago.edu
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