[Colloquium] Xia/MS Presentation/Nov. 4, 2005

[Margaret Jaffey]

This is a revised announcement of Fangfang Xia's Master's  
Presentation that will be held on Friday.  Please note that he has  
updated the title and abstract of his MS paper.  A revised version of  
his MS paper is available in Ry 161A.

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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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