Fordham University Department of Computer & Information
Science
and
Interdisciplinary Faculty Seminar on Biomedical Informatics
Present:
Clustering in the Space of Phylogenies
Dr. Li-San Wang
Penn Center for Bioinformatics
Institute for Aging
Department of Pahtology and Laboratory Medicine
School of Medicine
University of Pennsylvania
Date : Thursday, February 22, 2007
Time : 6:00pm-7:00pm
Location : Leo Lowenstein Building, LL 419
Abstract:
The reconstruction of the tree of evolutionary history, or phylogeny, of
species usually involve computationally intensive search algorithms in the
space of all phylogenies. Such analyses often produce thousands of candidate
trees; biologists resolve the conflict by computing the consensus of these
trees such as the strict and majority consensus methods. These methods all
produce only one consensus tree as a summary of common features and omit
conflicting ones. Though efficient as a means to reduce information, this
inherent limitation means single-tree consensus methods can be unsatisfactory
when the tree space "landscape" is complex. To address this issue, we
proposed an alternative approach by using clustering algorithms on the set of
candidate trees.
In the first half of my talk, I will briefly review the problem of
phylogeny reconstruction and common algorithms for tree space search and
consensus. I will then cover the frame work of clustering in the tree space
as a generalized consensus method. We propose bicriterion problems, in
particular using the concept of information loss, and new consensus trees
called representative trees that minimize the information loss. Our
empirical study using four biological datasets shows that our approach
provides a significant improvement in the information content with only a
small amount of overhead. Furthermore, the consensus trees we obtain for each
of our large clusters are more resolved than the single-tree consensus trees.
Bio:
Dr. Li-San Wang received an M.S. and a Ph.D. degree in Computer Science from
the University of Texas at Austin in 2000 and 2003. He was postdoctoral
fellow at the University of Pennsylvania from 2003 to 2006. Since 2006, he is
an Assistant Professor of Pathology & Laboratory Medicine in the School of
Medicine, University of Pennsylvania.
His research areas include disease-related bioinformatic research,
computational methods for microarray analysis and systems biology, and
computational phylogenetics. Dr. Wang has served as program committee member
of EITC/Bioinformatics 2004, RECOMB Satellite Workshop on Comparative
Genomics and as referee for Journal of Computational Biology, Mathematical
Biology, Systems Biology and RECOMB.
This talk is is in conjunction with Interdisciplinary Faculty Seminar on
Biomedical Informatics of Fordham College at Rose Hill.
For more information or directions, contact Ms. Diane Roche (718) 817-4480
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