CGB Roundtable Details
Hon Wai Leong, National University of Singapore
Gene Team Tree: Visualizing all Gene Teams
July 16, 2008 at 1:00 PM
Myers 209
Description:
The identification of conserved gene clusters is an important step
towards understanding genome evolution and predicting the function of
genes. Bergeron et. al. formalized the concept of gene teams, which
is a
model for conserved gene clusters that takes into account the position
of genes on a genome. Gene teams are also referred to as max-gap
clusters and they are widely used in practice. These methods require a
user-specified parameter, delta, that specifies the maximum distance
between adjacent genes in a gene team. However, determining reasonable
values for this delta is non-trivial. Furthermore, different regions
of
the genome may have different rates of rearrangement and hence require
different values of delta to discover meaningful gene clusters.
In this talk, we briefly survey approaches to finding gene teams.
Then, we present our new approach of generating a gene team tree
which is a compact representation of all the possible gene teams for
all possible value of the parameter delta. We also develop an
efficient
algorithm for computing the gene team tree. We verify the practicality
of our approach by running our algorithm on several biological
datasets.
We are also exploring new uses for the gene team tree.
(This is joint work with Melvin Zhang.)
Short Biographical Information of Dr. Hon Wai Leong
Hon Wai Leong is an Associate Professor in the Department
of Computer Science at the National University of Singapore.
He received the B.Sc. (Hon) degree in Mathematics from the
University of Malaya and the Ph.D. degree in Computer Science
from the University of Illinois at Urbana-Champaign.
His research interest is in the design of practical algorithms
for combinatorial optimization problems from diverse application areas
including VLSI-CAD, transportation logistics, multimedia systems,
and computational biology. In computational biology, his current
interests includes computational proteomics, sequencing-by-
hybridization,
fragment assembly, and genome rearrangement.
Homepage: http://www.comp.nus.edu.sg/~leonghw/
