COLLOQUIUM
Department of Computer Science and Engineering
University of South Carolina
 
Parallel Methods in Computational Genomics

Ananth Kalyanaraman

Department of Computer Engineering
Iowa State University

Date: March 1, 2006
Time: 1600-1700
Place: Swearingen 1C01 (Amoco Hall)

Abstract

Computational genomics has evolved into a vibrant field over the past
two decades. Questions that are of fundamental importance to genomic
science are being addressed through the development of computationally
effective solutions. Several of these biological discoveries are
direct outcomes of analyzing biological sequence data. With the
sequence repositories exponentially growing in their sizes, their
analysis is becoming increasingly complex. Concurrent with these
developments, supercomputing technologies have also advanced
tremendously. However, their computing potential remains relatively
untapped in computational genomics research. My research focuses on
the design and development of parallel algorithms and software for
analyzing large-scale sequence data.  Of particular interest are
problems with an impending need for scalable high-performance
computing solutions. In this talk, I will describe a parallel
clustering algorithm that we developed for the following two
applications: (i) clustering Expressed Sequence Tags (ESTs) which are
a type of DNA sequence data used in gene-related studies, and (ii)
clustering genomic data for maize genome assembly.  The novelty of our
approach lies in its space and time efficiency and its capability to
exploit the vast computing power and memory easily available through
distributed memory parallel computers. This work has significantly
enhanced the problem size reach while also drastically reducing the
time to solution.

Ananth Kalyanaraman is a doctoral candidate in Computer Engineering at
Iowa State University. He received his M.S. in Computer Science from
Iowa State University in 2002, and B.E. in Computer Science and
Engineering from Visvesvaraya National Institute of Technology,
Nagpur, India in 1998. His research interests include bioinformatics
and computational biology, parallel computing, and string algorithms.
Ananth is a recipient of IBM and Pioneer Hi-Bred graduate research
fellowships.  Recently, two of his publications were recognized with
best paper awards (in the IPDPS'06 and CSB'05 conferences). He is a
member of ACM, IEEE, and SIAM.  More information can be found at his
homepage: http://www.public.iastate.edu/~ananthk