COLLOQUIUM
Department of Computer Science and Engineering
University of South Carolina
 
Computational Challenges and Advances in Genome Assembly from Short Reads


Max Alekseyev

Department of Computer Science and Engineering
University of South Carolina

Date: May 25, 2011
Time: 1500-1600 (3pm-4pm)
Place: Swearingen 1A03 (Faculty Lounge)

Abstract

The next generation of sequencing technology provides a cheap and fast way for 
reading millions of short DNA fragments, thus promising an exponential growth 
in the number of sequenced genomes in the next few years and heightening the 
need for an efficient and accurate tool for assembling genomes from short 
reads. Existing assemblers face many obstacles such as errors in reads, 
presence of repeats, variations in repeat instances, gaps in reads coverage, 
inaccurate insert size, etc. There are still no sufficiently accurate 
assemblers that overcome all these obstacles.
In this talk I will describe computational challenges associated with these 
obstacles and present recent algorithmic advances developed at the Algorithmic 
Biology Lab at Saint Petersburg Academic University.

Max Alekseyev is an Assistant Professor in the Department of Computer Science 
and Engineering at the University of South Carolina. He is currently on leave 
at the Algorithmic Biology Lab in St. Petersburg, Russia, where he holds the 
position of scientific executive director. He received his PhD in Computer 
Science from the University of California at San Diego (UCSD) 2007. Prior to 
joining UCSD in 2001, he obtained the MS degree in Mathematics from Nizhni 
Novgorod State University, Russia. His research interests include 
computational molecular biology, bioinformatics, comparative genomics, graph 
theory, combinatorics, and discrete algorithms. He is Editor-in-Chief of the 
Online Encyclopedia of Integer Sequences (OEIS) and Associate Editor of 
Frontiers in Bioinformatics and Computational Biology.