Colloquia, Seminars and Conference News
Title : Virus Quasispecies Assembly using Network Flows
Date : October 7, 2009. (4:00 pm) Tea starts half an hour before each seminar
Location: ITEB 336
Speaker : Alex Zelikovsky
Abstract:
Understanding how the genomes of viruses mutate and evolve within
infected individuals is critically important in epidemiology. In this
talk I focus on optimization problems in sequence assembly for viruses
based on 454 Lifesciences system. Several formulations of the
quasispecies assembly problem and a measure of the assembly quality
will be given. I will describe a scalable assembling method for
quasispecies based on network flow and maximum likelihood formulations
and then give details of existing and novel methods for reliably
assembling quasipsecies that have very long common segments.
Finally, I report the results of assembling 44 quasispecies from the
1700 bp long E1E2 region of Hepatitis C Virus.
(Joint work with K. Wesbrooks, I. Astrovskaya (GSU) D. C. Rendon, Y.
Khudyakov (CDC), P. Berman (Penn State), I. Mandoiu (UConn))
Bio:Alex Zelikovsky is a Professor at Computer Science Department, Georgia
State University. His research areas include discrete algorithms and
applications in bioinformatics, VLSI CAD, and wireless networks. Out of his 160 refereed publications, 4 received best paper awards at the top international conferences and one journal paper won SIAM Outstanding Paper Prize. He is a chair and PC member of many international conferences, an editor of several special issues and on the editorial board of 5 international journals.
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