Alex Zelikovsky

Professor, Computer Science Department, Georgia State University

For more information please contact Dr. Mark Borodovsky at borodovsky@ gatech.edu

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"Virus Quasispecies Assembly using Network Flows"

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)

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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You are cordially invited to attend a reception between 1:30-2:00, before the seminar, to chat informally with faculty and students.

Refreshments will be provided

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