Author Profile

Sergei Pond

Institution: University of California San Diego

Department: Medicine

City: San Diego

State: CA

Country: USA

Following formal undergraduate training in computer science (at Kiev State University, Ukraine), I received a PhD from the interdisciplinary program in Applied Mathematics at the University of Arizona. My theoretical graduate research into statistical methodology for evolutionary analyses of coding sequence alignments found an application in an HIV research group at UCSD, which I joined as a postdoctoral fellow in 2003. Presently, I am an associate professor in the Divisions of Infectious Diseases and Biomedical Informatics in the UCSD Department of Medicine. In addition, I am the director the Bioinformatics, Evolutionary Analysis and Statistics Core at the UCSD Center of AIDS Research. My research interest include developing models and computational approaches for comparative analysis of sequence data, especially large and rich data set from measurably evolving pathogens, such as HIV-1, Influenza A virus and Hepatitis C virus. My group has published a number of methodological and applied papers applying evolutionary algorithms and machine learning techniques to complex problems in sequence evolution, especially in the context of HIV population history, adaptation to new hosts, transmission, immune escape, and the development of drug resistance. We have recently begun to develop the tools necessary to analyze and interpret large next generation sequencing data sets obtained from individual HIV positive subjects. I am also actively involved in open source software development. I am the primary developer of the molecular evolution package HyPhy (www.hyphy.org) and the companion evolutionary analysis webserver www.datamonkey.org.

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