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Sergei L Kosakovsky Pond

Associate Professor

Contact Information

Department of Medicine
University of California, San Diego
220 Dickinson St, Suite A
San Diego, CA 92103
Phone: 619-543-8898
Fax : 619-543-5066
E-mail: spond at ucsd dot edu

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 assistant 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 ( and the companion evolutionary analysis webserver I also contribute sequence analysis and metagenomics tools to the genome-scale analysis software framework Galaxy (

I am a Highly Cited researcher in computer science. Click here to see my Google Scholar profile and here to to see my full publication list in ResearcherID.

Research Interests

Methods, algorithms and software for statistical analysis, inference and hypothesis testing on molecular sequence data. In particular, I am interested in unique challenges posed by studying the evolution of HIV and other RNA viruses, with their extreme mutation and recombination rates, multiple adaptive mechanisms and computational difficulties involved in the analysis of very large molecular datasets.

Software projects

  • HyPhy. Hypothesis Testing Using Phylogenies: a platform for statistical analysis and hypothesis testing with genetic sequence data
  • Datamonkey. A web-based interface to MPI cluster versions of HyPhy to search for adaptive and purifying evolution in coding sequences, model selection and other tools
  • Galaxy. Evolutionary and data processing module development