Sergei L Kosakovsky Pond
Brief Academic Biography
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 (www.hyphy.org) and the companion evolutionary analysis webserver www.datamonkey.org. I also contribute sequence analysis and metagenomics tools to the genome-scale analysis software framework Galaxy (www.galaxyproject.org).
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.
Download Sergei's reasonably current CV File:Slkp cv.pdf
- 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
Five most cited publications
List last updated in March, 2013
- HyPhy: hypothesis testing using phylogenies (571 citations)
- Datamonkey: rapid detection of selective pressure on individual sites of codon alignments (314 citations)
- Not so different after all: A comparison of methods for detecting amino acid sites under selection (312 citations)
- Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection (175 citations)
- Automated phylogenetic detection of recombination using a genetic algorithm (159 citations)