Sergei L Kosakovsky Pond

Sergei L Kosakovsky Pond
Assistant Adjunct Professor
Department of Medicine
University of California, San Diego
220 Dickinson St, Suite A
San Diego, CA 92103
Phone: +1 619 543 8898
Fax : +1 619 543 5066
E-mail: email Sergei CV

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

• 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

List last updated on June 22, 2010

Search PubMed for the complete list of Sergei's papers

• HyPhy: hypothesis testing using phylogenies
• Not so different after all: A comparison of methods for detecting amino acid sites under selection
• Datamonkey: rapid detection of selective pressure on individual sites of codon alignments
• Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection
• Automated phylogenetic detection of recombination using a genetic algorithm