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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, with its extreme
mutation and recombination rates, multiple adaptive mechanisms and computational challenges
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 developed in collaboration with
Spencer Muse and
Simon Frost.
- 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 developed in collaboration with
Simon Frost.
- Galaxy
- Evolutionary and data processing module development
Conferences [this section is not current]
- 2006
- Sergei L Kosakovsky Pond, Spencer V Muse, Michael B Gravenor, Frank Mannino, Simon D W Frost
"Identifying Preferred and Suppressed Amino-Acid Substitutions in HIV-1 Genes Using Codon-Based Comparative Genetic Algorithm Analysis"
Talk at the 13th Workshop on HIV Dynamics and Evolution Woods Hole, MA, Apr 5th-8th, 2006.
- Sergei Kosakovsky Pond, D Smith, C Chappey, T Wrin, Y Liu, D Richman, S Little, S Frost, and E Daar
"Recombination during Intraclade HIV Dual Infection".
Poster presentation at the 13th Conference on Retroviruses and Opportunistic Infections. Denver, CO, Feb 22nd-25th, 2005.
[Abstract]
- S L Kosakovsky PondS D W Frost.
- 2005
- Sergei L Kosakovsky Pond, Douglas D Richman, Simon D W Frost
"Genetic Algorithms for Detecting Recombination"
Talk at the 12th Workshop on HIV Dynamics and Evolution Cleveland, OH, Apr 23rd-25th, 2005. [PDF]
- Sergei Kosakovsky Pond, S Frost, D Richman, and A Leigh Brown
"Footprints in Snow? Analyzing Host vs Population Selection in HIV Sequences".
Poster presentation at the 12th Conference on Retroviruses and Opportunistic Infections. Boston, MA, Feb 22nd-25th, 2005.
[Abstract]
- S L Kosakovsky PondS D W Frost.
"A genetic algortihms approach to identifying credible stochastic models of sequence evolution.".
Poster presentation at
the 10th Pacific Symposium in Biocomputing. Big Island, Hawaii, Jan 4th-8th, 2005.
- 2004
- S L Kosakovsky Pond, A J Leigh Brown, and S D W Frost.
"Comparing Adaptive and Purifying Selection Acting on HIV Genes in Different Populations".
Oral presentation at the
11th International Workshop on HIV Dynamics and Evolution. Stockholm, Sweden.
- S L Kosakovsky Pond, D D Richman, J A McCutchan, A J Leigh Brown, and S D W Frost.
"Natural Polymorphisms in HIV-1 Protease, Reverse Transcriptase, and Integrase are Maintained by Selection".
Poster presentation at the 11th Conference on Retroviruses and Opportunistic Infections. San Francisco, CA, Feb 8th-11th, 2004.
[Abstract]
- 2003
- S L Kosakovsky Pond, Spencer V Muse.
"Modeling evolution of protein coding DNA sequences". Invited talk at the
10th International Workshop on HIV Dynamics and Evolution. Lake Arrowhead, CA.
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