Sergei Pond






Kosakovsky Pond SL, Poon AFY, Velazquez R, Weaver S, Hepler NL, Murrell B, Shank SD, Magalis BR, Bouvier D, Nekrutenko A, Wisotsky S, Spielman SJ, Frost SDW, Muse SV. (2020). HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies. Molecular biology and evolution, 37(1)

Weaver S, Shank SD, Spielman SJ, Li M, Muse SV, Kosakovsky Pond SL. (2018). Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes. Molecular biology and evolution, 35(3)

Frost SD, Murrell B, Hossain AS, Silverman GJ, Pond SL. (2015). Assigning and visualizing germline genes in antibody repertoires. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 370(1676)

Edlefsen PT, Rolland M, Hertz T, Tovanabutra S, Gartland AJ, deCamp AC, Magaret CA, Ahmed H, Gottardo R, Juraska M, McCoy C, Larsen BB, Sanders-Buell E, Carrico C, Menis S, Kijak GH, Bose M, , Arroyo MA, O'Connell RJ, Nitayaphan S, Pitisuttithum P, Kaewkungwal J, Rerks-Ngarm S, Robb ML, Kirys T, Georgiev IS, Kwong PD, Scheffler K, Pond SL, Carlson JM, Michael NL, Schief WR, Mullins JI, Kim JH, Gilbert PB. (2015). Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial. PLoS computational biology, 11(2)

Hightower GK, May SJ, Pérez-Santiago J, Pacold ME, Wagner GA, Little SJ, Richman DD, Mehta SR, Smith DM, Pond SL. (2013). HIV-1 clade B pol evolution following primary infection. PLoS One, 8(6)

Pond SL, Murrell B, Poon AF. (2012). Evolution of viral genomes: interplay between selection, recombination, and other forces. Methods in molecular biology (Clifton, N.J.), (856)

Pond SL, Scheffler K, Gravenor MB, Poon AF, Frost SD. (2010). Evolutionary fingerprinting of genes. Molecular biology and evolution, 27(3)

Poon AF, Frost SD, Pond SL. (2009). Detecting signatures of selection from DNA sequences using Datamonkey. Methods in molecular biology (Clifton, N.J.), (537)

Pond SL, Frost SD, Grossman Z, Gravenor MB, Richman DD, Brown AJ. (2006). Adaptation to different human populations by HIV-1 revealed by codon-based analyses. PLoS computational biology, 2(6)

Huelsenbeck JP, Jain S, Frost SW, Pond SL. (2006). A Dirichlet process model for detecting positive selection in protein-coding DNA sequences. Proceedings of the National Academy of Sciences of the United States of America, 103(16)

Pond SL, Frost SD. (2005). Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics (Oxford, England), 21(10)

Pond SL, Frost SD, Muse SV. (2005). HyPhy: hypothesis testing using phylogenies. Bioinformatics (Oxford, England), 21(5)

Pond SL, Frost SD. (2005). A simple hierarchical approach to modeling distributions of substitution rates. Molecular biology and evolution, 22(2)

Pond SL, Frost SD. (2005). A genetic algorithm approach to detecting lineage-specific variation in selection pressure. Molecular biology and evolution, 22(3)