Sergei Pond






Mavian C, Pond SK, Marini S, Magalis BR, Vandamme AM, Dellicour S, Scarpino SV, Houldcroft C, Villabona-Arenas J, Paisie TK, Trovão NS, Boucher C, Zhang Y, Scheuermann RH, Gascuel O, Lam TT, Suchard MA, Abecasis A, Wilkinson E, de Oliveira T, Bento AI, Schmidt HA, Martin D, Hadfield J, Faria N, Grubaugh ND, Neher RA, Baele G, Lemey P, Stadler T, Albert J, Crandall KA, Leitner T, Stamatakis A, Prosperi M, Salemi M. (2020). Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable. Proceedings of the National Academy of Sciences of the United States of America

teams Galaxy and HyPhy developments, Nekrutenko Anton, Pond Sergei L Kosakovsky. (2020). No more business as usual: agile and effective responses to emerging pathogen threats require open data and open analytics. Cold Spring Harbor Laboratory

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)

Spielman SJ, Weaver S, Shank SD, Magalis BR, Li M, Kosakovsky Pond SL. Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces. Methods in molecular biology (Clifton, N.J.), (1910)

Shank SD, Weaver S, Kosakovsky Pond SL. (2018). phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics. BMC bioinformatics, 19(1)

Frost SDW, Magalis BR, Kosakovsky Pond SL. (2018). Neutral Theory and Rapidly Evolving Viral Pathogens. Molecular biology and evolution, 35(6)

Spielman SJ, Kosakovsky Pond SL. (2018). Relative evolutionary rates in proteins are largely insensitive to the substitution model. Molecular biology and evolution

Kosakovsky Pond SL, Weaver S, Leigh Brown AJ, Wertheim JO. (2018). HIV-TRACE (TRAnsmission Cluster Engine): a Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens. Molecular biology and evolution, 35(7)

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)

Landais E, Murrell B, Briney B, Murrell S, Rantalainen K, Berndsen ZT, Ramos A, Wickramasinghe L, Smith ML, Eren K, de Val N, Wu M, Cappelletti A, Umotoy J, Lie Y, Wrin T, Algate P, Chan-Hui PY, Karita E, , , Ward AB, Wilson IA, Burton DR, Smith D, Pond SLK, Poignard P. (2017). HIV Envelope Glycoform Heterogeneity and Localized Diversity Govern the Initiation and Maturation of a V2 Apex Broadly Neutralizing Antibody Lineage. Immunity, 47(5)

Choi JY, Pond SLK, Anderson CM, Richman DD, Smith DM. (2017). Molecular Features of the V1-V4 Coding Region of Sexually Transmitted Human Immunodeficiency Virus Type 1. The Journal of infectious diseases, 215(10)

Manasa J, Varghese V, Pond SLK, Rhee SY, Tzou PL, Fessel WJ, Jang KS, White E, Rögnvaldsson T, Katzenstein DA, Shafer RW. (2017). Evolution of gag and gp41 in Patients Receiving Ritonavir-Boosted Protease Inhibitors. Scientific reports, 7(1)

Lorenzo-Redondo R, Fryer HR, Bedford T, Kim EY, Archer J, Pond SLK, Chung YS, Penugonda S, Chipman J, Fletcher CV, Schacker TW, Malim MH, Rambaut A, Haase AT, McLean AR, Wolinsky SM. (2016). Persistent HIV-1 replication maintains the tissue reservoir during therapy. Nature, 530(7588)

Garcia-Knight MA, Slyker J, Payne BL, Pond SL, de Silva TI, Chohan B, Khasimwa B, Mbori-Ngacha D, John-Stewart G, Rowland-Jones SL, Esbjörnsson J. (2016). Viral Evolution and Cytotoxic T Cell Restricted Selection in Acute Infant HIV-1 Infection. Scientific reports, (6)

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)

Carter CC, Wagner GA, Hightower GK, Caballero G, Phung P, Richman DD, Pond SL, Smith DM. (2015). HIV-1 neutralizing antibody response and viral genetic diversity characterized with next generation sequencing. Virology, (474)

Volz E, Pond S. (2014). Phylodynamic analysis of ebola virus in the 2014 sierra leone epidemic. PLoS currents, (6)

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)

Aldous JL, Pond SK, Poon A, Jain S, Qin H, Kahn JS, Kitahata M, Rodriguez B, Dennis AM, Boswell SL, Haubrich R, Smith DM. (2012). Characterizing HIV transmission networks across the United States. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 55(8)

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)

Mehta SR, Wertheim JO, Delport W, Ene L, Tardei G, Duiculescu D, Pond SL, Smith DM. (2011). Using phylogeography to characterize the origins of the HIV-1 subtype F epidemic in Romania. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 11(5)

Pacold ME, Pond SL, Wagner GA, Delport W, Bourque DL, Richman DD, Little SJ, Smith DM. (2012). Clinical, virologic, and immunologic correlates of HIV-1 intraclade B dual infection among men who have sex with men. AIDS (London, England), 26(2)

Mehta SR, Delport W, Brouwer KC, Espitia S, Patterson T, Pond SK, Strathdee SA, Smith DM. (2010). The relatedness of HIV epidemics in the United States-Mexico border region. AIDS research and human retroviruses, 26(12)

Smith D, Delport W, Butler D, Little S, Richman D, Pond SK. (2010). Response to Comment on "The Origins of Sexually Transmitted HIV Among Men Who Have Sex with Men". Science translational medicine, 2(50)

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

Manosuthi W, Butler DM, Pérez-Santiago J, Poon AF, Pillai SK, Mehta SR, Pacold ME, Richman DD, Pond SK, Smith DM. (2010). Protease polymorphisms in HIV-1 subtype CRF01_AE represent selection by antiretroviral therapy and host immune pressure. AIDS (London, England), 24(3)

Poon AF, Brouwer KC, Strathdee SA, Firestone-Cruz M, Lozada RM, Pond SL, Heckathorn DD, Frost SD. (2009). Parsing social network survey data from hidden populations using stochastic context-free grammars. PloS one, 4(9)

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

Little SJ, Frost SD, Wong JK, Smith DM, Pond SL, Ignacio CC, Parkin NT, Petropoulos CJ, Richman DD. (2008). Persistence of transmitted drug resistance among subjects with primary human immunodeficiency virus infection. Journal of virology, 82(11)

Zárate S, Pond SL, Shapshak P, Frost SD. (2007). Comparative study of methods for detecting sequence compartmentalization in human immunodeficiency virus type 1. Journal of virology, 81(12)

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)

Pillai SK, Pond SL, Liu Y, Good BM, Strain MC, Ellis RJ, Letendre S, Smith DM, Günthard HF, Grant I, Marcotte TD, McCutchan JA, Richman DD, Wong JK. (2006). Genetic attributes of cerebrospinal fluid-derived HIV-1 env. Brain : a journal of neurology, 129(Pt 7)

Frost SD, Liu Y, Pond SL, Chappey C, Wrin T, Petropoulos CJ, Little SJ, Richman DD. (2005). Characterization of human immunodeficiency virus type 1 (HIV-1) envelope variation and neutralizing antibody responses during transmission of HIV-1 subtype B. Journal of virology, 79(10)

Pond SK, Muse SV. (2005). Site-to-site variation of synonymous substitution rates. Molecular biology and evolution, 22(12)

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 genetic algorithm approach to detecting lineage-specific variation in selection pressure. Molecular biology and evolution, 22(3)

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