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Sergei Pond

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Sergei Pond

  • College of Science and Technology

    • Biology

      • Professor

Courses Taught

Number

Name

Level

BIOL 3111

Genomics in Medicine

Undergraduate

BIOL 5111

Genomics in Medicine

Graduate

Selected Publications

Recent

  • Rahman, S., Pond, S.K., Webb, A., & Hey, J. (2021). Weak selection on synonymous codons substantially inflates dN/dS estimates in bacteria. Proceedings of the National Academy of Sciences of the United States of America, 118(20). doi: 10.1073/pnas.2023575118.

  • Lucaci, A., Wisotsky, S., Shank, S., Weaver, S., & Pond, S.K. (2021). Extra base hits: Widespread empirical support for instantaneous multiple-nucleotide changes. PLoS ONE, 16(3 March). doi: 10.1371/journal.pone.0248337.

  • Pond, S.K., Wisotsky, S., Escalante, A., Magalis, B., & Weaver, S. (2021). Contrast-FEL - A Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches. Molecular Biology and Evolution, 38(3), 1184-1198. doi: 10.1093/molbev/msaa263.

  • Wisotsky, S., Pond, S., Shank, S., & Muse, S. (2021). Synonymous site-to-site substitution rate variation dramatically inflates false positive rates of selection analyses: Ignore at your own peril. Molecular Biology and Evolution, 37(8), 2430-2439. doi: 10.1093/MOLBEV/MSAA037.

  • Pollock, D., Castoe, T., Perry, B., Lytras, S., Wade, K., Robertson, D., Holmes, E., Boni, M., Pond, S.K., Parry, R., Carlton, E., Wood, J., Pennings, P., & Goldstein, R. (2020). Viral CpG deficiency provides no evidence that dogs were intermediate hosts for SARS-CoV-2. Molecular Biology and Evolution, 37(9), 2706-2710. doi: 10.1093/molbev/msaa178.

  • Council, O., Zhou, S., McCann, C., Hoffman, I., Tegha, G., Kamwendo, D., Matoga, M., Pond, S.K., Cohen, M., & Swanstroma, R. (2020). Deep sequencing reveals compartmentalized HIV-1 in the semen of men with and without sexually transmitted infection-associated urethritis. Journal of Virology, 94(12). doi: 10.1128/JVI.00151-20.

  • Miura, S., Tamura, K., Tao, Q., Huuki, L., Pond, S.K., Priest, J., Deng, J., & Kumar, S. (2020). A new method for inferring timetrees from temporally sampled molecular sequences. PLoS Computational Biology, 16(1). doi: 10.1371/journal.pcbi.1007046.

  • RifeMagalis, B., Strickland, S.L., Shank, S.D., Autissier, P., Schuetz, A., Sithinamsuwan, P., Lerdlum, S., Fletcher, J.L., Souza, M.d., Ananworanich, J., Valcour, V., Williams, K.C., Pond, S.L.K., RattoKim, S., Salemi, M., & Grp, S.S. Phyloanatomic characterization of the distinct T cell and monocyte contributions to the peripheral blood HIV population within the host. VIRUS EVOLUTION, 6(1). 10.1093/ve/veaa005

  • Tzou, P., Pond, S.K., Avila-Rios, S., Holmes, S., Kantor, R., & Shafer, R. (2020). Analysis of unusual and signature APOBEC-mutations in HIV-1 pol next-generation sequences. PLoS ONE, 15(2). doi: 10.1371/journal.pone.0225352.

  • Pond, S.K., Poon, A., Velazquez, R., Weaver, S., Hepler, N., Murrell, B., Shank, S., Magalis, B., Bouvier, D., Nekrutenko, A., Wisotsky, S., Spielman, S., Frost, S., & Muse, S. (2020). HyPhy 2.5 - A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies. Molecular Biology and Evolution, 37(1), 295-299. doi: 10.1093/molbev/msz197.

  • Mannino, F., Wisotsky, S., Pond, S., & Muse, S. (2020). Equiprobable discrete models of site-specific substitution rates underestimate the extent of rate variability. PLoS ONE, 15(3). doi: 10.1371/journal.pone.0229493.

  • Avanzato, V., Oguntuyo, K., Escalera-Zamudio, M., Gutierrez, B., Golden, M., Pond, S.K., Pryce, R., Walter, T., Seow, J., Doores, K., Pybus, O., Munster, V., Lee, B., & Bowden, T. (2019). A structural basis for antibody-mediated neutralization of Nipah virus reveals a site of vulnerability at the fusion glycoprotein apex. Proceedings of the National Academy of Sciences of the United States of America, 116(50), 25057-25067. doi: 10.1073/pnas.1912503116.

  • Yan, Y., Maurer-Alcalá, X., Knight, R., Pond, S., & Katz, L. (2019). Single-cell transcriptomics reveal a correlation between genome architecture and gene family evolution in ciliates. MBio, 10(6). doi: 10.1128/mBio.02524-19.

  • Rhee, S., Magalis, B., Hurley, L., Silverberg, M., Marcus, J., Slome, S., Pond, S., & Shafer, R. (2019). National and international dimensions of human immunodeficiency virus-1 sequence clusters in a northern California clinical cohort. Open Forum Infectious Diseases, 6(4). doi: 10.1093/ofid/ofz135.

  • Rhee, S., Clutter, D., Fessel, W., Klein, D., Slome, S., Pinsky, B., Marcus, J., Hurley, L., Silverberg, M., Pond, S., & Shafer, R. (2019). Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted Human Immunodeficiency Virus Type 1 Drug Resistance in a Large US Clinic Population. Clinical Infectious Diseases, 68(2), 213-221. doi: 10.1093/cid/ciy453.

  • Tzou, P., Rhee, S., Pond, S., Manasa, J., & Shafer, R. (2018). Selection analyses of paired HIV-1 gag and gp41 sequences obtained before and after antiretroviral therapy. Scientific Data, 5(1). doi: 10.1038/sdata.2018.147.

  • Dalai, S., Junqueira, D., Wilkinson, E., Mehra, R., Pond, S.K., Levy, V., Israelski, D., Oliveira, T.D., & Katzenstein, D. (2018). Combining phylogenetic and network approaches to identify HIV-1 transmission links in San Mateo County, California. Frontiers in Microbiology, 9(DEC). doi: 10.3389/fmicb.2018.02799.

  • Eren, K., Weaver, S., Ketteringham, R., Valentyn, M., Smith, M.L., Kumar, V., Mohan, S., Pond, S.K., & Murrell, B. (2018). Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons. PLoS Computational Biology, 14(12). doi: 10.1371/journal.pcbi.1006498.

  • Wertheim, J., Murrell, B., Mehta, S., Forgione, L., Pond, S.K., Smith, D., & Torian, L. (2018). Growth of HIV-1 molecular transmission clusters in New York City. Journal of Infectious Diseases, 218(12), 1943-1953. doi: 10.1093/infdis/jiy431.

  • Spielman, S. & Pond, S.K. (2018). Relative evolutionary rates in proteins are largely insensitive to the substitution model. Molecular Biology and Evolution, 35(9), 2307-2317. doi: 10.1093/molbev/msy127.

  • Shank, S., Weaver, S., & Pond, S.K. (2018). phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics. BMC Bioinformatics, 19(1). doi: 10.1186/s12859-018-2283-2.

  • Pond, S.K., Weaver, S., Brown, A.L., & Wertheim, J. (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), 1812-1819. doi: 10.1093/molbev/msy016.

  • Frost, S., Magalis, B., & Pond, S.K. (2018). Neutral theory and rapidly evolving viral pathogens. Molecular Biology and Evolution, 35(6), 1348-1354. doi: 10.1093/molbev/msy088.

  • Weaver, S., Shank, S., Spielman, S., Li, M., Muse, S., & Pond, S.K. (2018). Datamonkey 2.0: A modern web application for characterizing selective and other evolutionary processes. Molecular Biology and Evolution, 35(3), 773-777. doi: 10.1093/molbev/msx335.

  • Pacheco, M., Matta, N., Valkiünas, G., Parker, P., Mello, B., Stanley, C., Lentino, M., Garcia-Amado, M., Cranfield, M., Pond, S., & Escalante, A. (2018). Mode and rate of evolution of haemosporidian mitochondrial genomes: Timing the radiation of avian parasites. Molecular Biology and Evolution, 35(2), 383-403. doi: 10.1093/molbev/msx285.

  • Spielman, S. & Pond, S. (2018). Relative evolutionary rate inference in HyPhy with LEISR. PeerJ, 2018(2). doi: 10.7717/peerj.4339.

  • Magalis, B.R., Pond, S.L.K., Summers, M.F., & Salemi, M. Evaluation of global HIV/SIV envelope gp120 RNA structure and evolution within and among infected hosts. VIRUS EVOLUTION, 4(1). 10.1093/ve/vey018

  • Braunstein, M., Bannoudi, H.E., Hay, M.A., Pond, S.L., & Silverman, G.J. (2017). Analysis of the IgA Heavy Chain Repertoire in Multiple Myeloma: Implications for Host-Microbiome Influences. BLOOD, 130. Retrieved from http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000432419700233&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=abcd71df5a6dac31fd219478b0a9c638.

  • Manasa, J., Varghese, V., Pond, S., Rhee, S., Tzou, P., Fessel, W., Jang, K., White, E., Rögnvaldsson, T., Katzenstein, D., & Shafer, R. (2017). Evolution of gag and gp41 in Patients Receiving Ritonavir-Boosted Protease Inhibitors. Scientific Reports, 7(1). doi: 10.1038/s41598-017-11893-8.

  • Lorenzo-Redondo, R., Fryer, H., Bedford, T., Kim, E., Archer, J., Pond, S., Chung, Y., Penugonda, S., Chipman, J., Fletcher, C., Schacker, T., Malim, M., Rambaut, A., Haase, A., McLean, A., & Wolinsky, S. (2017). Lorenzo-Redondo et al. reply. Nature, 551(7681), E10. doi: 10.1038/nature24635.

  • Landais, E., Murrell, B., Briney, B., Murrell, S., Rantalainen, K., Berndsen, Z., Ramos, A., Wickramasinghe, L., Smith, M., Eren, K., Val, N.d., Wu, M., Cappelletti, A., Umotoy, J., Lie, Y., Wrin, T., Algate, P., Chan-Hui, P., Karita, E., Ward, A., Wilson, I., Burton, D., Smith, D., Pond, S., & 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), 990-1003.e9. doi: 10.1016/j.immuni.2017.11.002.

  • Wagner, G., Landais, E., Caballero, G., Phung, P., Pond, S., Poignard, P., Richman, D., Little, S., & Smitha, D. (2017). Intrasubtype B HIV-1 superinfection correlates with delayed neutralizing antibody response. Journal of Virology, 91(17). doi: 10.1128/JVI.00475-17.

  • Forrester, N., Wertheim, J., Dugan, V., Auguste, A., Lin, D., Adams, A., Chen, R., Gorchakov, R., Leal, G., Estrada-Franco, J., Pandya, J., Halpin, R., Hari, K., Jain, R., Stockwell, T., Das, S., Wentworth, D., Smith, M., Pond, S.K., & Weaver, S. (2017). Evolution and spread of Venezuelan equine encephalitis complex alphavirus in the Americas. PLoS Neglected Tropical Diseases, 11(8). doi: 10.1371/journal.pntd.0005693.

  • Choi, J., Pond, S., Anderson, C., Richman, D., & Smith, D. (2017). Molecular Features of the V1-V4 Coding Region of Sexually Transmitted Human Immunodeficiency Virus Type 1. Journal of Infectious Diseases, 215(10), 1506-1513. doi: 10.1093/infdis/jix184.

  • Brayne, A., Dearlove, B., Lester, J., Pond, S., & Frost, S. (2017). Genotype-specific evolution of hepatitis E virus. Journal of Virology, 91(9). doi: 10.1128/JVI.02241-16.

  • Green, N., Hoenigl, M., Chaillon, A., Anderson, C., Pond, S., Smith, D., & Little, S. (2017). Partner services in adults with acute and early HIV infection. AIDS, 31(2), 287-293. doi: 10.1097/QAD.0000000000001308.

  • Bannoudi, H.E., Anquetil, C., Braunstein, M., Pond, S., & Silverman, G. (2017). Unbiased RACE-based massive parallel surveys of human IgA antibody repertoires. doi: 10.1007/978-1-4939-7180-0_5.

  • Wertheim, J., Pond, S.K., Forgione, L., Mehta, S., Murrell, B., Shah, S., Smith, D., Scheffler, K., & Torian, L. (2017). Social and Genetic Networks of HIV-1 Transmission in New York City. PLoS Pathogens, 13(1). doi: 10.1371/journal.ppat.1006000.