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Sergei Pond

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Sergei Pond

  • College of Science and Technology

    • Office of the Dean

      • Associate Dean

Courses Taught

Number

Name

Level

BIOL 3111

Genomics in Medicine

Undergraduate

BIOL 3113

Genome Analytics

Undergraduate

BIOL 5111

Genomics in Medicine

Graduate

BIOL 5466

Contemporary Biology

Graduate

Selected Publications

Recent

  • Verdonk, H., Pivirotto, A., Pavinato, V., Hey, J., & Pond, S.L. (2025). A New Comparative Framework for Estimating Selection on Synonymous Substitutions. Mol Biol Evol, 42(4). United States. 10.1093/molbev/msaf068

  • Selberg, A., Clark, N.L., Sackton, T.B., Muse, S.V., Lucaci, A.G., Weaver, S., Nekrutenko, A., Chikina, M., & Pond, S.L.K. (2025). Minus the Error: Testing for Positive Selection in the Presence of Residual Alignment Errors. BioRxiv. United States. 10.1101/2024.11.13.620707

  • Havens, J.L., Pond, S.L.K., Zehr, J.D., Pekar, J.E., Parker, E., Worobey, M., Andersen, K.G., & Wertheim, J.O. (2025). Dynamics of natural selection preceding human viral epidemics and pandemics. BioRxiv. United States. 10.1101/2025.02.26.640439

  • Verdonk, H., Pivirotto, A., Pavinato, V., Hey, J., & Pond, S.L. (2025). A new comparative framework for estimating selection on synonymous substitutions. BioRxiv. United States. 10.1101/2024.09.17.613331

  • Zarate, S., Bertram, M., Rodgers, C., Reed, K., Pelzel-McCluskey, A., Gomez-Romero, N., Rodriguez, L.L., Mayo, C., Mire, C., Pond, S.L.K., & Velazquez-Salinas, L. (2024). Phylogenomic Signatures of a Lineage of Vesicular Stomatitis Indiana Virus Circulating During the 2019-2020 Epidemic in the United States. Viruses, 16(11). Switzerland. 10.3390/v16111803

  • Misra, S., Gilbride, E., Ramasamy, S., Pond, S.L.K., & Kuchipudi, S.V. (2024). Enhanced Diversifying Selection on Polymerase Genes in H5N1 Clade 2.3.4.4b: A Key Driver of Altered Species Tropism and Host Range Expansion. BioRxiv. United States. 10.1101/2024.08.19.606826

  • Wirthlin, M.E., Schmid, T.A., Elie, J.E., Zhang, X., Kowalczyk, A., Redlich, R., Shvareva, V.A., Rakuljic, A., Ji, M.B., Bhat, N.S., Kaplow, I.M., Schäffer, D.E., Lawler, A.J., Wang, A.Z., Phan, B.N., Annaldasula, S., Brown, A.R., Lu, T., Lim, B.K., Azim, E., Consortium, Z., Clark, N.L., Meyer, W.K., Pond, S.L.K., Chikina, M., Yartsev, M.M., Pfenning, A.R., Andrews, G., Armstrong, J.C., Bianchi, M., Birren, B.W., Bredemeyer, K.R., Breit, A.M., Christmas, M.J., Clawson, H., Damas, J., Palma, F.D., Diekhans, M., Dong, M.X., Eizirik, E., Fan, K., Fanter, C., Foley, N.M., Forsberg-Nilsson, K., Garcia, C.J., Gatesy, J., Gazal, S., Genereux, D.P., Goodman, L., Grimshaw, J., Halsey, M.K., Harris, A.J., Hickey, G., Hiller, M., Hindle, A.G., Hubley, R.M., Hughes, G.M., Johnson, J., Juan, D., Kaplow, I.M., Karlsson, E.K., Keough, K.C., Kirilenko, B., Koepfli, K., Korstian, J.M., Kowalczyk, A., Kozyrev, S.V., Lawler, A.J., Lawless, C., Lehmann, T., Levesque, D.L., Lewin, H.A., Li, X., Lind, A., Lindblad-Toh, K., Mackay-Smith, A., Marinescu, V.D., Marques-Bonet, T., Mason, V.C., Meadows, J.R., Meyer, W.K., Moore, J.E., Moreira, L.R., Moreno-Santillan, D.D., Morrill, K.M., Muntané, G., Murphy, W.J., Navarro, A., Nweeia, M., Ortmann, S., Osmanski, A., Paten, B., Paulat, N.S., Pfenning, A.R., Phan, B.N., Pollard, K.S., Pratt, H.E., Ray, D.A., Reilly, S.K., Rosen, J.R., Ruf, I., Ryan, L., Ryder, O.A., Sabeti, P.C., Schäffer, D.E., Serres, A., Shapiro, B., Smit, A.F., Springer, M., Srinivasan, C., Steiner, C., Storer, J.M., Sullivan, K.A., Sullivan, P.F., Sundström, E., Supple, M.A., Swofford, R., Talbot, J., Teeling, E., Turner-Maier, J., Valenzuela, A., Wagner, F., Wallerman, O., Wang, C., Wang, J., Weng, Z., Wilder, A.P., Wirthlin, M.E., Xue, J.R., & Zhang, X. (2024). Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements. Science, 383(6690), eabn3263. United States. 10.1126/science.abn3263

  • Lucaci, A.G., Brew, W.E., Pond, S.L.K., & Moore, A.R. (2023). Evolutionary analysis of mammalian Rem2, a member of the RGK (Rem, Rem2, Rad, and Gem/Kir) family of small GTPases, reveals the role of selection and epistasis in shaping protein functional constraints. Cold Spring Harbor Laboratory. doi: 10.1101/2023.08.28.555117.

  • Tao, K., Rhee, S., Tzou, P.L., Osman, Z.A., Pond, S.L.K., Holmes, S.P., & Shafer, R.W. (2023). HIV-1 Group M Capsid Amino Acid Variability: Implications for Sequence Quality Control of Genotypic Resistance Testing. Viruses, 15(4). Switzerland. 10.3390/v15040992

  • Escalera-Zamudio, M., Pond, S.L.K., Viña, N.M.d.l., Gutiérrez, B., Inward, R.P., Thézé, J., Dorp, L.v., Castelán-Sánchez, H.G., Bowden, T.A., Pybus, O.G., & Hulswit, R.J. (2023). Identification of evolutionary trajectories shared across human betacoronaviruses. BioRxiv. United States. 10.1101/2021.05.24.445313

  • Tegally, H., Moir, M., Everatt, J., Giovanetti, M., Scheepers, C., Wilkinson, E., Subramoney, K., Makatini, Z., Moyo, S., Amoako, D.G., Baxter, C., Althaus, C.L., Anyaneji, U.J., Kekana, D., Viana, R., Giandhari, J., Lessells, R.J., Maponga, T., Maruapula, D., Choga, W., Matshaba, M., Mbulawa, M.B., Msomi, N., consortium, N., Naidoo, Y., Pillay, S., Sanko, T.J., San, J.E., Scott, L., Singh, L., Magini, N.A., Smith-Lawrence, P., Stevens, W., Dor, G., Tshiabuila, D., Wolter, N., Preiser, W., Treurnicht, F.K., Venter, M., Chiloane, G., McIntyre, C., O'Toole, A., Ruis, C., Peacock, T.P., Roemer, C., Pond, S.L.K., Williamson, C., Pybus, O.G., Bhiman, J.N., Glass, A., Martin, D.P., Jackson, B., Rambaut, A., Laguda-Akingba, O., Gaseitsiwe, S., Gottberg, A.v., & Oliveira, T.d. (2022). Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa. Nat Med, 28(9), 1785-1790. United States. 10.1038/s41591-022-01911-2

  • Benndorf, R., Velazquez, R., Zehr, J.D., Pond, S.L.K., Martin, J.L., & Lucaci, A.G. (2022). Human HspB1, HspB3, HspB5 and HspB8: Shaping these disease factors during vertebrate evolution. Cell Stress Chaperones, 27(4), 309-323. Netherlands. 10.1007/s12192-022-01268-y

  • Zehr, J.D., Pond, S.L.K., Martin, D.P., Ceres, K., Whittaker, G.R., Millet, J.K., Goodman, L.B., & Stanhope, M.J. (2022). Recent Zoonotic Spillover and Tropism Shift of a Canine Coronavirus Is Associated with Relaxed Selection and Putative Loss of Function in NTD Subdomain of Spike Protein. Viruses, 14(5). Switzerland. 10.3390/v14050853

  • Canuti, M., Bianchi, S., Kolbl, O., Pond, S.L.K., Kumar, S., Gori, M., Fappani, C., Colzani, D., Borghi, E., Zuccotti, G., Raviglione, M.C., Tanzi, E., & Amendola, A. (2022). Waiting for the truth: is reluctance in accepting an early origin hypothesis for SARS-CoV-2 delaying our understanding of viral emergence? BMJ Glob Health, 7(3). England. 10.1136/bmjgh-2021-008386

  • Rahman, S., Pond, S.L.K., Webb, A., & Hey, J. (2021). Weak selection on synonymous codons substantially inflates dN/dS estimates in bacteria. Proc Natl Acad Sci U S A, 118(20). United States. 10.1073/pnas.2023575118

  • Pond, S.L.K., Wisotsky, S.R., Escalante, A., Magalis, B.R., & Weaver, S. (2021). Contrast-FEL-A Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches. Mol Biol Evol, 38(3), 1184-1198. United States. 10.1093/molbev/msaa263

  • Lucaci, A.G., Wisotsky, S.R., Shank, S.D., Weaver, S., & Pond, S.L.K. (2021). Extra base hits: Widespread empirical support for instantaneous multiple-nucleotide changes. PLoS One, 16(3), e0248337. United States. 10.1371/journal.pone.0248337

  • Pollock, D.D., Castoe, T.A., Perry, B.W., Lytras, S., Wade, K.J., Robertson, D.L., Holmes, E.C., Boni, M.F., Pond, S.L.K., Parry, R., Carlton, E.J., Wood, J.L., Pennings, P.S., & Goldstein, R.A. (2020). Viral CpG Deficiency Provides No Evidence That Dogs Were Intermediate Hosts for SARS-CoV-2. Mol Biol Evol, 37(9), 2706-2710. United States. 10.1093/molbev/msaa178

  • Wisotsky, S.R., Pond, S.L.K., Shank, S.D., & Muse, S.V. (2020). Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril. Mol Biol Evol, 37(8), 2430-2439. United States. 10.1093/molbev/msaa037

  • Council, O.D., Zhou, S., McCann, C.D., Hoffman, I., Tegha, G., Kamwendo, D., Matoga, M., Pond, S.L.K., Cohen, M.S., & Swanstrom, R. (2020). Deep Sequencing Reveals Compartmentalized HIV-1 in the Semen of Men with and without Sexually Transmitted Infection-Associated Urethritis. J Virol, 94(12). United States. 10.1128/JVI.00151-20

  • Pond, S.L.K., Poon, A.F., Velazquez, R., Weaver, S., Hepler, N.L., Murrell, B., Shank, S.D., Magalis, B.R., Bouvier, D., Nekrutenko, A., Wisotsky, S., Spielman, S.J., Frost, S.D., & Muse, S.V. (2020). HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies. Mol Biol Evol, 37(1), 295-299. United States. 10.1093/molbev/msz197

  • Mannino, F., Wisotsky, S., Pond, S.L.K., & Muse, S.V. (2020). Equiprobable discrete models of site-specific substitution rates underestimate the extent of rate variability. PLoS One, 15(3), e0229493. United States. 10.1371/journal.pone.0229493

  • Miura, S., Tamura, K., Tao, Q., Huuki, L.A., Pond, S.L.K., Priest, J., Deng, J., & Kumar, S. (2020). A new method for inferring timetrees from temporally sampled molecular sequences. PLoS Comput Biol, 16(1), e1007046. United States. 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., Group, S.S., Williams, K.C., Pond, S.L.K., RattoKim, S., & Salemi, M. (2020). Phyloanatomic characterization of the distinct T cell and monocyte contributions to the peripheral blood HIV population within the host. Virus Evol, 6(1), veaa005. England. 10.1093/ve/veaa005

  • Tzou, P.L., Pond, S.L.K., Avila-Rios, S., Holmes, S.P., Kantor, R., & Shafer, R.W. (2020). Analysis of unusual and signature APOBEC-mutations in HIV-1 pol next-generation sequences. PLoS One, 15(2), e0225352. United States. 10.1371/journal.pone.0225352