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Sergei Pond

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Sergei Pond

  • College of Science and Technology

    • Office of the Dean

      • Associate Dean for Research and Innovation

    • Biology

      • Professor

Courses Taught

Number

Name

Level

BIOL 3111

Genomics in Medicine

Undergraduate

BIOL 5111

Genomics in Medicine

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

  • Zarate, S., Bertram, M.R., 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. MDPI AG. doi: 10.20944/preprints202410.0585.v1.

  • 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. openRxiv. 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