Publications
Art F.Y. Poon, Luke C. Swenson, Winnie W.Y. Dong, Wenjie Deng, Sergei L. Kosakovsky Pond, Zabrina L. Brumme, James I. Mullins, Douglas D. Richman, P. Richard Harrigan and Simon D.W. Frost Phylogenetic Analysis of Population-Based and Deep Sequencing Data to Identify Coevolving Sites in the nef Gene of HIV-1 Mol Biol Evol (2010) 27 (4): 819-832.
Volz, E., Koopman, J.S., Ward, M.J., Leigh Brown, A.J., and Frost, S.D.W. . Simple epidemiological dynamics explain phylogenetic clustering of HIV from patients with recent infection. PLoS Comp. Biol. 2012
McCreesh, N., Fros, S.D.W., Seeley, J., Katongole, J., Ndagire Tarsh, M., Ndungutse, R., Jichi, F., Tilson, M., Maher, D., Johnston, L.G., Sonnenberg, P., Copas, A., Hayes, R.J., and White, R.G. Empirical evaluation of Respondent-Driven Sampling. Epidemiology 2012 23:138-147.
Varela, M., Landskron, L., Lai, R.P.J., McKinley, T.J., Bogers,W.M., Verschoor, E.J., Dubbes, R., Barnett, S.W., Frost, S.D.W., and Heeney, J.L. Molecular evolution analysis of the human immunodeficiency virus type 1 envelope in simian/human immunodeficiency virusinfected macaques: implications for challenge dose selection. J. Virol. 2011 85:10332-10345.
Sergei L. Kosakovsky Pond and Simon D. W. Frost Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection Mol Biol Evol (May 2005) 22 (5): 1208-1222.
Simon D. W. Frost, Terri Wrin, Davey M. Smith , Sergei L. Kosakovsky Pond , Yang Liu, Ellen Paxinos, Colombe Chappey, Justin Galovich, Jeff Beauchaine, Christos J. Petropoulos, Susan J. Little, and Douglas D. Richman Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection PNAS December 20, 2005 vol. 102 no. 51 18514-18519
