Reader in Pathogen Dynamics
Evolution of immune responses
Simon Frost is accepting applications for PhD students.
Simon Frost is available for consultancy.
Departments and Institutes
My research interests focus on the use of mathematical and statistical modeling to understanding the dynamics and evolution of infectious diseases such as HIV, hepatitis C and influenza A. My work covers both within- and between-host dynamics, and while my past research has focused on viruses, it is broadening to examine the role of contact structure and heterogeneity in the host population. Current projects include the statistical modeling of evolutionary processes acting on genetic sequences, modeling viral and immune dynamics, designing diagnostics for viral infections, mining of large clinical databases, and investigating novel means of capturing social, sexual and disease transmission networks, particularly in the context of emerging infectious diseases.
- Sergei Kosakovsky Pond, UCSD
- Douglas Richman, UCSD
- Susan Little, UCSD
- Gerond Lake-Bakaar, Harvard/Beth Israel
- Andrew Leigh Brown, Edinburgh
- Douglas Heckatorn, Cornell
- Sharon Weir, UNC-Chapel Hill
- Eric Volz, University of Michigan
- Frost, S.D.W. and Volz, E.M. 2013. Modeling tree shape and structure in viral phylodynamics. Phil. Trans. Roy. Soc. B., in press.
- Volz, E., Koopman, J.S., Ward, M.J., Leigh Brown, A.J., and Frost, S.D.W. 2012. Simple epidemiological dynamics explain phylogenetic clustering of HIV from patients with recent infection. PLoS Comp. Biol.
- McCreesh, N., Frost, 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. (2012) Empirical evaluation of Respondent-Driven Sampling. Epidemiology 23:138-147.
- Drumright, L.N. and Frost, S.D.W. 2010 Rapid social network assessment for predicting HIV and STI risk among men attending bars and clubs in San Diego, California. Sex. Transm. Infect. 86 Suppl 3:iii17-23.
- Frost, S.D.W. and Volz, E.M. 2010 Viral phylodynamics and the search for an `effective number of infections'. Phil. Trans. Roy. Soc. B. 365:1879-1890.
- Volz, E.M., Kosakovsky Pond, S.L., Ward, M.J., Leigh Brown, A. J., and Frost, S.D.W. 2009 Phylodynamics of infectious disease dynamics. Genetics 183:1421-1430.
- Poon, A.F.Y., Brouwer, K.C., Strathdee, S.A., Firestone-Cruz, M., Lozada, R.M., Pond, S.L., Heckathorn, D.D., and Frost, S.D.W. (2009) Parsing social network survey data from hidden populations using stochastic context-free grammars. PLoS One 4:e6777.
- Frost, S.D.W. 2007 Using sexual affiliation networks to describe the sexual structure of a population. Sex. Transm. Inf. 83: (suppl 1): 137-142
- Poon, A.F.Y., Kosakovsky Pond, S.L., Bennett, P., Richman, D.D., Leigh Brown, A.J. and Frost, S.D.W. 2007 Adaptation to human populations is revealed by within-host polymorphism in HIV-1 and Hepatitis C virus. PLoS Pathog. 3:e45
- Poon, A.F.Y., Lewis, F.I., Kosakovsky Pond, S.L. and Frost, S.D.W. 2007 Detection of 'N-linked' glycan interactions by phylogenetic and Bayesian network analysis og HIV-1 envelope sequesces. PLoS Comp. Biol. 3:e45
- Frost, S.D.W. Brouwer, K.C., Firestone, M.A., Ramos, R., Ramos, M.E., Lozada, R.M., Magis-Rodriquez, C. and Strathdee, S.A. 2006 Respondent driven sampling of injection drug users in two U.S.- Mexico border cities: recruitment dynamics and impact on estimates of HIV and syphilis prevalence. J. Urban Health. 83: (suppl 7): 83-97
- Kosakovsky Pond, S.L., Posada, D., Gravenor, M.B., Woelk, C.H. and Frost, S.D.W. 2006 Automated phylogenetic detection of recombination using a genetic algorithm. Mol.Biol.Evol. 23: 1891-1901
- Frost, S.D.W., Wrin, T., Smith, D.M., Kosakovsky Pond, S.L., Liu, Y., Paxinos, E., Chappey, C., Galovich, J., Beauchaine, J., Petropoulos, C.J., Little, S.J. and Richman, D.D. 2005 Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection. Proc.Natl.Acad.Sci. 102: 18514-18519
- Frost, S.D.W., Liu, Y., Kosakovksy Pond, S.L., Chappey, C., Liu, Y., Wrin, T., Petropoulos, C.J., Little, S.J. and Richman, D.D. 2005 Characterization of HIV-1 envelope variation and neutralizing antibody responses during transmission of HIV-1 subtype B. Journal of Virology 79: 6523-6527
- Kosakovsky Pond, S.L. and Frost, S.D.W., 2005 Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol. Biol. Evol. 22: 1208-1222
- Frost, S.D.W., Martinez-Picado, J., Ruiz, L., Clotet, B., and Leigh Brown, A.J. 2002 Viral dynamics during structured therapy interruptions of chronic human immunodeficiency virus type 1 infection. J. Virol. 76:968-979.
- Frost, S.D.W., Dumaurier, M.-J., Wain-Hobson, S. and Leigh Brown, A.J. 2001 Genetic drift and within-host metapopulation dynamics of HIV-1 infection. Proc. Natl. Acad. Sci. USA 98:6975-6980.