Publications                                                    Publications before 2000

Conference WebCasts

Hughes G., Leigh-Brown A., Rambaut A., Lycett S., Lewis F., Fearnhill E., Recent Phylodynamics of the HIV Epidemic among MSM in the United Kingdom 15th Conference on Retroviruses and Opportunistic Infections, CROI, Boston, MA, USA, Feb 3-6 2008 Abstract CROI Webcast, slides 67-81

Journal Publications

Vermund, SH, Leigh Brown, A.J., The HIV Epidemic: High Income Nations. Chapter 19 in "Human Immunodeficiency Virus", Bushman, F.D., Nabel, G., Swanstrom, R., eds. Cold Spring Harbor Press. In press 2011

Leigh Brown AJ, Lycett SJ, Weinert L, Hughes GJ, Fearnhill E, Dunn DT, UK HIV Drug Resistance Collaboration. Transmission network parameters estimated from HIV sequences for a nationwide epidemic. J. Infect. Dis. 2011. Advance pub. link to journal article

McLeish NJ, Simmonds P, Robertson C, Handel I, McGilchrist M, Singh BK, Kerr S, Chase-Topping ME, Sinka K, Bronsvoort M, Porteous DJ, Carman W, McMenamin J, Leigh-Brown A, Woolhouse ME. Sero-Prevalence and Incidence of A/H1N1 2009 Influenza Infection in Scotland in Winter 2009-2010. PLoS One 6:e20358; 2011. link to journal article

Kosakovsky Pond, S. L., Posada, D., Stawiski, E., Chappey, C., Poon, A. F., Hughes, G., Fearnhill, E., Gravenor, M. B., Leigh Brown, A. J., and Frost, S. D. An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1. PLoS Comput.Biol. 5(11), e1000581. 2009. link to journal article

Volz, E., Kosakovsky Pond, S.L., Ward, M.J., Leigh Brown A.J. and Frost, S.D., Phylodynamics of infectious disease epidemics. Genetics. 2009 183: 1421-1430. link to journal article

Lycett,S.J. Ward, M., Lewis, F.I., Poon, A.F.Y., Kosakovsky Pond, S.L. and Leigh Brown, A.J. A Bayesian graphical model for the genetic determination of virulence of H5N1 influenza in mammals. J.Virol. 2009 83:9901-10. link to journal article

Hughes, G.J. Fearnhill, E., Dunn, D., Lycett, S.J., Rambaut,A. and Leigh Brown A.J. (on behalf of the UK HIV Drug Resistance Collaboration) Molecular phylodynamics of the heterosexual HIV epidemic in the United Kingdom. PLoS Pathogens 2009 5:e1000590. link to journal article

Kosakovsky Pond SL, Poon AF, Leigh Brown AJ, Frost SD. A maximum likelihood method for detecting directional evolution in protein sequences and its application to influenza A virus. Mol Biol Evol 2008;25:1809-24. pdf

Murray RJ, Lewis F, Miller, MD, Leigh Brown AJ Genetic basis of variation in tenofovir drug susceptibility. AIDS 2008, 22: 1113-1123. pdf

Lewis FI, Hughes GJ, Rambaut A, Pozniak A, Leigh Brown AJ. Episodic sexual transmission of HIV revealed by molecular phylodynamics. PLoS Med 5(3): e50 2008. link to journal article

Pillay D, Rambaut A, Geretti AM, Leigh Brown AJ. HIV phylogenetics. BMJ 2007 Sep 8;335(7618):460-1. pdf

Poon A.F.Y., Kosakovsky Pond S.L., Bennett P., Richman D.D., Leigh Brown A.J., Frost, S.D.W. Adaptation to human populations is revealed by within-host polymorphisms in HIV-1 and hepatitis C virus. PLoS Pathog 3(3), 2007: e45. pdf

Kosakovsky Pond S.L, Frost S.D.W, Grossman Z., Gravenor M.B., Richman D.D., Leigh Brown A.J. Adaptation to different human populations by HIV-1 revealed by codon-based analyses. PLoS Comput Biol. 2; e62, 2006. pdf

Yang, O.O., Daar, E.S., Jamieson, B.D., Balamururugam, A., Smith, D.M., Pitt, J.A., Petropoulos, C.J., Richman, D.D., Little, S.J. and Leigh Brown A.J. HIV-1 Clade B superinfection: evidence for differential immune containment of distinct clade B strains. J. Virol. 79, 860-868, 2005. pdf

Froebel, K. Howard, W., Schafer, J., Howie, F., Whitworth, J., Kaleebu, P., Leigh Brown, A. and Riley, E. Activation by malaria antigenes renders mononuclear cells susceptible to HIV infection and reactivates replication of endogenous HIV in cells from HIV infected donors. Parasite Immunol. 26, 213-217, 2004 pdf

Leigh Brown, A.J., Frost, S.D.W., Good, B., Daar, E.S., Simon, V., Markowitz, M., Collier, A.C., Connick, E., Conway, B., Margolick, J.B., Routy, J-P., Corbeil, J., Hellmann, N.S., Richman, D.D., Little, S.J. Genetic basis of hypersusceptibility to protease inhibitors and low replicative capacity of Human Immunodeficiency Virus Type strains in primary infection. J.Virol. 78, 2242-2246, 2004. pdf

De Pasquale, M.P., Leigh Brown, A.J., Allega, J., Caliendo, A.M., Sutton, L., Donahue, S., CuUvin, S., D'Aquila, R.T. Differences in HIV-1 pol sequences from female genital tract and blood during antiretroviral therapy. Journal of Acquired Immune Deficiency Syndromes, 34, 37-44, 2003.

Koelsch, K.K., Smith, D.M., Little, S.J., Ignacio, C.C., Leigh Brown, A.J., Petropoulos, C.C., Richman D.D. and Wong, J.K. Clade B HIV-1 Superinfection with Wild Type Virus Following Infection with Drug Resistant Clade B Virus. AIDS 17: F11-F16, 2003.

Strain, M.C., Gunthard, H.F., Havlir, D.V., Ignacio, C.C., Smith, D.M., Leigh Brown, A.J., Macaranas, T.R., Lam, R.Y., Daly, O.A., Fischer, M., Opravil, M., Levine, H., Bacheler, L., Spina, C., Richman, D.D. and Wong, J.K. Heterogeneous clearance rates of long-lived lymphocytes infected with HIV: intrinsic stability predicts lifelong persistence. Proc. Natl. Acad. Sci USA, 100, 4819-48 2003

Leigh Brown, A.J., Frost, S.D.W., Mathews, W. C., Whitcomb, J.M., Hellmann, N.S., Daar, E.S., Richman, D.D. and Little, S.J. Transmission fitness of drug resistant virus and the prevalence of resistance in the treated population, JID, 187, 683-686, 2003. pdf

Raposo, G., Moore, M., Innes, D., Leijendekker, R., Leigh-Brown, A., Benaroch, P., and Geuze, H. Human macrophages accumulate HIV-1 particles in MHC II compartments. Traffic, 3, 718-729, 2002

Quigg, M. Frost, S.D.W., McDonagh, S., Burns, S.M., Clutterbuck, D., MacMillan, A., Leen, C.S. and Leigh Brown, A.J. Association of antiretroviral resistance genotypes with response to therapy - comparison of three models. Antiviral Therapy, 7, 151-157, 2002. pdf

Bird, S.M. and Leigh Brown, A.J., Criminalisation of HIV transmission: implications for public health in Scotland. BMJ, 323, 1174-1177 2001. pdf

Frost, S.D.W., Martinez-Picado, J., Ruiz, L., Clotet, B. and Leigh Brown A.J. Viral dynamics during structured treatment interruptions of chronic human immunodeficiency virus type 1 infection. J. Virol., 76, 968-979, 2002. pdf

Jassal, S.R., Lairmore, M.D., Leigh Brown, A.J. and Brighty, D.W. Soluble recombinant HTLV-1 surface glycoprotein competitively inhibits syncytia formation and viral infection of cells. Virus Res. 78, 17-34, 2001.

Frost, S.D.W., Gunthard, H.F., Wong, J.K., Havlir,D., Richman, D.D and Leigh Brown,A.J. Evidence for positive selection driving the evolution of HIV env under potent antiretroviral therapy. Virology 284, 250-258, 2001. pdf

Lockett, S.F., Robertson, J.R., Brettle, R.P., Middleton, D., Yap, P.L. and Leigh Brown, A.J. Mismatched HLA alleles protect against HIV transmission in heterosexual infection. J. Acquir. Immun. Defic. Syndr. 27, 277-280, 2001. pdf

Frost, S.D.W. Dumaurier, M-J., Wain-Hobson, S. and Leigh Brown, A.J. Genetic drift and within-host metapopulation dynamics of HIV-1 infection. Proc. Natl. Acad. Sci. USA 98, 6975-6980, 2001. pdf

Leigh Brown, A.J., Precious, H.M., Whitcomb, J., Wong, J.K., Quigg, M., Daar, E., D'Aquila, R.T., Keiser, P., Connick, E., Hellmann, N., Petropoulos, C., Richman, D.D. and Little, S.J. Novel amino acid change affecting susceptibility to non-nucleoside reverse transcriptase inhibitors detected in primary HIV infection. J.Virol., 74, 10269-10273, 2000 pdf

Frost, S.D.W., Nijhuis, M., Schuurman, R., Boucher, C.A.B. and Leigh Brown, A.J. Variation in the rate of evolution of lamivudine (3TC) resistance in HIV-1 infected individuals and its relationship to effective population size. J. Virol., 74, 6262-6268, 2000. pdf

Hanna, G.J. Johnson, V.A. , Kuritzkes, D.R., Richman, D.D., Leigh Brown, A.J., Savara, A.V. Hazelwood, J.D. and D’Aquila, R.T. Patterns of resistance mutations selected by treatment of human immunodeficiency virus type 1 infection with zidovudine, didanosine and nevirapine. J.Infect.Dis., 181, 904-911, 2000.

Precious, H., Gunthard, H., Wong, J., D’Aquila, R.T., Johnson, V.A., Kuritzkes, D.R., Richman, D.D. and Leigh Brown, A.J., Multiple sites in HIV-1 reverse transcriptase associated with virological response to combination therapy. AIDS, 14, 31-36, 2000. pdf