Published in J Virol on November 11, 2015
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol (2010) 53.37
APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics (2004) 39.31
Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol (2012) 32.00
Vaccination with ALVAC and AIDSVAX to prevent HIV-1 infection in Thailand. N Engl J Med (2009) 28.62
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics (2014) 28.04
Efficacy assessment of a cell-mediated immunity HIV-1 vaccine (the Step Study): a double-blind, randomised, placebo-controlled, test-of-concept trial. Lancet (2008) 19.65
HyPhy: hypothesis testing using phylogenies. Bioinformatics (2004) 17.33
Association of highly active antiretroviral therapy coverage, population viral load, and yearly new HIV diagnoses in British Columbia, Canada: a population-based study. Lancet (2010) 12.82
Late escape from an immunodominant cytotoxic T-lymphocyte response associated with progression to AIDS. Nat Med (1997) 12.26
Antiviral pressure exerted by HIV-1-specific cytotoxic T lymphocytes (CTLs) during primary infection demonstrated by rapid selection of CTL escape virus. Nat Med (1997) 12.08
Human immunodeficiency virus genetic variation that can escape cytotoxic T cell recognition. Nature (1991) 10.85
Timing the ancestor of the HIV-1 pandemic strains. Science (2000) 10.42
HIV evolution: CTL escape mutation and reversion after transmission. Nat Med (2004) 10.21
Evidence of HIV-1 adaptation to HLA-restricted immune responses at a population level. Science (2002) 9.17
Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 update. PLoS One (2009) 8.37
Evolution and transmission of stable CTL escape mutations in HIV infection. Nature (2001) 6.57
Clustered mutations in HIV-1 gag are consistently required for escape from HLA-B27-restricted cytotoxic T lymphocyte responses. J Exp Med (2001) 6.51
Reversion of CTL escape-variant immunodeficiency viruses in vivo. Nat Med (2004) 6.33
Fitness cost of escape mutations in p24 Gag in association with control of human immunodeficiency virus type 1. J Virol (2006) 6.30
Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics (2010) 6.14
Escape from the dominant HLA-B27-restricted cytotoxic T-lymphocyte response in Gag is associated with a dramatic reduction in human immunodeficiency virus type 1 replication. J Virol (2007) 4.64
Founder effects in the assessment of HIV polymorphisms and HLA allele associations. Science (2007) 4.60
Adaptation of HIV-1 to human leukocyte antigen class I. Nature (2009) 4.24
Escape and compensation from early HLA-B57-mediated cytotoxic T-lymphocyte pressure on human immunodeficiency virus type 1 Gag alter capsid interactions with cyclophilin A. J Virol (2007) 3.93
Transmission and accumulation of CTL escape variants drive negative associations between HIV polymorphisms and HLA. J Exp Med (2005) 3.68
HLA and AIDS: a cautionary tale. Trends Mol Med (2001) 3.51
Is HIV-1 evolving to a less virulent form in humans? Nat Rev Microbiol (2007) 3.05
HIV seroprevalence among homeless and marginally housed adults in San Francisco. Am J Public Health (2004) 2.96
The emergence of HIV/AIDS in the Americas and beyond. Proc Natl Acad Sci U S A (2007) 2.89
FUBAR: a fast, unconstrained bayesian approximation for inferring selection. Mol Biol Evol (2013) 2.73
Rapid reversion of sequence polymorphisms dominates early human immunodeficiency virus type 1 evolution. J Virol (2006) 2.70
Evolution of HLA-B*5703 HIV-1 escape mutations in HLA-B*5703-positive individuals and their transmission recipients. J Exp Med (2009) 2.39
HLA-associated immune escape pathways in HIV-1 subtype B Gag, Pol and Nef proteins. PLoS One (2009) 2.16
HLA class I-driven evolution of human immunodeficiency virus type 1 subtype c proteome: immune escape and viral load. J Virol (2008) 2.14
Accurate model selection of relaxed molecular clocks in bayesian phylogenetics. Mol Biol Evol (2012) 2.13
Clustal Omega, accurate alignment of very large numbers of sequences. Methods Mol Biol (2014) 2.11
De novo generation of escape variant-specific CD8+ T-cell responses following cytotoxic T-lymphocyte escape in chronic human immunodeficiency virus type 1 infection. J Virol (2005) 2.04
The Vancouver Lymphadenopathy-AIDS Study: 6. HIV seroconversion in a cohort of homosexual men. CMAJ (1986) 2.01
Replicative fitness of historical and recent HIV-1 isolates suggests HIV-1 attenuation over time. AIDS (2005) 1.99
PATRISTIC: a program for calculating patristic distances and graphically comparing the components of genetic change. BMC Evol Biol (2006) 1.84
Definition of the viral targets of protective HIV-1-specific T cell responses. J Transl Med (2011) 1.73
Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial. PLoS Comput Biol (2015) 1.70
Estimating AIDS infection rates in the San Francisco cohort. AIDS (1988) 1.66
HIV-1 epitope-specific CD8+ T cell responses strongly associated with delayed disease progression cross-recognize epitope variants efficiently. J Immunol (2006) 1.64
Vaccine-elicited human T cells recognizing conserved protein regions inhibit HIV-1. Mol Ther (2013) 1.61
The social context of drinking, drug use, and unsafe sex in the Boston Young Men Study. J Acquir Immune Defic Syndr Hum Retrovirol (1998) 1.58
The evolution of the Fenway Community Health model. Am J Public Health (2001) 1.57
CTL responses of high functional avidity and broad variant cross-reactivity are associated with HIV control. PLoS One (2012) 1.48
Automating HIV drug resistance genotyping with RECall, a freely accessible sequence analysis tool. J Clin Microbiol (2012) 1.48
The Vancouver Lymphadenopathy-AIDS Study: 1. Persistent generalized lymphadenopathy. Can Med Assoc J (1985) 1.47
Gradual adaptation of HIV to human host populations: good or bad news? Nat Med (2003) 1.46
A molecular basis for the control of preimmune escape variants by HIV-specific CD8+ T cells. Immunity (2013) 1.41
Impact of HLA-driven HIV adaptation on virulence in populations of high HIV seroprevalence. Proc Natl Acad Sci U S A (2014) 1.40
The Vancouver Lymphadenopathy-AIDS Study: 2. Seroepidemiology of HTLV-III antibody. Can Med Assoc J (1985) 1.31
Transmission and long-term stability of compensated CD8 escape mutations. J Virol (2008) 1.29
Correlates of protective cellular immunity revealed by analysis of population-level immune escape pathways in HIV-1. J Virol (2012) 1.29
Reduced replication capacity of NL4-3 recombinant viruses encoding reverse transcriptase-integrase sequences from HIV-1 elite controllers. J Acquir Immune Defic Syndr (2011) 1.27
Statistical resolution of ambiguous HLA typing data. PLoS Comput Biol (2008) 1.25
Confronting the emergence of drug-resistant HIV type 1: impact of antiretroviral therapy on individual and population resistance. AIDS Res Hum Retroviruses (2005) 1.24
Frequent transmission of cytotoxic-T-lymphocyte escape mutants of human immunodeficiency virus type 1 in the highly HLA-A24-positive Japanese population. J Virol (2004) 1.18
HLA-associated clinical progression correlates with epitope reversion rates in early human immunodeficiency virus infection. J Virol (2008) 1.13
Sexual transmission of single human immunodeficiency virus type 1 virions encoding highly polymorphic multisite cytotoxic T-lymphocyte escape variants. J Virol (2005) 1.10
Cumulative impact of host and viral factors on HIV-1 viral-load control during early infection. J Virol (2012) 1.07
Modelling the evolution and spread of HIV immune escape mutants. PLoS Pathog (2010) 1.06
Crippling HIV one mutation at a time. J Exp Med (2008) 1.00
Apparent founder effect during the early years of the San Francisco HIV type 1 epidemic (1978-1979). AIDS Res Hum Retroviruses (2000) 0.99
Epidemiology of human immunodeficiency virus type 1 infection among homosexual men participating in hepatitis B vaccine trials in Amsterdam, New York City, and San Francisco, 1978-1990. Am J Epidemiol (1993) 0.98
Maternal versus paternal inheritance of HLA class I alleles among HIV-infected children: consequences for clinical disease progression. AIDS (2004) 0.97
Molecular evolution of human immunodeficiency virus type 1 upon transmission between human leukocyte antigen disparate donor-recipient pairs. PLoS One (2008) 0.96
HLA class I sequence-based typing using DNA recovered from frozen plasma. J Immunol Methods (2012) 0.93
Genotypic and functional impact of HIV-1 adaptation to its host population during the North American epidemic. PLoS Genet (2014) 0.91
Loss of HIV-1-derived cytotoxic T lymphocyte epitopes restricted by protective HLA-B alleles during the HIV-1 epidemic. AIDS (2011) 0.88
Significant reductions in Gag-protease-mediated HIV-1 replication capacity during the course of the epidemic in Japan. J Virol (2012) 0.88
Cytotoxic T-lymphocyte escape mutations identified by HLA association favor those which escape and revert rapidly. J Virol (2012) 0.85
HLA-driven convergence of HIV-1 viral subtypes B and F toward the adaptation to immune responses in human populations. PLoS One (2008) 0.85
Distinct HIV-1 escape patterns selected by cytotoxic T cells with identical epitope specificity. J Virol (2012) 0.84
Multiple transmissions of a stable human leucocyte antigen-B27 cytotoxic T-cell-escape strain of HIV-1 in The Netherlands. AIDS (2009) 0.79
Early immune adaptation in HIV-1 revealed by population-level approaches. Retrovirology (2014) 0.79
Switching and emergence of CTL epitopes in HIV-1 infection. Retrovirology (2014) 0.78
Global Database-Driven Assessment of HIV-1 Adaptation to the Immune Repertoires of Human Populations. J Virol (2015) 0.77
Impaired Nef function is associated with early control of HIV-1 viremia. J Virol (2014) 0.86
HIV-1 adaptation to HLA: a window into virus-host immune interactions. Trends Microbiol (2015) 0.84
Immune screening identifies novel T cell targets encoded by antisense reading frames of HIV-1. J Virol (2015) 0.77