Published in Science on March 16, 2007
Efficient control of population structure in model organism association mapping. Genetics (2008) 12.32
The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J Exp Med (2009) 6.22
Tiered categorization of a diverse panel of HIV-1 Env pseudoviruses for assessment of neutralizing antibodies. J Virol (2009) 5.91
Impact of MHC class I diversity on immune control of immunodeficiency virus replication. Nat Rev Immunol (2008) 5.17
Evolutionary analysis of the dynamics of viral infectious disease. Nat Rev Genet (2009) 4.56
Adaptation of HIV-1 to human leukocyte antigen class I. Nature (2009) 4.24
Transmission of HIV-1 Gag immune escape mutations is associated with reduced viral load in linked recipients. J Exp Med (2008) 3.20
Evidence of differential HLA class I-mediated viral evolution in functional and accessory/regulatory genes of HIV-1. PLoS Pathog (2007) 2.81
Central role of reverting mutations in HLA associations with human immunodeficiency virus set point. J Virol (2008) 2.72
Design and pre-clinical evaluation of a universal HIV-1 vaccine. PLoS One (2007) 2.61
Transmission of HIV-1 CTL escape variants provides HLA-mismatched recipients with a survival advantage. PLoS Pathog (2008) 2.59
Human immunodeficiency virus type 1 population genetics and adaptation in newly infected individuals. J Virol (2008) 2.56
Coordinate linkage of HIV evolution reveals regions of immunological vulnerability. Proc Natl Acad Sci U S A (2011) 2.37
Variable fitness impact of HIV-1 escape mutations to cytotoxic T lymphocyte (CTL) response. PLoS Pathog (2009) 2.36
Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag. PLoS Comput Biol (2008) 2.32
Reverse vaccinology: developing vaccines in the era of genomics. Immunity (2010) 2.25
T-cell vaccine strategies for human immunodeficiency virus, the virus with a thousand faces. J Virol (2009) 2.17
HLA-associated immune escape pathways in HIV-1 subtype B Gag, Pol and Nef proteins. PLoS One (2009) 2.16
HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBEC. PLoS Pathog (2009) 2.15
HLA class I-driven evolution of human immunodeficiency virus type 1 subtype c proteome: immune escape and viral load. J Virol (2008) 2.14
Viral sequence evolution in acute hepatitis C virus infection. J Virol (2007) 2.13
Extensive HLA class I allele promiscuity among viral CTL epitopes. Eur J Immunol (2007) 2.10
Genetic characterization of human immunodeficiency virus type 1 in elite controllers: lack of gross genetic defects or common amino acid changes. J Virol (2008) 1.94
An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope. PLoS Comput Biol (2007) 1.82
The origins of sexually transmitted HIV among men who have sex with men. Sci Transl Med (2010) 1.76
HLA/KIR restraint of HIV: surviving the fittest. Annu Rev Immunol (2011) 1.66
HIV-1 vaccine development after STEP. Annu Rev Med (2010) 1.64
Widespread impact of HLA restriction on immune control and escape pathways of HIV-1. J Virol (2012) 1.62
Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections. PLoS Pathog (2011) 1.57
Highly complex neutralization determinants on a monophyletic lineage of newly transmitted subtype C HIV-1 Env clones from India. Virology (2009) 1.51
Genetic signatures in the envelope glycoproteins of HIV-1 that associate with broadly neutralizing antibodies. PLoS Comput Biol (2010) 1.51
Frequent toggling between alternative amino acids is driven by selection in HIV-1. PLoS Pathog (2008) 1.49
Leveraging hierarchical population structure in discrete association studies. PLoS One (2007) 1.48
Demographic processes affect HIV-1 evolution in primary infection before the onset of selective processes. J Virol (2011) 1.41
Extensive intrasubtype recombination in South African human immunodeficiency virus type 1 subtype C infections. J Virol (2007) 1.37
Computational analysis of anti-HIV-1 antibody neutralization panel data to identify potential functional epitope residues. Proc Natl Acad Sci U S A (2013) 1.37
Conserved footprints of APOBEC3G on Hypermutated human immunodeficiency virus type 1 and human endogenous retrovirus HERV-K(HML2) sequences. J Virol (2008) 1.36
Human leukocyte antigen class I genotypes in relation to heterosexual HIV type 1 transmission within discordant couples. J Immunol (2008) 1.36
Evolution of human immunodeficiency virus type 1 cytotoxic T-lymphocyte epitopes: fitness-balanced escape. J Virol (2007) 1.35
Clade-specific differences between human immunodeficiency virus type 1 clades B and C: diversity and correlations in C3-V4 regions of gp120. J Virol (2006) 1.30
HLA footprints on human immunodeficiency virus type 1 are associated with interclade polymorphisms and intraclade phylogenetic clustering. J Virol (2009) 1.30
Correlates of protective cellular immunity revealed by analysis of population-level immune escape pathways in HIV-1. J Virol (2012) 1.29
Is the virulence of HIV changing? A meta-analysis of trends in prognostic markers of HIV disease progression and transmission. AIDS (2012) 1.29
Analysis of the evolutionary forces in an immunodominant CD8 epitope in hepatitis C virus at a population level. J Virol (2008) 1.28
Statistical resolution of ambiguous HLA typing data. PLoS Comput Biol (2008) 1.25
Progression to AIDS in South Africa is associated with both reverting and compensatory viral mutations. PLoS One (2011) 1.24
A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control. Elife (2013) 1.19
Viral adaptation to immune selection pressure by HLA class I-restricted CTL responses targeting epitopes in HIV frameshift sequences. J Exp Med (2010) 1.19
HLA-A*7401-mediated control of HIV viremia is independent of its linkage disequilibrium with HLA-B*5703. J Immunol (2011) 1.18
Mapping the landscape of host-pathogen coevolution: HLA class I binding and its relationship with evolutionary conservation in human and viral proteins. J Virol (2010) 1.17
Adaptive interactions between HLA and HIV-1: highly divergent selection imposed by HLA class I molecules with common supertype motifs. J Immunol (2010) 1.15
Frequent and variable cytotoxic-T-lymphocyte escape-associated fitness costs in the human immunodeficiency virus type 1 subtype B Gag proteins. J Virol (2013) 1.14
HLA-associated clinical progression correlates with epitope reversion rates in early human immunodeficiency virus infection. J Virol (2008) 1.13
An early HIV mutation within an HLA-B*57-restricted T cell epitope abrogates binding to the killer inhibitory receptor 3DL1. J Virol (2011) 1.13
Amino-acid co-variation in HIV-1 Gag subtype C: HLA-mediated selection pressure and compensatory dynamics. PLoS One (2010) 1.12
Attenuation of multiple Nef functions in HIV-1 elite controllers. Retrovirology (2013) 1.12
The emerging role of HLA-C in HIV-1 infection. Immunology (2011) 1.06
Modelling the evolution and spread of HIV immune escape mutants. PLoS Pathog (2010) 1.06
Human immunodeficiency virus vaccine trials. Cold Spring Harb Perspect Med (2012) 1.05
Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes. PLoS Comput Biol (2008) 1.05
Fluidity of HIV-1-specific T-cell responses during acute and early subtype C HIV-1 infection and associations with early disease progression. J Virol (2010) 1.04
Unique features of HLA-mediated HIV evolution in a Mexican cohort: a comparative study. Retrovirology (2009) 1.04
A signature in HIV-1 envelope leader peptide associated with transition from acute to chronic infection impacts envelope processing and infectivity. PLoS One (2011) 1.03
Disparate associations of HLA class I markers with HIV-1 acquisition and control of viremia in an African population. PLoS One (2011) 1.01
Autologous neutralizing antibodies to the transmitted/founder viruses emerge late after simian immunodeficiency virus SIVmac251 infection of rhesus monkeys. J Virol (2010) 1.01
Extensive HLA-driven viral diversity following a narrow-source HIV-1 outbreak in rural China. Blood (2011) 1.01
Host and viral factors contributing to CD8+ T cell failure in hepatitis C virus infection. World J Gastroenterol (2007) 0.99
Human leukocyte antigens and HIV type 1 viral load in early and chronic infection: predominance of evolving relationships. PLoS One (2010) 0.98
Translation of HLA-HIV associations to the cellular level: HIV adapts to inflate CD8 T cell responses against Nef and HLA-adapted variant epitopes. J Immunol (2011) 0.98
Nef-specific CD8+ T cell responses contribute to HIV-1 immune control. PLoS One (2013) 0.98
High-avidity, high-IFNγ-producing CD8 T-cell responses following immune selection during HIV-1 infection. Immunol Cell Biol (2011) 0.96
HLA targeting efficiency correlates with human T-cell response magnitude and with mortality from influenza A infection. Proc Natl Acad Sci U S A (2013) 0.96
Impact of pre-adapted HIV transmission. Nat Med (2016) 0.96
Host genes important to HIV replication and evolution. Cold Spring Harb Perspect Med (2012) 0.95
Identification of amino acid substitutions associated with neutralization phenotype in the human immunodeficiency virus type-1 subtype C gp120. Virology (2010) 0.94
HIV molecular epidemiology: transmission and adaptation to human populations. Curr Opin HIV AIDS (2009) 0.94
Adaptive changes in HIV-1 subtype C proteins during early infection are driven by changes in HLA-associated immune pressure. Virology (2009) 0.93
Uncommon pathways of immune escape attenuate HIV-1 integrase replication capacity. J Virol (2012) 0.93
All that glitters is not gold--founder effects complicate associations of flu mutations to disease severity. Virol J (2010) 0.93
HIV-1 Vpu Mediates HLA-C Downregulation. Cell Host Microbe (2016) 0.93
Viral adaptation to host immune responses occurs in chronic hepatitis B virus (HBV) infection, and adaptation is greatest in HBV e antigen-negative disease. J Virol (2011) 0.92
A quantitative quasispecies theory-based model of virus escape mutation under immune selection. Proc Natl Acad Sci U S A (2012) 0.92
Factors associated with viral rebound in HIV-1-infected individuals enrolled in a therapeutic HIV-1 gag vaccine trial. J Infect Dis (2011) 0.91
Genotypic and functional impact of HIV-1 adaptation to its host population during the North American epidemic. PLoS Genet (2014) 0.91
Immunogenicity and cross-reactivity of a representative ancestral sequence in hepatitis C virus infection. J Immunol (2012) 0.91
Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus. PLoS Pathog (2016) 0.90
Selective pressures of HLA genotypes and antiviral therapy on human immunodeficiency virus type 1 sequence mutation at a population level. Clin Vaccine Immunol (2007) 0.90
Genital tract sequestration of SIV following acute infection. PLoS Pathog (2011) 0.90
Epitope discovery with phylogenetic hidden Markov models. Mol Biol Evol (2010) 0.89
Significant reductions in Gag-protease-mediated HIV-1 replication capacity during the course of the epidemic in Japan. J Virol (2012) 0.88
SIV genome-wide pyrosequencing provides a comprehensive and unbiased view of variation within and outside CD8 T lymphocyte epitopes. PLoS One (2012) 0.87
Tracking the culprit: HIV-1 evolution and immune selection revealed by single-genome amplification. J Exp Med (2009) 0.86
Definition of the peptide binding motif within DRB1*1401 restricted epitopes by peptide competition and structural modeling. Mol Immunol (2008) 0.86
The distribution of CTL epitopes in HIV-1 appears to be random, and similar to that of other proteomes. BMC Evol Biol (2009) 0.86
Mapping protease inhibitor resistance to human immunodeficiency virus type 1 sequence polymorphisms within patients. J Virol (2007) 0.85
Cytotoxic T-lymphocyte escape mutations identified by HLA association favor those which escape and revert rapidly. J Virol (2012) 0.85
Constraints on viral evolution during chronic hepatitis C virus infection arising from a common-source exposure. J Virol (2012) 0.85
A hexanucleotide repeat expansion in C9ORF72 is the cause of chromosome 9p21-linked ALS-FTD. Neuron (2011) 18.73
Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc Natl Acad Sci U S A (2008) 16.54
A whole-genome association study of major determinants for host control of HIV-1. Science (2007) 15.19
Immune-correlates analysis of an HIV-1 vaccine efficacy trial. N Engl J Med (2012) 12.98
Efficient control of population structure in model organism association mapping. Genetics (2008) 12.32
CD8+ T-cell responses to different HIV proteins have discordant associations with viral load. Nat Med (2006) 10.34
The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science (2010) 9.61
Diversity considerations in HIV-1 vaccine selection. Science (2002) 9.60
Dominant influence of HLA-B in mediating the potential co-evolution of HIV and HLA. Nature (2004) 9.53
Comprehensive cross-clade neutralization analysis of a panel of anti-human immunodeficiency virus type 1 monoclonal antibodies. J Virol (2004) 8.99
Structure of a V3-containing HIV-1 gp120 core. Science (2005) 7.69
Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection. J Exp Med (2009) 7.01
FaST linear mixed models for genome-wide association studies. Nat Methods (2011) 6.52
Genetic and immunologic heterogeneity among persons who control HIV infection in the absence of therapy. J Infect Dis (2008) 6.43
Fitness cost of escape mutations in p24 Gag in association with control of human immunodeficiency virus type 1. J Virol (2006) 6.30
The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J Exp Med (2009) 6.22
Towards an HIV cure: a global scientific strategy. Nat Rev Immunol (2012) 5.52
Public health. A sound rationale needed for phase III HIV-1 vaccine trials. Science (2004) 5.31
Genital HIV-1 RNA predicts risk of heterosexual HIV-1 transmission. Sci Transl Med (2011) 5.21
Persistence of HIV in gut-associated lymphoid tissue despite long-term antiretroviral therapy. J Infect Dis (2008) 4.86
Low-dose rectal inoculation of rhesus macaques by SIVsmE660 or SIVmac251 recapitulates human mucosal infection by HIV-1. J Exp Med (2009) 4.79
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
Improved coreceptor usage prediction and genotypic monitoring of R5-to-X4 transition by motif analysis of human immunodeficiency virus type 1 env V3 loop sequences. J Virol (2003) 4.56
Immune selection for altered antigen processing leads to cytotoxic T lymphocyte escape in chronic HIV-1 infection. J Exp Med (2004) 4.52
Upregulation of CTLA-4 by HIV-specific CD4+ T cells correlates with disease progression and defines a reversible immune dysfunction. Nat Immunol (2007) 4.41
Origin of the human malaria parasite Plasmodium falciparum in gorillas. Nature (2010) 4.35
Adaptation of HIV-1 to human leukocyte antigen class I. Nature (2009) 4.24
Selection, transmission, and reversion of an antigen-processing cytotoxic T-lymphocyte escape mutation in human immunodeficiency virus type 1 infection. J Virol (2004) 4.20
HIV-1 superinfection despite broad CD8+ T-cell responses containing replication of the primary virus. Nature (2002) 4.20
Chromosome 9p21 in amyotrophic lateral sclerosis in Finland: a genome-wide association study. Lancet Neurol (2010) 4.19
Differential natural killer cell-mediated inhibition of HIV-1 replication based on distinct KIR/HLA subtypes. J Exp Med (2007) 4.14
Polyvalent vaccines for optimal coverage of potential T-cell epitopes in global HIV-1 variants. Nat Med (2006) 4.14
Advantage of rare HLA supertype in HIV disease progression. Nat Med (2003) 4.08
Tracking global patterns of N-linked glycosylation site variation in highly variable viral glycoproteins: HIV, SIV, and HCV envelopes and influenza hemagglutinin. Glycobiology (2004) 3.98
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
Increased HIV-1 vaccine efficacy against viruses with genetic signatures in Env V2. Nature (2012) 3.83
High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men. PLoS Pathog (2010) 3.68
Common genetic variation and the control of HIV-1 in humans. PLoS Genet (2009) 3.68
Transmission and accumulation of CTL escape variants drive negative associations between HIV polymorphisms and HLA. J Exp Med (2005) 3.68
The Los Alamos hepatitis C sequence database. Bioinformatics (2004) 3.67
HIV-infected individuals receiving effective antiviral therapy for extended periods of time continually replenish their viral reservoir. J Clin Invest (2005) 3.62
Tetherin-driven adaptation of Vpu and Nef function and the evolution of pandemic and nonpandemic HIV-1 strains. Cell Host Microbe (2009) 3.58
Decay of the HIV reservoir in patients receiving antiretroviral therapy for extended periods: implications for eradication of virus. J Infect Dis (2007) 3.50
HLA class I supertypes: a revised and updated classification. BMC Immunol (2008) 3.47
Mosaic HIV-1 vaccines expand the breadth and depth of cellular immune responses in rhesus monkeys. Nat Med (2010) 3.44
Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo. PLoS One (2009) 3.40
Clustering patterns of cytotoxic T-lymphocyte epitopes in human immunodeficiency virus type 1 (HIV-1) proteins reveal imprints of immune evasion on HIV-1 global variation. J Virol (2002) 3.38
Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection. PLoS Pathog (2012) 3.35
CCL3L1 and CCR5 influence cell-mediated immunity and affect HIV-AIDS pathogenesis via viral entry-independent mechanisms. Nat Immunol (2007) 3.31
Influence of HLA-C expression level on HIV control. Science (2013) 3.27
Efficacy trial of a DNA/rAd5 HIV-1 preventive vaccine. N Engl J Med (2013) 3.24
Control of human immunodeficiency virus replication by cytotoxic T lymphocytes targeting subdominant epitopes. Nat Immunol (2005) 3.23
Relative dominance of Gag p24-specific cytotoxic T lymphocytes is associated with human immunodeficiency virus control. J Virol (2006) 3.20
Transmission of HIV-1 Gag immune escape mutations is associated with reduced viral load in linked recipients. J Exp Med (2008) 3.20
Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naïve patients. Hepatology (2008) 3.14
Improved linear mixed models for genome-wide association studies. Nat Methods (2012) 3.09
Correction for hidden confounders in the genetic analysis of gene expression. Proc Natl Acad Sci U S A (2010) 3.08