Published in Epidemics on March 31, 2010
Panel of prototypical recombinant infectious molecular clones resistant to nevirapine, efavirenz, etravirine, and rilpivirine. Antimicrob Agents Chemother (2012) 0.81
Epistasis and Pleiotropy Affect the Modularity of the Genotype-Phenotype Map of Cross-Resistance in HIV-1. Mol Biol Evol (2016) 0.75
Rapid evolution of the neutralizing antibody response to HIV type 1 infection. Proc Natl Acad Sci U S A (2003) 12.75
Antiretroviral-drug resistance among patients recently infected with HIV. N Engl J Med (2002) 9.70
Comprehensive cross-clade neutralization analysis of a panel of anti-human immunodeficiency virus type 1 monoclonal antibodies. J Virol (2004) 8.99
Genetic and immunologic heterogeneity among persons who control HIV infection in the absence of therapy. J Infect Dis (2008) 6.43
Access of antibody molecules to the conserved coreceptor binding site on glycoprotein gp120 is sterically restricted on primary human immunodeficiency virus type 1. J Virol (2003) 4.49
Recommendations for the design and use of standard virus panels to assess neutralizing antibody responses elicited by candidate human immunodeficiency virus type 1 vaccines. J Virol (2005) 4.35
Development and characterization of a novel single-cycle recombinant-virus assay to determine human immunodeficiency virus type 1 coreceptor tropism. Antimicrob Agents Chemother (2006) 4.14
Evidence for positive epistasis in HIV-1. Science (2004) 4.12
Time trends in primary HIV-1 drug resistance among recently infected persons. JAMA (2002) 4.02
Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection. Proc Natl Acad Sci U S A (2005) 3.94
An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1. PLoS Comput Biol (2009) 3.11
Persistence of transmitted drug resistance among subjects with primary human immunodeficiency virus infection. J Virol (2008) 3.04
Characterization of human immunodeficiency virus type 1 (HIV-1) envelope variation and neutralizing antibody responses during transmission of HIV-1 subtype B. J Virol (2005) 2.83
A web-based genotyping resource for viral sequences. Nucleic Acids Res (2004) 2.68
A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase. Nat Genet (2011) 2.66
Emergence of drug-resistant influenza virus: population dynamical considerations. Science (2006) 2.46
Broad nucleoside reverse-transcriptase inhibitor cross-resistance in human immunodeficiency virus type 1 clinical isolates. J Infect Dis (2003) 2.30
Molecular epidemiology reveals long-term changes in HIV type 1 subtype B transmission in Switzerland. J Infect Dis (2010) 2.21
Molecular mechanisms of resistance to human immunodeficiency virus type 1 with reverse transcriptase mutations K65R and K65R+M184V and their effects on enzyme function and viral replication capacity. Antimicrob Agents Chemother (2002) 2.21
Loss of raltegravir susceptibility by human immunodeficiency virus type 1 is conferred via multiple nonoverlapping genetic pathways. J Virol (2009) 2.19
Dynamic variation in cycling of hematopoietic stem cells in steady state and inflammation. J Exp Med (2011) 2.18
Emergence of minor populations of human immunodeficiency virus type 1 carrying the M184V and L90M mutations in subjects undergoing structured treatment interruptions. J Infect Dis (2003) 2.17
Coreceptor tropism in human immunodeficiency virus type 1 subtype D: high prevalence of CXCR4 tropism and heterogeneous composition of viral populations. J Virol (2007) 2.14
The effect of opinion clustering on disease outbreaks. J R Soc Interface (2008) 2.12
Population biological principles of drug-resistance evolution in infectious diseases. Lancet Infect Dis (2011) 2.11
Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV). Proc Natl Acad Sci U S A (2012) 2.07
Quantitative constraints on the scope of negative selection. Trends Immunol (2003) 2.06
A novel substrate-based HIV-1 protease inhibitor drug resistance mechanism. PLoS Med (2007) 1.99
Experimental tests for an evolutionary trade-off between growth rate and yield in E. coli. Am Nat (2006) 1.99
Improving lopinavir genotype algorithm through phenotype correlations: novel mutation patterns and amprenavir cross-resistance. AIDS (2003) 1.96
Evolution of cooperation by generalized reciprocity. Proc Biol Sci (2005) 1.96
Cerebrospinal fluid HIV infection and pleocytosis: relation to systemic infection and antiretroviral treatment. BMC Infect Dis (2005) 1.91
Using an epidemiological model for phylogenetic inference reveals density dependence in HIV transmission. Mol Biol Evol (2013) 1.88
Estimating the basic reproductive number from viral sequence data. Mol Biol Evol (2011) 1.86
Assessing chemokine co-receptor usage in HIV. Curr Opin Infect Dis (2005) 1.84
HIV-1 tropism and survival in vertically infected Ugandan infants. J Infect Dis (2008) 1.83
Stable virulence levels in the HIV epidemic of Switzerland over two decades. AIDS (2006) 1.81
Amino acid substitutions at position 190 of human immunodeficiency virus type 1 reverse transcriptase increase susceptibility to delavirdine and impair virus replication. J Virol (2003) 1.79
Epistasis between deleterious mutations and the evolution of recombination. Trends Ecol Evol (2007) 1.79
Human immunodeficiency virus type 1 clade B superinfection: evidence for differential immune containment of distinct clade B strains. J Virol (2005) 1.77
Interruption of treatment with individual therapeutic drug classes in adults with multidrug-resistant HIV-1 infection. J Infect Dis (2005) 1.76
The HIV coreceptor switch: a population dynamical perspective. Trends Microbiol (2005) 1.76
Constraints on HIV-1 evolution and immunodominance revealed in monozygotic adult twins infected with the same virus. J Exp Med (2006) 1.72
Entry and transcription as key determinants of differences in CD4 T-cell permissiveness to human immunodeficiency virus type 1 infection. J Virol (2004) 1.68
Viral fitness cost prevents HIV-1 from evading dolutegravir drug pressure. Retrovirology (2013) 1.66
Ambiguous nucleotide calls from population-based sequencing of HIV-1 are a marker for viral diversity and the age of infection. Clin Infect Dis (2011) 1.64
Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load. PLoS Pathog (2010) 1.63
Strong cell-mediated immune responses are associated with the maintenance of low-level viremia in antiretroviral-treated individuals with drug-resistant human immunodeficiency virus type 1. J Infect Dis (2004) 1.58
Stochastic or deterministic: what is the effective population size of HIV-1? Trends Microbiol (2006) 1.58
An evolutionary scenario for the transition to undifferentiated multicellularity. Proc Natl Acad Sci U S A (2003) 1.55
The evolution of connectivity in metabolic networks. PLoS Biol (2005) 1.54
Recombination in HIV and the evolution of drug resistance: for better or for worse? Bioessays (2004) 1.54
Persistence of primary drug resistance among recently HIV-1 infected adults. AIDS (2004) 1.53
HIV drug resistance acquired through superinfection. AIDS (2005) 1.52
Clade B HIV-1 superinfection with wild-type virus after primary infection with drug-resistant clade B virus. AIDS (2003) 1.52
Long-term trends of HIV type 1 drug resistance prevalence among antiretroviral treatment-experienced patients in Switzerland. Clin Infect Dis (2009) 1.50
Hypersusceptibility to non-nucleoside reverse transcriptase inhibitors in HIV-1: clinical, phenotypic and genotypic correlates. AIDS (2002) 1.50
Inferring epidemic contact structure from phylogenetic trees. PLoS Comput Biol (2012) 1.47
CD4+ T cell kinetics and activation in human immunodeficiency virus-infected patients who remain viremic despite long-term treatment with protease inhibitor-based therapy. J Infect Dis (2002) 1.46
Evolution of cross-feeding in microbial populations. Am Nat (2004) 1.46
Baseline HIV type 1 coreceptor tropism predicts disease progression. Clin Infect Dis (2007) 1.46
In vivo fitness cost of the M184V mutation in multidrug-resistant human immunodeficiency virus type 1 in the absence of lamivudine. J Virol (2008) 1.45
Macaques infected with a CCR5-tropic simian/human immunodeficiency virus (SHIV) develop broadly reactive anti-HIV neutralizing antibodies. J Virol (2007) 1.44
Coreceptor tropism can be influenced by amino acid substitutions in the gp41 transmembrane subunit of human immunodeficiency virus type 1 envelope protein. J Virol (2008) 1.43
Neutralization profiles of newly transmitted human immunodeficiency virus type 1 by monoclonal antibodies 2G12, 2F5, and 4E10. J Virol (2004) 1.40
Relationship between in vitro human immunodeficiency virus type 1 replication rate and virus load in plasma. J Virol (2003) 1.40
The clinical relevance of non-nucleoside reverse transcriptase inhibitor hypersusceptibility: a prospective cohort analysis. AIDS (2002) 1.38
Comparison of standard PCR/cloning to single genome sequencing for analysis of HIV-1 populations. J Virol Methods (2010) 1.38
Estimating the stoichiometry of human immunodeficiency virus entry. J Virol (2008) 1.36
Treatment of advanced human immunodeficiency virus type 1 disease with the viral entry inhibitor PRO 542. Antimicrob Agents Chemother (2004) 1.34
Transmission of integrase strand-transfer inhibitor multidrug-resistant HIV-1: case report and response to raltegravir-containing antiretroviral therapy. Antivir Ther (2011) 1.34
Quantification of infectious HIV-1 plasma viral load using a boosted in vitro infection protocol. Virology (2004) 1.32
Simulating the evolution of signal transduction pathways. J Theor Biol (2006) 1.31
Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods. Philos Trans R Soc Lond B Biol Sci (2013) 1.31
The molecular basis of drug resistance against hepatitis C virus NS3/4A protease inhibitors. PLoS Pathog (2012) 1.30
The evolution of groups of cooperating bacteria and the growth rate versus yield trade-off. Microbiology (2005) 1.30
Substitutions at amino acid positions 143, 148, and 155 of HIV-1 integrase define distinct genetic barriers to raltegravir resistance in vivo. J Virol (2012) 1.28
Amprenavir-resistant HIV-1 exhibits lopinavir cross-resistance and reduced replication capacity. AIDS (2002) 1.28