Published in BMC Bioinformatics on October 25, 2010
Limited or no protection by weakly or nonneutralizing antibodies against vaginal SHIV challenge of macaques compared with a strongly neutralizing antibody. Proc Natl Acad Sci U S A (2011) 2.39
Sequential bottlenecks drive viral evolution in early acute hepatitis C virus infection. PLoS Pathog (2011) 2.13
Early low-titer neutralizing antibodies impede HIV-1 replication and select for virus escape. PLoS Pathog (2012) 1.61
Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection. PLoS Pathog (2017) 1.38
Quantifying the diversification of hepatitis C virus (HCV) during primary infection: estimates of the in vivo mutation rate. PLoS Pathog (2012) 1.30
Modeling the within-host dynamics of HIV infection. BMC Biol (2013) 1.29
Elucidation of hepatitis C virus transmission and early diversification by single genome sequencing. PLoS Pathog (2012) 1.28
Transmission of single and multiple viral variants in primary HIV-1 subtype C infection. PLoS One (2011) 1.16
The TRIM5 gene modulates penile mucosal acquisition of simian immunodeficiency virus in rhesus monkeys. J Virol (2011) 1.14
SIVmac251 is inefficiently transmitted to rhesus macaques by penile inoculation with a single SIVenv variant found in ramp-up phase plasma. AIDS Res Hum Retroviruses (2011) 1.13
Human Non-neutralizing HIV-1 Envelope Monoclonal Antibodies Limit the Number of Founder Viruses during SHIV Mucosal Infection in Rhesus Macaques. PLoS Pathog (2015) 1.11
Phylogenetic inferences on HIV-1 transmission: implications for the design of prevention and treatment interventions. AIDS (2013) 1.10
HIV-1 transmission during early antiretroviral therapy: evaluation of two HIV-1 transmission events in the HPTN 052 prevention study. PLoS One (2013) 1.04
Pilot studies for development of an HIV subtype panel for surveillance of global diversity. AIDS Res Hum Retroviruses (2012) 0.95
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
SHIV-162P3 infection of rhesus macaques given maraviroc gel vaginally does not involve resistant viruses. PLoS One (2011) 0.87
Treatment as Prevention: Characterization of Partner Infections in the HIV Prevention Trials Network 052 Trial. J Acquir Immune Defic Syndr (2017) 0.87
Short communication: HIV type 1 subtype C variants transmitted through the bottleneck of breastfeeding are sensitive to new generation broadly neutralizing antibodies directed against quaternary and CD4-binding site epitopes. AIDS Res Hum Retroviruses (2013) 0.86
Single-Genome Sequencing of Hepatitis C Virus in Donor-Recipient Pairs Distinguishes Modes and Models of Virus Transmission and Early Diversification. J Virol (2015) 0.86
Transmitted/Founder Viruses Rapidly Escape from CD8+ T Cell Responses in Acute Hepatitis C Virus Infection. J Virol (2015) 0.86
Future of phylogeny in HIV prevention. J Acquir Immune Defic Syndr (2013) 0.85
Limited nucleotide changes in the Rev response element (RRE) during HIV-1 infection alter overall Rev-RRE activity and Rev multimerization. J Virol (2013) 0.84
Low Multiplicity of HIV-1 Infection and No Vaccine Enhancement in VAX003 Injection Drug Users. Open Forum Infect Dis (2014) 0.84
Molecular mechanisms of HIV type 1 prophylaxis failure revealed by single-genome sequencing. J Infect Dis (2013) 0.84
Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) Identifies Immune-Selected HIV Variants. Viruses (2015) 0.82
Analysis of Viral Diversity in Relation to the Recency of HIV-1C Infection in Botswana. PLoS One (2016) 0.81
The number and genetic relatedness of transmitted/founder virus impact clinical outcome in vaginal R5 SHIVSF162P3N infection. Retrovirology (2014) 0.78
Brief Report: HIV-1 Evolution in Breakthrough Infections in a Human Trial of Oral Pre-exposure Prophylaxis With Emtricitabine and Tenofovir Disoproxil Fumarate. J Acquir Immune Defic Syndr (2016) 0.77
SPMM: estimating infection duration of multivariant HIV-1 infections. Bioinformatics (2015) 0.77
Transmitted/founder simian immunodeficiency virus envelope sequences in vesicular stomatitis and Semliki forest virus vector immunized rhesus macaques. PLoS One (2014) 0.76
Modeling sequence evolution in HIV-1 infection with recombination. J Theor Biol (2013) 0.76
Transmission of Multiple HIV-1 Subtype C Transmitted/founder Viruses into the Same Recipients Was not Determined by Modest Phenotypic Differences. Sci Rep (2016) 0.76
Using Combined Diagnostic Test Results to Hindcast Trends of Infection from Cross-Sectional Data. PLoS Comput Biol (2016) 0.75
Diversification in the HIV-1 Envelope Hyper-variable Domains V2, V4, and V5 and Higher Probability of Transmitted/Founder Envelope Glycosylation Favor the Development of Heterologous Neutralization Breadth. PLoS Pathog (2016) 0.75
Pairwise diversity and tMRCA as potential markers for HIV infection recency. Medicine (Baltimore) (2017) 0.75
Use of Dried Blood Spots to Elucidate Full-Length Transmitted/Founder HIV-1 Genomes. Pathog Immun (2016) 0.75
Genome sequencing in microfabricated high-density picolitre reactors. Nature (2005) 150.21
BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol (2007) 74.13
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
Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics (1991) 16.12
Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase. J Virol (1995) 9.02
Selective transmission of human immunodeficiency virus type-1 variants from mothers to infants. Science (1992) 7.44
Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection. J Exp Med (2009) 7.01
Natural variation in Vif: differential impact on APOBEC3G/3F and a potential role in HIV-1 diversification. PLoS Pathog (2005) 3.59
Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo. PLoS One (2009) 3.40
Modeling plasma virus concentration during primary HIV infection. J Theor Biol (2000) 3.40
Hepatitis C virus transmission bottlenecks analyzed by deep sequencing. J Virol (2010) 2.45
Modeling sequence evolution in acute HIV-1 infection. J Theor Biol (2009) 2.32
HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBEC. PLoS Pathog (2009) 2.15
Estimation of the initial viral growth rate and basic reproductive number during acute HIV-1 infection. J Virol (2010) 2.02
Homogeneous quasispecies in 16 out of 17 individuals during very early HIV-1 primary infection. AIDS (2002) 1.70
Target cell APOBEC3C can induce limited G-to-A mutation in HIV-1. PLoS Pathog (2007) 1.22
Current applications of single-cell PCR. Cell Mol Life Sci (2000) 1.14
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
Diversity considerations in HIV-1 vaccine selection. Science (2002) 9.60
Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission. Science (2004) 8.60
Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection. J Exp Med (2009) 7.01
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
Low-dose rectal inoculation of rhesus macaques by SIVsmE660 or SIVmac251 recapitulates human mucosal infection by HIV-1. J Exp Med (2009) 4.79
HIV-1 superinfection despite broad CD8+ T-cell responses containing replication of the primary virus. Nature (2002) 4.20
Polyvalent vaccines for optimal coverage of potential T-cell epitopes in global HIV-1 variants. Nat Med (2006) 4.14
A novel antiviral intervention results in more accurate assessment of human immunodeficiency virus type 1 replication dynamics and T-cell decay in vivo. J Virol (2003) 4.12
Breadth of human immunodeficiency virus-specific neutralizing activity in sera: clustering analysis and association with clinical variables. J Virol (2009) 3.85
Kinetics of influenza A virus infection in humans. J Virol (2006) 3.78
High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men. PLoS Pathog (2010) 3.68
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
A group M consensus envelope glycoprotein induces antibodies that neutralize subsets of subtype B and C HIV-1 primary viruses. Virology (2006) 3.26
Acute loss of intestinal CD4+ T cells is not predictive of simian immunodeficiency virus virulence. J Immunol (2007) 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 single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing. PLoS One (2010) 3.02
Persistent HIV-1 replication is associated with lower antiretroviral drug concentrations in lymphatic tissues. Proc Natl Acad Sci U S A (2014) 2.95
Antigenicity and immunogenicity of a synthetic human immunodeficiency virus type 1 group m consensus envelope glycoprotein. J Virol (2005) 2.89
Protective efficacy of a global HIV-1 mosaic vaccine against heterologous SHIV challenges in rhesus monkeys. Cell (2013) 2.88
Rapid emergence of protease inhibitor resistance in hepatitis C virus. Sci Transl Med (2010) 2.82
Evidence of differential HLA class I-mediated viral evolution in functional and accessory/regulatory genes of HIV-1. PLoS Pathog (2007) 2.81
Genetic and phenotypic analyses of human immunodeficiency virus type 1 escape from a small-molecule CCR5 inhibitor. J Virol (2004) 2.80
Modeling shows that the NS5A inhibitor daclatasvir has two modes of action and yields a shorter estimate of the hepatitis C virus half-life. Proc Natl Acad Sci U S A (2013) 2.79
Modelling how ribavirin improves interferon response rates in hepatitis C virus infection. Nature (2004) 2.74
Mosaic vaccines elicit CD8+ T lymphocyte responses that confer enhanced immune coverage of diverse HIV strains in monkeys. Nat Med (2010) 2.53
Viral dynamics and response differences in HCV-infected African American and white patients treated with IFN and ribavirin. Hepatology (2003) 2.50
Modeling sequence evolution in acute HIV-1 infection. J Theor Biol (2009) 2.32
Immediate antiviral therapy appears to restrict resting CD4+ cell HIV-1 infection without accelerating the decay of latent infection. Proc Natl Acad Sci U S A (2012) 2.27
The complexity of complexes in signal transduction. Biotechnol Bioeng (2003) 2.20
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
Extensive HLA class I allele promiscuity among viral CTL epitopes. Eur J Immunol (2007) 2.10
Vertical T cell immunodominance and epitope entropy determine HIV-1 escape. J Clin Invest (2012) 2.05
Intensification of antiretroviral therapy accelerates the decay of the HIV-1 latent reservoir and decreases, but does not eliminate, ongoing virus replication. J Acquir Immune Defic Syndr (2004) 2.05
Prevalence of broadly neutralizing antibody responses during chronic HIV-1 infection. AIDS (2014) 2.04
Different dynamics of CD4+ and CD8+ T cell responses during and after acute lymphocytic choriomeningitis virus infection. J Immunol (2003) 2.03
Estimation of the initial viral growth rate and basic reproductive number during acute HIV-1 infection. J Virol (2010) 2.02
Kinetics of hepatitis C virus reinfection after liver transplantation. Liver Transpl (2006) 2.01
Triphasic decline of hepatitis C virus RNA during antiviral therapy. Hepatology (2007) 2.00
CD8+ lymphocytes control viral replication in SIVmac239-infected rhesus macaques without decreasing the lifespan of productively infected cells. PLoS Pathog (2010) 1.99
Large-scale amplification, cloning and sequencing of near full-length HIV-1 subtype C genomes. J Virol Methods (2006) 1.99
Impact of HLA-B alleles, epitope binding affinity, functional avidity, and viral coinfection on the immunodominance of virus-specific CTL responses. J Immunol (2006) 1.99
The Thai Phase III HIV Type 1 Vaccine trial (RV144) regimen induces antibodies that target conserved regions within the V2 loop of gp120. AIDS Res Hum Retroviruses (2012) 1.94
Plasma IgG to linear epitopes in the V2 and V3 regions of HIV-1 gp120 correlate with a reduced risk of infection in the RV144 vaccine efficacy trial. PLoS One (2013) 1.94
Determining the relative efficacy of highly active antiretroviral therapy. J Infect Dis (2003) 1.90
Modeling hepatitis C virus dynamics: liver regeneration and critical drug efficacy. J Theor Biol (2007) 1.89
Designing a genome-based HIV incidence assay with high sensitivity and specificity. AIDS (2011) 1.88
Second-phase hepatitis C virus RNA decline during telaprevir-based therapy increases with drug effectiveness: implications for treatment duration. Hepatology (2011) 1.87
Turnover rates of B cells, T cells, and NK cells in simian immunodeficiency virus-infected and uninfected rhesus macaques. J Immunol (2003) 1.87
In vivo dynamics of T cell activation, proliferation, and death in HIV-1 infection: why are CD4+ but not CD8+ T cells depleted? Proc Natl Acad Sci U S A (2002) 1.82
A centralized gene-based HIV-1 vaccine elicits broad cross-clade cellular immune responses in rhesus monkeys. Proc Natl Acad Sci U S A (2008) 1.80
Quantifying the early immune response and adaptive immune response kinetics in mice infected with influenza A virus. J Virol (2010) 1.80
Modeling latently infected cell activation: viral and latent reservoir persistence, and viral blips in HIV-infected patients on potent therapy. PLoS Comput Biol (2009) 1.78
Kinetics of virus-specific CD8+ T cells and the control of human immunodeficiency virus infection. J Virol (2004) 1.77
Simulation and prediction of the adaptive immune response to influenza A virus infection. J Virol (2009) 1.76
Early ribavirin pharmacokinetics, HCV RNA and alanine aminotransferase kinetics in HIV/HCV co-infected patients during treatment with pegylated interferon and ribavirin. J Hepatol (2007) 1.74
Definition of the viral targets of protective HIV-1-specific T cell responses. J Transl Med (2011) 1.73
The prolonged culture of human immunodeficiency virus type 1 in primary lymphocytes increases its sensitivity to neutralization by soluble CD4. Virology (2004) 1.72
ON IDENTIFIABILITY OF NONLINEAR ODE MODELS AND APPLICATIONS IN VIRAL DYNAMICS. SIAM Rev Soc Ind Appl Math (2011) 1.69
Pharmacodynamics of PEG-IFN alpha differentiate HIV/HCV coinfected sustained virological responders from nonresponders. Hepatology (2006) 1.69
Polyspecificity of T cell and B cell receptor recognition. Semin Immunol (2007) 1.68
Cross-subtype T-cell immune responses induced by a human immunodeficiency virus type 1 group m consensus env immunogen. J Virol (2006) 1.63
Effect of ribavirin on viral kinetics and liver gene expression in chronic hepatitis C. Gut (2013) 1.63
Early low-titer neutralizing antibodies impede HIV-1 replication and select for virus escape. PLoS Pathog (2012) 1.61
Impact of thymectomy on the peripheral T cell pool in rhesus macaques before and after infection with simian immunodeficiency virus. Eur J Immunol (2005) 1.60
Fitness costs and diversity of the cytotoxic T lymphocyte (CTL) response determine the rate of CTL escape during acute and chronic phases of HIV infection. J Virol (2011) 1.57
Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections. PLoS Pathog (2011) 1.57
Parameter identifiability and estimation of HIV/AIDS dynamic models. Bull Math Biol (2008) 1.56
Drug resistance and influenza pandemics. Lancet (2002) 1.55
Transient viremia, plasma viral load, and reservoir replenishment in HIV-infected patients on antiretroviral therapy. J Acquir Immune Defic Syndr (2007) 1.54
Estimating lymphocyte division and death rates from CFSE data. Bull Math Biol (2006) 1.53
Modeling long-term HIV dynamics and antiretroviral response: effects of drug potency, pharmacokinetics, adherence, and drug resistance. J Acquir Immune Defic Syndr (2005) 1.52