Published in Mol Biol Evol on October 28, 2009
Viral phylodynamics and the search for an 'effective number of infections'. Philos Trans R Soc Lond B Biol Sci (2010) 1.76
Magnitude and breadth of a nonprotective neutralizing antibody response in an efficacy trial of a candidate HIV-1 gp120 vaccine. J Infect Dis (2010) 1.43
Mutation at a single position in the V2 domain of the HIV-1 envelope protein confers neutralization sensitivity to a highly neutralization-resistant virus. J Virol (2010) 1.14
Phylodynamics of HIV-1 from a phase III AIDS vaccine trial in Bangkok, Thailand. PLoS One (2011) 1.11
Monoclonal antibodies to the V2 domain of MN-rgp120: fine mapping of epitopes and inhibition of α4β7 binding. PLoS One (2012) 1.03
The evolution of HIV: inferences using phylogenetics. Mol Phylogenet Evol (2011) 0.94
Sequences in glycoprotein gp41, the CD4 binding site, and the V2 domain regulate sensitivity and resistance of HIV-1 to broadly neutralizing antibodies. J Virol (2012) 0.88
Phylogenetic relatedness of circulating HIV-1C variants in Mochudi, Botswana. PLoS One (2013) 0.88
Genetic and epidemiological insights into the emergence of peste des petits ruminants virus (PPRV) across Asia and Africa. Sci Rep (2014) 0.80
Characterization of HIV diversity, phylodynamics and drug resistance in Washington, DC. PLoS One (2017) 0.75
MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics (2003) 130.85
MODELTEST: testing the model of DNA substitution. Bioinformatics (1998) 101.19
BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol (2007) 74.13
On the number of segregating sites in genetical models without recombination. Theor Popul Biol (1975) 60.96
Viral load and heterosexual transmission of human immunodeficiency virus type 1. Rakai Project Study Group. N Engl J Med (2000) 41.18
Relaxed phylogenetics and dating with confidence. PLoS Biol (2006) 37.68
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol (2000) 35.86
MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res (2005) 31.64
Antibody neutralization and escape by HIV-1. Nature (2003) 21.48
Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol (2005) 18.57
HyPhy: hypothesis testing using phylogenies. Bioinformatics (2004) 17.33
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
Rapid evolution of the neutralizing antibody response to HIV type 1 infection. Proc Natl Acad Sci U S A (2003) 12.75
Dynamics of HIV viremia and antibody seroconversion in plasma donors: implications for diagnosis and staging of primary HIV infection. AIDS (2003) 11.66
Timing the ancestor of the HIV-1 pandemic strains. Science (2000) 10.42
Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J Virol (1999) 10.41
Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol (2005) 10.21
Placebo-controlled phase 3 trial of a recombinant glycoprotein 120 vaccine to prevent HIV-1 infection. J Infect Dis (2005) 10.20
Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission. Science (2004) 8.60
Transient high levels of viremia in patients with primary human immunodeficiency virus type 1 infection. N Engl J Med (1991) 7.83
A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics (2002) 7.41
High titers of cytopathic virus in plasma of patients with symptomatic primary HIV-1 infection. N Engl J Med (1991) 7.01
The acquired immunodeficiency syndrome in a cohort of homosexual men. A six-year follow-up study. Ann Intern Med (1985) 4.30
Neutralizing antibody responses in acute human immunodeficiency virus type 1 subtype C infection. J Virol (2007) 4.13
Independent introduction of two major HIV-1 genotypes into distinct high-risk populations in Thailand. Lancet (1993) 3.28
The emergence of HIV/AIDS in the Americas and beyond. Proc Natl Acad Sci U S A (2007) 2.89
The molecular epidemiology of HIV in Asia. AIDS (1994) 2.37
Human T-cell lymphotropic virus type III infection in a cohort of homosexual men in New York City. JAMA (1986) 1.90
Genetic diversity of HIV in Africa: impact on diagnosis, treatment, vaccine development and trials. AIDS (2003) 1.61
Evolution and diversity of HIV-1 in Africa--a review. Virus Genes (2003) 1.57
Ethnic differences in the adaptation rate of HIV gp120 from a vaccine trial. Retrovirology (2009) 0.93
High incidence of unusual cysteine variants in gp120 envelope proteins from early HIV type 1 infections from a Phase 3 vaccine efficacy trial. AIDS Res Hum Retroviruses (2006) 0.88
Bridging the gap between molecular epidemiologists and evolutionists. Trends Microbiol (2005) 0.85
The molecular epidemiology of HIV-1 in South and East Asia. Curr HIV Res (2003) 0.80
The manifestation of AIDS in Africa: an epidemiological overview. J Neurovirol (2005) 0.79
The frontline of HIV1 diffusion in the Central African region: a geographical and epidemiological perspective. Int J Epidemiol (1993) 0.77
jModelTest: phylogenetic model averaging. Mol Biol Evol (2008) 44.78
jModelTest 2: more models, new heuristics and parallel computing. Nat Methods (2012) 27.83
ProtTest: selection of best-fit models of protein evolution. Bioinformatics (2005) 19.16
Immune-correlates analysis of an HIV-1 vaccine efficacy trial. N Engl J Med (2012) 12.98
RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics (2010) 9.49
ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics (2011) 8.68
Automated phylogenetic detection of recombination using a genetic algorithm. Mol Biol Evol (2006) 5.94
ALTER: program-oriented conversion of DNA and protein alignments. Nucleic Acids Res (2010) 5.32
Correlation between immunologic responses to a recombinant glycoprotein 120 vaccine and incidence of HIV-1 infection in a phase 3 HIV-1 preventive vaccine trial. J Infect Dis (2005) 5.14
GARD: a genetic algorithm for recombination detection. Bioinformatics (2006) 4.88
Vaccine induction of antibodies against a structurally heterogeneous site of immune pressure within HIV-1 envelope protein variable regions 1 and 2. Immunity (2013) 4.82
Pharmacogenetic study of statin therapy and cholesterol reduction. JAMA (2004) 4.47
The causes and consequences of HIV evolution. Nat Rev Genet (2004) 4.34
Analysis of a clonal lineage of HIV-1 envelope V2/V3 conformational epitope-specific broadly neutralizing antibodies and their inferred unmutated common ancestors. J Virol (2011) 4.06
An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics (2007) 3.76
Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified. Proc Natl Acad Sci U S A (2008) 3.56
An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1. PLoS Comput Biol (2009) 3.11
The effect of recombination on the accuracy of phylogeny estimation. J Mol Evol (2002) 3.11
The impact of species concept on biodiversity studies. Q Rev Biol (2004) 2.91
Magnitude and breadth of the neutralizing antibody response in the RV144 and Vax003 HIV-1 vaccine efficacy trials. J Infect Dis (2012) 2.89
Recombination in evolutionary genomics. Annu Rev Genet (2002) 2.54
Vaccine-induced Env V1-V2 IgG3 correlates with lower HIV-1 infection risk and declines soon after vaccination. Sci Transl Med (2014) 2.47
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
TreeSAAP: selection on amino acid properties using phylogenetic trees. Bioinformatics (2003) 1.91
Subterranean phylogeography of freshwater crayfishes shows extensive gene flow and surprisingly large population sizes. Mol Ecol (2005) 1.90
International seroepidemiology of adenovirus serotypes 5, 26, 35, and 48 in pediatric and adult populations. Vaccine (2011) 1.88
Tree scanning: a method for using haplotype trees in phenotype/genotype association studies. Genetics (2004) 1.87
Parallel evolution of the genetic code in arthropod mitochondrial genomes. PLoS Biol (2006) 1.85
Population genetics of microbial pathogens estimated from multilocus sequence typing (MLST) data. Infect Genet Evol (2005) 1.72
HIV-1 virologic and immunologic progression and initiation of antiretroviral therapy among HIV-1-infected subjects in a trial of the efficacy of recombinant glycoprotein 120 vaccine. J Infect Dis (2005) 1.70
Pathoscope: species identification and strain attribution with unassembled sequencing data. Genome Res (2013) 1.62
Phylogeographic history of the land snail Candidula unifasciata (Helicellinae, Stylommatophora): fragmentation, corridor migration, and secondary contact. Evolution (2002) 1.62
A coalescent model of recombination hotspots. Genetics (2003) 1.60
Incorporating gaps as phylogenetic characters across eight DNA regions: ramifications for North American Psoraleeae (Leguminosae). Mol Phylogenet Evol (2007) 1.54
Phylogenetic models of molecular evolution: next-generation data, fit, and performance. J Mol Evol (2013) 1.45
Magnitude and breadth of a nonprotective neutralizing antibody response in an efficacy trial of a candidate HIV-1 gp120 vaccine. J Infect Dis (2010) 1.43
A comparison of phylogenetic network methods using computer simulation. PLoS One (2008) 1.40
Characterization of the follicular dendritic cell reservoir of human immunodeficiency virus type 1. J Virol (2008) 1.40
Candidate HIV/AIDS vaccines: lessons learned from the World's first phase III efficacy trials. AIDS (2003) 1.40
Evolutionary biology in biodiversity science, conservation, and policy: a call to action. Evolution (2010) 1.36
Unraveling the evolutionary radiation of the thoracican barnacles using molecular and morphological evidence: a comparison of several divergence time estimation approaches. Syst Biol (2004) 1.28
Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demography. BMC Bioinformatics (2007) 1.27
MtArt: a new model of amino acid replacement for Arthropoda. Mol Biol Evol (2006) 1.27
Perkinsoide chabelardi n. gen., a protozoan parasite with an intermediate evolutionary position: possible cause of the decrease of sardine fisheries? Environ Microbiol (2006) 1.26
The evolutionary value of recombination is constrained by genome modularity. PLoS Genet (2005) 1.26
Lost branches on the tree of life. PLoS Biol (2013) 1.26
The effect of recombination on the reconstruction of ancestral sequences. Genetics (2010) 1.25
Comparing phylogenetic codivergence between polyomaviruses and their hosts. J Virol (2006) 1.25
Antigenicity and immunogenicity of RV144 vaccine AIDSVAX clade E envelope immunogen is enhanced by a gp120 N-terminal deletion. J Virol (2012) 1.24
Pathogen typing in the genomics era: MLST and the future of molecular epidemiology. Infect Genet Evol (2013) 1.24
Model-based multi-locus estimation of decapod phylogeny and divergence times. Mol Phylogenet Evol (2005) 1.23
Recombination estimation under complex evolutionary models with the coalescent composite-likelihood method. Mol Biol Evol (2006) 1.23
A comprehensive and integrative reconstruction of evolutionary history for Anomura (Crustacea: Decapoda). BMC Evol Biol (2013) 1.20
Coalescent simulation of intracodon recombination. Genetics (2009) 1.20
Analysing recombination in nucleotide sequences. Mol Ecol Resour (2011) 1.18
Phase I/II study of a candidate vaccine designed against the B and E subtypes of HIV-1. J Acquir Immune Defic Syndr (2004) 1.18
LC16m8: an attenuated smallpox vaccine. Vaccine (2006) 1.16
Somatic mitochondrial DNA mutations in prostate cancer and normal appearing adjacent glands in comparison to age-matched prostate samples without malignant histology. J Mol Diagn (2006) 1.14
Genome scanning tests for comparing amino acid sequences between groups. Biometrics (2007) 1.14
Molecular characterization of crustacean visual pigments and the evolution of pancrustacean opsins. Mol Biol Evol (2006) 1.14
Mutation at a single position in the V2 domain of the HIV-1 envelope protein confers neutralization sensitivity to a highly neutralization-resistant virus. J Virol (2010) 1.14
Temporal trends in gonococcal population genetics in a high prevalence urban community. Infect Genet Evol (2006) 1.12
Phylodynamics of HIV-1 from a phase III AIDS vaccine trial in Bangkok, Thailand. PLoS One (2011) 1.11
Targeted amplicon sequencing (TAS): a scalable next-gen approach to multilocus, multitaxa phylogenetics. Genome Biol Evol (2011) 1.10
Evidence for survival of Pleistocene climatic changes in Northern refugia by the land snail Trochoidea geyeri (Soós 1926) (Helicellinae, Stylommatophora). BMC Evol Biol (2003) 1.10
Molecular taxonomy in the dark: evolutionary history, phylogeography, and diversity of cave crayfish in the subgenus Aviticambarus, genus Cambarus. Mol Phylogenet Evol (2006) 1.08
Divergence and diversification in North American Psoraleeae (Fabaceae) due to climate change. BMC Biol (2008) 1.08
Highly attenuated smallpox vaccine protects rabbits and mice against pathogenic orthopoxvirus challenge. Vaccine (2006) 1.08
Population genetics of Neisseria gonorrhoeae in a high-prevalence community using a hypervariable outer membrane porB and 13 slowly evolving housekeeping genes. Mol Biol Evol (2005) 1.05
Pleistocene glaciation leaves deep signature on the freshwater crab Aegla alacalufi in Chilean Patagonia. Mol Ecol (2009) 1.03
Monoclonal antibodies to the V2 domain of MN-rgp120: fine mapping of epitopes and inhibition of α4β7 binding. PLoS One (2012) 1.03
Evaluating the performance of likelihood methods for detecting population structure and migration. Mol Ecol (2004) 1.02
The tempo and mode of barnacle evolution. Mol Phylogenet Evol (2007) 1.01
Phylogenetic relationships and molecular adaptation dynamics of human rhinoviruses. Mol Biol Evol (2009) 1.01
DNA evidence for nonhybrid origins of parthenogenesis in natural populations of vertebrates. Evolution (2009) 1.01
Recombination favors the evolution of drug resistance in HIV-1 during antiretroviral therapy. Infect Genet Evol (2007) 1.00
Using models of nucleotide evolution to build phylogenetic trees. Dev Comp Immunol (2005) 1.00
Population genomics and phylogeography of an Australian dairy factory derived lytic bacteriophage. Genome Biol Evol (2012) 0.97
Phylogenetic evidence for multiple sympatric ecological diversification in a marine snail. Evolution (2007) 0.97