Published in Mol Biol Evol on July 03, 2006
Estimating the rate of intersubtype recombination in early HIV-1 group M strains. J Virol (2012) 12.78
Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics (2010) 6.14
Low-dose rectal inoculation of rhesus macaques by SIVsmE660 or SIVmac251 recapitulates human mucosal infection by HIV-1. J Exp Med (2009) 4.79
Quantitating the multiplicity of infection with human immunodeficiency virus type 1 subtype C reveals a non-poisson distribution of transmitted variants. J Virol (2009) 4.40
Persistent HIV-1 replication maintains the tissue reservoir during therapy. Nature (2016) 3.23
An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1. PLoS Comput Biol (2009) 3.11
Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage. Proc Natl Acad Sci U S A (2011) 2.78
Telomeric expression sites are highly conserved in Trypanosoma brucei. PLoS One (2008) 2.22
Evolutionary insights into the ecology of coronaviruses. J Virol (2007) 2.16
HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBEC. PLoS Pathog (2009) 2.15
A maximum likelihood method for detecting directional evolution in protein sequences and its application to influenza A virus. Mol Biol Evol (2008) 1.96
MHC genotypes associate with resistance to a frog-killing fungus. Proc Natl Acad Sci U S A (2011) 1.87
Serology-enabled discovery of genetically diverse hepaciviruses in a new host. J Virol (2012) 1.80
Complete genome analysis of coxsackievirus A2, A4, A5, and A10 strains isolated from hand, foot, and mouth disease patients in China revealing frequent recombination of human enterovirus A. J Clin Microbiol (2011) 1.71
Comparative study of methods for detecting sequence compartmentalization in human immunodeficiency virus type 1. J Virol (2007) 1.71
Sequence analyses of 2012 West Nile virus isolates from Texas fail to associate viral genetic factors with outbreak magnitude. Am J Trop Med Hyg (2013) 1.65
Comparative analysis reveals frequent recombination in the parvoviruses. J Gen Virol (2007) 1.64
Evolutionary fingerprinting of genes. Mol Biol Evol (2009) 1.64
Models of coding sequence evolution. Brief Bioinform (2008) 1.64
Identification of rodent homologs of hepatitis C virus and pegiviruses. MBio (2013) 1.61
HIV-specific probabilistic models of protein evolution. PLoS One (2007) 1.61
CodonTest: modeling amino acid substitution preferences in coding sequences. PLoS Comput Biol (2010) 1.56
Unprecedented levels of horizontal gene transfer among spatially co-occurring Shewanella bacteria from the Baltic Sea. ISME J (2010) 1.52
Evolutionary dynamics of the human ABO gene. Hum Genet (2008) 1.51
African origin of the malaria parasite Plasmodium vivax. Nat Commun (2014) 1.47
Detection of a novel and highly divergent coronavirus from asian leopard cats and Chinese ferret badgers in Southern China. J Virol (2007) 1.44
Immune activation promotes evolutionary conservation of T-cell epitopes in HIV-1. PLoS Biol (2013) 1.44
The association of recombination events in the founding and emergence of subgenogroup evolutionary lineages of human enterovirus 71. J Virol (2011) 1.40
Recombination in vaccine and circulating strains of porcine reproductive and respiratory syndrome viruses. Emerg Infect Dis (2009) 1.39
Partitioning the genetic diversity of a virus family: approach and evaluation through a case study of picornaviruses. J Virol (2012) 1.31
Identification of wheat gene Sr35 that confers resistance to Ug99 stem rust race group. Science (2013) 1.31
Role of donor genital tract HIV-1 diversity in the transmission bottleneck. Proc Natl Acad Sci U S A (2011) 1.30
A large new subset of TRIM genes highly diversified by duplication and positive selection in teleost fish. BMC Biol (2009) 1.28
454 sequencing reveals extreme complexity of the class II Major Histocompatibility Complex in the collared flycatcher. BMC Evol Biol (2010) 1.28
Origin and evolution of HIV-1 in breast milk determined by single-genome amplification and sequencing. J Virol (2010) 1.26
Mutability dynamics of an emergent single stranded DNA virus in a naïve host. PLoS One (2014) 1.25
The effect of recombination on the reconstruction of ancestral sequences. Genetics (2010) 1.25
Ecology, genetic diversity, and phylogeographic structure of andes virus in humans and rodents in Chile. J Virol (2008) 1.24
Evolution of new genotype of West Nile virus in North America. Emerg Infect Dis (2011) 1.20
Coalescent simulation of intracodon recombination. Genetics (2009) 1.20
Identification of a genomic reservoir for new TRIM genes in primate genomes. PLoS Genet (2011) 1.20
Convergence and divergence in the evolution of the APOBEC3G-Vif interaction reveal ancient origins of simian immunodeficiency viruses. PLoS Pathog (2013) 1.19
Wild waterfowl migration and domestic duck density shape the epidemiology of highly pathogenic H5N8 influenza in the Republic of Korea. Infect Genet Evol (2015) 1.18
Role of recombination in the evolution of the model plant pathogen Pseudomonas syringae pv. tomato DC3000, a very atypical tomato strain. Appl Environ Microbiol (2008) 1.17
Circulating coxsackievirus A16 identified as recombinant type A human enterovirus, China. Emerg Infect Dis (2011) 1.15
Co-circulation and genomic recombination of coxsackievirus A16 and enterovirus 71 during a large outbreak of hand, foot, and mouth disease in Central China. PLoS One (2014) 1.13
Restriction of HIV-1 genotypes in breast milk does not account for the population transmission genetic bottleneck that occurs following transmission. PLoS One (2010) 1.13
Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations. Proc Natl Acad Sci U S A (2012) 1.13
Evolution of the interferon alpha gene family in eutherian mammals. Gene (2007) 1.12
MHC adaptive divergence between closely related and sympatric African cichlids. PLoS One (2007) 1.10
The genetic bottleneck in vertical transmission of subtype C HIV-1 is not driven by selection of especially neutralization-resistant virus from the maternal viral population. J Virol (2011) 1.10
Evidence for limited genetic compartmentalization of HIV-1 between lung and blood. PLoS One (2009) 1.09
A new pheromone trail-based genetic algorithm for comparative genome assembly. Nucleic Acids Res (2008) 1.09
West Nile virus genetic diversity is maintained during transmission by Culex pipiens quinquefasciatus mosquitoes. PLoS One (2011) 1.08
Extensive HIV-1 intra-host recombination is common in tissues with abnormal histopathology. PLoS One (2009) 1.08
An exploratory algorithm to identify intra-host recombinant viral sequences. Mol Phylogenet Evol (2008) 1.07
Relative evolutionary rates of NBS-encoding genes revealed by soybean segmental duplication. Mol Genet Genomics (2010) 1.06
Differential evolution and neofunctionalization of snake venom metalloprotease domains. Mol Cell Proteomics (2012) 1.06
Molecular evolution of lineage 2 West Nile virus. J Gen Virol (2012) 1.05
The breadth of antiviral activity of Apobec3DE in chimpanzees has been driven by positive selection. J Virol (2011) 1.04
Genome diversity of Epstein-Barr virus from multiple tumor types and normal infection. J Virol (2015) 1.03
Evidence for natural recombination between mink enteritis virus and canine parvovirus. Virol J (2012) 1.02
Molecular evolution of West Nile virus in a northern temperate region: Connecticut, USA 1999-2008. Virology (2011) 1.01
Selection, recombination, and virulence gene diversity among group B streptococcal genotypes. J Bacteriol (2009) 1.01
Intercompartmental recombination of HIV-1 contributes to env intrahost diversity and modulates viral tropism and sensitivity to entry inhibitors. J Virol (2011) 1.00
Distinct evolutionary pressures underlie diversity in simian immunodeficiency virus and human immunodeficiency virus lineages. J Virol (2012) 1.00
Susceptibility of amphibians to chytridiomycosis is associated with MHC class II conformation. Proc Biol Sci (2015) 1.00
Phylogenomics and the dynamic genome evolution of the genus Streptococcus. Genome Biol Evol (2014) 0.99
Widespread distribution and a new recombinant species of Brazilian virus associated with cotton blue disease. Virol J (2008) 0.98
Contrasted evolutionary histories of two Toll-like receptors (Tlr4 and Tlr7) in wild rodents (MURINAE). BMC Evol Biol (2013) 0.98
High-throughput analysis of human cytomegalovirus genome diversity highlights the widespread occurrence of gene-disrupting mutations and pervasive recombination. J Virol (2015) 0.98
A network approach to analyzing highly recombinant malaria parasite genes. PLoS Comput Biol (2013) 0.97
Evolution stings: the origin and diversification of scorpion toxin peptide scaffolds. Toxins (Basel) (2013) 0.97
Restricted genetic diversity of HIV-1 subtype C envelope glycoprotein from perinatally infected Zambian infants. PLoS One (2010) 0.96
Molecular epidemiology of Powassan virus in North America. J Gen Virol (2010) 0.96
Analyses of pediatric isolates of Cryptococcus neoformans from South Africa. J Clin Microbiol (2010) 0.96
Circulating HFMD-associated coxsackievirus A16 is genetically and phenotypically distinct from the prototype CV-A16. PLoS One (2014) 0.95
Mammalian NPC1 genes may undergo positive selection and human polymorphisms associate with type 2 diabetes. BMC Med (2012) 0.94
Whole-genome enrichment and sequencing of Chlamydia trachomatis directly from clinical samples. BMC Infect Dis (2014) 0.94
Extraordinary intraspecific diversity in oyster sperm bindin. Proc Natl Acad Sci U S A (2008) 0.94
Factors associated with siman immunodeficiency virus transmission in a natural African nonhuman primate host in the wild. J Virol (2014) 0.94
Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences. Virol J (2008) 0.94
Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area. PLoS One (2013) 0.93
Genomic and phylogenetic characterization of Brazilian yellow fever virus strains. J Virol (2012) 0.93
Potent autologous and heterologous neutralizing antibody responses occur in HIV-2 infection across a broad range of infection outcomes. J Virol (2011) 0.93
Isolation and analysis of the genetic diversity of repertoires of VSG expression site containing telomeres from Trypanosoma brucei gambiense, T. b. brucei and T. equiperdum. BMC Genomics (2008) 0.93
Evidence of recombination in Hepatitis C Virus populations infecting a hemophiliac patient. Virol J (2009) 0.93
Active methamphetamine use is associated with transmitted drug resistance to non-nucleoside reverse transcriptase inhibitors in individuals with HIV infection of unknown duration. Open AIDS J (2007) 0.93
Estimating selection pressures on HIV-1 using phylogenetic likelihood models. Stat Med (2008) 0.92
Molecular basis and phylogenetic implications of deoxycylindrospermopsin biosynthesis in the cyanobacterium Raphidiopsis curvata. Appl Environ Microbiol (2012) 0.92
Extraordinary MHC class II B diversity in a non-passerine, wild bird: the Eurasian Coot Fulica atra (Aves: Rallidae). Ecol Evol (2014) 0.92
Extremely high MHC class I variation in a population of a long-distance migrant, the Scarlet Rosefinch (Carpodacus erythrinus). Immunogenetics (2009) 0.92
Genomic analysis of closely related astroviruses. J Virol (2008) 0.92
Intragenic recombination as a mechanism of genetic diversity in bluetongue virus. J Virol (2010) 0.91
Evolution in an ancient detoxification pathway is coupled with a transition to herbivory in the drosophilidae. Mol Biol Evol (2014) 0.91
Detecting phylogenetic breakpoints and discordance from genome-wide alignments for species tree reconstruction. Genome Biol Evol (2011) 0.90
Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data. BMC Evol Biol (2014) 0.90
Host range and specificity of the Drosophila C virus. PLoS One (2010) 0.90
Genital tract sequestration of SIV following acute infection. PLoS Pathog (2011) 0.90
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
HyPhy: hypothesis testing using phylogenies. Bioinformatics (2004) 17.33
Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol (2005) 10.21
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
Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics (2005) 8.62
Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics (2010) 6.14
ALTER: program-oriented conversion of DNA and protein alignments. Nucleic Acids Res (2010) 5.32
GARD: a genetic algorithm for recombination detection. Bioinformatics (2006) 4.88
Evaluation of respondent-driven sampling. Epidemiology (2012) 4.75
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
An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics (2007) 3.76
Highly precise measurement of HIV DNA by droplet digital PCR. PLoS One (2013) 3.53
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
A random effects branch-site model for detecting episodic diversifying selection. Mol Biol Evol (2011) 2.88
A genetic algorithm approach to detecting lineage-specific variation in selection pressure. Mol Biol Evol (2004) 2.65
Transmission fitness of drug-resistant human immunodeficiency virus and the prevalence of resistance in the antiretroviral-treated population. J Infect Dis (2003) 2.54
Adaptation to different human populations by HIV-1 revealed by codon-based analyses. PLoS Comput Biol (2006) 2.48
Immune-driven recombination and loss of control after HIV superinfection. J Exp Med (2008) 2.34
Phylodynamics of infectious disease epidemics. Genetics (2009) 2.15
Syringe possession arrests are associated with receptive syringe sharing in two Mexico-US border cities. Addiction (2007) 2.14
Lack of neutralizing antibody response to HIV-1 predisposes to superinfection. Virology (2006) 2.07
A maximum likelihood method for detecting directional evolution in protein sequences and its application to influenza A virus. Mol Biol Evol (2008) 1.96
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
An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope. PLoS Comput Biol (2007) 1.82
Phylogenetic evidence for adaptive evolution of dengue viruses in nature. J Gen Virol (2002) 1.82
A public health model for the molecular surveillance of HIV transmission in San Diego, California. AIDS (2009) 1.81
Comparative study of methods for detecting sequence compartmentalization in human immunodeficiency virus type 1. J Virol (2007) 1.71
High activity and Levy searches: jellyfish can search the water column like fish. Proc Biol Sci (2011) 1.68
Genetic constraints and the adaptive evolution of rabies virus in nature. Virology (2002) 1.65
Long-term persistence of transmitted HIV drug resistance in male genital tract secretions: implications for secondary transmission. J Infect Dis (2007) 1.64
Evolutionary fingerprinting of genes. Mol Biol Evol (2009) 1.64
Reduced positive selection in vector-borne RNA viruses. Mol Biol Evol (2002) 1.62
Phylogeographic history of the land snail Candidula unifasciata (Helicellinae, Stylommatophora): fragmentation, corridor migration, and secondary contact. Evolution (2002) 1.62
Comparative study of adaptive molecular evolution in different human immunodeficiency virus groups and subtypes. J Virol (2004) 1.61
A coalescent model of recombination hotspots. Genetics (2003) 1.60
Herpes simplex virus type 2 infection does not influence viral dynamics during early HIV-1 infection. J Infect Dis (2007) 1.59
Simple epidemiological dynamics explain phylogenetic clustering of HIV from patients with recent infection. PLoS Comput Biol (2012) 1.51
Phylogenetic models of molecular evolution: next-generation data, fit, and performance. J Mol Evol (2013) 1.45
A simple hierarchical approach to modeling distributions of substitution rates. Mol Biol Evol (2004) 1.42
A comparison of phylogenetic network methods using computer simulation. PLoS One (2008) 1.40
Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models. Bioinformatics (2008) 1.40
Using respondent-driven sampling in a hidden population at risk of HIV infection: who do HIV-positive recruiters recruit? Sex Transm Dis (2009) 1.37
Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1. Mol Biol Evol (2009) 1.37
Individual and network factors associated with prevalent hepatitis C infection among rural Appalachian injection drug users. Am J Public Health (2012) 1.35
Respondent driven sampling--where we are and where should we be going? Sex Transm Infect (2012) 1.35
Adaptation to human populations is revealed by within-host polymorphisms in HIV-1 and hepatitis C virus. PLoS Pathog (2007) 1.31
Risk factors for childhood obesity at age 5: analysis of the millennium cohort study. BMC Public Health (2009) 1.30
Amprenavir-resistant HIV-1 exhibits lopinavir cross-resistance and reduced replication capacity. AIDS (2002) 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
The effect of recombination on the reconstruction of ancestral sequences. Genetics (2010) 1.25
Evolutionary interactions between N-linked glycosylation sites in the HIV-1 envelope. PLoS Comput Biol (2006) 1.25
Viral evolution during structured treatment interruptions in chronically human immunodeficiency virus-infected individuals. J Virol (2002) 1.24
Recombination estimation under complex evolutionary models with the coalescent composite-likelihood method. Mol Biol Evol (2006) 1.23
Deep molecular characterization of HIV-1 dynamics under suppressive HAART. PLoS Pathog (2011) 1.21
Coalescent simulation of intracodon recombination. Genetics (2009) 1.20
Low-level plasma HIVs in patients on prolonged suppressive highly active antiretroviral therapy are produced mostly by cells other than CD4 T-cells. J Med Virol (2009) 1.19
Analysing recombination in nucleotide sequences. Mol Ecol Resour (2011) 1.18
Antiretroviral drug resistance and risk behavior among recently HIV-infected men who have sex with men. J Acquir Immune Defic Syndr (2008) 1.14
Evaluation of the role of location and distance in recruitment in respondent-driven sampling. Int J Health Geogr (2011) 1.14
Beyond bushmeat: animal contact, injury, and zoonotic disease risk in Western Uganda. Ecohealth (2014) 1.13
Capture-recapture methods and respondent-driven sampling: their potential and limitations. Sex Transm Infect (2011) 1.13
Selection of drug-resistant HIV-1 mutants in response to repeated structured treatment interruptions. AIDS (2002) 1.12
Evolution of the interferon alpha gene family in eutherian mammals. Gene (2007) 1.12
Phylodynamics of HIV-1 from a phase III AIDS vaccine trial in Bangkok, Thailand. PLoS One (2011) 1.11
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
Epidemiological bridging by injection drug use drives an early HIV epidemic. Epidemics (2010) 1.07
Whole serum 3D LC-nESI-FTMS quantitative proteomics reveals sexual dimorphism in the milieu intérieur of overweight and obese adults. J Proteome Res (2014) 1.06
Phenotypic hypersusceptibility to multiple protease inhibitors and low replicative capacity in patients who are chronically infected with human immunodeficiency virus type 1. J Virol (2005) 1.05
Parsing social network survey data from hidden populations using stochastic context-free grammars. PLoS One (2009) 1.04
A combined analysis of microarray gene expression studies of the human prefrontal cortex identifies genes implicated in schizophrenia. J Psychiatr Res (2012) 1.02
Induction of T helper type 1 and 2 responses to 19-kilodalton merozoite surface protein 1 in vaccinated healthy volunteers and adults naturally exposed to malaria. Infect Immun (2002) 1.02
Travelling waves in a network of SIR epidemic nodes with an approximation of weak coupling. Math Med Biol (2010) 1.02
Incidence, clinical patterns, and outcomes of primary sclerosing cholangitis in South Wales, United Kingdom. Gastroenterology (2004) 1.01
Detecting signatures of selection from DNA sequences using Datamonkey. Methods Mol Biol (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
Transmitted drug resistance in the CFAR network of integrated clinical systems cohort: prevalence and effects on pre-therapy CD4 and viral load. PLoS One (2011) 0.99
Evolutionary model selection with a genetic algorithm: a case study using stem RNA. Mol Biol Evol (2006) 0.97
Phylogenetic evidence for multiple sympatric ecological diversification in a marine snail. Evolution (2007) 0.97
Characteristics of recently HIV-infected men who use the Internet to find male sex partners and sexual practices with those partners. J Acquir Immune Defic Syndr (2006) 0.97
Phylogeography and diversification history of the day-gecko genus Phelsuma in the Seychelles islands. BMC Evol Biol (2013) 0.96