Published in Bioinformatics on November 16, 2006
Estimating the rate of intersubtype recombination in early HIV-1 group M strains. J Virol (2012) 12.78
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
Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics (2010) 6.14
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
High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men. PLoS Pathog (2010) 3.68
HIV rebounds from latently infected cells, rather than from continuing low-level replication. Proc Natl Acad Sci U S A (2008) 3.40
The ability of primate lentiviruses to degrade the monocyte restriction factor SAMHD1 preceded the birth of the viral accessory protein Vpx. Cell Host Microbe (2012) 2.79
Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage. Proc Natl Acad Sci U S A (2011) 2.78
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res (2014) 2.54
The apolipoprotein L family of programmed cell death and immunity genes rapidly evolved in primates at discrete sites of host-pathogen interactions. Genome Res (2009) 2.35
Novel human parvovirus 4 genotype 3 in infants, Ghana. Emerg Infect Dis (2010) 2.19
A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences. Nucleic Acids Res (2009) 2.06
Phylodynamic reconstruction reveals norovirus GII.4 epidemic expansions and their molecular determinants. PLoS Pathog (2010) 1.88
The artiodactyl APOBEC3 innate immune repertoire shows evidence for a multi-functional domain organization that existed in the ancestor of placental mammals. BMC Mol Biol (2008) 1.85
The genome sequence of Trypanosoma brucei gambiense, causative agent of chronic human african trypanosomiasis. PLoS Negl Trop Dis (2010) 1.83
Proposals for the classification of human rhinovirus species A, B and C into genotypically assigned types. J Gen Virol (2013) 1.82
The HIV-1 reservoir in eight patients on long-term suppressive antiretroviral therapy is stable with few genetic changes over time. Proc Natl Acad Sci U S A (2013) 1.80
The origins of sexually transmitted HIV among men who have sex with men. Sci Transl Med (2010) 1.76
Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica. BMC Genomics (2011) 1.64
Ancient adaptive evolution of tetherin shaped the functions of Vpu and Nef in human immunodeficiency virus and primate lentiviruses. J Virol (2010) 1.61
Molecular basis for specific recognition of bacterial ligands by NAIP/NLRC4 inflammasomes. Mol Cell (2014) 1.55
Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept. Genome Biol Evol (2010) 1.54
Unprecedented levels of horizontal gene transfer among spatially co-occurring Shewanella bacteria from the Baltic Sea. ISME J (2010) 1.52
Frequent toggling between alternative amino acids is driven by selection in HIV-1. PLoS Pathog (2008) 1.49
Molecular Characterisation of Chikungunya Virus Infections in Trinidad and Comparison of Clinical and Laboratory Features with Dengue and Other Acute Febrile Cases. PLoS Negl Trop Dis (2015) 1.47
Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning. BMC Bioinformatics (2009) 1.42
An evolutionary analysis of the Secoviridae family of viruses. PLoS One (2014) 1.40
Evidence of the recombinant origin of a bat severe acute respiratory syndrome (SARS)-like coronavirus and its implications on the direct ancestor of SARS coronavirus. J Virol (2007) 1.39
Genetic analysis of Israel acute paralysis virus: distinct clusters are circulating in the United States. J Virol (2008) 1.34
Estimating reassortment rates in co-circulating Eurasian swine influenza viruses. J Gen Virol (2012) 1.34
Evolutionary and transmission dynamics of reassortant H5N1 influenza virus in Indonesia. PLoS Pathog (2008) 1.31
Single cell analysis of lymph node tissue from HIV-1 infected patients reveals that the majority of CD4+ T-cells contain one HIV-1 DNA molecule. PLoS Pathog (2013) 1.31
Species delimitation using a combined coalescent and information-theoretic approach: an example from North American Myotis bats. Syst Biol (2010) 1.29
Trypanosoma cruzi I genotypes in different geographical regions and transmission cycles based on a microsatellite motif of the intergenic spacer of spliced-leader genes. Int J Parasitol (2010) 1.27
Dual host-virus arms races shape an essential housekeeping protein. PLoS Biol (2013) 1.22
Parallel evolution of a type IV secretion system in radiating lineages of the host-restricted bacterial pathogen Bartonella. PLoS Genet (2011) 1.21
The Discovery, Distribution, and Evolution of Viruses Associated with Drosophila melanogaster. PLoS Biol (2015) 1.17
Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter. Genome Res (2009) 1.15
Evolution and phylogenetic analysis of full-length VP3 genes of Eastern Mediterranean bluetongue virus isolates. PLoS One (2009) 1.12
A case for the ancient origin of coronaviruses. J Virol (2013) 1.12
Evolution of the interferon alpha gene family in eutherian mammals. Gene (2007) 1.12
Evolutionary history and molecular epidemiology of rabbit haemorrhagic disease virus in the Iberian Peninsula and Western Europe. BMC Evol Biol (2010) 1.11
Phylodynamics of HIV-1 from a phase III AIDS vaccine trial in Bangkok, Thailand. PLoS One (2011) 1.11
Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution. Genome Biol Evol (2011) 1.11
Discovery and genomic characterization of a novel ovine partetravirus and a new genotype of bovine partetravirus. PLoS One (2011) 1.10
Evolutionary history of the plant pathogenic bacterium Xanthomonas axonopodis. PLoS One (2013) 1.10
Evolutionary and molecular analysis of the emergent severe fever with thrombocytopenia syndrome virus. Epidemics (2012) 1.10
An expanded clade of rodent Trim5 genes. Virology (2009) 1.10
Clinical, virologic, and immunologic correlates of HIV-1 intraclade B dual infection among men who have sex with men. AIDS (2012) 1.10
AID can restrict L1 retrotransposition suggesting a dual role in innate and adaptive immunity. Nucleic Acids Res (2009) 1.09
An exploratory algorithm to identify intra-host recombinant viral sequences. Mol Phylogenet Evol (2008) 1.07
Functional consequences of sequence variation in the pheromone biosynthetic gene pgFAR for Ostrinia moths. Proc Natl Acad Sci U S A (2013) 1.05
Evolution and diversity of a fungal self/nonself recognition locus. PLoS One (2010) 1.03
Gene loss and adaptation to hominids underlie the ancient origin of HIV-1. Cell Host Microbe (2013) 1.02
Evolution and recombination of genes encoding HIV-1 drug resistance and tropism during antiretroviral therapy. Virology (2010) 1.02
Molecular epidemiology of Rabbit Haemorrhagic Disease Virus in Australia: when one became many. Mol Ecol (2013) 1.02
Origin and evolution of TRIM proteins: new insights from the complete TRIM repertoire of zebrafish and pufferfish. PLoS One (2011) 1.01
Southernmost Asia is the source of Japanese encephalitis virus (genotype 1) diversity from which the viruses disperse and evolve throughout Asia. PLoS Negl Trop Dis (2013) 1.00
Intercompartmental recombination of HIV-1 contributes to env intrahost diversity and modulates viral tropism and sensitivity to entry inhibitors. J Virol (2011) 1.00
Population dynamics of rhesus macaques and associated foamy virus in Bangladesh. Emerg Microbes Infect (2013) 1.00
Complex evolutionary history of the Aeromonas veronii group revealed by host interaction and DNA sequence data. PLoS One (2011) 0.99
Evolutionary origins of human herpes simplex viruses 1 and 2. Mol Biol Evol (2014) 0.99
Phylogenomics and the dynamic genome evolution of the genus Streptococcus. Genome Biol Evol (2014) 0.99
Contrasted evolutionary histories of two Toll-like receptors (Tlr4 and Tlr7) in wild rodents (MURINAE). BMC Evol Biol (2013) 0.98
Deep sequencing of viral genomes provides insight into the evolution and pathogenesis of varicella zoster virus and its vaccine in humans. Mol Biol Evol (2013) 0.98
Restricted genetic diversity of HIV-1 subtype C envelope glycoprotein from perinatally infected Zambian infants. PLoS One (2010) 0.96
The opportunistic pathogen Propionibacterium acnes: insights into typing, human disease, clonal diversification and CAMP factor evolution. PLoS One (2013) 0.96
Genome sequence and genetic diversity of European ash trees. Nature (2016) 0.95
Maintenance of Nef-mediated modulation of major histocompatibility complex class I and CD4 after sexual transmission of human immunodeficiency virus type 1. J Virol (2007) 0.95
Adaptive changes in HIV-1 subtype C proteins during early infection are driven by changes in HLA-associated immune pressure. Virology (2009) 0.93
Ethnic differences in the adaptation rate of HIV gp120 from a vaccine trial. Retrovirology (2009) 0.93
Env sequence determinants in CXCR4-using human immunodeficiency virus type-1 subtype C. Virology (2012) 0.93
The extraordinary evolutionary history of the reticuloendotheliosis viruses. PLoS Biol (2013) 0.91
Positive selection drives accelerated evolution of mosquito salivary genes associated with blood-feeding. Insect Mol Biol (2013) 0.91
Detecting phylogenetic breakpoints and discordance from genome-wide alignments for species tree reconstruction. Genome Biol Evol (2011) 0.90
Comparative genomics of marine mussels (Mytilus spp.) gender associated mtDNA: rapidly evolving atp8. J Mol Evol (2010) 0.90
The P1N-PISPO trans-Frame Gene of Sweet Potato Feathery Mottle Potyvirus Is Produced during Virus Infection and Functions as an RNA Silencing Suppressor. J Virol (2016) 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
Different regions of HIV-1 subtype C env are associated with placental localization and in utero mother-to-child transmission. J Virol (2011) 0.89
Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses. J Virol (2013) 0.88
Identification of potential recombination breakpoints in human parechoviruses. J Virol (2009) 0.88
Molecular evolution and phylogenetics of rodent malaria parasites. BMC Evol Biol (2012) 0.88
Positive evolutionary selection on the RIG-I-like receptor genes in mammals. PLoS One (2013) 0.88
Adaptive evolution of the matrix extracellular phosphoglycoprotein in mammals. BMC Evol Biol (2011) 0.87
Diversification across an altitudinal gradient in the Tiny Greenbul (Phyllastrephus debilis) from the Eastern Arc Mountains of Africa. BMC Evol Biol (2011) 0.87
Widespread gene conversion of alpha-2-fucosyltransferase genes in mammals. J Mol Evol (2009) 0.87
TAL effectors and activation of predicted host targets distinguish Asian from African strains of the rice pathogen Xanthomonas oryzae pv. oryzicola while strict conservation suggests universal importance of five TAL effectors. Front Plant Sci (2015) 0.87
Thermal adaptation and clinal mitochondrial DNA variation of European anchovy. Proc Biol Sci (2014) 0.87
Dynamics of viral evolution and neutralizing antibody response after HIV-1 superinfection. J Virol (2013) 0.86
Characterization of MHC class II B polymorphism in bottlenecked New Zealand saddlebacks reveals low levels of genetic diversity. Immunogenetics (2013) 0.86
Global Diversity within and between Human Herpesvirus 1 and 2 Glycoproteins. J Virol (2015) 0.86
Evolution and divergence of the mammalian SAMD9/SAMD9L gene family. BMC Evol Biol (2013) 0.86
Multilocus sequence analysis of xanthomonads causing bacterial spot of tomato and pepper plants reveals strains generated by recombination among species and recent global spread of Xanthomonas gardneri. Appl Environ Microbiol (2015) 0.86
Viral meningitis epidemics and a single, recent, recombinant and anthroponotic origin of swine vesicular disease virus. Evol Med Public Health (2015) 0.86
Adaptive evolution in the glucose transporter 4 gene Slc2a4 in Old World fruit bats (family: Pteropodidae). PLoS One (2012) 0.86
Genetic features of cerebrospinal fluid-derived subtype B HIV-1 tat. J Neurovirol (2012) 0.85
Global Spread of Human Chromoblastomycosis Is Driven by Recombinant Cladophialophora carrionii and Predominantly Clonal Fonsecaea Species. PLoS Negl Trop Dis (2015) 0.85
Heterogeneous rates of molecular evolution among cryptic species of the ciliate morphospecies Chilodonella uncinata. J Mol Evol (2012) 0.85
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
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
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
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
Evolutionary model selection with a genetic algorithm: a case study using stem RNA. Mol Biol Evol (2006) 0.97
Phylogeography and diversification history of the day-gecko genus Phelsuma in the Seychelles islands. BMC Evol Biol (2013) 0.96