Published in Virol J on July 16, 2009
Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses. Mol Biol Evol (2010) 1.80
Geminiviruses: masters at redirecting and reprogramming plant processes. Nat Rev Microbiol (2013) 1.55
Complex recombination patterns arising during geminivirus coinfections preserve and demarcate biologically important intra-genome interaction networks. PLoS Pathog (2011) 1.05
One misdated sequence of rabbit hemorrhagic disease virus prevents accurate estimation of its nucleotide substitution rate. BMC Evol Biol (2012) 0.94
High variability and rapid evolution of a nanovirus. J Virol (2010) 0.89
Dating the origins of the maize-adapted strain of maize streak virus, MSV-A. J Gen Virol (2009) 0.89
Evolutionary time-scale of the begomoviruses: evidence from integrated sequences in the Nicotiana genome. PLoS One (2011) 0.88
Sequence-based taxonomic framework for the classification of uncultured single-stranded DNA viruses of the family Genomoviridae. Virus Evol (2017) 0.83
Recombination hotspots and host susceptibility modulate the adaptive value of recombination during maize streak virus evolution. BMC Evol Biol (2011) 0.82
East African cassava mosaic-like viruses from Africa to Indian ocean islands: molecular diversity, evolutionary history and geographical dissemination of a bipartite begomovirus. BMC Evol Biol (2012) 0.81
Cultivated grapevines represent a symptomless reservoir for the transmission of hop stunt viroid to hop crops: 15 years of evolutionary analysis. PLoS One (2009) 0.80
The temporal evolution and global spread of Cauliflower mosaic virus, a plant pararetrovirus. PLoS One (2014) 0.79
Adaptive evolution by recombination is not associated with increased mutation rates in Maize streak virus. BMC Evol Biol (2012) 0.78
The global distribution of Banana bunchy top virus reveals little evidence for frequent recent, human-mediated long distance dispersal events. Virus Evol (2015) 0.77
Assessing constancy of substitution rates in viruses over evolutionary time. BMC Bioinformatics (2010) 0.77
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol (2007) 168.76
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol (2003) 102.57
BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol (2007) 74.13
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics (1989) 73.50
DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics (2003) 32.63
Statistical tests of neutrality of mutations. Genetics (1993) 24.94
HyPhy: hypothesis testing using phylogenies. Bioinformatics (2004) 17.33
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol (2001) 16.83
A constant rate of spontaneous mutation in DNA-based microbes. Proc Natl Acad Sci U S A (1991) 11.66
Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol (2005) 10.21
Bayesian selection of continuous-time Markov chain evolutionary models. Mol Biol Evol (2001) 8.69
Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics (2005) 8.62
A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics (2002) 7.41
RDP2: recombination detection and analysis from sequence alignments. Bioinformatics (2004) 7.29
Rates of evolutionary change in viruses: patterns and determinants. Nat Rev Genet (2008) 6.79
Estimation of evolutionary distances between homologous nucleotide sequences. Proc Natl Acad Sci U S A (1981) 5.34
Mispair specificity of methyl-directed DNA mismatch correction in vitro. J Biol Chem (1988) 4.20
A sensitive genetic assay for the detection of cytosine deamination: determination of rate constants and the activation energy. Biochemistry (1990) 3.51
Patterns of intra- and interhost nonsynonymous variation reveal strong purifying selection in dengue virus. J Virol (2003) 2.98
High rate of viral evolution associated with the emergence of carnivore parvovirus. Proc Natl Acad Sci U S A (2004) 2.83
Hantavirus evolution in relation to its rodent and insectivore hosts: no evidence for codivergence. Mol Biol Evol (2008) 2.04
Evolutionary history and phylogeography of human viruses. Annu Rev Microbiol (2008) 1.95
Mechanisms of plant virus evolution. Annu Rev Phytopathol (1997) 1.83
A simple method for cloning the complete begomovirus genome using the bacteriophage phi29 DNA polymerase. J Virol Methods (2004) 1.82
Mutagenic potentials of damaged nucleic acids produced by reactive oxygen/nitrogen species: approaches using synthetic oligonucleotides and nucleotides: survey and summary. Nucleic Acids Res (2003) 1.73
Phylogenetic evidence for rapid rates of molecular evolution in the single-stranded DNA begomovirus tomato yellow leaf curl virus. J Virol (2007) 1.68
Phylogenetic evidence for the rapid evolution of human B19 erythrovirus. J Virol (2006) 1.45
Nitric oxide-induced deamination of cytosine and guanine in deoxynucleosides and oligonucleotides. J Biol Chem (1998) 1.35
Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses. J Gen Virol (2009) 1.30
Genetic structure and population variability of tomato yellow leaf curl China virus. J Virol (2007) 1.26
Mutagenesis of 8-oxoguanine adjacent to an abasic site in simian kidney cells: tandem mutations and enhancement of G-->T transversions. Chem Res Toxicol (2005) 1.12
Recombination, decreased host specificity and increased mobility may have driven the emergence of maize streak virus as an agricultural pathogen. J Gen Virol (2008) 1.12
Parvovirus variation for disease: a difference with RNA viruses? Curr Top Microbiol Immunol (2006) 1.10
Quasispecies nature of three maize streak virus isolates obtained through different modes of selection from a population used to assess response to infection of maize cultivars. J Gen Virol (1998) 1.07
Human circoviruses. Vet Microbiol (2004) 1.05
A protocol for the rapid isolation of full geminivirus genomes from dried plant tissue. J Virol Methods (2008) 1.05
Spontaneous mutant frequency and mutation spectrum for gene A of phiX174 grown in E. coli. Environ Mol Mutagen (2004) 1.04
Observation of positive selection within hypervariable regions of a newly identified DNA virus (SEN virus)(1). FEBS Lett (2002) 1.04
JC virus evolution and its association with human populations. J Virol (2006) 1.04
Rapid host adaptation by extensive recombination. J Gen Virol (2009) 1.00
Successful application of FTA Classic Card technology and use of bacteriophage phi29 DNA polymerase for large-scale field sampling and cloning of complete maize streak virus genomes. J Virol Methods (2006) 1.00
A three-nucleotide mutation altering the Maize streak virus Rep pRBR-interaction motif reduces symptom severity in maize and partially reverts at high frequency without restoring pRBR-Rep binding. J Gen Virol (2005) 0.99
A novel cloning strategy for isolating, genotyping and phenotyping genetic variants of geminiviruses. Virol J (2008) 0.97
Transcription promotes guanine to thymine mutations in the non-transcribed strand of an Escherichia coli gene. DNA Repair (Amst) (2005) 0.96
Experimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution bias. Virol J (2008) 0.96
Restoration of native folding of single-stranded DNA sequences through reverse mutations: an indication of a new epigenetic mechanism. Arch Biochem Biophys (2006) 0.95
Differential selection and mutation between dsDNA and ssDNA phages shape the evolution of their genomic AT percentage. BMC Genet (2005) 0.93
Assessment of codivergence of mastreviruses with their plant hosts. BMC Evol Biol (2008) 0.90
Nucleotide sequence evidence for three distinct sugarcane streak mastreviruses. Arch Virol (1999) 0.85
High genetic diversity revealed by the study of TLMV infection in French hemodialysis patients. J Med Virol (2002) 0.85
High-frequency reversion of geminivirus replication protein mutants during infection. J Virol (2007) 0.81
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
Research capacity. Enabling the genomic revolution in Africa. Science (2014) 3.05
A random effects branch-site model for detecting episodic diversifying selection. Mol Biol Evol (2011) 2.88
Transmission of HIV-1 CTL escape variants provides HLA-mismatched recipients with a survival advantage. PLoS Pathog (2008) 2.59
Robust inference of positive selection from recombining coding sequences. Bioinformatics (2006) 2.43
Recombination patterns in aphthoviruses mirror those found in other picornaviruses. J Virol (2006) 2.36
Diverse circular ssDNA viruses discovered in dragonflies (Odonata: Epiprocta). J Gen Virol (2012) 2.18
A field guide to eukaryotic circular single-stranded DNA viruses: insights gained from metagenomics. Arch Virol (2012) 2.02
Diverse circovirus-like genome architectures revealed by environmental metagenomics. J Gen Virol (2009) 2.00
Single-cell genomics reveals organismal interactions in uncultivated marine protists. Science (2011) 1.90
The origins of sexually transmitted HIV among men who have sex with men. Sci Transl Med (2010) 1.76
Geminivirus disease complexes: an emerging threat. Trends Plant Sci (2003) 1.73
A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae). Arch Virol (2013) 1.69
Generation of genic diversity among Streptococcus pneumoniae strains via horizontal gene transfer during a chronic polyclonal pediatric infection. PLoS Pathog (2010) 1.66
Avoidance of protein fold disruption in natural virus recombinants. PLoS Pathog (2007) 1.62
The spread of tomato yellow leaf curl virus from the Middle East to the world. PLoS Pathog (2010) 1.62
Genome-wide analysis of the structure of the South African Coloured Population in the Western Cape. Hum Genet (2010) 1.61
Ecological speciation in South Atlantic island finches. Science (2007) 1.47
Dragonfly cyclovirus, a novel single-stranded DNA virus discovered in dragonflies (Odonata: Anisoptera). J Gen Virol (2011) 1.46
Molecular mechanisms of recombination restriction in the envelope gene of the human immunodeficiency virus. PLoS Pathog (2009) 1.45
Detection of minority resistance during early HIV-1 infection: natural variation and spurious detection rather than transmission and evolution of multiple viral variants. J Virol (2011) 1.44
Geminivirus disease complexes: the threat is spreading. Trends Plant Sci (2006) 1.42
Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning. BMC Bioinformatics (2009) 1.42
Establishment of three new genera in the family Geminiviridae: Becurtovirus, Eragrovirus and Turncurtovirus. Arch Virol (2014) 1.38
Novel myco-like DNA viruses discovered in the faecal matter of various animals. Virus Res (2013) 1.35
Revision of Begomovirus taxonomy based on pairwise sequence comparisons. Arch Virol (2015) 1.34
Genetic characteristics of HIV-1 subtype C envelopes inducing cross-neutralizing antibodies. Virology (2007) 1.31
Correcting the bias of empirical frequency parameter estimators in codon models. PLoS One (2010) 1.30
Cotton leaf curl disease - an emerging threat to cotton production worldwide. J Gen Virol (2013) 1.29
A model of directional selection applied to the evolution of drug resistance in HIV-1. Mol Biol Evol (2007) 1.27
The evolutionary value of recombination is constrained by genome modularity. PLoS Genet (2005) 1.26
High global diversity of cycloviruses amongst dragonflies. J Gen Virol (2013) 1.20
Development of phoH as a novel signature gene for assessing marine phage diversity. Appl Environ Microbiol (2011) 1.20
Recombination in eukaryotic single stranded DNA viruses. Viruses (2011) 1.20
Insights into the evolutionary history of an emerging livestock pathogen: porcine circovirus 2. J Virol (2009) 1.19
Cotton leaf curl disease in resistant cotton is associated with a single begomovirus that lacks an intact transcriptional activator protein. Virus Res (2010) 1.19
A proposal to change existing virus species names to non-Latinized binomials. Arch Virol (2010) 1.18
Exploring the diversity of plant DNA viruses and their satellites using vector-enabled metagenomics on whiteflies. PLoS One (2011) 1.17
Investigating the origin and spread of hepatitis C virus genotype 5a. J Virol (2006) 1.16
The Arabidopsis wall associated kinase-like 10 gene encodes a functional guanylyl cyclase and is co-expressed with pathogen defense related genes. PLoS One (2010) 1.14
Molecular characterisation of a novel cassava associated circular ssDNA virus. Virus Res (2012) 1.14
Suppressors of RNA silencing encoded by the components of the cotton leaf curl begomovirus-betasatellite complex. Mol Plant Microbe Interact (2011) 1.14
Contribution of the satellite encoded gene betaC1 to cotton leaf curl disease symptoms. Virus Res (2007) 1.13
Recombination, decreased host specificity and increased mobility may have driven the emergence of maize streak virus as an agricultural pathogen. J Gen Virol (2008) 1.12
Chimeric human papillomavirus type 16 (HPV-16) L1 particles presenting the common neutralizing epitope for the L2 minor capsid protein of HPV-6 and HPV-16. J Virol (2003) 1.11
Engineering novel traits in plants through RNA interference. Trends Plant Sci (2006) 1.11
Genetic diversity and phylogeography of cassava mosaic viruses in Kenya. J Gen Virol (2006) 1.10
Identification of a Novel Circular DNA Virus in New Zealand Fur Seal (Arctocephalus forsteri) Fecal Matter. Genome Announc (2013) 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
Systematic phylogenetic analysis of influenza A virus reveals many novel mosaic genome segments. Infect Genet Evol (2013) 1.09
A unicellular algal virus, Emiliania huxleyi virus 86, exploits an animal-like infection strategy. J Gen Virol (2009) 1.09
An unusual alphasatellite associated with monopartite begomoviruses attenuates symptoms and reduces betasatellite accumulation. J Gen Virol (2010) 1.08
Using phylogeography to characterize the origins of the HIV-1 subtype F epidemic in Romania. Infect Genet Evol (2011) 1.07
Extensive recombination detected among beak and feather disease virus isolates from breeding facilities in Poland. J Gen Virol (2013) 1.07
Post-transcriptional gene silencing suppressor activity of two non-pathogenic alphasatellites associated with a begomovirus. Virology (2010) 1.07
Evidence of unique genotypes of beak and feather disease virus in southern Africa. J Virol (2004) 1.06
Genetic variability among complete human respiratory syncytial virus subgroup A genomes: bridging molecular evolutionary dynamics and epidemiology. PLoS One (2012) 1.06
Replication promiscuity of DNA-beta satellites associated with monopartite begomoviruses; deletion mutagenesis of the Ageratum yellow vein virus DNA-beta satellite localizes sequences involved in replication. J Gen Virol (2008) 1.06
South West Indian Ocean islands tomato begomovirus populations represent a new major monopartite begomovirus group. J Gen Virol (2005) 1.06
Co-expression and promoter content analyses assign a role in biotic and abiotic stress responses to plant natriuretic peptides. BMC Plant Biol (2008) 1.06
Insights into the role and function of L2, the minor capsid protein of papillomaviruses. Arch Virol (2009) 1.05
Complex recombination patterns arising during geminivirus coinfections preserve and demarcate biologically important intra-genome interaction networks. PLoS Pathog (2011) 1.05
HIV type 1 subtype C gag and nef diversity in Southern Africa. AIDS Res Hum Retroviruses (2007) 1.05
A protocol for the rapid isolation of full geminivirus genomes from dried plant tissue. J Virol Methods (2008) 1.05
Discovery of a novel circular single-stranded DNA virus from porcine faeces. Arch Virol (2012) 1.04
Discovery of a novel mastrevirus and alphasatellite-like circular DNA in dragonflies (Epiprocta) from Puerto Rico. Virus Res (2012) 1.04
Occurrence of grapevine leafroll-associated virus complex in Napa Valley. PLoS One (2011) 1.03
More men than women make mucosal IgA antibodies to Human papillomavirus type 16 (HPV-16) and HPV-18: a study of oral HPV and oral HPV antibodies in a normal healthy population. BMC Infect Dis (2006) 1.03
Expression of HIV-1 antigens in plants as potential subunit vaccines. BMC Biotechnol (2008) 1.02
Post-translational cleavage of recombinantly expressed nitrilase from Rhodococcus rhodochrous J1 yields a stable, active helical form. FEBS J (2007) 1.02
Maintenance of an old world betasatellite by a new world helper begomovirus and possible rapid adaptation of the betasatellite. J Virol (2009) 1.01
Evidence of ancient papillomavirus recombination. J Gen Virol (2006) 1.01
Point mutation rate of bacteriophage PhiX174. Genetics (2009) 1.01
The comparative genomics of human respiratory syncytial virus subgroups A and B: genetic variability and molecular evolutionary dynamics. J Virol (2013) 1.01
Successful application of FTA Classic Card technology and use of bacteriophage phi29 DNA polymerase for large-scale field sampling and cloning of complete maize streak virus genomes. J Virol Methods (2006) 1.00