Published in BMC Evol Biol on June 26, 2015
Time-Dependent Rate Phenomenon in Viruses. J Virol (2016) 0.84
Marine origin of retroviruses in the early Palaeozoic Era. Nat Commun (2017) 0.78
Eleventh International Foamy Virus Conference-Meeting Report. Viruses (2016) 0.75
The molecular epidemiology of HIV-1 in the Comunidad Valenciana (Spain): analysis of transmission clusters. Sci Rep (2017) 0.75
Unique genome organization of non-mammalian papillomaviruses provides insights into the evolution of viral early proteins. Virus Evol (2017) 0.75
MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol (2011) 220.97
MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics (2003) 130.85
BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol (2007) 74.13
Relaxed phylogenetics and dating with confidence. PLoS Biol (2006) 37.68
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
Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature (2009) 17.96
The delayed rise of present-day mammals. Nature (2007) 15.98
Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics (2002) 10.63
Natural selection shaped regional mtDNA variation in humans. Proc Natl Acad Sci U S A (2002) 6.95
Rates of evolutionary change in viruses: patterns and determinants. Nat Rev Genet (2008) 6.79
Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol Biol Evol (2005) 6.77
Effects of purifying and adaptive selection on regional variation in human mtDNA. Science (2004) 5.87
Human Y chromosome base-substitution mutation rate measured by direct sequencing in a deep-rooting pedigree. Curr Biol (2009) 5.70
A molecular phylogeny of living primates. PLoS Genet (2011) 5.61
Correcting for purifying selection: an improved human mitochondrial molecular clock. Am J Hum Genet (2009) 5.37
Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis. J Mol Evol (2002) 5.24
Comparisons of dN/dS are time dependent for closely related bacterial genomes. J Theor Biol (2005) 5.20
A high observed substitution rate in the human mitochondrial DNA control region. Nat Genet (1997) 5.07
Estimation of primate speciation dates using local molecular clocks. Mol Biol Evol (2000) 5.06
High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome. Nature (2004) 4.79
Evolution of human influenza A viruses over 50 years: rapid, uniform rate of change in NS gene. Science (1986) 4.64
Bayesian random local clocks, or one rate to rule them all. BMC Biol (2010) 3.44
A recalibrated molecular clock and independent origins for the cholera pandemic clones. PLoS One (2008) 3.16
Revisiting the insect mitochondrial molecular clock: the mid-Aegean trench calibration. Mol Biol Evol (2010) 2.98
Time-dependent rates of molecular evolution. Mol Ecol (2011) 2.82
High direct estimate of the mutation rate in the mitochondrial genome of Caenorhabditis elegans. Science (2000) 2.78
Ancient co-speciation of simian foamy viruses and primates. Nature (2005) 2.71
Age of cichlids: new dates for ancient lake fish radiations. Mol Biol Evol (2007) 2.50
Purifying selection can obscure the ancient age of viral lineages. Mol Biol Evol (2011) 2.43
Accounting for bias from sequencing error in population genetic estimates. Mol Biol Evol (2007) 2.36
HIV evolutionary dynamics within and among hosts. AIDS Rev (2006) 2.32
Evidence for time dependency of molecular rate estimates. Syst Biol (2007) 2.26
Structural constraints on RNA virus evolution. J Virol (1999) 2.24
The pedigree rate of sequence divergence in the human mitochondrial genome: there is a difference between phylogenetic and pedigree rates. Am J Hum Genet (2003) 2.23
Molecular clock of viral evolution, and the neutral theory. Proc Natl Acad Sci U S A (1990) 2.15
The molecular clock of HIV-1 unveiled through analysis of a known transmission history. Proc Natl Acad Sci U S A (1999) 2.11
A large variation in the rates of synonymous substitution for RNA viruses and its relationship to a diversity of viral infection and transmission modes. Mol Biol Evol (2004) 2.07
Molecular clocks and the puzzle of RNA virus origins. J Virol (2003) 2.07
Rapid, global demographic expansions after the origins of agriculture. Proc Natl Acad Sci U S A (2011) 1.96
Direct estimation of the mitochondrial DNA mutation rate in Drosophila melanogaster. PLoS Biol (2008) 1.94
Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses. Mol Biol Evol (2010) 1.80
Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales). Syst Biol (2011) 1.77
An evaluation of R2 as an inadequate measure for nonlinear models in pharmacological and biochemical research: a Monte Carlo approach. BMC Pharmacol (2010) 1.65
Macroevolution of complex retroviruses. Science (2009) 1.63
Sequencing errors and molecular evolutionary analysis. Mol Biol Evol (1992) 1.58
Genomic fossils calibrate the long-term evolution of hepadnaviruses. PLoS Biol (2010) 1.57
Characterizing the time dependency of human mitochondrial DNA mutation rate estimates. Mol Biol Evol (2008) 1.53
The mode and tempo of hepatitis C virus evolution within and among hosts. BMC Evol Biol (2011) 1.46
Geological dates and molecular rates: fish DNA sheds light on time dependency. Mol Biol Evol (2008) 1.45
Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning. BMC Bioinformatics (2009) 1.42
Understanding differences between phylogenetic and pedigree-derived mtDNA mutation rate: a model using families from the Azores Islands (Portugal). Mol Biol Evol (2005) 1.38
Alarm bells for the molecular clock? No support for Ho et al.'s model of time-dependent molecular rate estimates. Syst Biol (2007) 1.32
Mutation and evolutionary rates in adélie penguins from the antarctic. PLoS Genet (2008) 1.31
High mitogenomic evolutionary rates and time dependency. Trends Genet (2009) 1.28
Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates. Proc Biol Sci (2014) 1.28
Mutation accumulation and the effect of copia insertions in Drosophila melanogaster. Genet Res (2004) 1.24
Different population dynamics of human T cell lymphotropic virus type II in intravenous drug users compared with endemically infected tribes. Proc Natl Acad Sci U S A (1999) 1.24
Quantitative prediction of molecular clock and ka/ks at short timescales. Mol Biol Evol (2009) 1.23
A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times. Bioinformatics (2002) 1.21
Within-host and between-host evolutionary rates across the HIV-1 genome. Retrovirology (2013) 1.21
Understanding the origins of AIDS viruses. Nature (1988) 1.15
Rates of viral evolution are linked to host geography in bat rabies. PLoS Pathog (2012) 1.15
Bayesian estimation of sequence damage in ancient DNA. Mol Biol Evol (2007) 1.13
An endogenous foamy virus in the aye-aye (Daubentonia madagascariensis). J Virol (2012) 1.05
More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure. Philos Trans R Soc Lond B Biol Sci (2010) 1.05
Genetic stability of foamy viruses: long-term study in an African green monkey population. J Virol (1999) 1.03
Endogenous viruses: Connecting recent and ancient viral evolution. Virology (2015) 1.02
From molecular genetics to phylodynamics: evolutionary relevance of mutation rates across viruses. PLoS Pathog (2012) 0.99
Species-specific inhibition of foamy viruses from South American monkeys by New World Monkey TRIM5{alpha} proteins. J Virol (2010) 0.97
A tenth crucial question regarding model use in phylogenetics. Trends Ecol Evol (2007) 0.97
The impact of calibration and clock-model choice on molecular estimates of divergence times. Mol Phylogenet Evol (2014) 0.95
In vitro fidelity of the prototype primate foamy virus (PFV) RT compared to HIV-1 RT. Virology (2007) 0.93
Accuracy estimation of foamy virus genome copying. Retrovirology (2009) 0.92
Discovery of prosimian and afrotherian foamy viruses and potential cross species transmissions amidst stable and ancient mammalian co-evolution. Retrovirology (2014) 0.91
The influence of rate heterogeneity among sites on the time dependence of molecular rates. Mol Biol Evol (2012) 0.91
Foamy virus vectors for gene transfer. Expert Opin Biol Ther (2009) 0.88
Evolutionary dynamics of human retroviruses investigated through full-genome scanning. Mol Biol Evol (2005) 0.87
Identification and characterization of highly divergent simian foamy viruses in a wide range of new world primates from Brazil. PLoS One (2013) 0.85
Endogenous viral sequences from the Cape golden mole (Chrysochloris asiatica) reveal the presence of foamy viruses in all major placental mammal clades. PLoS One (2014) 0.82
Time dependency of molecular evolutionary rates? Yes and no. Genome Biol Evol (2011) 0.82
Evolutionary strategies of human T-cell lymphotropic virus type II. Gene (2000) 0.82
Evolutionary dynamics of the N1 neuraminidases of the main lineages of influenza A viruses. Mol Phylogenet Evol (2010) 0.81
Foamy virus vectors come of age. Mol Ther (2008) 0.80
Selective constraints determine the time dependency of molecular rates for human nuclear genomes. Genome Biol Evol (2012) 0.78
Wide distribution and ancient evolutionary history of simian foamy viruses in New World primates. Retrovirology (2015) 0.80