Published in Mol Biol Evol on July 04, 2008
Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science (2010) 18.45
Insights into hominid evolution from the gorilla genome sequence. Nature (2012) 4.12
Bayesian species delimitation using multilocus sequence data. Proc Natl Acad Sci U S A (2010) 3.56
A comprehensive map of mobile element insertion polymorphisms in humans. PLoS Genet (2011) 3.14
Bayesian inference of ancient human demography from individual genome sequences. Nat Genet (2011) 3.03
Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution. Proc Natl Acad Sci U S A (2012) 2.54
A direct characterization of human mutation based on microsatellites. Nat Genet (2012) 2.38
Molecular phylogenetics: principles and practice. Nat Rev Genet (2012) 2.08
Rates and fitness consequences of new mutations in humans. Genetics (2012) 2.01
Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection. Genome Res (2011) 1.88
Fine-scale phylogenetic discordance across the house mouse genome. PLoS Genet (2009) 1.83
Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome. PLoS Genet (2011) 1.54
Ancestral population genomics: the coalescent hidden Markov model approach. Genetics (2009) 1.54
Genomic DNA sequences from mastodon and woolly mammoth reveal deep speciation of forest and savanna elephants. PLoS Biol (2010) 1.53
Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle. Nat Genet (2013) 1.45
Estimating divergence parameters with small samples from a large number of loci. Genetics (2009) 1.45
Chimpanzee genomic diversity reveals ancient admixture with bonobos. Science (2016) 1.41
Evidence for pervasive adaptive protein evolution in wild mice. PLoS Genet (2010) 1.39
Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidden Markov model. PLoS Genet (2011) 1.37
Single-locus species delimitation: a test of the mixed Yule-coalescent model, with an empirical application to Philippine round-leaf bats. Proc Biol Sci (2012) 1.24
A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species. PLoS Genet (2012) 1.23
Genetic diversity in India and the inference of Eurasian population expansion. Genome Biol (2010) 1.13
Phylogenomics of primates and their ancestral populations. Genome Res (2009) 1.12
Doubts about complex speciation between humans and chimpanzees. Trends Ecol Evol (2009) 1.10
Accurate and fast methods to estimate the population mutation rate from error prone sequences. BMC Bioinformatics (2009) 1.10
Improved reversible jump algorithms for Bayesian species delimitation. Genetics (2013) 1.05
A likelihood ratio test of speciation with gene flow using genomic sequence data. Genome Biol Evol (2010) 1.01
Critical assessment of coalescent simulators in modeling recombination hotspots in genomic sequences. BMC Bioinformatics (2014) 0.99
Female-to-male breeding ratio in modern humans-an analysis based on historical recombinations. Am J Hum Genet (2010) 0.99
How reticulated are species? Bioessays (2015) 0.96
A comparative approach shows differences in patterns of numt insertion during hominoid evolution. J Mol Evol (2009) 0.96
The (r)evolution of SINE versus LINE distributions in primate genomes: sex chromosomes are important. Genome Res (2010) 0.95
Mobile elements reveal small population size in the ancient ancestors of Homo sapiens. Proc Natl Acad Sci U S A (2010) 0.94
Contrasting X-linked and autosomal diversity across 14 human populations. Am J Hum Genet (2014) 0.92
Divergence, demography and gene loss along the human lineage. Philos Trans R Soc Lond B Biol Sci (2010) 0.89
Mutation rate distribution inferred from coincident SNPs and coincident substitutions. Genome Biol Evol (2011) 0.88
Factors influencing ascertainment bias of microsatellite allele sizes: impact on estimates of mutation rates. Genetics (2013) 0.88
Great ape genomics. ILAR J (2013) 0.87
The impact of the rate prior on Bayesian estimation of divergence times with multiple Loci. Syst Biol (2014) 0.86
An autosomal analysis gives no genetic evidence for complex speciation of humans and chimpanzees. Mol Biol Evol (2011) 0.83
Bayesian species delimitation can be robust to guide-tree inference errors. Syst Biol (2014) 0.83
Robust estimates of divergence times and selection with a poisson random field model: a case study of comparative phylogeographic data. Genetics (2013) 0.82
Neutral nuclear variation in Baboons (genus Papio) provides insights into their evolutionary and demographic histories. Am J Phys Anthropol (2014) 0.80
Reconstructing the demographic history of the human lineage using whole-genome sequences from human and three great apes. Genome Biol Evol (2012) 0.78
Hypertension increases with aging and obesity in chimpanzees (Pan troglodytes). Zoo Biol (2012) 0.78
Does Gene Tree Discordance Explain the Mismatch between Macroevolutionary Models and Empirical Patterns of Tree Shape and Branching Times? Syst Biol (2016) 0.78
Multilocus phylogeny and cryptic diversity in Asian shrew-like moles (Uropsilus, Talpidae): implications for taxonomy and conservation. BMC Evol Biol (2013) 0.78
Challenges in Species Tree Estimation Under the Multispecies Coalescent Model. Genetics (2016) 0.77
Population genetic studies in the genomic sequencing era. Dongwuxue Yanjiu (2015) 0.77
Catalysis and Structure of Zebrafish Urate Oxidase Provide Insights into the Origin of Hyperuricemia in Hominoids. Sci Rep (2016) 0.76
Context-dependent codon partition models provide significant increases in model fit in atpB and rbcL protein-coding genes. BMC Evol Biol (2011) 0.76
Unraveling recombination rate evolution using ancestral recombination maps. Bioessays (2014) 0.75
In silico phylogenomics using complete genomes: a case study on the evolution of hominoids. Genome Res (2016) 0.75
Estimation of the ancestral effective population sizes of African great apes under different selection regimes. Genetica (2014) 0.75
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol (2005) 8.74
Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics (2003) 7.05
Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics (2004) 4.22
Bayesian models of episodic evolution support a late precambrian explosive diversification of the Metazoa. Mol Biol Evol (2003) 4.10
Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics (2003) 3.89
Inferring speciation times under an episodic molecular clock. Syst Biol (2007) 3.85
INDELible: a flexible simulator of biological sequence evolution. Mol Biol Evol (2009) 3.29
Accuracy and power of bayes prediction of amino acid sites under positive selection. Mol Biol Evol (2002) 3.26
The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times. Syst Biol (2009) 3.04
Phylogenetic inference using whole genomes. Annu Rev Genomics Hum Genet (2008) 2.98
A new time-scale for ray-finned fish evolution. Proc Biol Sci (2007) 2.92
Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proc Biol Sci (2012) 2.68
Best practices for justifying fossil calibrations. Syst Biol (2011) 2.51
Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA. Mol Biol Evol (2003) 2.29
Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny. Syst Biol (2002) 2.15
Divergence dates for Malagasy lemurs estimated from multiple gene loci: geological and evolutionary context. Mol Ecol (2004) 2.01
The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection. Mol Biol Evol (2010) 2.01
Dating primate divergences through an integrated analysis of palaeontological and molecular data. Syst Biol (2010) 1.85
Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites. Mol Biol Evol (2007) 1.77
Exploring uncertainty in the calibration of the molecular clock. Biol Lett (2011) 1.74
A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. J Mol Evol (2004) 1.70
An empirical examination of the utility of codon-substitution models in phylogeny reconstruction. Syst Biol (2005) 1.69
Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales. Curr Biol (2015) 1.66
Maximum likelihood methods for detecting adaptive evolution after gene duplication. J Struct Funct Genomics (2003) 1.61
Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times. Mol Biol Evol (2011) 1.58
Widespread adaptive evolution in the human immunodeficiency virus type 1 genome. J Mol Evol (2003) 1.49
Host-symbiont conflicts: positive selection on an outer membrane protein of parasitic but not mutualistic Rickettsiaceae. Mol Biol Evol (2002) 1.46
Evaluation of a bayesian coalescent method of species delimitation. Syst Biol (2011) 1.34
PAMLX: a graphical user interface for PAML. Mol Biol Evol (2013) 1.30
Detecting site-specific physicochemical selective pressures: applications to the Class I HLA of the human major histocompatibility complex and the SRK of the plant sporophytic self-incompatibility system. J Mol Evol (2005) 1.19
Phylogenomic analysis of natural selection pressure in Streptococcus genomes. BMC Evol Biol (2007) 1.14
The role of positive selection in determining the molecular cause of species differences in disease. BMC Evol Biol (2008) 1.11
MtZoa: a general mitochondrial amino acid substitutions model for animal evolutionary studies. Mol Phylogenet Evol (2009) 1.10
Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals. Biol Lett (2014) 1.08
Tail paradox, partial identifiability, and influential priors in Bayesian branch length inference. Mol Biol Evol (2011) 1.06
Improved reversible jump algorithms for Bayesian species delimitation. Genetics (2013) 1.05
The influence of gene flow on species tree estimation: a simulation study. Syst Biol (2013) 1.04
Rapid evolution of a pollen-specific oleosin-like gene family from Arabidopsis thaliana and closely related species. Mol Biol Evol (2004) 1.04
Robustness of compound Dirichlet priors for Bayesian inference of branch lengths. Syst Biol (2012) 1.04
Somatosensory projections to cochlear nucleus are upregulated after unilateral deafness. J Neurosci (2012) 1.02
Population genetics of speciation in nonmodel organisms: I. Ancestral polymorphism in mangroves. Mol Biol Evol (2007) 0.99
Rate variation and estimation of divergence times using strict and relaxed clocks. BMC Evol Biol (2011) 0.97
In defense of statistical methods for detecting positive selection. Proc Natl Acad Sci U S A (2009) 0.96
The trouble with sliding windows and the selective pressure in BRCA1. PLoS One (2008) 0.96
Duplicated paralogous genes subject to positive selection in the genome of Trypanosoma brucei. PLoS One (2008) 0.95
A likelihood look at the supermatrix-supertree controversy. Gene (2008) 0.94
Maximum likelihood implementation of an isolation-with-migration model with three species for testing speciation with gene flow. Mol Biol Evol (2012) 0.93
Looking for Darwin in genomic sequences--validity and success of statistical methods. Mol Biol Evol (2012) 0.92
Evolutionary rate variation among vertebrate beta globin genes: implications for dating gene family duplication events. Gene (2006) 0.92
Proposed standard nomenclature for the alpha- and beta-globin gene families. Genes Genet Syst (2006) 0.90
Gene conversion and functional divergence in the beta-globin gene family. J Mol Evol (2004) 0.90
Introduction. Statistical and computational challenges in molecular phylogenetics and evolution. Philos Trans R Soc Lond B Biol Sci (2008) 0.90
Unusual conservation among genes encoding small secreted salivary gland proteins from a gall midge. BMC Evol Biol (2010) 0.89
Dating phylogenies with sequentially sampled tips. Syst Biol (2013) 0.88
Efficient simulation under a population genetics model of carcinogenesis. Bioinformatics (2011) 0.88
Bayesian dating of shallow phylogenies with a relaxed clock. Syst Biol (2009) 0.88
Multilocus estimation of divergence times and ancestral effective population sizes of Oryza species and implications for the rapid diversification of the genus. New Phytol (2013) 0.87
A unique amino acid substitution, T126I, in human genotype C of hepatitis B virus S gene and its possible influence on antigenic structural change. Gene (2006) 0.87
Duplication and adaptive evolution of the chalcone synthase genes of Dendranthema (Asteraceae). Mol Biol Evol (2002) 0.87
Molecular evolution of the hepatitis delta virus antigen gene: recombination or positive selection? J Mol Evol (2004) 0.86
Bayesian relaxed clock estimation of divergence times in foraminifera. Mol Phylogenet Evol (2011) 0.86
Change of positive selection pressure on HIV-1 envelope gene inferred by early and recent samples. PLoS One (2011) 0.85
Diversifying and purifying selection in the peptide binding region of DRB in mammals. J Mol Evol (2008) 0.84
Likelihood analysis of the chalcone synthase genes suggests the role of positive selection in morning glories (Ipomoea). J Mol Evol (2004) 0.84
Why do more divergent sequences produce smaller nonsynonymous/synonymous rate ratios in pairwise sequence comparisons? Genetics (2013) 0.81
Molecular evolutionary characterization of a V1R subfamily unique to strepsirrhine primates. Genome Biol Evol (2014) 0.80
Comparative genomics coming of age. Heredity (Edinb) (2003) 0.76