Published in J Struct Funct Genomics on January 01, 2003
A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. J Mol Evol (2004) 1.70
fog-2 and the evolution of self-fertile hermaphroditism in Caenorhabditis. PLoS Biol (2004) 1.58
Comparative analysis of protein coding sequences from human, mouse and the domesticated pig. BMC Biol (2005) 1.51
Comprehensive analysis of animal TALE homeobox genes: new conserved motifs and cases of accelerated evolution. J Mol Evol (2007) 1.44
Genome-wide survey for biologically functional pseudogenes. PLoS Comput Biol (2006) 1.38
Accelerated FoxP2 evolution in echolocating bats. PLoS One (2007) 1.34
Darwinian adaptation of proteorhodopsin to different light intensities in the marine environment. Proc Natl Acad Sci U S A (2004) 1.34
Relaxed selection among duplicate floral regulatory genes in Lamiales. J Mol Evol (2006) 1.25
Reconstructing the evolutionary history of paralogous APETALA1/FRUITFULL-like genes in grasses (Poaceae). Genetics (2006) 1.24
Evolution of the relaxin-like peptide family. BMC Evol Biol (2005) 1.20
At the crossroads of homoeostasis and disease: roles of the PACS proteins in membrane traffic and apoptosis. Biochem J (2009) 1.15
Adaptive functional divergence among triplicated alpha-globin genes in rodents. Genetics (2008) 1.14
Molecular evolution of the ependymin protein family: a necessary update. BMC Evol Biol (2007) 1.09
Evolution of a microbial nitrilase gene family: a comparative and environmental genomics study. BMC Evol Biol (2005) 1.05
Diversification and adaptive sequence evolution of Caenorhabditis lysozymes (Nematoda: Rhabditidae). BMC Evol Biol (2008) 1.04
RELAX: detecting relaxed selection in a phylogenetic framework. Mol Biol Evol (2014) 1.03
Gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates. Biol Direct (2009) 1.02
The venom-gland transcriptome of the eastern coral snake (Micrurus fulvius) reveals high venom complexity in the intragenomic evolution of venoms. BMC Genomics (2013) 1.00
Adaptive evolution of scorpion sodium channel toxins. J Mol Evol (2004) 0.99
Adaptive evolution in rodent seminal vesicle secretion proteins. Mol Biol Evol (2008) 0.97
Evolutionary rate patterns of the Gibberellin pathway genes. BMC Evol Biol (2009) 0.95
Understanding phylogenetic incongruence: lessons from phyllostomid bats. Biol Rev Camb Philos Soc (2012) 0.91
Duplicative and conservative transpositions of larval serum protein 1 genes in the genus Drosophila. Genetics (2004) 0.91
Adaptive molecular evolution of the Major Histocompatibility Complex genes, DRA and DQA, in the genus Equus. BMC Evol Biol (2011) 0.91
Gene conversion and functional divergence in the beta-globin gene family. J Mol Evol (2004) 0.90
Phylogenomics of the benzoxazinoid biosynthetic pathway of Poaceae: gene duplications and origin of the Bx cluster. BMC Evol Biol (2012) 0.88
Positive selection shaped the convergent evolution of independently expanded kallikrein subfamilies expressed in mouse and rat saliva proteomes. PLoS One (2011) 0.87
Fish lateral line innovation: insights into the evolutionary genomic dynamics of a unique mechanosensory organ. Mol Biol Evol (2012) 0.86
Gene conversion among paralogs results in moderate false detection of positive selection using likelihood methods. J Mol Evol (2009) 0.86
The roles of gene duplication, gene conversion and positive selection in rodent Esp and Mup pheromone gene families with comparison to the Abp family. PLoS One (2012) 0.86
Adaptive evolution in the glucose transporter 4 gene Slc2a4 in Old World fruit bats (family: Pteropodidae). PLoS One (2012) 0.86
The protein chaperone HSP90 can facilitate the divergence of gene duplicates. Genetics (2013) 0.85
Change of positive selection pressure on HIV-1 envelope gene inferred by early and recent samples. PLoS One (2011) 0.85
Positive and negative selection in the beta-esterase gene cluster of the Drosophila melanogaster subgroup. J Mol Evol (2006) 0.84
Molecular evolution of a gene cluster of serine proteases expressed in the Anopheles gambiae female reproductive tract. BMC Evol Biol (2011) 0.84
Birth-and-death of KLK3 and KLK2 in primates: evolution driven by reproductive biology. Genome Biol Evol (2012) 0.83
Evidence of positive selection at codon sites localized in extracellular domains of mammalian CC motif chemokine receptor proteins. BMC Evol Biol (2010) 0.83
Early evolution of ionotropic GABA receptors and selective regimes acting on the mammalian-specific theta and epsilon subunits. PLoS One (2007) 0.83
Molecular population genetics and gene expression analysis of duplicated CBF genes of Arabidopsis thaliana. BMC Plant Biol (2008) 0.83
Novel male-biased expression in paralogs of the aphid slimfast nutrient amino acid transporter expansion. BMC Evol Biol (2011) 0.83
Evolutionary history of the alpha2,8-sialyltransferase (ST8Sia) gene family: tandem duplications in early deuterostomes explain most of the diversity found in the vertebrate ST8Sia genes. BMC Evol Biol (2008) 0.82
Variation in opsin genes correlates with signalling ecology in North American fireflies. Mol Ecol (2015) 0.82
Molecular evolution of the deuterolysin (M35) family genes in Coccidioides. PLoS One (2012) 0.82
Diversity and evolutionary history of the MHC DQA gene in leporids. Immunogenetics (2008) 0.82
Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals. Proc Biol Sci (2004) 0.82
Evolution of a domain conserved in microtubule-associated proteins of eukaryotes. Adv Appl Bioinform Chem (2008) 0.81
Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example. BMC Evol Biol (2005) 0.81
The Molecular Evolutionary Patterns of the Insulin/FOXO Signaling Pathway. Evol Bioinform Online (2013) 0.81
Independent expansion of zincin metalloproteinases in Onygenales fungi may be associated with their pathogenicity. PLoS One (2014) 0.81
Molecular evolutionary characterization of a V1R subfamily unique to strepsirrhine primates. Genome Biol Evol (2014) 0.80
The evolution of vertebrate tetraspanins: gene loss, retention, and massive positive selection after whole genome duplications. BMC Evol Biol (2010) 0.80
GATA transcription factors in vertebrates: evolutionary, structural and functional interplay. Mol Genet Genomics (2013) 0.79
A candidate subspecies discrimination system involving a vomeronasal receptor gene with different alleles fixed in M. m. domesticus and M. m. musculus. PLoS One (2010) 0.79
Positively selected sites in the Arabidopsis receptor-like kinase gene family. J Mol Evol (2005) 0.79
Divergence and adaptive evolution of the gibberellin oxidase genes in plants. BMC Evol Biol (2015) 0.78
Molecular evolution and functional divergence of tubulin superfamily in the fungal tree of life. Sci Rep (2014) 0.78
Population genetics of duplicated alternatively spliced exons of the Dscam gene in Daphnia and Drosophila. PLoS One (2011) 0.78
Distinctive patterns of evolution of the δ-globin gene (HBD) in primates. PLoS One (2015) 0.78
Phosphoenolpyruvate carboxykinase 1 gene (Pck1) displays parallel evolution between Old World and New World fruit bats. PLoS One (2015) 0.77
Molecular evolution of the duplicated TFIIAgamma genes in Oryzeae and its relatives. BMC Evol Biol (2010) 0.77
Sequence diversity of Pan troglodytes subspecies and the impact of WFDC6 selective constraints in reproductive immunity. Genome Biol Evol (2013) 0.77
Molecular adaptation in plant hemoglobin, a duplicated gene involved in plant-bacteria symbiosis. J Mol Evol (2004) 0.76
Natural Selection at the Brush-Border: Adaptations to Carbohydrate Diets in Humans and Other Mammals. Genome Biol Evol (2015) 0.76
Functional Divergence in Teleost Cardiac Troponin Paralogs Guides Variation in the Interaction of TnI Switch Region with TnC. Genome Biol Evol (2016) 0.76
Molecular evolution of a family of resistance gene analogs of nucleotide-binding site sequences in Solanum lycopersicum. Genetica (2011) 0.76
Troponin-I is present as an essential component of muscles in echinoderm larvae. Sci Rep (2017) 0.75
Molecular evolution of the ent-kaurenoic acid oxidase gene in Oryzeae. Genet Mol Biol (2012) 0.75
Positive selection and functional divergence of farnesyl pyrophosphate synthase genes in plants. BMC Mol Biol (2017) 0.75
Phylogenic analysis of adhesion related genes Mad1 revealed a positive selection for the evolution of trapping devices of nematode-trapping fungi. Sci Rep (2016) 0.75
The birth of a human-specific neural gene by incomplete duplication and gene fusion. Genome Biol (2017) 0.75
Adaptive molecular evolution of the two-pore channel 1 gene TPC1 in the karst-adapted genus Primulina (Gesneriaceae). Ann Bot (2016) 0.75
Gene-pseudogene evolution: a probabilistic approach. BMC Genomics (2015) 0.75
Mechanistic insights into molecular evolution of species-specific differential glycosaminoglycan binding surfaces in growth-related oncogene chemokines. R Soc Open Sci (2017) 0.75
The glycogen synthase 2 gene (Gys2) displays parallel evolution between Old World and New World fruit bats. J Mol Evol (2013) 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
Estimation of hominoid ancestral population sizes under bayesian coalescent models incorporating mutation rate variation and sequencing errors. Mol Biol Evol (2008) 2.90
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
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
Gene conversion and functional divergence in the beta-globin gene family. J Mol Evol (2004) 0.90
Proposed standard nomenclature for the alpha- and beta-globin gene families. Genes Genet Syst (2006) 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
Duplication and adaptive evolution of the chalcone synthase genes of Dendranthema (Asteraceae). Mol Biol Evol (2002) 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
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
Likelihood analysis of the chalcone synthase genes suggests the role of positive selection in morning glories (Ipomoea). J Mol Evol (2004) 0.84
Diversifying and purifying selection in the peptide binding region of DRB in mammals. J Mol Evol (2008) 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