Published in Mol Biol Evol on January 01, 2002
Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G. PLoS Biol (2004) 4.76
Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics (2004) 4.22
Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics (2003) 3.89
Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization. Genome Res (2004) 3.00
A random effects branch-site model for detecting episodic diversifying selection. Mol Biol Evol (2011) 2.88
Simultaneous amino acid substitutions at antigenic sites drive influenza A hemagglutinin evolution. Proc Natl Acad Sci U S A (2007) 2.67
Adaptation to different human populations by HIV-1 revealed by codon-based analyses. PLoS Comput Biol (2006) 2.48
Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thaliana. Genome Res (2002) 2.27
Estimating diversifying selection and functional constraint in the presence of recombination. Genetics (2005) 2.02
Adaptive evolution in two large families of ubiquitin-ligase adapters in nematodes and plants. Genome Res (2006) 1.84
Comparative genomics and the evolution of human mitochondrial DNA: assessing the effects of selection. Am J Hum Genet (2004) 1.80
Population genetics of microbial pathogens estimated from multilocus sequence typing (MLST) data. Infect Genet Evol (2005) 1.72
Evolutionary fingerprinting of genes. Mol Biol Evol (2009) 1.64
Models of coding sequence evolution. Brief Bioinform (2008) 1.64
Diversifying selection in human papillomavirus type 16 lineages based on complete genome analyses. J Virol (2005) 1.57
Comparative genomic analysis of the odorant-binding protein family in 12 Drosophila genomes: purifying selection and birth-and-death evolution. Genome Biol (2007) 1.44
The dynamic genetic repertoire of microbial communities. FEMS Microbiol Rev (2008) 1.42
The power of phylogenetic comparison in revealing protein function. Proc Natl Acad Sci U S A (2005) 1.31
Coevolution of interacting fertilization proteins. PLoS Genet (2009) 1.26
Relaxed selection among duplicate floral regulatory genes in Lamiales. J Mol Evol (2006) 1.25
Molecular evolution and population genetic analysis of candidate female reproductive genes in Drosophila. Genetics (2006) 1.19
Epidemic history and evolutionary dynamics of hepatitis B virus infection in two remote communities in rural Nigeria. PLoS One (2010) 1.17
Adaptive evolution in the SRZ chemoreceptor families of Caenorhabditis elegans and Caenorhabditis briggsae. Proc Natl Acad Sci U S A (2005) 1.16
Isoform-specific targeting and interaction domains in human nicotinamide mononucleotide adenylyltransferases. J Biol Chem (2010) 1.15
Integrating sequence variation and protein structure to identify sites under selection. Mol Biol Evol (2012) 1.15
Positive selection on hemagglutinin and neuraminidase genes of H1N1 influenza viruses. Virol J (2011) 1.14
Evolution and comparative genomics of odorant- and pheromone-associated genes in rodents. Genome Res (2004) 1.14
SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis. Nucleic Acids Res (2006) 1.12
Olfactory expression of a single and highly variable V1r pheromone receptor-like gene in fish species. Proc Natl Acad Sci U S A (2005) 1.11
MHC adaptive divergence between closely related and sympatric African cichlids. PLoS One (2007) 1.10
Sequence diversity in three tomato species: SNPs, markers, and molecular evolution. BMC Plant Biol (2009) 1.10
Spontaneous dominant mutations in chlamydomonas highlight ongoing evolution by gene diversification. Plant Cell (2015) 1.09
Predicting functional alternative splicing by measuring RNA selection pressure from multigenome alignments. PLoS Comput Biol (2009) 1.06
Diversification and adaptive sequence evolution of Caenorhabditis lysozymes (Nematoda: Rhabditidae). BMC Evol Biol (2008) 1.04
Analyses of 32 loci clarify phylogenetic relationships among Trypanosoma cruzi lineages and support a single hybridization prior to human contact. PLoS Negl Trop Dis (2011) 1.02
Gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates. Biol Direct (2009) 1.02
Prestin and the cholinergic receptor of hair cells: positively-selected proteins in mammals. Hear Res (2010) 1.00
Evolution under strong balancing selection: how many codons determine specificity at the female self-incompatibility gene SRK in Brassicaceae? BMC Evol Biol (2007) 1.00
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
Positive selection on nucleotide substitutions and indels in accessory gland proteins of the Drosophila pseudoobscura subgroup. J Mol Evol (2006) 0.98
Gene discovery in the threatened elkhorn coral: 454 sequencing of the Acropora palmata transcriptome. PLoS One (2011) 0.98
Identification of physicochemical selective pressure on protein encoding nucleotide sequences. BMC Bioinformatics (2006) 0.97
Adaptive evolution of SCML1 in primates, a gene involved in male reproduction. BMC Evol Biol (2008) 0.96
Purifying selection in mitochondria, free-living and obligate intracellular proteobacteria. BMC Evol Biol (2007) 0.96
Ancient and recent adaptive evolution of primate non-homologous end joining genes. PLoS Genet (2010) 0.96
Rapid evolution by positive Darwinian selection in T-cell antigen CD4 in primates. J Mol Evol (2008) 0.96
Relaxed genetic constraint is ancestral to the evolution of phenotypic plasticity. Integr Comp Biol (2012) 0.91
Positive selection drives accelerated evolution of mosquito salivary genes associated with blood-feeding. Insect Mol Biol (2013) 0.91
Orthology, function and evolution of accessory gland proteins in the Drosophila repleta group. Genetics (2008) 0.90
Maximum-likelihood model averaging to profile clustering of site types across discrete linear sequences. PLoS Comput Biol (2009) 0.90
The Diversity and Molecular Evolution of B-Cell Receptors during Infection. Mol Biol Evol (2016) 0.89
Phylogenomic analyses of nuclear genes reveal the evolutionary relationships within the BEP clade and the evidence of positive selection in Poaceae. PLoS One (2013) 0.89
Polymorphism and selection in the major histocompatibility complex DRA and DQA genes in the family Equidae. Immunogenetics (2009) 0.87
Methods for selecting fixed-effect models for heterogeneous codon evolution, with comments on their application to gene and genome data. BMC Evol Biol (2007) 0.87
Differential stepwise evolution of SARS coronavirus functional proteins in different host species. BMC Evol Biol (2009) 0.87
Isolation of a 97-kb minimal essential MHC B locus from a new reverse-4D BAC library of the golden pheasant. PLoS One (2012) 0.86
Rubisco evolution in C₄ eudicots: an analysis of Amaranthaceae sensu lato. PLoS One (2012) 0.86
Evolutionary patterning: a novel approach to the identification of potential drug target sites in Plasmodium falciparum. PLoS One (2008) 0.85
Natural selection and mammalian BRCA1 sequences: elucidating functionally important sites relevant to breast cancer susceptibility in humans. Mamm Genome (2006) 0.85
RNA-seq and high-definition mass spectrometry reveal the complex and divergent venoms of two rear-fanged colubrid snakes. BMC Genomics (2014) 0.85
Viral cystatin evolution and three-dimensional structure modelling: a case of directional selection acting on a viral protein involved in a host-parasitoid interaction. BMC Biol (2008) 0.84
MHC evolution in three salmonid species: a comparison between class II alpha and beta genes. Immunogenetics (2010) 0.84
Positively selected codons in immune-exposed loops of the vaccine candidate OMP-P1 of Haemophilus influenzae. J Mol Evol (2007) 0.84
Diversifying and purifying selection in the peptide binding region of DRB in mammals. J Mol Evol (2008) 0.84
Tempo and mode of gene duplication in mammalian ribosomal protein evolution. PLoS One (2014) 0.84
Defining the turkey MHC: identification of expressed class I- and class IIB-like genes independent of the MHC-B. Immunogenetics (2011) 0.83
Eco-immunology of fish invasions: the role of MHC variation. Immunogenetics (2014) 0.83
Time dependence of evolutionary metrics during the 2009 pandemic influenza virus outbreak. Virus Evol (2015) 0.82
Accuracy and power of the likelihood ratio test for comparing evolutionary rates among genes. J Mol Evol (2005) 0.82
The evolutionary history of the SAL1 gene family in eutherian mammals. BMC Evol Biol (2011) 0.81
Divergent evolution and purifying selection of the flaA gene sequences in Aeromonas. Biol Direct (2009) 0.81
Characterizing molecular adaptation: a hierarchical approach to assess the selective influence of amino acid properties. Bioinformatics (2010) 0.81
On characterizing adaptive events unique to modern humans. Genome Biol Evol (2011) 0.81
Sexual selection halts the relaxation of protamine 2 among rodents. PLoS One (2011) 0.81
Selective constraint and the evolution of the RNA polymerase II C-Terminal Domain. Transcription (2013) 0.80
A Comparison of One-Rate and Two-Rate Inference Frameworks for Site-Specific dN/dS Estimation. Genetics (2016) 0.80
MHC class II DRB diversity in raccoons (Procyon lotor) reveals associations with raccoon rabies virus (Lyssavirus). Immunogenetics (2010) 0.80
Positive and purifying selection influence the evolution of doublesex in the Anastrepha fraterculus species group. PLoS One (2012) 0.80
Molecular evolution of the transmembrane domains of G protein-coupled receptors. PLoS One (2011) 0.80
Molecular evolution of rbcL in three gymnosperm families: identifying adaptive and coevolutionary patterns. Biol Direct (2011) 0.79
Evidence for positive selection in the gene fruitless in Anastrepha fruit flies. BMC Evol Biol (2010) 0.79
Recombination Rate Variation Modulates Gene Sequence Evolution Mainly via GC-Biased Gene Conversion, Not Hill-Robertson Interference, in an Avian System. Mol Biol Evol (2015) 0.79
Patterns of molecular evolution of the germ line specification gene oskar suggest that a novel domain may contribute to functional divergence in Drosophila. Dev Genes Evol (2014) 0.79
Divergence and adaptive evolution of the gibberellin oxidase genes in plants. BMC Evol Biol (2015) 0.78
Rapid evolution, genetic variations, and functional association of the human spermatogenesis-related gene NYD-SP12. J Mol Evol (2007) 0.78
Evolutionary mode and functional divergence of vertebrate NMDA receptor subunit 2 genes. PLoS One (2010) 0.78
Target-Driven Evolution of Scorpion Toxins. Sci Rep (2015) 0.78
Adaptive evolution of the chrysanthemyl diphosphate synthase gene involved in irregular monoterpene metabolism. BMC Evol Biol (2012) 0.78
Molecular evolution of a malaria resistance gene (DARC) in primates. Immunogenetics (2012) 0.78
Population genetics of duplicated alternatively spliced exons of the Dscam gene in Daphnia and Drosophila. PLoS One (2011) 0.78
Molecular evolution of anthocyanin pigmentation genes following losses of flower color. BMC Evol Biol (2016) 0.77
Utility of computational methods to identify the apoptosis machinery in unicellular eukaryotes. Bioinform Biol Insights (2008) 0.77
Variation in positively selected major histocompatibility complex class I loci in rufous-collared sparrows (Zonotrichia capensis). Immunogenetics (2014) 0.77
Functional Divergence of the Nuclear Receptor NR2C1 as a Modulator of Pluripotentiality During Hominid Evolution. Genetics (2016) 0.77
Protein-protein interfaces from cytochrome c oxidase I evolve faster than nonbinding surfaces, yet negative selection is the driving force. Genome Biol Evol (2014) 0.77
New methods for inferring population dynamics from microbial sequences. Infect Genet Evol (2006) 0.77
Heterogeneity of [Formula: see text] Ratios at the Classical HLA Class I Genes over Divergence Time and Across the Allelic Phylogeny. J Mol Evol (2015) 0.76
Molecular adaptation and expression evolution following duplication of genes for organellar ribosomal protein S13 in rosids. BMC Evol Biol (2008) 0.76
Selection and demographic history shape the molecular evolution of the gamete compatibility protein bindin in Pisaster sea stars. Ecol Evol (2014) 0.76
Adaptive evolution of formyl peptide receptors in mammals. J Mol Evol (2015) 0.76
Proteomics reveals novel Drosophila seminal fluid proteins transferred at mating. PLoS Biol (2008) 2.09
Evolution of reproductive proteins from animals and plants. Reproduction (2006) 2.05
Pervasive adaptive evolution in primate seminal proteins. PLoS Genet (2005) 1.85
Speciation in birds: genes, geography, and sexual selection. Proc Natl Acad Sci U S A (2005) 1.55
A test for faster X evolution in Drosophila. Mol Biol Evol (2002) 1.46
Molecular evolution of seminal proteins in field crickets. Mol Biol Evol (2006) 1.45
Positive selection in the human genome: from genome scans to biological significance. Annu Rev Genomics Hum Genet (2008) 1.38
Proteomic discovery of previously unannotated, rapidly evolving seminal fluid genes in Drosophila. Genome Res (2009) 1.37
Coevolution of interacting fertilization proteins. PLoS Genet (2009) 1.26
Positive selection in the egg receptor for abalone sperm lysin. Proc Natl Acad Sci U S A (2003) 1.26
Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection. Genome Res (2011) 1.20
Identification and comparative analysis of accessory gland proteins in Orthoptera. Genome (2006) 1.20
Molecular evolution and population genetic analysis of candidate female reproductive genes in Drosophila. Genetics (2006) 1.19
Rapid evolution of reproductive proteins in abalone and Drosophila. Philos Trans R Soc Lond B Biol Sci (2006) 1.19
Rapidly evolving zona pellucida domain proteins are a major component of the vitelline envelope of abalone eggs. Proc Natl Acad Sci U S A (2006) 1.16
Adaptive evolution in the SRZ chemoreceptor families of Caenorhabditis elegans and Caenorhabditis briggsae. Proc Natl Acad Sci U S A (2005) 1.16
Proteomics and comparative genomic investigations reveal heterogeneity in evolutionary rate of male reproductive proteins in mice (Mus domesticus). Mol Biol Evol (2009) 1.07
TRPV6 exhibits unusual patterns of polymorphism and divergence in worldwide populations. Hum Mol Genet (2006) 1.06
Gene duplication and adaptive evolution of digestive proteases in Drosophila arizonae female reproductive tracts. PLoS Genet (2007) 1.06
Proteomics enhances evolutionary and functional analysis of reproductive proteins. Bioessays (2010) 1.02
Selection in the rapid evolution of gamete recognition proteins in marine invertebrates. Cold Spring Harb Perspect Biol (2011) 1.02
Duplication and selection on abalone sperm lysin in an allopatric population. Mol Biol Evol (2007) 1.01
Full-length sequence of VERL, the egg vitelline envelope receptor for abalone sperm lysin. Gene (2002) 1.00
Detecting coevolution through allelic association between physically unlinked loci. Am J Hum Genet (2010) 0.97
Adaptive evolution in rodent seminal vesicle secretion proteins. Mol Biol Evol (2008) 0.97
ZP domain proteins in the abalone egg coat include a paralog of VERL under positive selection that binds lysin and 18-kDa sperm proteins. Mol Biol Evol (2010) 0.95
Molecular population genetics of the gene encoding the human fertilization protein zonadhesin reveals rapid adaptive evolution. Am J Hum Genet (2006) 0.95
A perforin-like protein from a marine mollusk. Biochem Biophys Res Commun (2004) 0.94
Evidence of amino acid diversity-enhancing selection within humans and among primates at the candidate sperm-receptor gene PKDREJ. Am J Hum Genet (2007) 0.92
Identification of ejaculated proteins in the house mouse (Mus domesticus) via isotopic labeling. BMC Genomics (2011) 0.91
Positive selection in the carbohydrate recognition domains of sea urchin sperm receptor for egg jelly (suREJ) proteins. Mol Biol Evol (2004) 0.88
Dietary change and adaptive evolution of enamelin in humans and among primates. Genetics (2008) 0.88
Reproduction and immunity-driven natural selection in the human WFDC locus. Mol Biol Evol (2013) 0.84
Population genetics of accessory gland proteins and sexual behavior in Drosophila melanogaster populations from Evolution Canyon. Evolution (2003) 0.83
Adaptive evolution in an avian reproductive protein: ZP3. J Mol Evol (2007) 0.82
Positive selection within a diatom species acts on putative protein interactions and transcriptional regulation. Mol Biol Evol (2012) 0.80
Beyond the phenotypic gambit: molecular behavioural ecology and the evolution of genetic architecture. Mol Ecol (2011) 0.79
Evolution of the egg: new findings and challenges. Annu Rev Genomics Hum Genet (2012) 0.79
Oyster sperm bindin is a combinatorial fucose lectin with remarkable intra-species diversity. Int J Dev Biol (2008) 0.79
Functional diversification and evolution of antifreeze proteins in the antarctic fish Lycodichthys dearborni. J Mol Evol (2010) 0.78
Bindin from a sea star. Evol Dev (2009) 0.78
Targeted resequencing of two genes, RAGE and POLL, confirms findings from a genome-wide scan for adaptive evolution and provides evidence for positive selection in additional populations. Hum Mol Genet (2008) 0.78
Sequence diversity of Pan troglodytes subspecies and the impact of WFDC6 selective constraints in reproductive immunity. Genome Biol Evol (2013) 0.77
Detecting coevolution in mammalian sperm-egg fusion proteins. Mol Reprod Dev (2014) 0.77
Mass spectrometry and next-generation sequencing reveal an abundant and rapidly evolving abalone sperm protein. Mol Reprod Dev (2013) 0.77
Selection on plant male function genes identifies candidates for reproductive isolation of yellow monkeyflowers. PLoS Genet (2013) 0.76
The Tegula tango: a coevolutionary dance of interacting, positively selected sperm and egg proteins. Evolution (2012) 0.76
Duplicate abalone egg coat proteins bind sperm lysin similarly, but evolve oppositely, consistent with molecular mimicry at fertilization. PLoS Genet (2013) 0.76