Published in J Mol Evol on March 01, 2005
CodonTest: modeling amino acid substitution preferences in coding sequences. PLoS Comput Biol (2010) 1.56
Detecting groups of coevolving positions in a molecule: a clustering approach. BMC Evol Biol (2007) 1.03
Structural modules for receptor dimerization in the S-locus receptor kinase extracellular domain. Proc Natl Acad Sci U S A (2007) 1.01
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
Directionality in the evolution of influenza A haemagglutinin. Proc Biol Sci (2008) 0.97
Identification of physicochemical selective pressure on protein encoding nucleotide sequences. BMC Bioinformatics (2006) 0.97
Detecting patches of protein sites of influenza A viruses under positive selection. Mol Biol Evol (2012) 0.95
Evolution of the S-locus region in Arabidopsis relatives. Plant Physiol (2011) 0.91
In vivo detection of residues required for ligand-selective activation of the S-locus receptor in Arabidopsis. Curr Biol (2009) 0.90
Bayesian comparisons of codon substitution models. Genetics (2008) 0.90
Detecting site-specific biochemical constraints through substitution mapping. J Mol Evol (2008) 0.86
Molecular characterization of Lal2, an SRK-like gene linked to the S-locus in the wild mustard Leavenworthia alabamica. Genetics (2008) 0.84
Reconstructing the phylogenetic history of long-term effective population size and life-history traits using patterns of amino acid replacement in mitochondrial genomes of mammals and birds. Genome Biol Evol (2013) 0.84
Benchmarking multi-rate codon models. PLoS One (2010) 0.84
Independent expansion of zincin metalloproteinases in Onygenales fungi may be associated with their pathogenicity. PLoS One (2014) 0.81
Self-incompatibility in Brassicaceae crops: lessons for interspecific incompatibility. Breed Sci (2014) 0.81
Characterizing molecular adaptation: a hierarchical approach to assess the selective influence of amino acid properties. Bioinformatics (2010) 0.81
Site-specific N-glycosylation of the S-locus receptor kinase and its role in the self-incompatibility response of the brassicaceae. Plant Cell (2014) 0.77
New methods for inferring population dynamics from microbial sequences. Infect Genet Evol (2006) 0.77
Origin and diversification dynamics of self-incompatibility haplotypes. Genetics (2011) 0.76
Bayesian factor models in characterizing molecular adaptation. J Appl Stat (2013) 0.75
Bayesian semiparametric regression models to characterize molecular evolution. BMC Bioinformatics (2012) 0.75
Detecting positively selected sites from amino Acid sequences: an implicit codon model. Conf Proc IEEE Eng Med Biol Soc (2007) 0.75
Role of sexual selection in speciation in Drosophila. Genetica (2013) 0.75
Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol (1981) 67.56
Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol (1986) 36.06
Amino acid difference formula to help explain protein evolution. Science (1974) 15.19
Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature (1988) 15.05
Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics (2000) 14.84
Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules. Nature (1991) 13.90
Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics (1998) 11.25
Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol (2002) 7.21
The male determinant of self-incompatibility in Brassica. Science (1999) 5.03
The three-dimensional structure of peptide-MHC complexes. Annu Rev Immunol (1995) 4.60
Two types of amino acid substitutions in protein evolution. J Mol Evol (1979) 4.34
Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Mol Biol Evol (2001) 4.03
Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics (2003) 3.89
Enhanced immunological surveillance in mice heterozygous at the H-2 gene complex. Nature (1975) 3.49
Models of amino acid substitution and applications to mitochondrial protein evolution. Mol Biol Evol (1998) 3.03
Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals. Proc Natl Acad Sci U S A (2001) 2.80
Rates of conservative and radical nonsynonymous nucleotide substitutions in mammalian nuclear genes. J Mol Evol (2000) 2.48
Genetic analysis of protein stability and function. Annu Rev Genet (1989) 2.47
Positive Darwinian selection promotes charge profile diversity in the antigen-binding cleft of class I major-histocompatibility-complex molecules. Mol Biol Evol (1990) 2.41
Physical linkage of the SLG and SRK genes at the self-incompatibility locus of Brassica oleracea. Mol Gen Genet (1993) 2.39
Evidence for balancing selection at HLA. Genetics (1983) 2.35
The self-incompatibility (S) haplotypes of Brassica contain highly divergent and rearranged sequences of ancient origin. Plant Cell (1997) 2.19
Sequence variability analysis of human class I and class II MHC molecules: functional and structural correlates of amino acid polymorphisms. J Mol Biol (2003) 1.88
DNA sequences of self-incompatibility genes from Brassica campestris and B. oleracea: polymorphism predating speciation. Plant Mol Biol (1991) 1.87
A naturally selected dimorphism within the HLA-B44 supertype alters class I structure, peptide repertoire, and T cell recognition. J Exp Med (2003) 1.72
A generalized least-squares estimate for the origin of sporophytic self-incompatibility. Genetics (1995) 1.70
Determining the physical limits of the Brassica S locus by recombinational analysis. Plant Cell (2000) 1.67
SRK, the stigma-specific S locus receptor kinase of Brassica, is targeted to the plasma membrane in transgenic tobacco. Plant Cell (1996) 1.63
Ratios of radical to conservative amino acid replacement are affected by mutational and compositional factors and may not be indicative of positive Darwinian selection. Mol Biol Evol (2002) 1.60
Polymorphism in the alpha 1 helix of the HLA-B heavy chain can have an overriding influence on peptide-binding specificity. J Immunol (1997) 1.52
Relations between chemical structure and biological activity in peptides. J Theor Biol (1966) 1.51
Coevolution of the S-locus genes SRK, SLG and SP11/SCR in Brassica oleracea and B. rapa. Genetics (2002) 1.42
Bound water structure and polymorphic amino acids act together to allow the binding of different peptides to MHC class I HLA-B53. Immunity (1996) 1.27
Recognition and rejection of self in plant reproduction. Science (2002) 1.27
Haplotype structure of the stigmatic self-incompatibility gene in natural populations of Arabidopsis lyrata. Mol Biol Evol (2003) 1.25
Non-randomness of amino-acid changes in the evolution of homologous proteins. Nature (1967) 1.24
Heterozygosity at individual amino acid sites: extremely high levels for HLA-A and -B genes. Proc Natl Acad Sci U S A (1991) 1.23
Selective constraints on amino-acid substitutions during the evolution of proteins. Nature (1970) 1.15
HLA-B27 subtypes differentially associated with disease exhibit subtle structural alterations. J Biol Chem (2002) 1.13
HLA polymorphism in the Havasupai: evidence for balancing selection. Am J Hum Genet (1993) 1.12
Recombination within the human MHC. Immunol Rev (1999) 1.10
Self-incompatibility in the Brassicaceae: receptor-ligand signaling and cell-to-cell communication. Plant Cell (2002) 1.10
Strong balancing selection at HLA loci: evidence from segregation in South Amerindian families. Proc Natl Acad Sci U S A (1997) 1.06
Comparison of the P2 specificity pocket in three human histocompatibility antigens: HLA-A*6801, HLA-A*0201, and HLA-B*2705. Proc Natl Acad Sci U S A (1993) 1.04
Codon and rate variation models in molecular phylogeny. Mol Biol Evol (2002) 0.94
Structural studies of class I major histocompatibility complex proteins: insights into antigen presentation. FASEB J (1995) 0.90
Antigenicity of HLA-A2 and HLA-B7. Loss and gain of serologic determinants induced by site-specific mutagenesis at residues 62 to 80. Hum Immunol (1991) 0.76
The diploid genome sequence of an Asian individual. Nature (2008) 46.29
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21
The sequence and de novo assembly of the giant panda genome. Nature (2009) 15.76
A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature (2012) 11.68
Sequencing of 50 human exomes reveals adaptation to high altitude. Science (2010) 11.27
Bayes empirical bayes inference of amino acid sites under positive selection. Mol Biol Evol (2005) 11.26
Natural selection on protein-coding genes in the human genome. Nature (2005) 10.84
Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science (2003) 9.20
The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One (2007) 9.17
Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet (2008) 8.92
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol (2005) 8.74
Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res (2005) 8.38
Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics (2004) 7.79
Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature (2010) 7.51
Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol (2002) 7.21
The evolution of gene expression levels in mammalian organs. Nature (2011) 7.16
Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics (2003) 7.05
Ascertainment bias in studies of human genome-wide polymorphism. Genome Res (2005) 6.63
Proportionally more deleterious genetic variation in European than in African populations. Nature (2008) 6.61
Simultaneous inference of selection and population growth from patterns of variation in the human genome. Proc Natl Acad Sci U S A (2005) 5.94
Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc Natl Acad Sci U S A (2007) 5.64
Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet (2010) 5.44
Localizing recent adaptive evolution in the human genome. PLoS Genet (2007) 5.11
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol (2011) 4.84
An Aboriginal Australian genome reveals separate human dispersals into Asia. Science (2011) 4.84
Patterns of positive selection in six Mammalian genomes. PLoS Genet (2008) 4.69
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
Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genet (2007) 3.83
The cost of inbreeding in Arabidopsis. Nature (2002) 3.80
Ancient biomolecules from deep ice cores reveal a forested southern Greenland. Science (2007) 3.79
Linkage disequilibrium as a signature of selective sweeps. Genetics (2004) 3.52
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature (2013) 3.45
Pervasive adaptive evolution in mammalian fertilization proteins. Mol Biol Evol (2003) 3.42
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
Stochastic mapping of morphological characters. Syst Biol (2003) 3.08
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
Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science (2009) 2.68
Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proc Biol Sci (2012) 2.68
Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques. Science (2007) 2.62
Species-specific responses of Late Quaternary megafauna to climate and humans. Nature (2011) 2.60
Adaptive genic evolution in the Drosophila genomes. Proc Natl Acad Sci U S A (2007) 2.56
Ascertainment biases in SNP chips affect measures of population divergence. Mol Biol Evol (2010) 2.56
Inference of historical changes in migration rate from the lengths of migrant tracts. Genetics (2008) 2.53
Best practices for justifying fossil calibrations. Syst Biol (2011) 2.51
Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals. Genome Res (2008) 2.46
Signatures of environmental genetic adaptation pinpoint pathogens as the main selective pressure through human evolution. PLoS Genet (2011) 2.44
Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques. Nat Biotechnol (2011) 2.37
Radiation of extant cetaceans driven by restructuring of the oceans. Syst Biol (2009) 2.33
Population genetic inference from genomic sequence variation. Genome Res (2010) 2.29
Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA. Mol Biol Evol (2003) 2.29
Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Mol Biol Evol (2008) 2.25
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
Balancing selection maintains a form of ERAP2 that undergoes nonsense-mediated decay and affects antigen presentation. PLoS Genet (2010) 2.14
Statistical assignment of DNA sequences using Bayesian phylogenetics. Syst Biol (2008) 2.13
Estimation of 2Nes from temporal allele frequency data. Genetics (2008) 2.12
Ancient DNA reveals late survival of mammoth and horse in interior Alaska. Proc Natl Acad Sci U S A (2009) 2.10
Design of association studies with pooled or un-pooled next-generation sequencing data. Genet Epidemiol (2010) 2.06
Relatedness mapping and tracts of relatedness for genome-wide data in the presence of linkage disequilibrium. Genet Epidemiol (2009) 2.02
Divergence dates for Malagasy lemurs estimated from multiple gene loci: geological and evolutionary context. Mol Ecol (2004) 2.01
Comparative genome analyses of Arabidopsis spp.: inferring chromosomal rearrangement events in the evolutionary history of A. thaliana. Genome Res (2005) 2.01
The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection. Mol Biol Evol (2010) 2.01
Using nuclear haplotypes with microsatellites to study gene flow between recently separated Cichlid species. Mol Ecol (2004) 1.99
Population size changes reshape genomic patterns of diversity. Evolution (2007) 1.95
Estimation of allele frequency and association mapping using next-generation sequencing data. BMC Bioinformatics (2011) 1.93
Generation of self-incompatible Arabidopsis thaliana by transfer of two S locus genes from A. lyrata. Science (2002) 1.89
A likelihood ratio test for species membership based on DNA sequence data. Philos Trans R Soc Lond B Biol Sci (2005) 1.85
Dating primate divergences through an integrated analysis of palaeontological and molecular data. Syst Biol (2010) 1.85
Ancient bacteria show evidence of DNA repair. Proc Natl Acad Sci U S A (2007) 1.81
Unlocking the vault: next-generation museum population genomics. Mol Ecol (2013) 1.77
Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites. Mol Biol Evol (2007) 1.77
Inferring demographic history from a spectrum of shared haplotype lengths. PLoS Genet (2013) 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
Genes under positive selection in Escherichia coli. Genome Res (2007) 1.70
Maximum likelihood and Bayesian methods for estimating the distribution of selective effects among classes of mutations using DNA polymorphism data. Theor Popul Biol (2003) 1.69
An empirical examination of the utility of codon-substitution models in phylogeny reconstruction. Syst Biol (2005) 1.69
Targets of balancing selection in the human genome. Mol Biol Evol (2009) 1.69
Human genomics: disclosure of variation. Nature (2005) 1.67
Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales. Curr Biol (2015) 1.66
The evolution of selfing in Arabidopsis thaliana. Science (2007) 1.62
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
Linkage disequilibrium and inference of ancestral recombination in 538 single-nucleotide polymorphism clusters across the human genome. Am J Hum Genet (2003) 1.58
Adaptive evolution of cytochrome c oxidase: Infrastructure for a carnivorous plant radiation. Proc Natl Acad Sci U S A (2004) 1.56
Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome. PLoS Genet (2011) 1.54
A maximum likelihood method for analyzing pseudogene evolution: implications for silent site evolution in humans and rodents. Mol Biol Evol (2002) 1.54
Natural selection and the distribution of identity-by-descent in the human genome. Genetics (2010) 1.52
Rational design of DNA sequence-based strategies for subtyping Listeria monocytogenes. J Clin Microbiol (2002) 1.51