Published in Mol Biol Evol on February 02, 2005
PyCogent: a toolkit for making sense from sequence. Genome Biol (2007) 20.64
Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics (2010) 6.14
Patterns of positive selection in six Mammalian genomes. PLoS Genet (2008) 4.69
INDELible: a flexible simulator of biological sequence evolution. Mol Biol Evol (2009) 3.29
Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition. Genome Biol (2007) 3.10
Emergence of young human genes after a burst of retroposition in primates. PLoS Biol (2005) 3.08
PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes. Nucleic Acids Res (2006) 3.04
A random effects branch-site model for detecting episodic diversifying selection. Mol Biol Evol (2011) 2.88
FUBAR: a fast, unconstrained bayesian approximation for inferring selection. Mol Biol Evol (2013) 2.73
Adaptive evolution has targeted the C-terminal domain of the RXLR effectors of plant pathogenic oomycetes. Plant Cell (2007) 2.66
Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst Biol (2011) 2.66
RXLR effector reservoir in two Phytophthora species is dominated by a single rapidly evolving superfamily with more than 700 members. Proc Natl Acad Sci U S A (2008) 2.65
Selectionism and neutralism in molecular evolution. Mol Biol Evol (2005) 2.64
Adaptive evolution in zinc finger transcription factors. PLoS Genet (2009) 2.35
Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates. Proc Natl Acad Sci U S A (2008) 2.34
Wave-like spread of Ebola Zaire. PLoS Biol (2005) 2.23
Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach. Nucleic Acids Res (2007) 2.21
Genetic variability of human respiratory syncytial virus A strains circulating in Ontario: a novel genotype with a 72 nucleotide G gene duplication. PLoS One (2012) 2.21
HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBEC. PLoS Pathog (2009) 2.15
Anti-fungal innate immunity in C. elegans is enhanced by evolutionary diversification of antimicrobial peptides. PLoS Pathog (2008) 1.97
Reliabilities of identifying positive selection by the branch-site and the site-prediction methods. Proc Natl Acad Sci U S A (2009) 1.94
Function and evolution of a gene family encoding odorant binding-like proteins in a social insect, the honey bee (Apis mellifera). Genome Res (2006) 1.92
Evolution of highly pathogenic H5N1 avian influenza viruses in Vietnam between 2001 and 2007. PLoS One (2008) 1.91
Positive selection driving diversification in plant secondary metabolism. Proc Natl Acad Sci U S A (2006) 1.89
Pervasive adaptive evolution in primate seminal proteins. PLoS Genet (2005) 1.85
Adaptive evolution of young gene duplicates in mammals. Genome Res (2009) 1.82
Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation. Genome Biol Evol (2010) 1.81
Three members of the 6-cys protein family of Plasmodium play a role in gamete fertility. PLoS Pathog (2010) 1.72
Evolutionary fingerprinting of genes. Mol Biol Evol (2009) 1.64
Models of coding sequence evolution. Brief Bioinform (2008) 1.64
In planta expression screens of Phytophthora infestans RXLR effectors reveal diverse phenotypes, including activation of the Solanum bulbocastanum disease resistance protein Rpi-blb2. Plant Cell (2009) 1.57
Positive selection of a duplicated UV-sensitive visual pigment coincides with wing pigment evolution in Heliconius butterflies. Proc Natl Acad Sci U S A (2010) 1.57
Positive selection and increased antiviral activity associated with the PARP-containing isoform of human zinc-finger antiviral protein. PLoS Genet (2008) 1.52
Coevolution of retroelements and tandem zinc finger genes. Genome Res (2011) 1.46
Coral life history and symbiosis: functional genomic resources for two reef building Caribbean corals, Acropora palmata and Montastraea faveolata. BMC Genomics (2008) 1.45
Detection of minority resistance during early HIV-1 infection: natural variation and spurious detection rather than transmission and evolution of multiple viral variants. J Virol (2011) 1.44
The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits. Nat Genet (2013) 1.42
Diversity and evolution of effector loci in natural populations of the plant pathogen Melampsora lini. Mol Biol Evol (2009) 1.42
Adaptive evolution in the toxicity of a spider's venom enzymes. BMC Evol Biol (2015) 1.41
Evolutionary analysis of inter-farm transmission dynamics in a highly pathogenic avian influenza epidemic. PLoS Pathog (2011) 1.40
Evolutionary trends of A(H1N1) influenza virus hemagglutinin since 1918. PLoS One (2009) 1.40
Rapid sequence and expression divergence suggest selection for novel function in primate-specific KRAB-ZNF genes. Mol Biol Evol (2010) 1.38
Widespread positive selection in the photosynthetic Rubisco enzyme. BMC Evol Biol (2007) 1.37
Proteomic discovery of previously unannotated, rapidly evolving seminal fluid genes in Drosophila. Genome Res (2009) 1.37
An effector-targeted protease contributes to defense against Phytophthora infestans and is under diversifying selection in natural hosts. Plant Physiol (2010) 1.35
Adaptation and constraint at Toll-like receptors in primates. Mol Biol Evol (2010) 1.34
Gene duplication and fragmentation in the zebra finch major histocompatibility complex. BMC Biol (2010) 1.34
High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes. Genome Res (2011) 1.32
Evolution and diverse roles of the CUP-SHAPED COTYLEDON genes in Arabidopsis leaf development. Plant Cell (2011) 1.29
Extensive functional diversification of the Populus glutathione S-transferase supergene family. Plant Cell (2009) 1.29
Reconstruction of ancestral metabolic enzymes reveals molecular mechanisms underlying evolutionary innovation through gene duplication. PLoS Biol (2012) 1.27
The evolution of nuclear auxin signalling. BMC Evol Biol (2009) 1.27
Evolutionary trajectories of beta-lactamase CTX-M-1 cluster enzymes: predicting antibiotic resistance. PLoS Pathog (2010) 1.26
Patterns of evolution of host proteins involved in retroviral pathogenesis. Retrovirology (2006) 1.26
Network-level molecular evolutionary analysis of the insulin/TOR signal transduction pathway across 12 Drosophila genomes. Genome Res (2009) 1.20
Feline lentivirus evolution in cross-species infection reveals extensive G-to-A mutation and selection on key residues in the viral polymerase. J Virol (2006) 1.20
Complete mtDNA genomes of Anopheles darlingi and an approach to anopheline divergence time. Malar J (2010) 1.19
An experimentally determined evolutionary model dramatically improves phylogenetic fit. Mol Biol Evol (2014) 1.19
Molecular evolution and population genetic analysis of candidate female reproductive genes in Drosophila. Genetics (2006) 1.19
Coevolution between a family of parasite virulence effectors and a class of LINE-1 retrotransposons. PLoS One (2009) 1.15
Codon-based tests of positive selection, branch lengths, and the evolution of mammalian immune system genes. Immunogenetics (2008) 1.15
Evolution and functional divergence of NLRP genes in mammalian reproductive systems. BMC Evol Biol (2009) 1.14
The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC. Mol Biol Evol (2013) 1.14
Phylogenomic analysis of natural selection pressure in Streptococcus genomes. BMC Evol Biol (2007) 1.14
Adaptive functional divergence among triplicated alpha-globin genes in rodents. Genetics (2008) 1.14
Applications and implications of neutral versus non-neutral markers in molecular ecology. Int J Mol Sci (2011) 1.12
Statistics and truth in phylogenomics. Mol Biol Evol (2011) 1.12
The role of positive selection in determining the molecular cause of species differences in disease. BMC Evol Biol (2008) 1.11
A depauperate immune repertoire precedes evolution of sociality in bees. Genome Biol (2015) 1.11
Compartmentalization of HIV-1 within the female genital tract is due to monotypic and low-diversity variants not distinct viral populations. PLoS One (2009) 1.11
Insights into the evolution of longevity from the bowhead whale genome. Cell Rep (2015) 1.09
Molecular evolution of the ependymin protein family: a necessary update. BMC Evol Biol (2007) 1.09
Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence. BMC Genomics (2013) 1.09
Directional and balancing selection in human beta-defensins. BMC Evol Biol (2008) 1.09
Molecular evolution, functional variation, and proposed nomenclature of the gene family that includes sphingomyelinase D in sicariid spider venoms. Mol Biol Evol (2008) 1.09
Positive selection of Iris, a retroviral envelope-derived host gene in Drosophila melanogaster. PLoS Genet (2005) 1.09
Evolution of functional and sequence variants of the mammalian XPR1 receptor for mouse xenotropic gammaretroviruses and the human-derived retrovirus XMRV. J Virol (2010) 1.08
Identification of innate immunity elicitors using molecular signatures of natural selection. Proc Natl Acad Sci U S A (2012) 1.08
Patterns of positive selection in seven ant genomes. Mol Biol Evol (2014) 1.08
Co-evolution of primate SAMHD1 and lentivirus Vpx leads to the loss of the vpx gene in HIV-1 ancestor. PLoS One (2012) 1.07
Phylodynamic analysis of clinical and environmental Vibrio cholerae isolates from Haiti reveals diversification driven by positive selection. MBio (2014) 1.07
Long-wavelength sensitive visual pigments of the guppy (Poecilia reticulata): six opsins expressed in a single individual. BMC Evol Biol (2007) 1.06
Origin, antiviral function and evidence for positive selection of the gammaretrovirus restriction gene Fv1 in the genus Mus. Proc Natl Acad Sci U S A (2009) 1.06
Linking genomics and ecology to investigate the complex evolution of an invasive Drosophila pest. Genome Biol Evol (2013) 1.06
A novel system of polymorphic and diverse NK cell receptors in primates. PLoS Genet (2009) 1.06
Differential evolution and neofunctionalization of snake venom metalloprotease domains. Mol Cell Proteomics (2012) 1.06
Gene duplication and adaptive evolution of digestive proteases in Drosophila arizonae female reproductive tracts. PLoS Genet (2007) 1.06
A history of recurrent positive selection at the toll-like receptor 5 in primates. Mol Biol Evol (2009) 1.05
Rapid evolution by positive selection and gene gain and loss: PLA(2) venom genes in closely related Sistrurus rattlesnakes with divergent diets. J Mol Evol (2008) 1.05
Diversification and adaptive sequence evolution of Caenorhabditis lysozymes (Nematoda: Rhabditidae). BMC Evol Biol (2008) 1.04
Analysis of core housekeeping and virulence genes reveals cryptic lineages of Clostridium perfringens that are associated with distinct disease presentations. Genetics (2006) 1.04
Patterns of selection in anti-malarial immune genes in malaria vectors: evidence for adaptive evolution in LRIM1 in Anopheles arabiensis. PLoS One (2007) 1.04
Mitochondrial targeting adaptation of the hominoid-specific glutamate dehydrogenase driven by positive Darwinian selection. PLoS Genet (2008) 1.04
The breadth of antiviral activity of Apobec3DE in chimpanzees has been driven by positive selection. J Virol (2011) 1.04
Molecular evolution of the CPP-like gene family in plants: insights from comparative genomics of Arabidopsis and rice. J Mol Evol (2008) 1.04
Duplication, selection and gene conversion in a Drosophila mojavensis female reproductive protein family. Genetics (2009) 1.04
Causes of evolutionary rate variation among protein sites. Nat Rev Genet (2016) 1.03
Episodic evolution and adaptation of chloroplast genomes in ancestral grasses. PLoS One (2009) 1.03
Adaptive evolution of Mus Apobec3 includes retroviral insertion and positive selection at two clusters of residues flanking the substrate groove. PLoS Pathog (2010) 1.03
Adaptive signals in algal Rubisco reveal a history of ancient atmospheric carbon dioxide. Philos Trans R Soc Lond B Biol Sci (2012) 1.03
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
Rate of de novo mutations and the importance of father's age to disease risk. Nature (2012) 11.92
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
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
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
Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs. Bioinformatics (2012) 5.04
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
Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics (2003) 3.89
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
Stochastic mapping of morphological characters. Syst Biol (2003) 3.08
Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science (2009) 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
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
Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Mol Biol Evol (2008) 2.25
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
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
A likelihood ratio test for species membership based on DNA sequence data. Philos Trans R Soc Lond B Biol Sci (2005) 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
Inferring demographic history from a spectrum of shared haplotype lengths. PLoS Genet (2013) 1.77
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
Targets of balancing selection in the human genome. Mol Biol Evol (2009) 1.69
Human genomics: disclosure of variation. Nature (2005) 1.67
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
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 affects multiple aspects of genetic variation at putatively neutral sites across the human genome. PLoS Genet (2011) 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
Detecting selection in noncoding regions of nucleotide sequences. Genetics (2004) 1.50
Evolution of the integral membrane desaturase gene family in moths and flies. Genetics (2002) 1.47
Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing. BMC Genomics (2013) 1.46
Correcting estimators of theta and Tajima's D for ascertainment biases caused by the single-nucleotide polymorphism discovery process. Genetics (2008) 1.44
Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor? Mol Biol Evol (2007) 1.44
Whole-exome sequencing of 2,000 Danish individuals and the role of rare coding variants in type 2 diabetes. Am J Hum Genet (2013) 1.43
A method for detecting IBD regions simultaneously in multiple individuals--with applications to disease genetics. Genome Res (2011) 1.41
Quantifying population genetic differentiation from next-generation sequencing data. Genetics (2013) 1.41
Microsatellite mutation models: insights from a comparison of humans and chimpanzees. Genetics (2004) 1.38
Discerning between recurrent gene flow and recent divergence under a finite-site mutation model applied to North Atlantic and Mediterranean Sea fin whale (Balaenoptera physalus) populations. Evolution (2004) 1.35
Genetic signatures reveal high-altitude adaptation in a set of ethiopian populations. Mol Biol Evol (2013) 1.33
Distinguishing between selective sweeps from standing variation and from a de novo mutation. PLoS Genet (2012) 1.31
Fast phylogenetic DNA barcoding. Philos Trans R Soc Lond B Biol Sci (2008) 1.27
On detecting incomplete soft or hard selective sweeps using haplotype structure. Mol Biol Evol (2014) 1.25
Genomics: In search of rare human variants. Nature (2010) 1.20
Bayesian estimation of genomic distance. Genetics (2004) 1.19
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
Radiation and speciation of pelagic organisms during periods of global warming: the case of the common minke whale, Balaenoptera acutorostrata. Mol Ecol (2007) 1.16
Bacterial natural transformation by highly fragmented and damaged DNA. Proc Natl Acad Sci U S A (2013) 1.15
Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation. Genome Res (2013) 1.12
An investigation of the statistical power of neutrality tests based on comparative and population genetic data. Mol Biol Evol (2008) 1.11
Detecting coevolving amino acid sites using Bayesian mutational mapping. Bioinformatics (2005) 1.11
Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data. BMC Bioinformatics (2013) 1.10
The impact of founder events on chromosomal variability in multiply mating species. Mol Biol Evol (2008) 1.05
Bayesian estimation of the number of inversions in the history of two chromosomes. J Comput Biol (2002) 1.04
Genetic architecture of vitamin B12 and folate levels uncovered applying deeply sequenced large datasets. PLoS Genet (2013) 1.04
Patterns of mutation and selection at synonymous sites in Drosophila. Mol Biol Evol (2007) 1.03
Evidence for positive selection on a number of MicroRNA regulatory interactions during recent human evolution. PLoS Genet (2012) 1.03