Published in Mol Biol Evol on March 10, 2004
Metagenomic biomarker discovery and explanation. Genome Biol (2011) 11.29
Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. Proc Natl Acad Sci U S A (2006) 5.13
Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics (2004) 4.22
A random effects branch-site model for detecting episodic diversifying selection. Mol Biol Evol (2011) 2.88
Selectionism and neutralism in molecular evolution. Mol Biol Evol (2005) 2.64
Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates. Proc Natl Acad Sci U S A (2008) 2.34
A maximum likelihood method for detecting directional evolution in protein sequences and its application to influenza A virus. Mol Biol Evol (2008) 1.96
Pervasive adaptive evolution in primate seminal proteins. PLoS Genet (2005) 1.85
Comparative analysis of protein coding sequences from human, mouse and the domesticated pig. BMC Biol (2005) 1.51
Evolution of the relaxin-like peptide family. BMC Evol Biol (2005) 1.20
Selective pressures on the olfactory receptor repertoire since the human-chimpanzee divergence. Proc Natl Acad Sci U S A (2004) 1.18
Molecular evolution of glutathione S-transferases in the genus Drosophila. Genetics (2007) 1.14
The evolution of amastin surface glycoproteins in trypanosomatid parasites. Mol Biol Evol (2010) 1.10
Evolution of a microbial nitrilase gene family: a comparative and environmental genomics study. BMC Evol Biol (2005) 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
The complexity of selection at the major primate beta-defensin locus. BMC Evol Biol (2005) 1.02
Positive selection on nucleotide substitutions and indels in accessory gland proteins of the Drosophila pseudoobscura subgroup. J Mol Evol (2006) 0.98
Heterogeneous evolutionary processes affect R gene diversity in natural populations of Solanum pimpinellifolium. Proc Natl Acad Sci U S A (2004) 0.96
Evidence of positive Darwinian selection in Omp85, a highly conserved bacterial outer membrane protein essential for cell viability. J Mol Evol (2005) 0.94
Adaptive history of single copy genes highly expressed in the term human placenta. Genomics (2008) 0.92
Evidence of positive Darwinian selection in putative meningococcal vaccine antigens. J Mol Evol (2005) 0.89
Variation and molecular evolution of HmbR, the Neisseria meningitidis haemoglobin receptor. Microbiology (2010) 0.89
Global Diversity within and between Human Herpesvirus 1 and 2 Glycoproteins. J Virol (2015) 0.86
High variability and non-neutral evolution of the mammalian avpr1a gene. BMC Evol Biol (2007) 0.86
Positive Darwinian selection at single amino acid sites conferring plant virus resistance. J Mol Evol (2008) 0.85
Nucleotide sequence polymorphism in circoviruses. Infect Genet Evol (2007) 0.85
Evidence for positive selection on a sexual reproduction gene in the diatom genus Thalassiosira (Bacillariophyta). J Mol Evol (2006) 0.85
Evolutionary analysis of phycobiliproteins: implications for their structural and functional relationships. J Mol Evol (2006) 0.82
Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals. Proc Biol Sci (2004) 0.82
Polymorphism, natural selection, and structural modeling of class Ia MHC in the African clawed frog (Xenopus laevis). Immunogenetics (2006) 0.81
Structural and functional implications of positive selection at the primate angiogenin gene. BMC Evol Biol (2007) 0.81
Microevolutionary dynamics of a macroevolutionary key innovation in a Lepidopteran herbivore. BMC Evol Biol (2010) 0.80
UVPAR: fast detection of functional shifts in duplicate genes. BMC Bioinformatics (2006) 0.80
Positive selection within a diatom species acts on putative protein interactions and transcriptional regulation. Mol Biol Evol (2012) 0.80
Molecular evolution of the genomic RNA of Apple stem grooving capillovirus. J Mol Evol (2012) 0.79
Structural and molecular diversification of the Anguimorpha lizard mandibular venom gland system in the arboreal species Abronia graminea. J Mol Evol (2012) 0.79
Testing for adaptive evolution of the female reproductive protein ZPC in mammals, birds and fishes reveals problems with the M7-M8 likelihood ratio test. BMC Evol Biol (2005) 0.79
'Obesity' is healthy for cetaceans? Evidence from pervasive positive selection in genes related to triacylglycerol metabolism. Sci Rep (2015) 0.77
Codon-based detection of positive selection can be biased by heterogeneous distribution of polar amino acids along protein sequences. Comput Syst Bioinformatics Conf (2006) 0.76
Rapid adaptive evolution of the tumor suppressor gene Pten in an insect lineage. J Mol Evol (2006) 0.76
The site-wise log-likelihood score is a good predictor of genes under positive selection. J Mol Evol (2013) 0.76
Positive Selection or Free to Vary? Assessing the Functional Significance of Sequence Change Using Molecular Dynamics. PLoS One (2016) 0.75
MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol (2011) 220.97
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol (2007) 168.76
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform (2004) 72.40
MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform (2008) 24.69
Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A (2004) 20.53
Estimation of divergence times for major lineages of primate species. Mol Biol Evol (2003) 3.52
POPTREE2: Software for constructing population trees from allele frequency data and computing other population statistics with Windows interface. Mol Biol Evol (2009) 2.68
Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc Natl Acad Sci U S A (2002) 2.63
Extensive gains and losses of olfactory receptor genes in mammalian evolution. PLoS One (2007) 2.35
Evolutionary dynamics of olfactory receptor genes in fishes and tetrapods. Proc Natl Acad Sci U S A (2005) 2.32
Evolution of olfactory receptor genes in the human genome. Proc Natl Acad Sci U S A (2003) 1.97
Evolutionary dynamics of olfactory and other chemosensory receptor genes in vertebrates. J Hum Genet (2006) 1.94
Reliabilities of identifying positive selection by the branch-site and the site-prediction methods. Proc Natl Acad Sci U S A (2009) 1.94
Genomic drift and copy number variation of sensory receptor genes in humans. Proc Natl Acad Sci U S A (2007) 1.80
Acceleration of genomic evolution caused by enhanced mutation rate in endocellular symbionts. Proc Natl Acad Sci U S A (2002) 1.79
Origins and evolution of the recA/RAD51 gene family: evidence for ancient gene duplication and endosymbiotic gene transfer. Proc Natl Acad Sci U S A (2006) 1.72
Evolution of F-box genes in plants: different modes of sequence divergence and their relationships with functional diversification. Proc Natl Acad Sci U S A (2009) 1.70
Type I MADS-box genes have experienced faster birth-and-death evolution than type II MADS-box genes in angiosperms. Proc Natl Acad Sci U S A (2004) 1.62
Comparative evolutionary analysis of olfactory receptor gene clusters between humans and mice. Gene (2005) 1.55
Simulation study of the reliability and robustness of the statistical methods for detecting positive selection at single amino acid sites. Mol Biol Evol (2002) 1.50
Molecular evolution of the nontandemly repeated genes of the histone 3 multigene family. Mol Biol Evol (2002) 1.50
Evolutionary dynamics of olfactory receptor genes in Drosophila species. Proc Natl Acad Sci U S A (2007) 1.48
Evolutionary change of the numbers of homeobox genes in bilateral animals. Mol Biol Evol (2005) 1.37
Evolutionary changes of the number of olfactory receptor genes in the human and mouse lineages. Gene (2004) 1.32
Origins and evolution of microRNA genes in Drosophila species. Genome Biol Evol (2010) 1.31
Reanalysis of Murphy et al.'s data gives various mammalian phylogenies and suggests overcredibility of Bayesian trees. J Mol Evol (2003) 1.30
Antiquity and evolution of the MADS-box gene family controlling flower development in plants. Mol Biol Evol (2003) 1.24
Heterogeneous but conserved natural killer receptor gene complexes in four major orders of mammals. Proc Natl Acad Sci U S A (2006) 1.21
Empirical tests of the reliability of phylogenetic trees constructed with microsatellite DNA. Genetics (2008) 1.20
Origins and evolution of microRNA genes in plant species. Genome Biol Evol (2012) 1.20
Origin and evolution of influenza virus hemagglutinin genes. Mol Biol Evol (2002) 1.19
Concerted and nonconcerted evolution of the Hsp70 gene superfamily in two sibling species of nematodes. Mol Biol Evol (2003) 1.17
Birth-and-death evolution in primate MHC class I genes: divergence time estimates. Mol Biol Evol (2003) 1.11
The origins and early evolution of DNA mismatch repair genes--multiple horizontal gene transfers and co-evolution. Nucleic Acids Res (2007) 1.10
Purifying selection and birth-and-death evolution in the histone H4 gene family. Mol Biol Evol (2002) 1.09
Evolutionary dynamics of the immunoglobulin heavy chain variable region genes in vertebrates. Immunogenetics (2008) 1.09
Rapid expansion of killer cell immunoglobulin-like receptor genes in primates and their coevolution with MHC Class I genes. Gene (2005) 1.09
Evolutionary redefinition of immunoglobulin light chain isotypes in tetrapods using molecular markers. Proc Natl Acad Sci U S A (2008) 1.05
Origins and evolution of the formin multigene family that is involved in the formation of actin filaments. Mol Biol Evol (2008) 1.03
Ultraconserved coding regions outside the homeobox of mammalian Hox genes. BMC Evol Biol (2008) 0.98
Origin and evolution of the Ig-like domains present in mammalian leukocyte receptors: insights from chicken, frog, and fish homologues. Immunogenetics (2005) 0.98
Adaptive evolution of variable region genes encoding an unusual type of immunoglobulin in camelids. Mol Biol Evol (2002) 0.97
Genomic organization and evolutionary analysis of Ly49 genes encoding the rodent natural killer cell receptors: rapid evolution by repeated gene duplication. Immunogenetics (2004) 0.96
Origin and evolution of the chicken leukocyte receptor complex. Proc Natl Acad Sci U S A (2005) 0.95
Evolutionary changes of the target sites of two microRNAs encoded in the Hox gene cluster of Drosophila and other insect species. Genome Biol Evol (2010) 0.88
Analysis of the immunoglobulin light chain genes in zebra finch: evolutionary implications. Mol Biol Evol (2010) 0.86
Genomic drift and evolution of microsatellite DNAs in human populations. Mol Biol Evol (2009) 0.85
Genomic organization and evolution of immunoglobulin kappa gene enhancers and kappa deleting element in mammals. Mol Immunol (2009) 0.79
Eighty percent of proteins are different between humans and chimpanzees. Gene (2005) 0.79
A simple method for predicting the functional differentiation of duplicate genes and its application to MIKC-type MADS-box genes. Nucleic Acids Res (2005) 0.79
Evolution of the sex-lethal gene in insects and origin of the sex-determination system in Drosophila. J Mol Evol (2013) 0.78
Is positive selection responsible for the evolution of a duplicate UV-sensitive opsin gene in Heliconius butterflies? Proc Natl Acad Sci U S A (2010) 0.78
Random fluctuation of selection coefficients and the extent of nucleotide variation in human populations. Proc Natl Acad Sci U S A (2013) 0.75