Published in Brief Bioinform on June 01, 2004
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol (2006) 57.72
MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform (2008) 24.69
NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res (2006) 23.67
Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A (2004) 20.53
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res (2006) 16.26
DNA barcoding Australia's fish species. Philos Trans R Soc Lond B Biol Sci (2005) 11.37
Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak. PLoS Med (2006) 11.14
Dendroscope: An interactive viewer for large phylogenetic trees. BMC Bioinformatics (2007) 11.03
DNA barcodes distinguish species of tropical Lepidoptera. Proc Natl Acad Sci U S A (2006) 10.35
Molecular analysis of human forearm superficial skin bacterial biota. Proc Natl Acad Sci U S A (2007) 9.73
DNA barcodes reveal cryptic host-specificity within the presumed polyphagous members of a genus of parasitoid flies (Diptera: Tachinidae). Proc Natl Acad Sci U S A (2006) 6.23
Introducing TreeClimber, a test to compare microbial community structures. Appl Environ Microbiol (2006) 5.69
Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature (2010) 5.08
Global genetic population structure of Bacillus anthracis. PLoS One (2007) 4.94
Genetic detection and characterization of Lujo virus, a new hemorrhagic fever-associated arenavirus from southern Africa. PLoS Pathog (2009) 4.88
Genetic variation and population structure in native Americans. PLoS Genet (2007) 4.87
Emergence of azole resistance in Aspergillus fumigatus and spread of a single resistance mechanism. PLoS Med (2008) 4.68
A revision of Malagasy species of Anochetus mayr and Odontomachus latreille (Hymenoptera: Formicidae). PLoS One (2008) 4.28
The Schistosoma japonicum genome reveals features of host-parasite interplay. Nature (2009) 4.19
Pathway analysis of seven common diseases assessed by genome-wide association. Genomics (2008) 4.11
Chikungunya outbreaks caused by African genotype, India. Emerg Infect Dis (2006) 3.97
Evolutionary genetics of the capsular locus of serogroup 6 pneumococci. J Bacteriol (2004) 3.81
Variation in virulence among clades of Escherichia coli O157:H7 associated with disease outbreaks. Proc Natl Acad Sci U S A (2008) 3.69
Vaccine escape recombinants emerge after pneumococcal vaccination in the United States. PLoS Pathog (2007) 3.65
Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified. Proc Natl Acad Sci U S A (2008) 3.56
Panmicrobial oligonucleotide array for diagnosis of infectious diseases. Emerg Infect Dis (2007) 3.51
RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons. PLoS Biol (2005) 3.50
TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses. BMC Bioinformatics (2010) 3.38
Prevalence and genetic diversity of coronaviruses in bats from China. J Virol (2006) 3.37
Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains. Nucleic Acids Res (2005) 3.36
Studies of reservoir hosts for Marburg virus. Emerg Infect Dis (2007) 3.35
Red colouration in apple fruit is due to the activity of the MYB transcription factor, MdMYB10. Plant J (2006) 3.33
Common functions for diverse small RNAs of land plants. Plant Cell (2007) 3.30
Characterisation of the genetic diversity of Brucella by multilocus sequencing. BMC Microbiol (2007) 3.25
Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution. Plant Cell (2008) 3.25
Gene losses during human origins. PLoS Biol (2006) 3.17
Density-dependent cladogenesis in birds. PLoS Biol (2008) 3.14
Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. Plant Cell (2006) 3.10
Does the DNA barcoding gap exist? - a case study in blue butterflies (Lepidoptera: Lycaenidae). Front Zool (2007) 3.08
Comparative analysis of twelve genomes of three novel group 2c and group 2d coronaviruses reveals unique group and subgroup features. J Virol (2006) 3.07
Toward a unified nomenclature system for highly pathogenic avian influenza virus (H5N1). Emerg Infect Dis (2008) 3.06
Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res (2006) 3.02
Streptococcal toxic shock syndrome caused by Streptococcus suis serotype 2. PLoS Med (2006) 2.99
A statistical phylogeography of influenza A H5N1. Proc Natl Acad Sci U S A (2007) 2.91
A previously unknown reovirus of bat origin is associated with an acute respiratory disease in humans. Proc Natl Acad Sci U S A (2007) 2.88
Reductive genome evolution from the mother of Rickettsia. PLoS Genet (2007) 2.87
Salicylic acid-independent ENHANCED DISEASE SUSCEPTIBILITY1 signaling in Arabidopsis immunity and cell death is regulated by the monooxygenase FMO1 and the Nudix hydrolase NUDT7. Plant Cell (2006) 2.87
MultiSeq: unifying sequence and structure data for evolutionary analysis. BMC Bioinformatics (2006) 2.81
Rapid evolution of pandemic noroviruses of the GII.4 lineage. PLoS Pathog (2010) 2.80
A deficit of detoxification enzymes: pesticide sensitivity and environmental response in the honeybee. Insect Mol Biol (2006) 2.80
The diversity of reproductive parasites among arthropods: Wolbachia do not walk alone. BMC Biol (2008) 2.76
Emergence and pathogenicity of highly virulent Cryptococcus gattii genotypes in the northwest United States. PLoS Pathog (2010) 2.67
MLST of housekeeping genes captures geographic population structure and suggests a European origin of Borrelia burgdorferi. Proc Natl Acad Sci U S A (2008) 2.67
A dominant clone of Leptospira interrogans associated with an outbreak of human leptospirosis in Thailand. PLoS Negl Trop Dis (2007) 2.65
Whole genome sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection. Proc Natl Acad Sci U S A (2005) 2.64
Comprehensive DNA barcode coverage of North American birds. Mol Ecol Notes (2007) 2.64
The rice tapetum degeneration retardation gene is required for tapetum degradation and anther development. Plant Cell (2006) 2.62
Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). OMICS (2006) 2.57
The emerging amphibian pathogen Batrachochytrium dendrobatidis globally infects introduced populations of the North American bullfrog, Rana catesbeiana. Biol Lett (2006) 2.53
Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proc Natl Acad Sci U S A (2008) 2.53
Functional noncoding sequences derived from SINEs in the mammalian genome. Genome Res (2006) 2.50
Hepatitis B virus taxonomy and hepatitis B virus genotypes. World J Gastroenterol (2007) 2.50
The genome of the square archaeon Haloquadratum walsbyi : life at the limits of water activity. BMC Genomics (2006) 2.48
The AP-2 family of transcription factors. Genome Biol (2005) 2.46
Isolation and molecular characterization of Aichi viruses from fecal specimens collected in Japan, Bangladesh, Thailand, and Vietnam. J Clin Microbiol (2007) 2.45
Evolutionary genomics reveals conserved structural determinants of signaling and adaptation in microbial chemoreceptors. Proc Natl Acad Sci U S A (2007) 2.42
Molecular phylogenetics of Candida albicans. Eukaryot Cell (2007) 2.41
Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case. Proc Natl Acad Sci U S A (2007) 2.41
The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum). Environ Microbiol (2008) 2.40
Akirins are highly conserved nuclear proteins required for NF-kappaB-dependent gene expression in drosophila and mice. Nat Immunol (2007) 2.36
Proanthocyanidin synthesis and expression of genes encoding leucoanthocyanidin reductase and anthocyanidin reductase in developing grape berries and grapevine leaves. Plant Physiol (2005) 2.35
FLOWERING LOCUS T protein may act as the long-distance florigenic signal in the cucurbits. Plant Cell (2007) 2.35
Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens. PLoS Genet (2006) 2.35
Genomic patterns of pathogen evolution revealed by comparison of Burkholderia pseudomallei, the causative agent of melioidosis, to avirulent Burkholderia thailandensis. BMC Microbiol (2006) 2.35
Proboscidean mitogenomics: chronology and mode of elephant evolution using mastodon as outgroup. PLoS Biol (2007) 2.34
Role of APOBEC3 in genetic diversity among endogenous murine leukemia viruses. PLoS Genet (2007) 2.33
Multilocus sequence typing method for identification and genotypic classification of pathogenic Leptospira species. Ann Clin Microbiol Antimicrob (2006) 2.33
The grapevine transcription factor VvMYBPA1 regulates proanthocyanidin synthesis during fruit development. Plant Physiol (2007) 2.33
Cryptic properties of a cluster of dominant flavivirus cross-reactive antigenic sites. J Virol (2006) 2.33
Native Great Lakes wolves were not restored. Biol Lett (2008) 2.31
Pathogenesis of avian influenza (H7) virus infection in mice and ferrets: enhanced virulence of Eurasian H7N7 viruses isolated from humans. J Virol (2007) 2.30
A novel lineage of proteobacteria involved in formation of marine Fe-oxidizing microbial mat communities. PLoS One (2007) 2.28
Determination of molecular phylogenetics of Vibrio parahaemolyticus strains by multilocus sequence typing. J Bacteriol (2008) 2.28
Establishment of influenza A virus (H6N1) in minor poultry species in southern China. J Virol (2007) 2.26
Exploring systemic RNA interference in insects: a genome-wide survey for RNAi genes in Tribolium. Genome Biol (2008) 2.25
Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and Arabidopsis. Plant Physiol (2006) 2.25
Distinguishing molecular features and clinical characteristics of a putative new rhinovirus species, human rhinovirus C (HRV C). PLoS One (2008) 2.23
Natural selection drives recurrent formation of activating killer cell immunoglobulin-like receptor and Ly49 from inhibitory homologues. J Exp Med (2005) 2.23
Metagenomic characterization of Chesapeake Bay virioplankton. Appl Environ Microbiol (2007) 2.22
Genetic variation in the zebrafish. Genome Res (2006) 2.22
Multi-gene phylogenies and phenotypic characters distinguish two species within the Colletogloeopsis zuluensis complex associated with Eucalyptus stem cankers. Stud Mycol (2006) 2.21
An R2R3 MYB transcription factor associated with regulation of the anthocyanin biosynthetic pathway in Rosaceae. BMC Plant Biol (2010) 2.19
Use of phylogenetic and phenotypic analyses to identify nonhemolytic streptococci isolated from bacteremic patients. J Clin Microbiol (2005) 2.18
Globalization and the population structure of Toxoplasma gondii. Proc Natl Acad Sci U S A (2006) 2.17
Antagonistic HLH/bHLH transcription factors mediate brassinosteroid regulation of cell elongation and plant development in rice and Arabidopsis. Plant Cell (2009) 2.17
Phylogeny and ecology of the ubiquitous saprobe Cladosporium sphaerospermum, with descriptions of seven new species from hypersaline environments. Stud Mycol (2007) 2.16
Genetic characterization of the influenza A pandemic (H1N1) 2009 virus isolates from India. PLoS One (2010) 2.15
Coreceptor tropism in human immunodeficiency virus type 1 subtype D: high prevalence of CXCR4 tropism and heterogeneous composition of viral populations. J Virol (2007) 2.14
CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens. Nucleic Acids Res (2008) 2.14
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
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
MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis. Bioinformatics (2012) 13.09
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
False-positive selection identified by ML-based methods: examples from the Sig1 gene of the diatom Thalassiosira weissflogii and the tax gene of a human T-cell lymphotropic virus. Mol Biol Evol (2004) 1.64
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
Replication origin of mitochondrial DNA in insects. Genetics (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
Statistics and truth in phylogenomics. Mol Biol Evol (2011) 1.12
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
A novel chimeric gene, siren, with retroposed promoter sequence in the Drosophila bipectinata complex. Genetics (2005) 0.96
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
MEGA-MD: molecular evolutionary genetics analysis software with mutational diagnosis of amino acid variation. Bioinformatics (2014) 0.87
Experimental study on the hemostatc activity of Pollen Typhae: a traditional folk medicine used by external and oral application. Blood Coagul Fibrinolysis (2011) 0.86
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
Phylogenetic placement of metagenomic reads using the minimum evolution principle. BMC Genomics (2015) 0.83
Phylogenetic relationships between Sophophora and Lordiphosa, with proposition of a hypothesis on the vicariant divergences of tropical lineages between the Old and New Worlds in the family Drosophilidae. Mol Phylogenet Evol (2011) 0.83
Phylogeny of the Drosophila immigrans species group (Diptera: Drosophilidae) based on Adh and Gpdh sequences. Zoolog Sci (2007) 0.81
Genomic organization and evolution of immunoglobulin kappa gene enhancers and kappa deleting element in mammals. Mol Immunol (2009) 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
Eighty percent of proteins are different between humans and chimpanzees. Gene (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
Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Unusual evolution of interspersed repeat sequences in the Drosophila ananassae subgroup. Mol Biol Evol (2006) 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
Extensive differences in antifungal immune response in two Drosophila species revealed by comparative transcriptome analysis. Int J Genomics (2013) 0.76
Cold tolerance and metabolic rate increased by cold acclimation in Drosophila albomicans from natural populations. Genes Genet Syst (2013) 0.76
Random fluctuation of selection coefficients and the extent of nucleotide variation in human populations. Proc Natl Acad Sci U S A (2013) 0.75