Published in Mol Biol Evol on May 07, 2007
Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics (2012) 26.90
MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform (2008) 24.69
The human oral microbiome. J Bacteriol (2010) 9.00
Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nat Methods (2010) 8.86
The genome of the mesopolyploid crop species Brassica rapa. Nat Genet (2011) 8.23
The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res (2009) 7.87
Whole-genome molecular haplotyping of single cells. Nat Biotechnol (2010) 6.77
A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS One (2007) 5.62
ALTER: program-oriented conversion of DNA and protein alignments. Nucleic Acids Res (2010) 5.32
Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet (2010) 5.20
Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res (2008) 5.00
Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved. Nat Genet (2010) 4.94
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol (2011) 4.84
High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol (2008) 4.74
Mechanisms of GII.4 norovirus persistence in human populations. PLoS Med (2008) 4.57
Quantitating the multiplicity of infection with human immunodeficiency virus type 1 subtype C reveals a non-poisson distribution of transmitted variants. J Virol (2009) 4.40
VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. Nucleic Acids Res (2011) 4.36
Examining the global distribution of dominant archaeal populations in soil. ISME J (2010) 4.24
The population structure of Acinetobacter baumannii: expanding multiresistant clones from an ancestral susceptible genetic pool. PLoS One (2010) 4.19
Evaluation of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry in comparison to 16S rRNA gene sequencing for species identification of nonfermenting bacteria. J Clin Microbiol (2008) 4.18
Probable person to person transmission of novel avian influenza A (H7N9) virus in Eastern China, 2013: epidemiological investigation. BMJ (2013) 4.17
Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies. PLoS One (2009) 4.13
Sequencing and analyses of all known human rhinovirus genomes reveal structure and evolution. Science (2009) 3.94
Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs. Proc Natl Acad Sci U S A (2010) 3.92
An emerging recombinant human enterovirus 71 responsible for the 2008 outbreak of hand foot and mouth disease in Fuyang city of China. Virol J (2010) 3.90
The population genetics of dN/dS. PLoS Genet (2008) 3.88
Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling. Cell (2009) 3.69
Selection of internal control genes for quantitative real-time RT-PCR studies during tomato development process. BMC Plant Biol (2008) 3.57
Substantial alterations of the cutaneous bacterial biota in psoriatic lesions. PLoS One (2008) 3.56
Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET. Nature (2010) 3.55
Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes. Nat Genet (2011) 3.44
Evolutionary toggling of the MAPT 17q21.31 inversion region. Nat Genet (2008) 3.42
HIV rebounds from latently infected cells, rather than from continuing low-level replication. Proc Natl Acad Sci U S A (2008) 3.40
Propionibacterium acnes strain populations in the human skin microbiome associated with acne. J Invest Dermatol (2013) 3.32
Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus. BMC Microbiol (2007) 3.25
The XC chemokine receptor 1 is a conserved selective marker of mammalian cells homologous to mouse CD8alpha+ dendritic cells. J Exp Med (2010) 3.20
The draft genome of a diploid cotton Gossypium raimondii. Nat Genet (2012) 3.18
Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli. Proc Natl Acad Sci U S A (2009) 3.17
Recent human-to-poultry host jump, adaptation, and pandemic spread of Staphylococcus aureus. Proc Natl Acad Sci U S A (2009) 3.10
Viral entry and escape from antibody-mediated neutralization influence hepatitis C virus reinfection in liver transplantation. J Exp Med (2010) 3.09
Novel surveillance network for norovirus gastroenteritis outbreaks, United States. Emerg Infect Dis (2011) 3.06
Constraint and turnover in sex-biased gene expression in the genus Drosophila. Nature (2007) 3.04
qnrD, a novel gene conferring transferable quinolone resistance in Salmonella enterica serovar Kentucky and Bovismorbificans strains of human origin. Antimicrob Agents Chemother (2008) 3.00
Detection and prevalence patterns of group I coronaviruses in bats, northern Germany. Emerg Infect Dis (2008) 3.00
Endogenous non-retroviral RNA virus elements in mammalian genomes. Nature (2010) 2.91
Rapid evolution of pandemic noroviruses of the GII.4 lineage. PLoS Pathog (2010) 2.80
Plasmodium falciparum erythrocyte membrane protein 1 diversity in seven genomes--divide and conquer. PLoS Comput Biol (2010) 2.80
Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nat Commun (2010) 2.77
Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nat Genet (2013) 2.76
Glypicans. Genome Biol (2008) 2.76
Single cell genome amplification accelerates identification of the apratoxin biosynthetic pathway from a complex microbial assemblage. PLoS One (2011) 2.73
Limited neutralizing antibody specificities drive neutralization escape in early HIV-1 subtype C infection. PLoS Pathog (2009) 2.70
Recovery of divergent avian bornaviruses from cases of proventricular dilatation disease: identification of a candidate etiologic agent. Virol J (2008) 2.69
POPTREE2: Software for constructing population trees from allele frequency data and computing other population statistics with Windows interface. Mol Biol Evol (2009) 2.68
Plasmodium knowlesi in humans, macaques and mosquitoes in peninsular Malaysia. Parasit Vectors (2008) 2.62
Null mutations in human and mouse orthologs frequently result in different phenotypes. Proc Natl Acad Sci U S A (2008) 2.60
Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species. Genome Biol (2010) 2.60
On the diversity of malaria parasites in African apes and the origin of Plasmodium falciparum from Bonobos. PLoS Pathog (2010) 2.60
Abraham's children in the genome era: major Jewish diaspora populations comprise distinct genetic clusters with shared Middle Eastern Ancestry. Am J Hum Genet (2010) 2.54
Distant relatives of severe acute respiratory syndrome coronavirus and close relatives of human coronavirus 229E in bats, Ghana. Emerg Infect Dis (2009) 2.52
Role of conjugative elements in the evolution of the multidrug-resistant pandemic clone Streptococcus pneumoniaeSpain23F ST81. J Bacteriol (2008) 2.51
blaCMY-2-positive IncA/C plasmids from Escherichia coli and Salmonella enterica are a distinct component of a larger lineage of plasmids. Antimicrob Agents Chemother (2009) 2.51
Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118. Proc Natl Acad Sci U S A (2009) 2.51
Phylogenetic and genomic diversity of human bacteremic Escherichia coli strains. BMC Genomics (2008) 2.51
Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species. Genome Res (2010) 2.50
Bursts of retrotransposition reproduced in Arabidopsis. Nature (2009) 2.50
Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis. Mol Syst Biol (2008) 2.49
Assigning strains to bacterial species via the internet. BMC Biol (2009) 2.49
Novel astroviruses in insectivorous bats. J Virol (2008) 2.48
Uncultivated bacteria as etiologic agents of intra-amniotic inflammation leading to preterm birth. J Clin Microbiol (2008) 2.45
Acquisition of human-type receptor binding specificity by new H5N1 influenza virus sublineages during their emergence in birds in Egypt. PLoS Pathog (2011) 2.45
A comprehensive mapping of HIV-1 genotypes in various risk groups and regions across China based on a nationwide molecular epidemiologic survey. PLoS One (2012) 2.44
Identifying the fundamental units of bacterial diversity: a paradigm shift to incorporate ecology into bacterial systematics. Proc Natl Acad Sci U S A (2008) 2.44
The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nat Commun (2014) 2.43
Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics. Proc Natl Acad Sci U S A (2010) 2.43
Continued evolution of highly pathogenic avian influenza A (H5N1): updated nomenclature. Influenza Other Respir Viruses (2011) 2.41
Evolution of Streptococcus pneumoniae and its close commensal relatives. PLoS One (2008) 2.41
Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome. World J Gastroenterol (2010) 2.41
Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biol (2009) 2.40
Resistant starches types 2 and 4 have differential effects on the composition of the fecal microbiota in human subjects. PLoS One (2010) 2.39
Development and validation of a real-time PCR for detection of pathogenic leptospira species in clinical materials. PLoS One (2009) 2.36
Circulation of 3 lineages of a novel Saffold cardiovirus in humans. Emerg Infect Dis (2008) 2.35
Control of flowering and storage organ formation in potato by FLOWERING LOCUS T. Nature (2011) 2.32
Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos. PLoS One (2011) 2.32
Novel staphylococcal cassette chromosome mec type, tentatively designated type VIII, harboring class A mec and type 4 ccr gene complexes in a Canadian epidemic strain of methicillin-resistant Staphylococcus aureus. Antimicrob Agents Chemother (2008) 2.30
HIV-1 persistence in CD4+ T cells with stem cell-like properties. Nat Med (2014) 2.30
Tembusu virus in ducks, china. Emerg Infect Dis (2011) 2.30
A single regulatory gene is sufficient to alter bacterial host range. Nature (2009) 2.29
Genetic characterization of toggenburg orbivirus, a new bluetongue virus, from goats, Switzerland. Emerg Infect Dis (2008) 2.28
Evidence of molecular evolution driven by recombination events influencing tropism in a novel human adenovirus that causes epidemic keratoconjunctivitis. PLoS One (2009) 2.27
Viremia, resuppression, and time to resistance in human immunodeficiency virus (HIV) subtype C during first-line antiretroviral therapy in South Africa. Clin Infect Dis (2009) 2.25
Incidence of Acinetobacter species other than A. baumannii among clinical isolates of Acinetobacter: evidence for emerging species. J Clin Microbiol (2010) 2.24
Proportions of Mycobacterium massiliense and Mycobacterium bolletii strains among Korean Mycobacterium chelonae-Mycobacterium abscessus group isolates. J Clin Microbiol (2008) 2.24
Cardioviruses are genetically diverse and cause common enteric infections in South Asian children. J Virol (2009) 2.23
African swine fever virus isolate, Georgia, 2007. Emerg Infect Dis (2008) 2.22
Rift Valley fever during rainy seasons, Madagascar, 2008 and 2009. Emerg Infect Dis (2010) 2.22
DNA methylation profiling identifies epigenetic dysregulation in pancreatic islets from type 2 diabetic patients. EMBO J (2012) 2.21
Evidence for a new avian paramyxovirus serotype 10 detected in rockhopper penguins from the Falkland Islands. J Virol (2010) 2.21
MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol (2011) 220.97
MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol (2013) 112.81
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
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
Precision of molecular time estimates. Trends Genet (2004) 15.94
Estimating divergence times in large molecular phylogenies. Proc Natl Acad Sci U S A (2012) 13.49
Bioinformatics software for biologists in the genomics era. Bioinformatics (2007) 10.70
TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics (2006) 10.24
Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference. Mol Biol Evol (2003) 7.78
Fast and slow implementations of relaxed-clock methods show similar patterns of accuracy in estimating divergence times. Mol Biol Evol (2011) 6.93
Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol Biol Evol (2003) 5.30
Performance of relaxed-clock methods in estimating evolutionary divergence times and their credibility intervals. Mol Biol Evol (2010) 5.13
Estimation of divergence times for major lineages of primate species. Mol Biol Evol (2003) 3.52
Evolutionary diagnosis method for variants in personal exomes. Nat Methods (2012) 3.32
Constraint and turnover in sex-biased gene expression in the genus Drosophila. Nature (2007) 3.04
Genomic clocks and evolutionary timescales. Trends Genet (2003) 2.83
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
Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome. Genetics (2004) 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
Evolutionary distance estimation under heterogeneous substitution pattern among lineages. Mol Biol Evol (2002) 2.23
Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree. J Exp Zool B Mol Dev Evol (2005) 2.22
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
Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes. Genome Res (2003) 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
Evolutionary anatomies of positions and types of disease-associated and neutral amino acid mutations in the human genome. BMC Genomics (2006) 1.87
Bone and Joint day - India. Indian J Orthop (2013) 1.84
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
Nullomers: really a matter of natural selection? PLoS One (2007) 1.67
Clinical and laboratory features and response to treatment in patients presenting with vitamin B12 deficiency-related neurological syndromes. Neurol India (2005) 1.66
Identifying spatially similar gene expression patterns in early stage fruit fly embryo images: binary feature versus invariant moment digital representations. BMC Bioinformatics (2004) 1.64
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
FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease. Genome Biol (2008) 1.58
Genomics. Vertebrate genomes compared. Science (2002) 1.57
Evolution of modern birds revealed by mitogenomics: timing the radiation and origin of major orders. Mol Biol Evol (2011) 1.55
Comparative evolutionary analysis of olfactory receptor gene clusters between humans and mice. Gene (2005) 1.55
Zinc oxide nanoparticles selectively induce apoptosis in human cancer cells through reactive oxygen species. Int J Nanomedicine (2012) 1.54
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
Automated annotation of Drosophila gene expression patterns using a controlled vocabulary. Bioinformatics (2008) 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
Performance of computational tools in evaluating the functional impact of laboratory-induced amino acid mutations. Bioinformatics (2012) 1.46
Decompressive surgery for severe cerebral venous sinus thrombosis. Neurol India (2010) 1.46
Drosophila Gene Expression Pattern Annotation Using Sparse Features and Term-Term Interactions. KDD (2009) 1.45
Taxon sampling, bioinformatics, and phylogenomics. Syst Biol (2003) 1.44
Improved lignocellulose conversion to biofuels with thermophilic bacteria and thermostable enzymes. Bioresour Technol (2012) 1.40
Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials. PLoS Biol (2010) 1.40
Evolutionary change of the numbers of homeobox genes in bilateral animals. Mol Biol Evol (2005) 1.37
Bilateral anterior shoulder dislocation: a case report. Eur J Emerg Med (2005) 1.35
A bag-of-words approach for Drosophila gene expression pattern annotation. BMC Bioinformatics (2009) 1.34
Classification of Drosophila embryonic developmental stage range based on gene expression pattern images. Comput Syst Bioinformatics Conf (2006) 1.33
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
Comparison of embryonic expression within multigene families using the FlyExpress discovery platform reveals more spatial than temporal divergence. Dev Dyn (2011) 1.27
Genomic sequence of a ranavirus (family Iridoviridae) associated with salamander mortalities in North America. Virology (2003) 1.27
Antiquity and evolution of the MADS-box gene family controlling flower development in plants. Mol Biol Evol (2003) 1.24
Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis. BMC Res Notes (2012) 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
Local or general anesthesia for open hernia repair: a randomized trial. Ann Surg (2003) 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
The origin of Metazoa: a transition from temporal to spatial cell differentiation. Bioessays (2009) 1.16
Patterns of transitional mutation biases within and among mammalian genomes. Mol Biol Evol (2003) 1.13
Maximum likelihood outperforms maximum parsimony even when evolutionary rates are heterotachous. Mol Biol Evol (2005) 1.12
Higher intensity of purifying selection on >90% of the human genes revealed by the intrinsic replacement mutation rates. Mol Biol Evol (2006) 1.12
Birth-and-death evolution in primate MHC class I genes: divergence time estimates. Mol Biol Evol (2003) 1.11
Signatures of ecological resource availability in the animal and plant proteomes. Mol Biol Evol (2006) 1.10
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
Outcome of laparoscopic cholecystectomy in patients 80 years and older. World J Surg (2004) 1.09
Branding: a harmful practice. Indian Pediatr (2005) 1.07
More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure. Philos Trans R Soc Lond B Biol Sci (2010) 1.05
Nanotoxicity of pure silica mediated through oxidant generation rather than glutathione depletion in human lung epithelial cells. Toxicology (2010) 1.05
Evolutionary redefinition of immunoglobulin light chain isotypes in tetrapods using molecular markers. Proc Natl Acad Sci U S A (2008) 1.05
Contamination levels and spatial distribution of organochlorine pesticides in soils from India. Ecotoxicol Environ Saf (2011) 1.04
The spectrum of human rhodopsin disease mutations through the lens of interspecific variation. Gene (2004) 1.04
Origins and evolution of the formin multigene family that is involved in the formation of actin filaments. Mol Biol Evol (2008) 1.03
Human genomic disease variants: a neutral evolutionary explanation. Genome Res (2012) 1.02
Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster. Bioinformatics (2009) 1.02
Isolated dorsal dislocation of the intermediate cunieform: a case report and review of the literature. Arch Orthop Trauma Surg (2003) 1.02
Developmental Stage Annotation of Drosophila Gene Expression Pattern Images via an Entire Solution Path for LDA. ACM Trans Knowl Discov Data (2008) 1.02
Magnetic resonance evaluation of tubercular lesion in spine. Int Orthop (2011) 1.01
The role of simultaneous gap arthroplasty and distraction osteogenesis in the management of temporo-mandibular joint ankylosis with mandibular deformity in children. J Craniomaxillofac Surg (2004) 1.01