Published in J Mol Evol on January 01, 1982
Human mitochondrial DNA variation and evolution: analysis of nucleotide sequences from seven individuals. Genetics (1983) 9.22
Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proc Natl Acad Sci U S A (2004) 7.42
Variation in the mutation rate across mammalian genomes. Nat Rev Genet (2011) 3.09
Boundaries of somatic mutation in rearranged immunoglobulin genes: 5' boundary is near the promoter, and 3' boundary is approximately 1 kb from V(D)J gene. J Exp Med (1990) 2.98
Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucleic Acids Res (2003) 2.85
A genome-wide view of Caenorhabditis elegans base-substitution mutation processes. Proc Natl Acad Sci U S A (2009) 2.69
Transcription-induced mutations: increase in C to T mutations in the nontranscribed strand during transcription in Escherichia coli. Proc Natl Acad Sci U S A (1996) 2.65
Neighboring-nucleotide effects on single nucleotide polymorphisms: a study of 2.6 million polymorphisms across the human genome. Genome Res (2002) 2.49
Genetic polymorphism and natural selection in the malaria parasite Plasmodium falciparum. Genetics (1998) 2.36
An isochore map of human chromosomes. Genome Res (2006) 2.36
SIMAP: the similarity matrix of proteins. Nucleic Acids Res (2006) 2.26
Nature and structure of human genes that generate retropseudogenes. Genome Res (2000) 2.21
Two distinct mechanisms cause heterogeneity of 16S rRNA. J Bacteriol (1999) 1.94
Patterns of nucleotide substitution in Drosophila and mammalian genomes. Proc Natl Acad Sci U S A (1999) 1.89
Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome. Nucleic Acids Res (2001) 1.85
Haplotype test reveals departure from neutrality in a segment of the white gene of Drosophila melanogaster. Genetics (1995) 1.85
Mutation patterns in cancer genomes. Proc Natl Acad Sci U S A (2009) 1.69
The visna virus genome: evidence for a hypervariable site in the env gene and sequence homology among lentivirus envelope proteins. J Virol (1987) 1.63
Molecular evolution and nucleotide sequences of the maize plastid genes for the alpha subunit of CF1 (atpA) and the proteolipid subunit of CF0 (atpH). Genetics (1987) 1.59
Molecular evolution of angiosperm mitochondrial introns and exons. Proc Natl Acad Sci U S A (1997) 1.56
Dependence of mutational asymmetry on gene-expression levels in the human genome. Am J Hum Genet (2003) 1.50
The neoselectionist theory of genome evolution. Proc Natl Acad Sci U S A (2007) 1.46
Neighboring base composition and transversion/transition bias in a comparison of rice and maize chloroplast noncoding regions. Proc Natl Acad Sci U S A (1995) 1.44
Comparative sequencing of human and chimpanzee MHC class I regions unveils insertions/deletions as the major path to genomic divergence. Proc Natl Acad Sci U S A (2003) 1.43
Similar compositional biases are caused by very different mutational effects. Genome Res (2006) 1.41
Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes. Nucleic Acids Res (2002) 1.40
Transition-transversion bias is not universal: a counter example from grasshopper pseudogenes. PLoS Genet (2007) 1.38
Transcription-coupled and splicing-coupled strand asymmetries in eukaryotic genomes. Nucleic Acids Res (2004) 1.38
Molecular evolution of the major capsid protein VP1 of enterovirus 70. J Virol (1994) 1.29
Human members of the eukaryotic protein kinase family. Genome Biol (2002) 1.25
Mutational hot spots in Ig V region genes of human follicular lymphomas. J Exp Med (1988) 1.25
Genomic evidence for elevated mutation rates in highly expressed genes. EMBO Rep (2012) 1.19
The coevolution of genes and genetic codes: Crick's frozen accident revisited. J Mol Evol (2006) 1.02
Differing patterns of selection in alternative and constitutive splice sites. Genome Res (2007) 1.02
Accelerated evolution as a consequence of transitions to mutualism. Proc Natl Acad Sci U S A (1997) 1.01
Contribution of mutation and RNA recombination to the evolution of a plant pathogenic RNA. J Mol Evol (1997) 0.99
Directionality of point mutation and 5-methylcytosine deamination rates in the chimpanzee genome. BMC Genomics (2006) 0.97
A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites. Nucleic Acids Res (2006) 0.97
Isolation and characterization of two alleles of the chicken cytochrome c gene. Nucleic Acids Res (1983) 0.97
Single-nucleotide polymorphism markers from de-novo assembly of the pomegranate transcriptome reveal germplasm genetic diversity. PLoS One (2014) 0.94
Differential selection and mutation between dsDNA and ssDNA phages shape the evolution of their genomic AT percentage. BMC Genet (2005) 0.93
Genomic changes in nucleotide and dinucleotide frequencies in Pasteurella multocida cultured under high temperature. Genetics (2002) 0.93
High correlation between the turnover of nucleotides under mutational pressure and the DNA composition. BMC Evol Biol (2001) 0.92
Powerful mutators lurking in the genome. Philos Trans R Soc Lond B Biol Sci (2009) 0.92
Processed pseudogenes, processed genes, and spontaneous mutations in the Arabidopsis genome. J Mol Evol (2006) 0.91
Inferring the pattern of spontaneous mutation from the pattern of substitution in unitary pseudogenes of Mycobacterium leprae and a comparison of mutation patterns among distantly related organisms. J Mol Evol (2005) 0.91
Estimation of DNA sequence context-dependent mutation rates using primate genomic sequences. J Mol Evol (2007) 0.90
Origin and evolution of processed pseudogenes that stabilize functional Makorin1 mRNAs in mice, primates and other mammals. Genetics (2006) 0.90
The rDNA ITS region in the lessepsian marine angiosperm Halophila stipulacea (Forssk.) Aschers. (Hydrocharitaceae): intragenomic variability and putative pseudogenic sequences. J Mol Evol (2004) 0.88
A strong deletion bias in nonallelic gene conversion. PLoS Genet (2012) 0.88
Extensive sequence variation in rice blast resistance gene Pi54 makes it broad spectrum in nature. Front Plant Sci (2015) 0.86
Nucleotide diversity and molecular evolution of the WAG-2 gene in common wheat (Triticum aestivum L) and its relatives. Genet Mol Biol (2011) 0.84
High-throughput marker discovery in melon using a self-designed oligo microarray. BMC Genomics (2010) 0.84
Comparison of methods for estimating the nucleotide substitution matrix. BMC Bioinformatics (2008) 0.83
Large-scale inference of the point mutational spectrum in human segmental duplications. BMC Genomics (2009) 0.83
Advantages of a mechanistic codon substitution model for evolutionary analysis of protein-coding sequences. PLoS One (2011) 0.82
Molecular nature of spontaneous mutations in mouse lactate dehydrogenase-A processed pseudogenes. Genetics (1987) 0.82
Molecular evolution of V(H)9 germline genes isolated from DBA, BALB, 129 and C57BL mouse strains and sublines. Immunogenetics (2003) 0.81
To the beat of a different drum: determinants implicated in the asymmetric sequence divergence of Caenorhabditis elegans paralogs. BMC Evol Biol (2013) 0.81
Patterns of nucleotides that flank substitutions in human orthologous genes. BMC Genomics (2010) 0.80
Mispair formation in DNA can involve rare tautomeric forms in the template. Nucleic Acids Res (1988) 0.79
Simulating pseudogene evolution in vitro: determining the true number of mutations in a lineage. Proc Natl Acad Sci U S A (2001) 0.79
Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide Substitution. Genetics (2015) 0.78
Personalized pathway enrichment map of putative cancer genes from next generation sequencing data. PLoS One (2012) 0.77
Assessing constancy of substitution rates in viruses over evolutionary time. BMC Bioinformatics (2010) 0.77
Isolation, identification and computational studies on Pseudomonas aeruginosa sp. strain MPC1 in tannery effluent. Bioinformation (2011) 0.76
Multiplicity of alleles of nuclear 18S rRNA gene of Amur sturgeons: genes and pseudogenes? Dokl Biochem Biophys (2008) 0.76
Are Synonymous Sites in Primates and Rodents Functionally Constrained? J Mol Evol (2015) 0.75
A novel statistical method to estimate the effective SNP size in vertebrate genomes and categorized genomic regions. BMC Genomics (2006) 0.75
Are sites with multiple single nucleotide variants in cancer genomes a consequence of drivers, hypermutable sites or sequencing errors? PeerJ (2016) 0.75
Transition and Transversion Mutations Are Biased towards GC in Transposons of Chilo suppressalis (Lepidoptera: Pyralidae). Genes (Basel) (2016) 0.75
Molecular archeology of an SP100 splice variant revisited: dating the retrotranscription and Alu insertion events. Genome Biol (2001) 0.75
Genome digging: insight into the mitochondrial genome of Homo. PLoS One (2010) 0.75
RNA-Seq of Guar (Cyamopsis tetragonoloba, L. Taub.) Leaves: De novo Transcriptome Assembly, Functional Annotation and Development of Genomic Resources. Front Plant Sci (2017) 0.75
Extreme mutation bias and high AT content in Plasmodium falciparum. Nucleic Acids Res (2017) 0.75
Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A (1979) 41.08
The transcriptional landscape of the mammalian genome. Science (2005) 37.63
Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol (1986) 36.06
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature (2002) 28.79
The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res (1987) 26.51
Statistical tests of neutrality of mutations. Genetics (1993) 24.94
Functional annotation of a full-length mouse cDNA collection. Nature (2001) 23.61
DNA data bank of Japan (DDBJ) in collaboration with mass sequencing teams. Nucleic Acids Res (2000) 15.69
Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci U S A (1987) 10.66
DNA Data Bank of Japan dealing with large-scale data submission. Nucleic Acids Res (1999) 10.26
Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol (1993) 9.43
Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. Am J Hum Genet (2001) 9.35
Evidence for higher rates of nucleotide substitution in rodents than in man. Proc Natl Acad Sci U S A (1985) 8.18
Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Res (2000) 7.88
Mutation rates differ among regions of the mammalian genome. Nature (1989) 7.63
Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc Natl Acad Sci U S A (1989) 6.99
DDBJ in the stream of various biological data. Nucleic Acids Res (2004) 6.24
Large-scale search for genes on which positive selection may operate. Mol Biol Evol (1996) 6.14
Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons. Nucleic Acids Res (1986) 5.68
DDBJ with new system and face. Nucleic Acids Res (2007) 5.33
Linkage disequilibrium in subdivided populations. Genetics (1973) 5.22
Distribution of nucleotide differences between two randomly chosen cistrons in a finite population. Genetics (1977) 5.22
An evolutionary perspective on synonymous codon usage in unicellular organisms. J Mol Evol (1986) 5.05
Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol Biol Evol (1995) 4.88
Codon usage tabulated from the GenBank genetic sequence data. Nucleic Acids Res (1986) 4.83
Drift variances of heterozygosity and genetic distance in transient states. Genet Res (1975) 4.45
DNA Data Bank of Japan at work on genome sequence data. Nucleic Acids Res (1998) 4.43
Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications. J Mol Evol (1984) 4.42
Rates of nucleotide substitution in angiosperm mitochondrial DNA sequences and dates of divergence between Brassica and other angiosperm lineages. J Mol Evol (1999) 4.37
Pseudogenes as a paradigm of neutral evolution. Nature (1981) 4.33
Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. I. Four taxa with a molecular clock. Mol Biol Evol (1992) 4.31
The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias. Mol Biol Evol (1987) 4.30
Complete nucleotide sequence of an infectious clone of human T-cell leukemia virus type II: an open reading frame for the protease gene. Proc Natl Acad Sci U S A (1985) 4.28
Codon usage tabulated from the GenBank Genetic Sequence Data. Nucleic Acids Res (1988) 4.26
Is the guinea-pig a rodent? Nature (1991) 4.25
Transposable elements are found in a large number of human protein-coding genes. Trends Genet (2001) 3.89
DNA Data Bank of Japan (DDBJ) in XML. Nucleic Acids Res (2003) 3.87
Classification, nomenclature, and database development for hepatitis C virus (HCV) and related viruses: proposals for standardization. International Committee on Virus Taxonomy. Arch Virol (1998) 3.77
Human hepatic lipase. Cloned cDNA sequence, restriction fragment length polymorphisms, chromosomal localization, and evolutionary relationships with lipoprotein lipase and pancreatic lipase. J Biol Chem (1988) 3.74
On the rate of DNA sequence evolution in Drosophila. J Mol Evol (1989) 3.74
Non-random association between electromorphs and inversion chromosomes in finite populations. Genet Res (1980) 3.69
DNA Data Bank of Japan (DDBJ) for genome scale research in life science. Nucleic Acids Res (2002) 3.64
A method for detecting positive selection at single amino acid sites. Mol Biol Evol (1999) 3.58
Codon usage tabulated from the GenBank genetic sequence data. Nucleic Acids Res (1990) 3.54
Estimation of average number of nucleotide substitutions when the rate of substitution varies with nucleotide. J Mol Evol (1982) 3.45
The molecular clock runs more slowly in man than in apes and monkeys. Nature (1987) 3.42
DDBJ in collaboration with mass-sequencing teams on annotation. Nucleic Acids Res (2005) 3.14
ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J Mol Biol (2001) 3.14
Simple method for constructing phylogenetic trees from distance matrices. Proc Natl Acad Sci U S A (1981) 3.09
Evolutionary motif and its biological and structural significance. J Mol Evol (1997) 3.03
Codon usage tabulated from the GenBank genetic sequence data. Nucleic Acids Res (1991) 3.01
Codon usage tabulated from the GenBank genetic sequence data. Nucleic Acids Res (1992) 2.95
Probability of identical monomorphism in related species. Genet Res (1975) 2.91
Male-driven evolution of DNA sequences. Nature (1993) 2.86
The size distribution of insertions and deletions in human and rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment. J Mol Evol (1995) 2.77
Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes. Mol Biol Evol (1999) 2.68
Worldwide DNA sequence variation in a 10-kilobase noncoding region on human chromosome 22. Proc Natl Acad Sci U S A (2000) 2.67
Estimating the age of the common ancestor of a sample of DNA sequences. Mol Biol Evol (1997) 2.64
Global patterns of human DNA sequence variation in a 10-kb region on chromosome 1. Mol Biol Evol (2001) 2.64
A fast algorithm for joint reconstruction of ancestral amino acid sequences. Mol Biol Evol (2000) 2.59
Molecular cloning and expression of a member of the aquaporin family with permeability to glycerol and urea in addition to water expressed at the basolateral membrane of kidney collecting duct cells. Proc Natl Acad Sci U S A (1994) 2.54
Sequence of a novel simian immunodeficiency virus from a wild-caught African mandrill. Nature (1989) 2.45
Coalescing into the 21st century: An overview and prospects of coalescent theory. Theor Popul Biol (1999) 2.38
Evolutionary mechanisms and population dynamics of the third variable envelope region of HIV within single hosts. Proc Natl Acad Sci U S A (1997) 2.35
Patterns and rates of indel evolution in processed pseudogenes from humans and murids. Gene (1997) 2.33
Accumulation of mutations in sexual and asexual populations. Genet Res (1987) 2.30
Genome plasticity as a paradigm of eubacteria evolution. J Mol Evol (1997) 2.29
Models of nearly neutral mutations with particular implications for nonrandom usage of synonymous codons. J Mol Evol (1987) 2.27
Monophyletic origin and unique dispersal patterns of domestic fowls. Proc Natl Acad Sci U S A (1996) 2.27
Rates of evolution of the retroviral oncogene of Moloney murine sarcoma virus and of its cellular homologues. Proc Natl Acad Sci U S A (1985) 2.25
Mitochondrial DNA polymorphism in Japanese. I. Analysis with restriction enzymes of six base pair recognition. Hum Genet (1984) 2.17
Codon usage tabulated from the international DNA sequence databases. Nucleic Acids Res (1997) 2.10
Maximum likelihood estimation of population parameters. Genetics (1993) 2.01
Amino acid composition and the evolutionary rates of protein-coding genes. J Mol Evol (1985) 2.00
Total number of individuals affected by a single deleterious mutation in a finite population. Am J Hum Genet (1972) 1.98
High polymorphism at the human melanocortin 1 receptor locus. Genetics (1999) 1.94
Stable linkage disequilibrium without epistasis in subdivided populations. Theor Popul Biol (1974) 1.93
Mitochondrial DNA polymorphism among five Asian populations. Am J Hum Genet (1988) 1.86
Distribution of nucleotide differences between two randomly chosen cistrons in a subdivided population: the finite island model. Theor Popul Biol (1976) 1.86
Sequence, structure, receptor-binding domains and internal repeats of human apolipoprotein B-100. Nature (1986) 1.85
Molecular phylogeny of extant gymnosperms and seed plant evolution: analysis of nuclear 18S rRNA sequences. Mol Biol Evol (1997) 1.85
Molecular phylogeny of the kingdoms Animalia, Plantae, and Fungi. Mol Biol Evol (1989) 1.83
Evolutionary origin of pathogenic determinants in enterotoxigenic Escherichia coli and Vibrio cholerae O1. J Bacteriol (1987) 1.80
Host-independent evolution and a genetic classification of the hepadnavirus family based on nucleotide sequences. Proc Natl Acad Sci U S A (1989) 1.76
Deletions in processed pseudogenes accumulate faster in rodents than in humans. J Mol Evol (1989) 1.73
The transient distribution of allele frequencies under mutation pressure. Genet Res (1976) 1.70
Chromosomal location and evolutionary rate variation in enterobacterial genes. Science (1989) 1.67
The molecular clock ticks regularly in muroid rodents and hamsters. J Mol Evol (1992) 1.66
Neuroendocrine differentiation in 32 cases of so-called sclerosing hemangioma of the lung: identified by immunohistochemical and ultrastructural study. Am J Surg Pathol (1997) 1.64
Selective constraints, amino acid composition, and the rate of protein evolution. Mol Biol Evol (2000) 1.63
Molecular evolution of hemagglutinin genes of H1N1 swine and human influenza A viruses. J Mol Evol (1991) 1.63
Genomic divergence between human and chimpanzee estimated from large-scale alignments of genomic sequences. J Hered (2002) 1.63
Higher rates of amino acid substitution in rodents than in humans. Mol Phylogenet Evol (1992) 1.61
Rates of synonymous substitution and base composition of nuclear genes in Drosophila. Genetics (1992) 1.57
Statistical analysis of nucleotide sequences of the hemagglutinin gene of human influenza A viruses. Proc Natl Acad Sci U S A (1994) 1.55
Persistence of common alleles in two related populations or species. Genetics (1977) 1.54
Rapid evolution of goat and sheep globin genes following gene duplication. Mol Biol Evol (1983) 1.52
Reevaluation of amino acid variability of the human immunodeficiency virus type 1 gp120 envelope glycoprotein and prediction of new discontinuous epitopes. J Virol (2000) 1.51
A rapid heuristic algorithm for finding minimum evolution trees. Mol Phylogenet Evol (2000) 1.50