Published in Mol Biol Evol on May 23, 2007
Learning a prior on regulatory potential from eQTL data. PLoS Genet (2009) 3.31
Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes. Genome Res (2011) 1.91
Origin and evolution of spliceosomal introns. Biol Direct (2012) 1.65
Adaptive evolution of genes underlying schizophrenia. Proc Biol Sci (2007) 1.58
The IGF1 small dog haplotype is derived from Middle Eastern grey wolves. BMC Biol (2010) 1.57
Translational selection is ubiquitous in prokaryotes. PLoS Genet (2010) 1.45
Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity. Nucleic Acids Res (2013) 1.44
Constraints and plasticity in genome and molecular-phenome evolution. Nat Rev Genet (2010) 1.41
Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs. Genome Biol Evol (2011) 1.23
Incomplete sex chromosome dosage compensation in the Indian meal moth, Plodia interpunctella, based on de novo transcriptome assembly. Genome Biol Evol (2012) 1.19
Positive selection acting on splicing motifs reflects compensatory evolution. Genome Res (2008) 1.18
Spliceosomal introns as tools for genomic and evolutionary analysis. Nucleic Acids Res (2008) 1.12
Statistics and truth in phylogenomics. Mol Biol Evol (2011) 1.12
An evolutionary and structural characterization of mammalian protein complex organization. BMC Genomics (2008) 1.03
Detecting positive and purifying selection at synonymous sites in yeast and worm. Mol Biol Evol (2010) 1.00
Evolution of alternative splicing in primate brain transcriptomes. Hum Mol Genet (2010) 0.99
Purifying selection on splice-related motifs, not expression level nor RNA folding, explains nearly all constraint on human lincRNAs. Mol Biol Evol (2014) 0.93
Coupling between protein level selection and codon usage optimization in the evolution of bacteria and archaea. MBio (2014) 0.87
Duplications and functional divergence of ADP-glucose pyrophosphorylase genes in plants. BMC Evol Biol (2008) 0.86
Shifts in the selection-drift balance drive the evolution and epidemiology of foot-and-mouth disease virus. J Virol (2008) 0.86
Complex interplay of evolutionary forces in the ladybird homeobox genes of Drosophila melanogaster. PLoS One (2011) 0.82
Unraveling patterns of site-to-site synonymous rates variation and associated gene properties of protein domains and families. PLoS One (2014) 0.81
Positive Selection Underlies Faster-Z Evolution of Gene Expression in Birds. Mol Biol Evol (2015) 0.81
Genome-wide functional divergence after the symbiosis of proteobacteria with insects unraveled through a novel computational approach. PLoS Comput Biol (2009) 0.79
Cut thy neighbor: cyclic birth and death of recombination hotspots via genetic conflict. Genetics (2008) 0.79
Mutational dynamics of murine angiogenin duplicates. BMC Evol Biol (2010) 0.79
The meaning of biological information. Philos Trans A Math Phys Eng Sci (2016) 0.78
Genomic evidence for non-random endemic populations of decaying exons from mammalian genes. BMC Genomics (2009) 0.77
Impairment of translation in neurons as a putative causative factor for autism. Biol Direct (2014) 0.77
Molecular evolution of PKD2 gene family in mammals. Genetica (2009) 0.77
Interspecific and intragenic differences in codon usage bias among vertebrate myosin heavy-chain genes. J Mol Evol (2011) 0.77
Head Transcriptomes of Two Closely Related Species of Fruit Flies of the Anastrepha fraterculus Group Reveals Divergent Genes in Species with Extensive Gene Flow. G3 (Bethesda) (2016) 0.76
Recombination and selection in the major histocompatibility complex of the endangered forest musk deer (Moschus berezovskii). Sci Rep (2015) 0.76
Human rhinovirus diversity and evolution: How strange the change from Major to minor. J Virol (2017) 0.75
The human retinoblastoma susceptibility gene (RB1): an evolutionary story in primates. Mamm Genome (2017) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol (1980) 113.75
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet (2000) 69.26
A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A (2004) 44.81
The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res (1987) 26.51
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2006) 18.85
Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol (1985) 16.88
Natural selection on protein-coding genes in the human genome. Nature (2005) 10.84
Non-coding RNA. Hum Mol Genet (2006) 10.57
Statistical methods for detecting molecular adaptation. Trends Ecol Evol (2000) 10.10
Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol (1993) 9.43
The 'effective number of codons' used in a gene. Gene (1990) 9.26
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol (2005) 8.74
A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol (2005) 8.32
Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics (1994) 6.83
Highly expressed genes in yeast evolve slowly. Genetics (2001) 6.28
High genomic deleterious mutation rates in hominids. Nature (1999) 6.23
Hearing silence: non-neutral evolution at synonymous sites in mammals. Nat Rev Genet (2006) 5.97
Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Mol Biol Evol (2000) 4.70
Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nat Biotechnol (2005) 4.68
The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends Genet (2002) 4.46
Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res (2003) 3.90
Evolution of the Zfx and Zfy genes: rates and interdependence between the genes. Mol Biol Evol (1993) 3.78
Variation in sequence and organization of splicing regulatory elements in vertebrate genes. Proc Natl Acad Sci U S A (2004) 3.34
Distribution and characterization of regulatory elements in the human genome. Genome Res (2002) 3.34
Mammalian gene evolution: nucleotide sequence divergence between mouse and rat. J Mol Evol (1993) 2.97
Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals. Genome Biol (2005) 2.94
Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. Mol Biol Evol (2005) 2.85
Comparative evolutionary rates of introns and exons in murine rodents. J Mol Evol (1997) 2.75
Selection on human genes as revealed by comparisons to chimpanzee cDNA. Genome Res (2003) 2.48
Statistical test for the comparison of samples from mutational spectra. J Mol Biol (1987) 2.33
Synonymous codon bias is related to gene length in Escherichia coli: selection for translational accuracy? Mol Biol Evol (1996) 2.28
A periodic pattern of mRNA secondary structure created by the genetic code. Nucleic Acids Res (2006) 2.24
Evolutionary significance of gene expression divergence. Gene (2004) 2.04
Chromosomal location effects on gene sequence evolution in mammals. Curr Biol (1999) 2.02
Positive selection on the human genome. Hum Mol Genet (2004) 1.95
Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes. Genome Res (2003) 1.94
Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites. J Theor Biol (2005) 1.88
Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences. Proc Natl Acad Sci U S A (2005) 1.88
Frequencies of synonymous substitutions in mammals are gene-specific and correlated with frequencies of nonsynonymous substitutions. J Mol Evol (1995) 1.81
Translational selection and molecular evolution. Curr Opin Genet Dev (1998) 1.79
Synonymous and nonsynonymous substitution distances are correlated in mouse and rat genes. J Mol Evol (1998) 1.79
A test of translational selection at 'silent' sites in the human genome: base composition comparisons in alternatively spliced genes. Gene (2000) 1.75
Small fitness effect of mutations in highly conserved non-coding regions. Hum Mol Genet (2005) 1.73
Nucleotide frequency variation across human genes. Genome Res (2003) 1.68
OWEN: aligning long collinear regions of genomes. Bioinformatics (2002) 1.60
Similar rates but different modes of sequence evolution in introns and at exonic silent sites in rodents: evidence for selectively driven codon usage. Mol Biol Evol (2004) 1.55
Unifying measures of gene function and evolution. Proc Biol Sci (2006) 1.55
Mammalian mutation pressure, synonymous codon choice, and mRNA degradation. J Mol Evol (2003) 1.48
Interaction of silent and replacement changes in eukaryotic coding sequences. J Mol Evol (1985) 1.18
Genomic regionality in rates of evolution is not explained by clustering of genes of comparable expression profile. Genome Res (2004) 1.14
The SPANX gene family of cancer/testis-specific antigens: rapid evolution and amplification in African great apes and hominids. Proc Natl Acad Sci U S A (2004) 1.09
The effect of tandem substitutions on the correlation between synonymous and nonsynonymous rates in rodents. Genetics (1999) 1.03
Estimating the neutral rate of nucleotide substitution using introns. Mol Biol Evol (2006) 1.00
Rapid evolution of a cyclin A inhibitor gene, roughex, in Drosophila. Mol Biol Evol (2001) 0.81
The COG database: an updated version includes eukaryotes. BMC Bioinformatics (2003) 60.98
Small CRISPR RNAs guide antiviral defense in prokaryotes. Science (2008) 17.79
Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol (2011) 17.11
De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-kappaB signalling. Nature (2004) 12.41
A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol Direct (2006) 11.31
Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. Science (2002) 7.49
Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet (2002) 7.25
Classification and evolution of P-loop GTPases and related ATPases. J Mol Biol (2002) 6.85
The ecoresponsive genome of Daphnia pulex. Science (2011) 6.55
Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res (2002) 6.08
Regeneration of peroxiredoxins by p53-regulated sestrins, homologs of bacterial AhpD. Science (2004) 5.88
Genetic basis for individual variations in pain perception and the development of a chronic pain condition. Hum Mol Genet (2004) 5.87
Selection in the evolution of gene duplications. Genome Biol (2002) 5.58
Role of predicted metalloprotease motif of Jab1/Csn5 in cleavage of Nedd8 from Cul1. Science (2002) 4.95
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol (2004) 4.94
Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol Biol (2003) 4.70
Evolutionary history and higher order classification of AAA+ ATPases. J Struct Biol (2004) 4.68
Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. Virus Res (2006) 4.49
A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res (2002) 4.39
Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends Genet (2003) 4.39
The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res (2002) 4.28
Selection for short introns in highly expressed genes. Nat Genet (2002) 4.04
Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Res (2002) 4.00
Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol Direct (2011) 3.92
Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res (2003) 3.90
Genome trees and the tree of life. Trends Genet (2002) 3.79
The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc Natl Acad Sci U S A (2002) 3.72
Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Curr Biol (2003) 3.72
Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Proc Natl Acad Sci U S A (2003) 3.55
'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucleic Acids Res (2004) 3.50
Diversity and function of adaptive immune receptors in a jawless vertebrate. Science (2005) 3.39
Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus. Biol Direct (2006) 3.18
Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes. Biol Direct (2009) 3.17
Introns and the origin of nucleus-cytosol compartmentalization. Nature (2006) 3.16
One-component systems dominate signal transduction in prokaryotes. Trends Microbiol (2005) 3.09
No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly. BMC Evol Biol (2003) 3.07
A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats. J Biol Chem (2008) 3.00
A universal trend of amino acid gain and loss in protein evolution. Nature (2005) 2.81
Conservation and coevolution in the scale-free human gene coexpression network. Mol Biol Evol (2004) 2.78
A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol Microbiol (2010) 2.70
Search for a 'Tree of Life' in the thicket of the phylogenetic forest. J Biol (2009) 2.66
Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex. Cell Cycle (2004) 2.65
Differential arginylation of actin isoforms is regulated by coding sequence-dependent degradation. Science (2010) 2.62
Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging. Nucleic Acids Res (2004) 2.62
Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). OMICS (2006) 2.57
Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea. Biol Direct (2007) 2.53
Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms. Proc Natl Acad Sci U S A (2009) 2.52
Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation. Proc Natl Acad Sci U S A (2003) 2.52
Evolution and classification of P-loop kinases and related proteins. J Mol Biol (2003) 2.52
The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages. Proc Natl Acad Sci U S A (2009) 2.50
Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members. Nucleic Acids Res (2005) 2.49
Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis. Genome Res (2004) 2.42
New dimensions of the virus world discovered through metagenomics. Trends Microbiol (2009) 2.41
A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends Genet (2004) 2.40
Origin and evolution of human microRNAs from transposable elements. Genetics (2007) 2.39
Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems. Nucleic Acids Res (2013) 2.35
Connected gene neighborhoods in prokaryotic genomes. Nucleic Acids Res (2002) 2.35
129-derived strains of mice are deficient in DNA polymerase iota and have normal immunoglobulin hypermutation. J Exp Med (2003) 2.26
A periodic pattern of mRNA secondary structure created by the genetic code. Nucleic Acids Res (2006) 2.24
Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces. Appl Environ Microbiol (2002) 2.24
Complete pathway for protein disulfide bond formation encoded by poxviruses. Proc Natl Acad Sci U S A (2002) 2.19
A korarchaeal genome reveals insights into the evolution of the Archaea. Proc Natl Acad Sci U S A (2008) 2.16
Computational methods for Gene Orthology inference. Brief Bioinform (2011) 2.16
Origins and evolution of eukaryotic RNA interference. Trends Ecol Evol (2008) 2.15
Dimeric dUTPases, HisE, and MazG belong to a new superfamily of all-alpha NTP pyrophosphohydrolases with potential "house-cleaning" functions. J Mol Biol (2005) 2.14
Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution. Virol J (2009) 2.13
The cyanobacterial genome core and the origin of photosynthesis. Proc Natl Acad Sci U S A (2006) 2.11
Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family. J Biol Chem (2006) 2.10
STAND, a class of P-loop NTPases including animal and plant regulators of programmed cell death: multiple, complex domain architectures, unusual phyletic patterns, and evolution by horizontal gene transfer. J Mol Biol (2004) 2.10
Functional and evolutionary implications of gene orthology. Nat Rev Genet (2013) 2.07
Three distinct modes of intron dynamics in the evolution of eukaryotes. Genome Res (2007) 2.06
Evolutionary significance of gene expression divergence. Gene (2004) 2.04
Kinase activity of overexpressed HipA is required for growth arrest and multidrug tolerance in Escherichia coli. J Bacteriol (2006) 2.04
Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life. Virus Res (2006) 2.02
Classification and evolutionary history of the single-strand annealing proteins, RecT, Redbeta, ERF and RAD52. BMC Genomics (2002) 1.99
Provirophages and transpovirons as the diverse mobilome of giant viruses. Proc Natl Acad Sci U S A (2012) 1.96
The relationship of protein conservation and sequence length. BMC Evol Biol (2002) 1.95
Myosin XI-K Is required for rapid trafficking of Golgi stacks, peroxisomes, and mitochondria in leaf cells of Nicotiana benthamiana. Plant Physiol (2008) 1.95
Microevolutionary genomics of bacteria. Theor Popul Biol (2002) 1.95
Duplicated genes evolve slower than singletons despite the initial rate increase. BMC Evol Biol (2004) 1.95
SPOUT: a class of methyltransferases that includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases. J Mol Microbiol Biotechnol (2002) 1.95
Abundance of type I toxin-antitoxin systems in bacteria: searches for new candidates and discovery of novel families. Nucleic Acids Res (2010) 1.93