Published in Trends Genet on February 01, 2003
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res (2005) 44.08
Distribution and intensity of constraint in mammalian genomic sequence. Genome Res (2005) 18.85
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res (2007) 7.05
Analysis of repetitive element DNA methylation by MethyLight. Nucleic Acids Res (2005) 6.49
Transposable elements and the evolution of regulatory networks. Nat Rev Genet (2008) 6.11
Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome. Plant Cell (2003) 3.45
Retroelements and the human genome: new perspectives on an old relation. Proc Natl Acad Sci U S A (2004) 3.43
Retroviral elements and their hosts: insertional mutagenesis in the mouse germ line. PLoS Genet (2006) 3.07
The ancient Virus World and evolution of cells. Biol Direct (2006) 3.06
On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol (2013) 3.00
Strong selective sweep associated with a transposon insertion in Drosophila simulans. Proc Natl Acad Sci U S A (2004) 2.65
What fraction of the human genome is functional? Genome Res (2011) 2.46
Origin and evolution of human microRNAs from transposable elements. Genetics (2007) 2.39
A large family of ancient repeat elements in the human genome is under strong selection. Proc Natl Acad Sci U S A (2006) 2.23
Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals. Nat Genet (2011) 2.22
Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PLoS Genet (2013) 2.07
Global methylation profiles in DNA from different blood cell types. Epigenetics (2011) 1.94
Darwinian evolution in the light of genomics. Nucleic Acids Res (2009) 1.92
The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate? Biol Direct (2006) 1.88
Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome. Genome Res (2007) 1.82
Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes. BMC Genomics (2006) 1.80
Heterotachy in mammalian promoter evolution. PLoS Genet (2006) 1.71
Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes. Genome Res (2004) 1.70
Transposable elements re-wire and fine-tune the transcriptome. PLoS Genet (2013) 1.70
Cis-regulatory elements in the Accord retrotransposon result in tissue-specific expression of the Drosophila melanogaster insecticide resistance gene Cyp6g1. Genetics (2006) 1.66
The struggle for life of the genome's selfish architects. Biol Direct (2011) 1.64
DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nat Genet (2013) 1.64
The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons. Nucleic Acids Res (2006) 1.62
Integration target site selection by a resurrected human endogenous retrovirus. Genes Dev (2009) 1.62
Members of a large retroposon family are determinants of post-transcriptional gene expression in Leishmania. PLoS Pathog (2007) 1.59
Sequencing of pooled DNA samples (Pool-Seq) uncovers complex dynamics of transposable element insertions in Drosophila melanogaster. PLoS Genet (2012) 1.59
An endogenous retroviral long terminal repeat is the dominant promoter for human beta1,3-galactosyltransferase 5 in the colon. Proc Natl Acad Sci U S A (2003) 1.56
Long-term evolution of transposable elements. Proc Natl Acad Sci U S A (2007) 1.55
High rate of recent transposable element-induced adaptation in Drosophila melanogaster. PLoS Biol (2008) 1.52
All y'all need to know 'bout retroelements in cancer. Semin Cancer Biol (2010) 1.52
The evolution and functional diversification of animal microRNA genes. Cell Res (2008) 1.49
Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids. Genome Biol (2008) 1.49
Evolution of genome architecture. Int J Biochem Cell Biol (2008) 1.48
tRNA genes protect a reporter gene from epigenetic silencing in mouse cells. Cell Cycle (2011) 1.47
Repeated recruitment of LTR retrotransposons as promoters by the anti-apoptotic locus NAIP during mammalian evolution. PLoS Genet (2006) 1.46
Environmental exposures and gene regulation in disease etiology. Environ Health Perspect (2007) 1.44
Transposable elements donate lineage-specific regulatory sequences to host genomes. Cytogenet Genome Res (2005) 1.44
Global DNA hypomethylation in peripheral blood leukocytes as a biomarker for cancer risk: a meta-analysis. PLoS One (2012) 1.43
The mouse immunoglobulin heavy chain V-D intergenic sequence contains insulators that may regulate ordered V(D)J recombination. J Biol Chem (2010) 1.39
Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells. Nucleic Acids Res (2007) 1.38
Multiple effects govern endogenous retrovirus survival patterns in human gene introns. Genome Biol (2006) 1.37
Evolution of hydra, a recently evolved testis-expressed gene with nine alternative first exons in Drosophila melanogaster. PLoS Genet (2007) 1.36
Measuring the evolutionary rewiring of biological networks. PLoS Comput Biol (2011) 1.35
Prenatal smoke exposure and genomic DNA methylation in a multiethnic birth cohort. Cancer Epidemiol Biomarkers Prev (2011) 1.32
Widespread contribution of transposable elements to the innovation of gene regulatory networks. Genome Res (2014) 1.31
TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates. Nucleic Acids Res (2007) 1.30
Global methylation in exposure biology and translational medical science. Environ Health Perspect (2011) 1.28
Text-mining assisted regulatory annotation. Genome Biol (2008) 1.26
Impact of Alu repeats on the evolution of human p53 binding sites. Biol Direct (2011) 1.25
DNA transposons: nature and applications in genomics. Curr Genomics (2010) 1.25
SREBP controls oxygen-dependent mobilization of retrotransposons in fission yeast. PLoS Genet (2007) 1.21
Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses. Genome Biol (2006) 1.20
Gene expression in trypanosomatid parasites. J Biomed Biotechnol (2010) 1.18
Coding sequences of functioning human genes derived entirely from mobile element sequences. Proc Natl Acad Sci U S A (2004) 1.18
Transposon variants and their effects on gene expression in Arabidopsis. PLoS Genet (2013) 1.17
Transactivation of elements in the human endogenous retrovirus W family by viral infection. Retrovirology (2006) 1.16
How repetitive are genomes? BMC Bioinformatics (2006) 1.16
Comparative analysis of chromatin landscape in regulatory regions of human housekeeping and tissue specific genes. BMC Bioinformatics (2005) 1.13
Functional diversity of human basic helix-loop-helix transcription factor TCF4 isoforms generated by alternative 5' exon usage and splicing. PLoS One (2011) 1.12
Evolution of microbes and viruses: a paradigm shift in evolutionary biology? Front Cell Infect Microbiol (2012) 1.11
Comparative genomic analysis of prion genes. BMC Genomics (2007) 1.11
Exaptation of transposable elements into novel cis-regulatory elements: is the evidence always strong? Mol Biol Evol (2013) 1.11
Retrotranspositions in orthologous regions of closely related grass species. BMC Evol Biol (2006) 1.11
Viral ancestors of antiviral systems. Viruses (2011) 1.11
Gene function and expression level influence the insertion/fixation dynamics of distinct transposon families in mammalian introns. Genome Biol (2006) 1.07
Evaluating the protein coding potential of exonized transposable element sequences. Biol Direct (2007) 1.05
Transposable element derived DNaseI-hypersensitive sites in the human genome. Biol Direct (2006) 1.04
Organization and evolution of two SIDER retroposon subfamilies and their impact on the Leishmania genome. BMC Genomics (2009) 1.04
Tissue-specific and ubiquitous expression patterns from alternative promoters of human genes. PLoS One (2010) 1.04
Human endogenous retroviruses: transposable elements with potential? Clin Exp Immunol (2004) 1.03
Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA. BMC Genomics (2008) 1.02
Proliferation of Ty3/gypsy-like retrotransposons in hybrid sunflower taxa inferred from phylogenetic data. BMC Biol (2009) 1.02
Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogaster genome. BMC Biol (2005) 1.00
Mobile DNA and the TE-Thrust hypothesis: supporting evidence from the primates. Mob DNA (2011) 1.00
Coding region structural heterogeneity and turnover of transcription start sites contribute to divergence in expression between duplicate genes. Genome Biol (2009) 1.00
Exonization of the LTR transposable elements in human genome. BMC Genomics (2007) 0.99
ZBED evolution: repeated utilization of DNA transposons as regulators of diverse host functions. PLoS One (2013) 0.98
A novel protein isoform of the multicopy human NAIP gene derives from intragenic Alu SINE promoters. PLoS One (2009) 0.98
29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome. PLoS One (2012) 0.97
Evolution of prokaryotic genes by shift of stop codons. J Mol Evol (2010) 0.97
Repetitive DNA elements, nucleosome binding and human gene expression. Gene (2009) 0.96
Intra- and inter-specific variations in the copy number of two types of retrotransposons from the ectomycorrhizal basidiomycete Tricholoma matsutake. Mycorrhiza (2005) 0.96
The effect of transposable element insertions on gene expression evolution in rodents. PLoS One (2009) 0.96
Transformation of a transposon into a derived prolactin promoter with function during human pregnancy. Proc Natl Acad Sci U S A (2012) 0.96
Human genetics and genomics a decade after the release of the draft sequence of the human genome. Hum Genomics (2011) 0.95
CENP-B cooperates with Set1 in bidirectional transcriptional silencing and genome organization of retrotransposons. Mol Cell Biol (2012) 0.94
Association between hypermethylation of DNA repetitive elements in white blood cell DNA and early-onset colorectal cancer. Epigenetics (2013) 0.94
A novel mode of enhancer evolution: the Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity. Genome Res (2008) 0.94
Long-term balancing selection maintains trans-specific polymorphisms in the human TRIM5 gene. Hum Genet (2010) 0.93
Effect of divergence time and recombination rate on molecular evolution of Drosophila INE-1 transposable elements and other candidates for neutrally evolving sites. J Mol Evol (2007) 0.93
Repetitive elements and enforced transcriptional repression co-operate to enhance DNA methylation spreading into a promoter CpG-island. Nucleic Acids Res (2012) 0.93
Computational and biological inference of gene regulatory networks of the LINE-1 retrotransposon. Genomics (2007) 0.93
Patterns of selection against transposons inferred from the distribution of Tc1, Tc3 and Tc5 insertions in the mut-7 line of the nematode Caenorhabditis elegans. Genetics (2003) 0.92
The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site. Nucleic Acids Res (2008) 0.92
The Fine LINE: Methylation Drawing the Cancer Landscape. Biomed Res Int (2015) 0.91
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
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
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
Evolution and diversification of lamprey antigen receptors: evidence for involvement of an AID-APOBEC family cytosine deaminase. Nat Immunol (2007) 3.14
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
Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc Natl Acad Sci U S A (2002) 2.63
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
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
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
Microevolutionary genomics of bacteria. Theor Popul Biol (2002) 1.95
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
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
GINS, a central nexus in the archaeal DNA replication fork. EMBO Rep (2006) 1.91
The rhomboids: a nearly ubiquitous family of intramembrane serine proteases that probably evolved by multiple ancient horizontal gene transfers. Genome Biol (2003) 1.91
The deep archaeal roots of eukaryotes. Mol Biol Evol (2008) 1.90
Analysis of evolution of exon-intron structure of eukaryotic genes. Brief Bioinform (2005) 1.89
Birth and death of protein domains: a simple model of evolution explains power law behavior. BMC Evol Biol (2002) 1.86
Evolutionary genomics of lactic acid bacteria. J Bacteriol (2006) 1.84
Phylogenomics of prokaryotic ribosomal proteins. PLoS One (2012) 1.82
Evolution of protein domain promiscuity in eukaryotes. Genome Res (2008) 1.82