Published in Mob DNA on October 19, 2011
Comparative analysis of transposable elements highlights mobilome diversity and evolution in vertebrates. Genome Biol Evol (2015) 1.11
ZBED evolution: repeated utilization of DNA transposons as regulators of diverse host functions. PLoS One (2013) 0.98
Dynamics and innovations within oomycete genomes: insights into biology, pathology, and evolution. Eukaryot Cell (2012) 0.97
MITEs in the promoters of effector genes allow prediction of novel virulence genes in Fusarium oxysporum. BMC Genomics (2013) 0.94
Evidence for small RNAs homologous to effector-encoding genes and transposable elements in the oomycete Phytophthora infestans. PLoS One (2012) 0.89
ZMYM3 regulates BRCA1 localization at damaged chromatin to promote DNA repair. Genes Dev (2017) 0.77
Genetic Drift, Not Life History or RNAi, Determine Long-Term Evolution of Transposable Elements. Genome Biol Evol (2016) 0.76
Insight into different environmental niches adaptation and allergenicity from the Cladosporium sphaerospermum genome, a common human allergy-eliciting Dothideomycetes. Sci Rep (2016) 0.75
The evolution of tyrosine-recombinase elements in Nematoda. PLoS One (2014) 0.75
Standardized, systemic phenotypic analysis reveals kidney dysfunction as main alteration of Kctd1 (I27N) mutant mice. J Biomed Sci (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
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol (2010) 53.37
MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res (2005) 31.64
Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst Biol (2006) 12.96
The FLP recombinase of yeast catalyzes site-specific recombination in the Drosophila genome. Cell (1989) 8.93
The telomere terminal transferase of Tetrahymena is a ribonucleoprotein enzyme with two kinds of primer specificity. Cell (1987) 8.32
Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell (1996) 8.21
PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res (2005) 8.20
Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics (2006) 5.50
Replication and recombination functions associated with the yeast plasmid, 2 mu circle. Cell (1980) 5.46
NDC10: a gene involved in chromosome segregation in Saccharomyces cerevisiae. J Cell Biol (1993) 4.96
Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse. Nature (1997) 4.39
Somatic diversification of variable lymphocyte receptors in the agnathan sea lamprey. Nature (2004) 4.37
Similarities and differences among 105 members of the Int family of site-specific recombinases. Nucleic Acids Res (1998) 3.71
RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons. PLoS Biol (2005) 3.50
A universal classification of eukaryotic transposable elements implemented in Repbase. Nat Rev Genet (2008) 3.17
PSF and p54(nrb)/NonO--multi-functional nuclear proteins. FEBS Lett (2002) 3.06
Osmotic stress-induced gene expression in Saccharomyces cerevisiae requires Msn1p and the novel nuclear factor Hot1p. Mol Cell Biol (1999) 3.04
Isolation and characterization of a gene (CBF2) specifying a protein component of the budding yeast kinetochore. J Cell Biol (1993) 2.72
Turning junk into gold: domestication of transposable elements and the creation of new genes in eukaryotes. Bioessays (2006) 2.71
Evolution of filamentous plant pathogens: gene exchange across eukaryotic kingdoms. Curr Biol (2006) 2.55
The GCR1 gene encodes a positive transcriptional regulator of the enolase and glyceraldehyde-3-phosphate dehydrogenase gene families in Saccharomyces cerevisiae. Mol Cell Biol (1987) 2.14
The outs and ins of transposition: from mu to kangaroo. Nat Rev Mol Cell Biol (2003) 2.06
Ohnologs in the human genome are dosage balanced and frequently associated with disease. Proc Natl Acad Sci U S A (2010) 2.02
FGFR1 is fused with a novel zinc-finger gene, ZNF198, in the t(8;13) leukaemia/lymphoma syndrome. Nat Genet (1998) 1.96
Transposases are the most abundant, most ubiquitous genes in nature. Nucleic Acids Res (2010) 1.91
Timing of genome duplications relative to the origin of the vertebrates: did cyclostomes diverge before or after? Mol Biol Evol (2008) 1.90
Identification of the endonuclease domain encoded by R2 and other site-specific, non-long terminal repeat retrotransposable elements. Proc Natl Acad Sci U S A (1999) 1.79
Molecular evolutionary analysis of the widespread piggyBac transposon family and related "domesticated" sequences. Mol Genet Genomics (2003) 1.76
A candidate X-linked mental retardation gene is a component of a new family of histone deacetylase-containing complexes. J Biol Chem (2002) 1.67
Self-synthesizing DNA transposons in eukaryotes. Proc Natl Acad Sci U S A (2006) 1.65
An Arabidopsis hAT-like transposase is essential for plant development. Nature (2005) 1.59
Complex formation between activator and RNA polymerase as the basis for transcriptional activation by MarA and SoxS in Escherichia coli. Mol Microbiol (2002) 1.53
Harbinger transposons and an ancient HARBI1 gene derived from a transposase. DNA Cell Biol (2004) 1.47
The pogo transposable element family of Drosophila melanogaster. Mol Gen Genet (1992) 1.37
Convergent domestication of pogo-like transposases into centromere-binding proteins in fission yeast and mammals. Mol Biol Evol (2007) 1.36
Telomere-associated endonuclease-deficient Penelope-like retroelements in diverse eukaryotes. Proc Natl Acad Sci U S A (2007) 1.29
P-element homologous sequences are tandemly repeated in the genome of Drosophila guanche. Proc Natl Acad Sci U S A (1992) 1.18
The putative Drosophila transcription factor woc is required to prevent telomeric fusions. Mol Cell (2005) 1.16
Cryptons: a group of tyrosine-recombinase-encoding DNA transposons from pathogenic fungi. Microbiology (2003) 1.14
Prp8, the pivotal protein of the spliceosomal catalytic center, evolved from a retroelement-encoded reverse transcriptase. RNA (2011) 1.13
The splicing-factor related protein SFPQ/PSF interacts with RAD51D and is necessary for homology-directed repair and sister chromatid cohesion. Nucleic Acids Res (2010) 1.12
MCAF1/AM is involved in Sp1-mediated maintenance of cancer-associated telomerase activity. J Biol Chem (2008) 1.10
Drosophila HP1c isoform interacts with the zinc-finger proteins WOC and Relative-of-WOC to regulate gene expression. Genes Dev (2008) 1.10
Reiterative AP2a activity controls sequential steps in the neural crest gene regulatory network. Proc Natl Acad Sci U S A (2010) 1.09
Reverse transcriptase and endonuclease activities encoded by Penelope-like retroelements. Proc Natl Acad Sci U S A (2004) 1.08
New superfamilies of eukaryotic DNA transposons and their internal divisions. Mol Biol Evol (2009) 1.08
The DIRS1 group of retrotransposons. Mol Biol Evol (2001) 1.08
A new group of tyrosine recombinase-encoding retrotransposons. Mol Biol Evol (2004) 1.08
ZNF198 stabilizes the LSD1-CoREST-HDAC1 complex on chromatin through its MYM-type zinc fingers. PLoS One (2008) 1.06
Cloning and characterization of DXS6673E, a candidate gene for X-linked mental retardation in Xq13.1. Hum Mol Genet (1996) 1.04
Homologs of Drosophila P transposons were mobile in zebrafish but have been domesticated in a common ancestor of chicken and human. Mol Biol Evol (2004) 0.98
The interaction of KCTD1 with transcription factor AP-2alpha inhibits its transactivation. J Cell Biochem (2009) 0.96
Probing the Escherichia coli transcriptional activator MarA using alanine-scanning mutagenesis: residues important for DNA binding and activation. J Mol Biol (2000) 0.95
Ginger DNA transposons in eukaryotes and their evolutionary relationships with long terminal repeat retrotransposons. Mob DNA (2010) 0.91
The VIPER elements of trypanosomes constitute a novel group of tyrosine recombinase-enconding retrotransposons. Mol Biochem Parasitol (2005) 0.91
An extraordinary retrotransposon family encoding dual endonucleases. Genome Res (2005) 0.90
Kctd15 inhibits neural crest formation by attenuating Wnt/beta-catenin signaling output. Development (2010) 0.90
Selection on the genes of Euplotes crassus Tec1 and Tec2 transposons: evolutionary appearance of a programmed frameshift in a Tec2 gene encoding a tyrosine family site-specific recombinase. Eukaryot Cell (2003) 0.89
ZNF198 protein, involved in rearrangement in myeloproliferative disease, forms complexes with the DNA repair-associated HHR6A/6B and RAD18 proteins. Oncogene (2003) 0.88
Mass spectroscopy identifies the splicing-associated proteins, PSF, hnRNP H3, hnRNP A2/B1, and TLS/FUS as interacting partners of the ZNF198 protein associated with rearrangement in myeloproliferative disease. Exp Cell Res (2005) 0.87
Tec3, a new developmentally eliminated DNA element in Euplotes crassus. Eukaryot Cell (2003) 0.84
PTB-associated splicing factor (PSF) functions as a repressor of STAT6-mediated Ig epsilon gene transcription by recruitment of HDAC1. J Biol Chem (2010) 0.84
Identification of novel Smad binding proteins. Biochem Biophys Res Commun (2003) 0.82
The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science (2004) 9.97
Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science (2007) 9.79
The amphioxus genome and the evolution of the chordate karyotype. Nature (2008) 8.03
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature (2007) 7.91
Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature (2005) 7.74
Analyses of pig genomes provide insight into porcine demography and evolution. Nature (2012) 5.58
Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics (2006) 5.50
The genome of the Western clawed frog Xenopus tropicalis. Science (2010) 4.70
Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Nature (2006) 4.68
Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri. Science (2010) 3.70
RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons. PLoS Biol (2005) 3.50
A universal classification of eukaryotic transposable elements implemented in Repbase. Nat Rev Genet (2008) 3.17
Molecular paleontology of transposable elements in the Drosophila melanogaster genome. Proc Natl Acad Sci U S A (2003) 3.09
Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution. PLoS Genet (2009) 2.07
Evolutionary history of 7SL RNA-derived SINEs in Supraprimates. Trends Genet (2007) 2.00
The microcephaly ASPM gene is expressed in proliferating tissues and encodes for a mitotic spindle protein. Hum Mol Genet (2005) 1.88
Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica. Genome Res (2007) 1.79
Helitrons on a roll: eukaryotic rolling-circle transposons. Trends Genet (2007) 1.74
Dfam: a database of repetitive DNA based on profile hidden Markov models. Nucleic Acids Res (2012) 1.74
Self-synthesizing DNA transposons in eukaryotes. Proc Natl Acad Sci U S A (2006) 1.65
Shuffling of genes within low-copy repeats on 22q11 (LCR22) by Alu-mediated recombination events during evolution. Genome Res (2003) 1.62
Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion. PLoS Biol (2004) 1.54
Harbinger transposons and an ancient HARBI1 gene derived from a transposase. DNA Cell Biol (2004) 1.47
A novel class of SINE elements derived from 5S rRNA. Mol Biol Evol (2003) 1.42
Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust. PLoS One (2011) 1.33
Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequences. Gene (2009) 1.30
The esterase and PHD domains in CR1-like non-LTR retrotransposons. Mol Biol Evol (2003) 1.23
Genes, pseudogenes, and Alu sequence organization across human chromosomes 21 and 22. Proc Natl Acad Sci U S A (2002) 1.23
HERVd: the Human Endogenous RetroViruses Database: update. Nucleic Acids Res (2004) 1.17
Evolution of the tumor suppressor BRCA1 locus in primates: implications for cancer predisposition. Hum Mol Genet (2004) 1.17
Retroposition of processed pseudogenes: the impact of RNA stability and translational control. Trends Genet (2005) 1.10
Potential for retroposition by old Alu subfamilies. J Mol Evol (2003) 1.09
New superfamilies of eukaryotic DNA transposons and their internal divisions. Mol Biol Evol (2009) 1.08
Comprehensive analysis of two Alu Yd subfamilies. J Mol Evol (2003) 1.06
Dynamic structure of the SPANX gene cluster mapped to the prostate cancer susceptibility locus HPCX at Xq27. Genome Res (2005) 1.04
Analysis of the human Alu Ye lineage. BMC Evol Biol (2005) 1.03
Transposition of a reconstructed Harbinger element in human cells and functional homology with two transposon-derived cellular genes. Proc Natl Acad Sci U S A (2008) 1.02
Evolutionary diversification of SPANX-N sperm protein gene structure and expression. PLoS One (2007) 1.02
Identification of sequence motifs at the breakpoint junctions in three t(1;9)(p36.3;q34) and delineation of mechanisms involved in generating balanced translocations. Hum Genet (2006) 0.99
VisualRepbase: an interface for the study of occurrences of transposable element families. BMC Bioinformatics (2008) 0.96
Traffic of genetic information between segmental duplications flanking the typical 22q11.2 deletion in velo-cardio-facial syndrome/DiGeorge syndrome. Genome Res (2005) 0.95
SINEs, evolution and genome structure in the opossum. Gene (2007) 0.92
Ginger DNA transposons in eukaryotes and their evolutionary relationships with long terminal repeat retrotransposons. Mob DNA (2010) 0.91
A superfamily of DNA transposons targeting multicopy small RNA genes. PLoS One (2013) 0.90
Evolutionary diversity and potential recombinogenic role of integration targets of Non-LTR retrotransposons. Mol Biol Evol (2005) 0.89
Recent expansion of a new Ingi-related clade of Vingi non-LTR retrotransposons in hedgehogs. Mol Biol Evol (2010) 0.89
Tracing genetic history of modern humans using X-chromosome lineages. Hum Genet (2007) 0.88
Homologues of bacterial TnpB_IS605 are widespread in diverse eukaryotic transposable elements. Mob DNA (2013) 0.87
Positive selection on the nonhomologous end-joining factor Cernunnos-XLF in the human lineage. Biol Direct (2006) 0.87
Genomic impact of eukaryotic transposable elements. Mob DNA (2012) 0.84
Horizontal transfers of Mariner transposons between mammals and insects. Mob DNA (2012) 0.82
Origin and evolution of LINE-1 derived "half-L1" retrotransposons (HAL1). Gene (2010) 0.82
Introduction for the Gene special issue dedicated to the meeting "Genomic impact of eukaryotic transposable elements" at Asilomar. Gene (2006) 0.77
"Genomic Impact of Eukaryotic Transposable Elements", Pacific Grove, California, February 6-10, 2009. Gene (2009) 0.77