Published in Bioinformatics on September 24, 2010
ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat Rev Genet (2012) 3.23
Fast computation and applications of genome mappability. PLoS One (2012) 2.73
On the presence and role of human gene-body DNA methylation. Oncotarget (2012) 2.10
Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data. PLoS Comput Biol (2011) 1.86
DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nat Genet (2013) 1.64
DICER- and AGO3-dependent generation of retinoic acid-induced DR2 Alu RNAs regulates human stem cell proliferation. Nat Struct Mol Biol (2012) 1.03
Transcriptional landscape of repetitive elements in normal and cancer human cells. BMC Genomics (2014) 1.01
TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets. Bioinformatics (2015) 0.94
Epigenetic regulation of human cis-natural antisense transcripts. Nucleic Acids Res (2012) 0.91
Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline. Genome Res (2014) 0.88
Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite. BMC Syst Biol (2011) 0.82
Cell type-specific termination of transcription by transposable element sequences. Mob DNA (2012) 0.80
Next generation quantitative genetics in plants. Front Plant Sci (2011) 0.79
MMR: a tool for read multi-mapper resolution. Bioinformatics (2015) 0.78
Do human transposable element small RNAs serve primarily as genome defenders or genome regulators? Mob Genet Elements (2012) 0.78
CNV-guided multi-read allocation for ChIP-seq. Bioinformatics (2014) 0.77
Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping. PLoS Comput Biol (2015) 0.77
A comprehensive hybridization model allows whole HERV transcriptome profiling using high density microarray. BMC Genomics (2017) 0.75
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
The human genome browser at UCSC. Genome Res (2002) 168.23
Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res (2008) 157.44
High-resolution profiling of histone methylations in the human genome. Cell (2007) 85.74
Model-based analysis of ChIP-Seq (MACS). Genome Biol (2008) 51.63
Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science (1993) 36.84
The UCSC Table Browser data retrieval tool. Nucleic Acids Res (2004) 25.12
ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet (2009) 13.12
Transposable elements and the evolution of regulatory networks. Nat Rev Genet (2008) 6.11
Gibbs motif sampling: detection of bacterial outer membrane protein repeats. Protein Sci (1995) 5.96
A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. Genomics (2008) 3.19
Identification of higher-order functional domains in the human ENCODE regions. Genome Res (2007) 2.62
Computational epigenetics. Bioinformatics (2007) 1.92
Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite. Bioinformatics (2009) 1.32
A topoisomerase IIbeta-mediated dsDNA break required for regulated transcription. Science (2006) 6.71
Sensors and signals: a coactivator/corepressor/epigenetic code for integrating signal-dependent programs of transcriptional response. Genes Dev (2006) 6.32
Inhibition of activated pericentromeric SINE/Alu repeat transcription in senescent human adult stem cells reinstates self-renewal. Cell Cycle (2011) 3.11
A family of human microRNA genes from miniature inverted-repeat transposable elements. PLoS One (2007) 2.63
A computational genomics pipeline for prokaryotic sequencing projects. Bioinformatics (2010) 2.63
Origin and evolution of human microRNAs from transposable elements. Genetics (2007) 2.39
On the presence and role of human gene-body DNA methylation. Oncotarget (2012) 2.10
Dual coding of siRNAs and miRNAs by plant transposable elements. RNA (2008) 1.76
Purifying and directional selection in overlapping prokaryotic genes. Trends Genet (2002) 1.74
Retrotransposons and their recognition of pol II promoters: a comprehensive survey of the transposable elements from the complete genome sequence of Schizosaccharomyces pombe. Genome Res (2003) 1.63
An induced Ets repressor complex regulates growth arrest during terminal macrophage differentiation. Cell (2002) 1.63
APOBEC4, a new member of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases predicted by computational analysis. Cell Cycle (2005) 1.49
Human cis natural antisense transcripts initiated by transposable elements. Trends Genet (2008) 1.35
Global similarity and local divergence in human and mouse gene co-expression networks. BMC Evol Biol (2006) 1.32
Dasheng and RIRE2. A nonautonomous long terminal repeat element and its putative autonomous partner in the rice genome. Plant Physiol (2002) 1.24
Flow-dependent epigenetic DNA methylation regulates endothelial gene expression and atherosclerosis. J Clin Invest (2014) 1.18
Epigenetics: judge, jury and executioner of stem cell fate. Epigenetics (2012) 1.17
Genome sequences for six Rhodanobacter strains, isolated from soils and the terrestrial subsurface, with variable denitrification capabilities. J Bacteriol (2012) 1.16
No rest for REST: REST/NRSF regulation of neurogenesis. Cell (2005) 1.14
Retroviral promoters in the human genome. Bioinformatics (2008) 1.10
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
Epigenetic histone modifications of human transposable elements: genome defense versus exaptation. Mob DNA (2010) 1.04
Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA. BMC Genomics (2008) 1.02
Multiple independent evolutionary solutions to core histone gene regulation. Genome Biol (2006) 1.00
Transposable elements and the evolution of eukaryotic complexity. Curr Issues Mol Biol (2002) 0.99
Epigenetic regulation of transposable element derived human gene promoters. Gene (2011) 0.98
BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets. Bioinformatics (2013) 0.98
Genome sequence of the Mycobacterium colombiense type strain, CECT 3035. J Bacteriol (2011) 0.98
Repetitive DNA elements, nucleosome binding and human gene expression. Gene (2009) 0.96
Genome-wide prediction and analysis of human chromatin boundary elements. Nucleic Acids Res (2011) 0.93
Epigenetic regulation of human cis-natural antisense transcripts. Nucleic Acids Res (2012) 0.91
Identification of a tumor-suppressive human-specific microRNA within the FHIT tumor-suppressor gene. Cancer Res (2014) 0.90
Chromatin signature discovery via histone modification profile alignments. Nucleic Acids Res (2012) 0.89
Endogenous retroviruses of the chicken genome. Biol Direct (2008) 0.89
Prediction of transposable element derived enhancers using chromatin modification profiles. PLoS One (2011) 0.88
Neisseria Base: a comparative genomics database for Neisseria meningitidis. Database (Oxford) (2011) 0.88
Transcription factor binding sites are highly enriched within microRNA precursor sequences. Biol Direct (2011) 0.88
Co-evolutionary rates of functionally related yeast genes. Evol Bioinform Online (2006) 0.88
Meningococcus genome informatics platform: a system for analyzing multilocus sequence typing data. Nucleic Acids Res (2009) 0.86
Epigenetic regulation of Mammalian genomes by transposable elements. Ann N Y Acad Sci (2009) 0.86
Benchmarking computational tools for polymorphic transposable element detection. Brief Bioinform (2016) 0.85
A c-Myc regulatory subnetwork from human transposable element sequences. Mol Biosyst (2009) 0.85
A method for visualization of "omic" datasets for sphingolipid metabolism to predict potentially interesting differences. J Lipid Res (2011) 0.84
Depletion of nuclear histone H2A variants is associated with chronic DNA damage signaling upon drug-evoked senescence of human somatic cells. Aging (Albany NY) (2012) 0.83
Effect of the transposable element environment of human genes on gene length and expression. Genome Biol Evol (2011) 0.82
Highly conserved regimes of neighbor-base-dependent mutation generated the background primary-structural heterogeneities along vertebrate chromosomes. PLoS One (2008) 0.82
Relating the disease mutation spectrum to the evolution of the cystic fibrosis transmembrane conductance regulator (CFTR). PLoS One (2012) 0.81
Protein interactions with piALU RNA indicates putative participation of retroRNA in the cell cycle, DNA repair and chromatin assembly. Mob Genet Elements (2012) 0.81
Adult stem cells: simply a tool for regenerative medicine or an additional piece in the puzzle of human aging? Cell Cycle (2011) 0.81
Using single-nucleotide polymorphisms to discriminate disease-associated from carried genomes of Neisseria meningitidis. J Bacteriol (2011) 0.80
Analysis of transposable element sequences using CENSOR and RepeatMasker. Methods Mol Biol (2009) 0.80
Genomic basis of a polyagglutinating isolate of Neisseria meningitidis. J Bacteriol (2012) 0.80
Cell type-specific termination of transcription by transposable element sequences. Mob DNA (2012) 0.80
Population differences in transcript-regulator expression quantitative trait loci. PLoS One (2012) 0.80
The deaf community and culture at a crossroads: issues and challenges. J Soc Work Disabil Rehabil (2010) 0.79
Genome sequence-based discriminator for vancomycin-intermediate Staphylococcus aureus. J Bacteriol (2013) 0.79
Origin and evolution of the cystic fibrosis transmembrane regulator protein R domain. Gene (2013) 0.79
Epigenetics components of aging in the central nervous system. Neurotherapeutics (2013) 0.79
Transcriptional activity, chromosomal distribution and expression effects of transposable elements in Coffea genomes. PLoS One (2013) 0.79
Do human transposable element small RNAs serve primarily as genome defenders or genome regulators? Mob Genet Elements (2012) 0.78
Identification of transcription factor binding sites derived from transposable element sequences using ChIP-seq. Methods Mol Biol (2010) 0.77
Compound cis-regulatory elements with both boundary and enhancer sequences in the human genome. Bioinformatics (2013) 0.75