Published in Proc Natl Acad Sci U S A on August 18, 2009
A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol (2011) 16.53
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13
Charting histone modifications and the functional organization of mammalian genomes. Nat Rev Genet (2010) 7.39
Most "dark matter" transcripts are associated with known genes. PLoS Biol (2010) 6.60
Global epigenomic reconfiguration during mammalian brain development. Science (2013) 6.14
Histone modification levels are predictive for gene expression. Proc Natl Acad Sci U S A (2010) 4.00
Evaluation of algorithm performance in ChIP-seq peak detection. PLoS One (2010) 3.99
Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation. Genome Res (2009) 3.30
Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nucleic Acids Res (2009) 2.74
The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding. Genome Biol (2011) 2.68
Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development. PLoS Genet (2011) 2.65
Systematic bias in high-throughput sequencing data and its correction by BEADS. Nucleic Acids Res (2011) 2.48
ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions. Genome Biol (2011) 2.47
A twin approach to unraveling epigenetics. Trends Genet (2011) 2.38
Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches. PLoS Genet (2011) 2.38
Annotating non-coding regions of the genome. Nat Rev Genet (2010) 2.38
Genomic views of STAT function in CD4+ T helper cell differentiation. Nat Rev Immunol (2011) 2.09
DNA methylation status predicts cell type-specific enhancer activity. EMBO J (2011) 1.98
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
Chromatin landscape dictates HSF binding to target DNA elements. PLoS Genet (2010) 1.82
ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis. BMC Genomics (2011) 1.80
High-throughput sequencing for biology and medicine. Mol Syst Biol (2013) 1.75
H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells. BMC Genomics (2012) 1.73
A Statistical Framework for the Analysis of ChIP-Seq Data. J Am Stat Assoc (2012) 1.58
Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb. Genome Res (2012) 1.57
High-resolution mapping of transcription factor binding sites on native chromatin. Nat Methods (2013) 1.55
Mutations in regulators of the epigenome and their connections to global chromatin patterns in cancer. Nat Rev Genet (2013) 1.53
MYRF is a membrane-associated transcription factor that autoproteolytically cleaves to directly activate myelin genes. PLoS Biol (2013) 1.45
Wide-ranging functions of E2F4 in transcriptional activation and repression revealed by genome-wide analysis. Nucleic Acids Res (2011) 1.43
A computational pipeline for comparative ChIP-seq analyses. Nat Protoc (2011) 1.42
RNA-seq: impact of RNA degradation on transcript quantification. BMC Biol (2014) 1.41
Widespread misinterpretable ChIP-seq bias in yeast. PLoS One (2013) 1.36
High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation. Genome Res (2011) 1.24
ChIP on Chip: surprising results are often artifacts. BMC Genomics (2010) 1.24
Large-scale quality analysis of published ChIP-seq data. G3 (Bethesda) (2014) 1.23
Uniform, optimal signal processing of mapped deep-sequencing data. Nat Biotechnol (2013) 1.17
Motif-based analysis of large nucleotide data sets using MEME-ChIP. Nat Protoc (2014) 1.15
Limitations and possibilities of low cell number ChIP-seq. BMC Genomics (2012) 1.09
Complex exon-intron marking by histone modifications is not determined solely by nucleosome distribution. PLoS One (2010) 1.09
Mapping yeast transcriptional networks. Genetics (2013) 1.06
Non-random DNA fragmentation in next-generation sequencing. Sci Rep (2014) 1.01
Surveying the epigenomic landscape, one base at a time. Genome Biol (2012) 0.99
The histone chaperone CAF-1 safeguards somatic cell identity. Nature (2015) 0.97
An evolutionary consequence of dosage compensation on Drosophila melanogaster female X-chromatin structure? BMC Genomics (2010) 0.95
DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data. Genes Cells (2013) 0.95
Non-targeted transcription factors motifs are a systemic component of ChIP-seq datasets. Genome Biol (2014) 0.93
Direct regulation of nucleosome density by the conserved AAA-ATPase Yta7. Proc Natl Acad Sci U S A (2011) 0.92
Comparative analysis of 4C-Seq data generated from enzyme-based and sonication-based methods. BMC Genomics (2013) 0.92
Centromere-like regions in the budding yeast genome. PLoS Genet (2013) 0.90
Single molecule and single cell epigenomics. Methods (2014) 0.89
Non-canonical protein-DNA interactions identified by ChIP are not artifacts. BMC Genomics (2013) 0.87
Expanded roles of the origin recognition complex in the architecture and function of silenced chromatin in Saccharomyces cerevisiae. Mol Cell Biol (2009) 0.87
Processing and analyzing ChIP-seq data: from short reads to regulatory interactions. Brief Funct Genomics (2010) 0.84
Dynamic chromatin technologies: from individual molecules to epigenomic regulation in cells. Nat Rev Genet (2017) 0.84
Identifying and characterizing regulatory sequences in the human genome with chromatin accessibility assays. Genes (Basel) (2012) 0.83
Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment. BMC Genomics (2014) 0.83
Unraveling the 3D genome: genomics tools for multiscale exploration. Trends Genet (2015) 0.83
Epigenomic annotation of gene regulatory alterations during evolution of the primate brain. Nat Neurosci (2016) 0.82
Computational methodology for ChIP-seq analysis. Quant Biol (2013) 0.82
Metastases suppressor NME2 associates with telomere ends and telomerase and reduces telomerase activity within cells. Nucleic Acids Res (2011) 0.82
Predictive models of gene regulation from high-throughput epigenomics data. Comp Funct Genomics (2012) 0.81
Genomic approaches for the discovery of CFTR regulatory elements. Transcription (2012) 0.81
Cell context dependent p53 genome-wide binding patterns and enrichment at repeats. PLoS One (2014) 0.80
BIDCHIPS: bias decomposition and removal from ChIP-seq data clarifies true binding signal and its functional correlates. Epigenetics Chromatin (2015) 0.78
Chromatin tandem affinity purification sequencing. Nat Protoc (2013) 0.78
Establishment of active chromatin structure at enhancer elements by mixed-lineage leukemia 1 to initiate estrogen-dependent gene expression. Nucleic Acids Res (2013) 0.78
Next-generation sequencing of apoptotic DNA breakpoints reveals association with actively transcribed genes and gene translocations. PLoS One (2011) 0.77
Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast. BMC Genomics (2014) 0.77
Most transcription factor binding sites are in a few mosaic classes of the human genome. BMC Genomics (2010) 0.76
NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing data. BMC Genomics (2017) 0.76
Z-DNA-forming sites identified by ChIP-Seq are associated with actively transcribed regions in the human genome. DNA Res (2016) 0.76
Global analysis of transcription factor-binding sites in yeast using ChIP-Seq. Methods Mol Biol (2014) 0.75
Iterative Fragmentation Improves the Detection of ChIP-seq Peaks for Inactive Histone Marks. Bioinform Biol Insights (2016) 0.75
High-resolution profiling of histone methylations in the human genome. Cell (2007) 85.74
Genome-wide mapping of in vivo protein-DNA interactions. Science (2007) 64.92
Model-based analysis of ChIP-Seq (MACS). Genome Biol (2008) 51.63
Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature (2001) 21.55
Ensembl 2008. Nucleic Acids Res (2007) 20.67
NCBI GEO: mining tens of millions of expression profiles--database and tools update. Nucleic Acids Res (2006) 19.42
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods (2008) 11.61
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol (2009) 11.28
A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci U S A (2006) 10.63
Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Biotechniques (2008) 10.02
Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res (2008) 8.89
FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res (2006) 7.72
Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc (2006) 7.29
Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs. Nature (2009) 6.88
DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nat Methods (2006) 6.25
Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res (2007) 4.59
Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding. Genome Res (2008) 4.11
ChIP-chip: a genomic approach for identifying transcription factor binding sites. Methods Enzymol (2002) 3.32
Cell cycle-specified fluctuation of nucleosome occupancy at gene promoters. PLoS Genet (2006) 3.08
Genomewide demarcation of RNA polymerase II transcription units revealed by physical fractionation of chromatin. Proc Natl Acad Sci U S A (2003) 2.33
Global changes in STAT target selection and transcription regulation upon interferon treatments. Genes Dev (2005) 2.01
Chromatin immunoprecipitation for determining the association of proteins with specific genomic sequences in vivo. Curr Protoc Cell Biol (2004) 1.98
Open conformation chromatin and pluripotency. Genes Dev (2007) 1.83
The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci. Genome Res (2007) 1.56
Polycomb gene expression and histone H3 lysine 27 trimethylation changes during bovine preimplantation development. Reproduction (2008) 0.98
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77
The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods (2007) 45.04
Functional profiling of the Saccharomyces cerevisiae genome. Nature (2002) 36.10
Paired-end mapping reveals extensive structural variation in the human genome. Science (2007) 30.46
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature (2006) 24.29
Landscape of transcription in human cells. Nature (2012) 20.18
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
Global identification of human transcribed sequences with genome tiling arrays. Science (2004) 17.85
Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell (2004) 16.15
A map of the interactome network of the metazoan C. elegans. Science (2004) 15.60
Mapping copy number variation by population-scale genome sequencing. Nature (2011) 12.55
Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell (2012) 12.32
A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (2003) 12.07
Unlocking the secrets of the genome. Nature (2009) 11.80
Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol Cell (2003) 11.78
Annotation of functional variation in personal genomes using RegulomeDB. Genome Res (2012) 11.47
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol (2009) 11.28
High-quality binary protein interaction map of the yeast interactome network. Science (2008) 10.65
An epigenetic switch involving NF-kappaB, Lin28, Let-7 MicroRNA, and IL6 links inflammation to cell transformation. Cell (2009) 10.09
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
Variation in transcription factor binding among humans. Science (2010) 9.33
Genomic analysis of regulatory network dynamics reveals large topological changes. Nature (2004) 9.32
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell (2012) 8.41
The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24
Subcellular localization of the yeast proteome. Genes Dev (2002) 7.93
Global analysis of protein phosphorylation in yeast. Nature (2005) 7.46
HTRA1 promoter polymorphism in wet age-related macular degeneration. Science (2006) 7.12
Performance comparison of exome DNA sequencing technologies. Nat Biotechnol (2011) 7.11
Divergence of transcription factor binding sites across related yeast species. Science (2007) 7.10
Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol (2003) 6.98
CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res (2011) 6.97
The transcriptional activity of human Chromosome 22. Genes Dev (2003) 6.82
Metformin selectively targets cancer stem cells, and acts together with chemotherapy to block tumor growth and prolong remission. Cancer Res (2009) 6.74
TREX is a conserved complex coupling transcription with messenger RNA export. Nature (2002) 6.53
Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat Genet (2004) 6.33
Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. Mol Cell (2005) 6.17
Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes Dev (2005) 6.14
Performance comparison of whole-genome sequencing platforms. Nat Biotechnol (2011) 5.79
Relating whole-genome expression data with protein-protein interactions. Genome Res (2002) 5.78
STAT3 activation of miR-21 and miR-181b-1 via PTEN and CYLD are part of the epigenetic switch linking inflammation to cancer. Mol Cell (2010) 5.67
The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol (2007) 5.63
Methylation of H3-lysine 79 is mediated by a new family of HMTases without a SET domain. Curr Biol (2002) 5.53
Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res (2003) 5.49
Linking disease associations with regulatory information in the human genome. Genome Res (2012) 5.47
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res (2004) 5.26
Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nat Biotechnol (2009) 5.13
Nucleosome positioning signals in genomic DNA. Genome Res (2007) 4.99
What is a gene, post-ENCODE? History and updated definition. Genome Res (2007) 4.96
High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. Proc Natl Acad Sci U S A (2006) 4.84
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res (2012) 4.80
A cis-regulatory map of the Drosophila genome. Nature (2011) 4.80
Eaf3 chromodomain interaction with methylated H3-K36 links histone deacetylation to Pol II elongation. Mol Cell (2005) 4.77
AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol (2011) 4.71
Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat Struct Mol Biol (2009) 4.64
New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Genes Dev (2007) 4.62
Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res (2007) 4.59
Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells. Mol Cell (2006) 4.51
Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol (2004) 4.48