Published in Cold Spring Harb Protoc on February 01, 2010
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DNase I sensitivity QTLs are a major determinant of human expression variation. Nature (2012) 6.17
High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Res (2010) 4.69
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res (2011) 4.43
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol (2012) 3.61
ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat Rev Genet (2012) 3.23
Epigenetic expansion of VHL-HIF signal output drives multiorgan metastasis in renal cancer. Nat Med (2012) 2.95
Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape. Nat Biotechnol (2014) 2.70
Dual role of FoxA1 in androgen receptor binding to chromatin, androgen signalling and prostate cancer. EMBO J (2011) 2.55
Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci. Cell Metab (2010) 2.21
Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples. Nature (2015) 1.86
Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA. Nat Protoc (2012) 1.84
Nucleoporin-mediated regulation of cell identity genes. Genes Dev (2016) 1.48
Unbiased, genome-wide in vivo mapping of transcriptional regulatory elements reveals sex differences in chromatin structure associated with sex-specific liver gene expression. Mol Cell Biol (2010) 1.45
ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr Protoc Mol Biol (2015) 1.44
The functional consequences of variation in transcription factor binding. PLoS Genet (2014) 1.38
Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes. Genome Res (2012) 1.35
Discovery of active enhancers through bidirectional expression of short transcripts. Genome Biol (2011) 1.34
Machine learning applications in genetics and genomics. Nat Rev Genet (2015) 1.32
Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements. Nat Methods (2015) 1.27
Global mapping of cell type-specific open chromatin by FAIRE-seq reveals the regulatory role of the NFI family in adipocyte differentiation. PLoS Genet (2011) 1.24
Chromatin: constructing the big picture. EMBO J (2011) 1.24
Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development. Genome Biol (2014) 1.24
Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection. PLoS Genet (2012) 1.22
The ensembl regulatory build. Genome Biol (2015) 1.21
Epigenomic comparison reveals activation of "seed" enhancers during transition from naive to primed pluripotency. Cell Stem Cell (2014) 1.17
Distinct properties of cell-type-specific and shared transcription factor binding sites. Mol Cell (2013) 1.16
Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity. Genome Biol (2012) 1.15
Regulation of the Ifng locus in the context of T-lineage specification and plasticity. Immunol Rev (2010) 1.12
Chromatin accessibility data sets show bias due to sequence specificity of the DNase I enzyme. PLoS One (2013) 1.07
Deletions of chromosomal regulatory boundaries are associated with congenital disease. Genome Biol (2014) 1.07
Chromatin accessibility: a window into the genome. Epigenetics Chromatin (2014) 1.06
A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity. Genome Res (2013) 1.05
Genome-wide analysis of the relationships between DNaseI HS, histone modifications and gene expression reveals distinct modes of chromatin domains. Nucleic Acids Res (2011) 1.01
Surveying the epigenomic landscape, one base at a time. Genome Biol (2012) 0.99
Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum. Nat Neurosci (2015) 0.98
Ascl1 Coordinately Regulates Gene Expression and the Chromatin Landscape during Neurogenesis. Cell Rep (2015) 0.97
Rapid genome-scale mapping of chromatin accessibility in tissue. Epigenetics Chromatin (2012) 0.97
Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants. Plant Cell (2016) 0.95
Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators. Genome Res (2015) 0.92
Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection. Nucleic Acids Res (2014) 0.92
Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal. Genome Res (2014) 0.91
Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape. Genome Res (2014) 0.91
Genome accessibility is widely preserved and locally modulated during mitosis. Genome Res (2014) 0.91
Current bioinformatic approaches to identify DNase I hypersensitive sites and genomic footprints from DNase-seq data. Front Genet (2012) 0.90
Cancer genome sequencing: understanding malignancy as a disease of the genome, its conformation, and its evolution. Cancer Lett (2012) 0.89
The open chromatin landscape of Kaposi's sarcoma-associated herpesvirus. J Virol (2013) 0.87
Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes. PLoS Genet (2012) 0.87
A comparison of peak callers used for DNase-Seq data. PLoS One (2014) 0.87
Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome. Cell (2016) 0.86
Chromatin remodeling in cancer: a gateway to regulate gene transcription. Mol Oncol (2012) 0.86
Mapping genome-wide transcription factor binding sites in frozen tissues. Epigenetics Chromatin (2013) 0.86
Uncovering correlated variability in epigenomic datasets using the Karhunen-Loeve transform. BioData Min (2015) 0.85
The decade of the epigenomes? Genes Cancer (2011) 0.84
Genome-wide mapping of DNase I hypersensitive sites and association analysis with gene expression in MSB1 cells. Front Genet (2014) 0.83
Uncovering drug-responsive regulatory elements. Pharmacogenomics (2015) 0.83
Disease-associated variants in different categories of disease located in distinct regulatory elements. BMC Genomics (2015) 0.83
Identifying and characterizing regulatory sequences in the human genome with chromatin accessibility assays. Genes (Basel) (2012) 0.83
Measuring Arabidopsis chromatin accessibility using DNase I-polymerase chain reaction and DNase I-chip assays. Plant Physiol (2013) 0.83
Unraveling the 3D genome: genomics tools for multiscale exploration. Trends Genet (2015) 0.83
Epigenetic landscape during osteoblastogenesis defines a differentiation-dependent Runx2 promoter region. Gene (2014) 0.83
Ensembl regulation resources. Database (Oxford) (2016) 0.82
Map of open and closed chromatin domains in Drosophila genome. BMC Genomics (2014) 0.82
Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome. Nucleic Acids Res (2013) 0.82
Hormone-induced repression of genes requires BRG1-mediated H1.2 deposition at target promoters. EMBO J (2016) 0.81
Characterization of chromatin accessibility with a transposome hypersensitive sites sequencing (THS-seq) assay. Genome Biol (2016) 0.81
DNase I digestion of isolated nulcei for genome-wide mapping of DNase hypersensitivity sites in chromatin. Methods Mol Biol (2013) 0.81
Mapping nucleosome positions using DNase-seq. Genome Res (2016) 0.81
Assaying the epigenome in limited numbers of cells. Methods (2014) 0.80
Chromosomal organization at the level of gene complexes. Cell Mol Life Sci (2010) 0.80
Next-Generation Sequencing Approaches in Cancer: Where Have They Brought Us and Where Will They Take Us? Cancers (Basel) (2015) 0.80
Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse. Nucleic Acids Res (2016) 0.79
Genomic approaches for understanding the genetics of complex disease. Genome Res (2015) 0.79
Interrogation of allelic chromatin states in human cells by high-density ChIP-genotyping. Epigenetics (2014) 0.79
Elucidating MicroRNA Regulatory Networks Using Transcriptional, Post-transcriptional, and Histone Modification Measurements. Cell Rep (2015) 0.79
CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome. Nat Biotechnol (2017) 0.78
Statistical Methods in Integrative Genomics. Annu Rev Stat Appl (2016) 0.78
Progesterone receptor induces bcl-x expression through intragenic binding sites favoring RNA polymerase II elongation. Nucleic Acids Res (2013) 0.78
Removing reference mapping biases using limited or no genotype data identifies allelic differences in protein binding at disease-associated loci. BMC Med Genomics (2015) 0.78
Embryonic Stem Cells: A Perfect Tool for Studying Mammalian Transcriptional Enhancers. J Stem Cell Res Ther (2012) 0.78
Tissue specific CTCF occupancy and boundary function at the human growth hormone locus. Nucleic Acids Res (2014) 0.78
Genomic analysis reveals distinct mechanisms and functional classes of SOX10-regulated genes in melanocytes. Hum Mol Genet (2015) 0.78
The bone-specific Runx2-P1 promoter displays conserved three-dimensional chromatin structure with the syntenic Supt3h promoter. Nucleic Acids Res (2014) 0.78
Chromatin Dynamics in the Regulation of CFTR Expression. Genes (Basel) (2015) 0.78
Isolation of nuclei for use in genome-wide DNase hypersensitivity assays to probe chromatin structure. Methods Mol Biol (2013) 0.77
Transcriptional Enhancers in the Regulation of T Cell Differentiation. Front Immunol (2015) 0.77
Improved DNase-seq protocol facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana. Plant Methods (2015) 0.77
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
Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research. Prog Retin Eye Res (2016) 0.76
Proteogenomics analysis reveals specific genomic orientations of distal regulatory regions composed by non-canonical histone variants. Epigenetics Chromatin (2015) 0.76
A quantitative analysis of the impact on chromatin accessibility by histone modifications and binding of transcription factors in DNase I hypersensitive sites. Biomed Res Int (2013) 0.76
TargetOrtho: a phylogenetic footprinting tool to identify transcription factor targets. Genetics (2014) 0.76
Genetic variants and cellular stressors associated with exfoliation syndrome modulate promoter activity of a lncRNA within the LOXL1 locus. Hum Mol Genet (2015) 0.76
SuRFing the genomics wave: an R package for prioritising SNPs by functionality. Genome Med (2014) 0.76
Prediction of DNase I hypersensitive sites by using pseudo nucleotide compositions. ScientificWorldJournal (2014) 0.76
Past Roadblocks and New Opportunities in Transcription Factor Network Mapping. Trends Genet (2016) 0.76
Genome-Wide Identification of Regulatory Sequences Undergoing Accelerated Evolution in the Human Genome. Mol Biol Evol (2016) 0.75
The Cartography of UV-induced DNA Damage Formation and DNA Repair. Photochem Photobiol (2016) 0.75
Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes. Nucleic Acids Res (2016) 0.75
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
High-resolution mapping and characterization of open chromatin across the genome. Cell (2008) 15.93
The 5' ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature (1980) 14.11
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Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods (2009) 10.17
Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat Methods (2006) 8.52
DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nat Methods (2006) 6.25
Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet (2007) 5.93
The chromatin structure of specific genes: II. Disruption of chromatin structure during gene activity. Cell (1979) 5.13
DNase I hypersensitive sites in Drosophila chromatin occur at the 5' ends of regions of transcription. Proc Natl Acad Sci U S A (1981) 3.39
Chromatin fine structure of active and repressed genes. Nature (1981) 1.70
Mapping regulatory elements by DNaseI hypersensitivity chip (DNase-Chip). Methods Mol Biol (2009) 1.33
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet (2007) 32.41
Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature (2009) 24.41
The accessible chromatin landscape of the human genome. Nature (2012) 16.86
High-resolution mapping and characterization of open chromatin across the genome. Cell (2008) 15.93
DNase I sensitivity QTLs are a major determinant of human expression variation. Nature (2012) 6.17
Heritable individual-specific and allele-specific chromatin signatures in humans. Science (2010) 5.94
Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet (2007) 5.93
RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat Methods (2013) 4.85
F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics (2008) 4.77
High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Res (2010) 4.69
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res (2011) 4.43
An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol (2012) 4.15
Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res (2013) 3.61
Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen arrays. Methods Enzymol (2006) 3.53
Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A (2014) 3.35
Synergistic and tunable human gene activation by combinations of synthetic transcription factors. Nat Methods (2013) 3.26
Epigenetic instability of cytokine and transcription factor gene loci underlies plasticity of the T helper 17 cell lineage. Immunity (2010) 3.24
Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis. PLoS Genet (2006) 2.62
Dissecting the regulatory architecture of gene expression QTLs. Genome Biol (2012) 2.51
Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns. Genome Res (2009) 2.31
Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci. Cell Metab (2010) 2.21
CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression. PLoS Genet (2010) 2.20
Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Res (2011) 2.07
Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. Genome Res (2012) 1.99
Predicting cell-type-specific gene expression from regions of open chromatin. Genome Res (2012) 1.78
Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions. Genome Res (2013) 1.69
Interferon regulatory factors are transcriptional regulators of adipogenesis. Cell Metab (2008) 1.55
Site-specific silencing of regulatory elements as a mechanism of X inactivation. Cell (2012) 1.54
Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. Genome Res (2011) 1.53
Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU.1 and HMGA1. Cancer Res (2007) 1.34
Mapping regulatory elements by DNaseI hypersensitivity chip (DNase-Chip). Methods Mol Biol (2009) 1.33
Intronic enhancers coordinate epithelial-specific looping of the active CFTR locus. Proc Natl Acad Sci U S A (2009) 1.29
A complex intronic enhancer regulates expression of the CFTR gene by direct interaction with the promoter. J Cell Mol Med (2009) 1.23
Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection. PLoS Genet (2012) 1.22
High-resolution mapping of open chromatin in the rice genome. Genome Res (2011) 1.19
Modular utilization of distal cis-regulatory elements controls Ifng gene expression in T cells activated by distinct stimuli. Immunity (2010) 1.17
Distinct properties of cell-type-specific and shared transcription factor binding sites. Mol Cell (2013) 1.16
Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity. Genome Biol (2012) 1.15
Gene expression during normal and FSHD myogenesis. BMC Med Genomics (2011) 1.12
The hypersensitive glucocorticoid response specifically regulates period 1 and expression of circadian genes. Mol Cell Biol (2012) 1.06
A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity. Genome Res (2013) 1.05
Early de novo DNA methylation and prolonged demethylation in the muscle lineage. Epigenetics (2013) 1.00
Distant conserved sequences flanking endothelial-specific promoters contain tissue-specific DNase-hypersensitive sites and over-represented motifs. Hum Mol Genet (2006) 1.00
Allele-specific and heritable chromatin signatures in humans. Hum Mol Genet (2010) 0.96
H3K4me3 inversely correlates with DNA methylation at a large class of non-CpG-island-containing start sites. Genome Med (2012) 0.90
A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function. Thorax (2011) 0.88
Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes. PLoS Genet (2012) 0.87
DNA methylation and differentiation: HOX genes in muscle cells. Epigenetics Chromatin (2013) 0.86
DNaseI hypersensitivity at gene-poor, FSH dystrophy-linked 4q35.2. Nucleic Acids Res (2009) 0.85
A genome-wide analysis of open chromatin in human epididymis epithelial cells reveals candidate regulatory elements for genes coordinating epididymal function. Biol Reprod (2013) 0.85
Discovering sequences with potential regulatory characteristics. Genomics (2008) 0.83
DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types. Genome Res (2013) 0.80
Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proc Natl Acad Sci U S A (2014) 0.76
Correction: Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association. PLoS Genet (2015) 0.75
Corrigendum: Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal. Genome Res (2016) 0.75