Published in Nature on August 02, 2012
Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature (2012) 18.23
Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell (2013) 9.55
Super-enhancers in the control of cell identity and disease. Cell (2013) 7.50
An atlas of active enhancers across human cell types and tissues. Nature (2014) 6.57
Global epigenomic reconfiguration during mammalian brain development. Science (2013) 6.14
Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat Rev Genet (2013) 4.38
Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell (2013) 3.83
CTCF: an architectural protein bridging genome topology and function. Nat Rev Genet (2014) 3.64
The hierarchy of the 3D genome. Mol Cell (2013) 3.54
Reversing DNA methylation: mechanisms, genomics, and biological functions. Cell (2014) 3.17
Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming. Cell (2013) 3.13
Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes. Cell (2014) 3.13
Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics. Cell (2013) 3.09
Enhancer transcripts mark active estrogen receptor binding sites. Genome Res (2013) 2.82
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Multiple knockout mouse models reveal lincRNAs are required for life and brain development. Elife (2013) 2.66
Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription. Cell (2014) 2.64
CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function. Cell (2015) 2.59
Cohesin-mediated interactions organize chromosomal domain architecture. EMBO J (2013) 2.48
Mapping human epigenomes. Cell (2013) 2.44
Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nat Methods (2012) 2.42
Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. Nat Genet (2014) 2.42
Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nat Genet (2013) 2.41
Global analysis of DNA methylation variation in adipose tissue from twins reveals links to disease-associated variants in distal regulatory elements. Am J Hum Genet (2013) 2.40
Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants. Nat Genet (2014) 2.38
Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations. Nature (2013) 2.25
BET bromodomains mediate transcriptional pause release in heart failure. Cell (2013) 2.17
Fine tuning of craniofacial morphology by distant-acting enhancers. Science (2013) 2.16
Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits. Genome Res (2013) 2.14
Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation. Blood (2013) 2.12
Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation. Genes Dev (2013) 2.07
Nkx2-1 represses a latent gastric differentiation program in lung adenocarcinoma. Mol Cell (2013) 2.05
Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments. Genome Res (2013) 2.05
Genome-wide inference of natural selection on human transcription factor binding sites. Nat Genet (2013) 2.03
Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture. Cell Rep (2015) 2.00
H3K4me3 interactions with TAF3 regulate preinitiation complex assembly and selective gene activation. Cell (2013) 2.00
Programming and inheritance of parental DNA methylomes in mammals. Cell (2014) 1.85
Genome-scale functional characterization of Drosophila developmental enhancers in vivo. Nature (2014) 1.82
The pluripotent genome in three dimensions is shaped around pluripotency factors. Nature (2013) 1.82
Genome-wide identification and characterization of functional neuronal activity-dependent enhancers. Nat Neurosci (2014) 1.82
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Genome-wide nucleosome positioning during embryonic stem cell development. Nat Struct Mol Biol (2012) 1.80
Rapid and pervasive changes in genome-wide enhancer usage during mammalian development. Cell (2013) 1.79
Epigenetic priming of enhancers predicts developmental competence of hESC-derived endodermal lineage intermediates. Cell Stem Cell (2015) 1.78
Th17 Cell Induction by Adhesion of Microbes to Intestinal Epithelial Cells. Cell (2015) 1.76
High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states. Nat Protoc (2013) 1.73
Functional importance of cardiac enhancer-associated noncoding RNAs in heart development and disease. J Mol Cell Cardiol (2014) 1.71
The 3D genome in transcriptional regulation and pluripotency. Cell Stem Cell (2014) 1.70
Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts. Genome Res (2014) 1.69
RFECS: a random-forest based algorithm for enhancer identification from chromatin state. PLoS Comput Biol (2013) 1.66
Bayesian inference of spatial organizations of chromosomes. PLoS Comput Biol (2013) 1.66
Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization. Cell Stem Cell (2013) 1.65
Genome organization and long-range regulation of gene expression by enhancers. Curr Opin Cell Biol (2013) 1.63
LRP8-Reelin-Regulated Neuronal Enhancer Signature Underlying Learning and Memory Formation. Neuron (2015) 1.61
The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements. Genome Res (2015) 1.58
High-throughput genome scaffolding from in vivo DNA interaction frequency. Nat Biotechnol (2013) 1.53
Partially redundant enhancers cooperatively maintain Mammalian pomc expression above a critical functional threshold. PLoS Genet (2015) 1.53
Endogenous retroviruses function as species-specific enhancer elements in the placenta. Nat Genet (2013) 1.52
The evolution of lineage-specific regulatory activities in the human embryonic limb. Cell (2013) 1.51
Chromatin insulators: linking genome organization to cellular function. Mol Cell (2013) 1.51
Distinct roles of the methylcytosine oxidases Tet1 and Tet2 in mouse embryonic stem cells. Proc Natl Acad Sci U S A (2014) 1.50
What does our genome encode? Genome Res (2012) 1.47
Enhancers: five essential questions. Nat Rev Genet (2013) 1.46
Segmental folding of chromosomes: a basis for structural and regulatory chromosomal neighborhoods? Bioessays (2013) 1.45
A statistical approach for inferring the 3D structure of the genome. Bioinformatics (2014) 1.45
The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances. Dev Cell (2016) 1.45
Lin28A Binds Active Promoters and Recruits Tet1 to Regulate Gene Expression. Mol Cell (2015) 1.44
Functional and topological characteristics of mammalian regulatory domains. Genome Res (2014) 1.43
Multi-tiered Reorganization of the Genome during B Cell Affinity Maturation Anchored by a Germinal Center-Specific Locus Control Region. Immunity (2016) 1.43
Long-lasting alterations to DNA methylation and ncRNAs could underlie the effects of fetal alcohol exposure in mice. Dis Model Mech (2013) 1.42
5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation. Mol Cell (2014) 1.42
Direct reprogramming of fibroblasts into renal tubular epithelial cells by defined transcription factors. Nat Cell Biol (2016) 1.42
Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs. Genome Biol (2013) 1.41
Shared Enhancer Activity in the Limbs and Phallus and Functional Divergence of a Limb-Genital cis-Regulatory Element in Snakes. Dev Cell (2015) 1.40
High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Res (2012) 1.40
Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biol (2015) 1.40
ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs. Genome Res (2014) 1.37
The genomic landscape of cohesin-associated chromatin interactions. Genome Res (2013) 1.36
Synergistic binding of transcription factors to cell-specific enhancers programs motor neuron identity. Nat Neurosci (2013) 1.36
Principles of regulatory information conservation between mouse and human. Nature (2014) 1.34
Evolution of transcription factor binding in metazoans - mechanisms and functional implications. Nat Rev Genet (2014) 1.33
CTCF: the protein, the binding partners, the binding sites and their chromatin loops. Philos Trans R Soc Lond B Biol Sci (2013) 1.32
ANP32E is a histone chaperone that removes H2A.Z from chromatin. Nature (2014) 1.32
Long noncoding RNAs in development and cancer: potential biomarkers and therapeutic targets. Mol Cell Ther (2015) 1.32
Chromatin organization and transcriptional regulation. Curr Opin Genet Dev (2012) 1.31
Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease. Nat Commun (2014) 1.31
Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model. Nat Genet (2013) 1.30
TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells. Genome Res (2012) 1.29
Identification of alternative topological domains in chromatin. Algorithms Mol Biol (2014) 1.29
Global chromatin state analysis reveals lineage-specific enhancers during the initiation of human T helper 1 and T helper 2 cell polarization. Immunity (2013) 1.27
A method for calculating probabilities of fitness consequences for point mutations across the human genome. Nat Genet (2015) 1.27
Identification of active regulatory regions from DNA methylation data. Nucleic Acids Res (2013) 1.26
BRD4 assists elongation of both coding and enhancer RNAs by interacting with acetylated histones. Nat Struct Mol Biol (2014) 1.25
Genome-wide Hi-C analyses in wild-type and mutants reveal high-resolution chromatin interactions in Arabidopsis. Mol Cell (2014) 1.24
Reprogramming to pluripotency using designer TALE transcription factors targeting enhancers. Stem Cell Reports (2013) 1.22
Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome. Nat Genet (2015) 1.21
H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction. Genome Res (2013) 1.20
Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation. Genes Dev (2014) 1.20
Role of Tet proteins in enhancer activity and telomere elongation. Genes Dev (2014) 1.19
Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis. Genome Res (2014) 1.19
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
High-resolution profiling of histone methylations in the human genome. Cell (2007) 85.74
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res (2006) 48.10
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res (2005) 44.08
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet (2007) 32.41
Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (2009) 29.83
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell (2008) 28.29
Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature (2009) 24.41
Mapping and analysis of chromatin state dynamics in nine human cell types. Nature (2011) 24.37
A high-resolution map of active promoters in the human genome. Nature (2005) 24.35
ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature (2009) 18.38
Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature (2012) 18.23
Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell (2007) 16.66
A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol (2011) 16.53
Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A (2010) 15.13
Mediator and cohesin connect gene expression and chromatin architecture. Nature (2010) 14.34
A unique chromatin signature uncovers early developmental enhancers in humans. Nature (2010) 14.02
Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature (2012) 9.75
Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res (2009) 9.40
Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell (2010) 8.74
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell (2012) 8.41
Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science (2010) 7.41
VISTA Enhancer Browser--a database of tissue-specific human enhancers. Nucleic Acids Res (2006) 7.04
CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus. Genes Dev (2006) 6.32
Genomic views of distant-acting enhancers. Nature (2009) 6.27
Enhancer function: new insights into the regulation of tissue-specific gene expression. Nat Rev Genet (2011) 5.27
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (2002) 43.52
Human DNA methylomes at base resolution show widespread epigenomic differences. Nature (2009) 34.27
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
A high-resolution map of active promoters in the human genome. Nature (2005) 24.35
ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature (2009) 18.38
Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature (2012) 18.23
Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell (2007) 16.66
The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol (2010) 13.99
Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature (2011) 13.94
Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39
Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell (2010) 8.74
A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells. Proc Natl Acad Sci U S A (2003) 7.30
Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell (2012) 7.09
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol (2010) 7.00
Genome-wide analysis of protein-DNA interactions. Annu Rev Genomics Hum Genet (2006) 6.47
9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response. Nature (2011) 6.25
Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet (2007) 5.93
Next-generation genomics: an integrative approach. Nat Rev Genet (2010) 5.88
Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell (2011) 5.27
A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature (2013) 5.18
A cis-regulatory map of the Drosophila genome. Nature (2011) 4.80
ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet (2010) 4.32
An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol (2012) 4.15
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res (2008) 4.08
Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome. Cell (2012) 4.00
ASF/SF2-regulated CaMKIIdelta alternative splicing temporally reprograms excitation-contraction coupling in cardiac muscle. Cell (2005) 3.96
Profiling alternative splicing on fiber-optic arrays. Nat Biotechnol (2002) 3.94
Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell (2013) 3.81
An assessment of histone-modification antibody quality. Nat Struct Mol Biol (2010) 3.72
Direct isolation and identification of promoters in the human genome. Genome Res (2005) 3.68
Discovery and annotation of functional chromatin signatures in the human genome. PLoS Comput Biol (2009) 3.61
ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome. PLoS Comput Biol (2008) 3.46
Progressive degeneration of human neural stem cells caused by pathogenic LRRK2. Nature (2012) 3.38
Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res (2011) 3.36
Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A (2014) 3.35
Predictive chromatin signatures in the mammalian genome. Hum Mol Genet (2009) 3.25
Chromatin-bound nuclear pore components regulate gene expression in higher eukaryotes. Cell (2010) 3.04
Finding distal regulatory elements in the human genome. Curr Opin Genet Dev (2009) 3.02
Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. PLoS Genet (2011) 2.87
Chromatin architecture reorganization during stem cell differentiation. Nature (2015) 2.71
Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells. Proc Natl Acad Sci U S A (2013) 2.71
The novel BORIS + CTCF gene family is uniquely involved in the epigenetics of normal biology and cancer. Semin Cancer Biol (2002) 2.66
A lymphotoxin-driven pathway to hepatocellular carcinoma. Cancer Cell (2009) 2.64
BORIS, a novel male germ-line-specific protein associated with epigenetic reprogramming events, shares the same 11-zinc-finger domain with CTCF, the insulator protein involved in reading imprinting marks in the soma. Proc Natl Acad Sci U S A (2002) 2.62
Tumor-associated zinc finger mutations in the CTCF transcription factor selectively alter tts DNA-binding specificity. Cancer Res (2002) 2.52
Follicular dendritic cells emerge from ubiquitous perivascular precursors. Cell (2012) 2.50
Mapping human epigenomes. Cell (2013) 2.44
Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nat Genet (2013) 2.41
Bcl-6 and NF-kappaB cistromes mediate opposing regulation of the innate immune response. Genes Dev (2010) 2.31
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Role of the histone H3 lysine 4 methyltransferase, SET7/9, in the regulation of NF-kappaB-dependent inflammatory genes. Relevance to diabetes and inflammation. J Biol Chem (2008) 2.17
Sensitive ChIP-DSL technology reveals an extensive estrogen receptor alpha-binding program on human gene promoters. Proc Natl Acad Sci U S A (2007) 2.17
Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. Genome Res (2007) 2.16
Fine tuning of craniofacial morphology by distant-acting enhancers. Science (2013) 2.16
Identification of the transcriptional targets of FOXP2, a gene linked to speech and language, in developing human brain. Am J Hum Genet (2007) 2.08
Conditional expression of the CTCF-paralogous transcriptional factor BORIS in normal cells results in demethylation and derepression of MAGE-A1 and reactivation of other cancer-testis genes. Cancer Res (2005) 2.08
Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing. Nat Biotechnol (2013) 2.05
No sex differences in memory formation during general anesthesia. Anesthesiology (2006) 2.04
Dilated cardiomyopathy caused by tissue-specific ablation of SC35 in the heart. EMBO J (2004) 1.88
Endogenous retroviruses and neighboring genes are coordinately repressed by LSD1/KDM1A. Genes Dev (2011) 1.86
Genome-wide prediction of transcription factor binding sites using an integrated model. Genome Biol (2010) 1.84
HiCNorm: removing biases in Hi-C data via Poisson regression. Bioinformatics (2012) 1.77
Reciprocal binding of CTCF and BORIS to the NY-ESO-1 promoter coincides with derepression of this cancer-testis gene in lung cancer cells. Cancer Res (2005) 1.74
Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency. Cell Res (2011) 1.72
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Genome-wide mapping of allele-specific protein-DNA interactions in human cells. Nat Methods (2008) 1.69
RFECS: a random-forest based algorithm for enhancer identification from chromatin state. PLoS Comput Biol (2013) 1.66