Published in J Biol Chem on September 05, 2012
Insights into neural crest development and evolution from genomic analysis. Genome Res (2013) 1.02
Understanding spatial organizations of chromosomes via statistical analysis of Hi-C data. Quant Biol (2013) 0.93
Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes. Crit Rev Biochem Mol Biol (2015) 0.85
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
The sequence of the human genome. Science (2001) 101.55
High-resolution profiling of histone methylations in the human genome. Cell (2007) 85.74
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature (2007) 65.18
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
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods (2007) 45.04
Genome-wide location and function of DNA binding proteins. Science (2000) 31.25
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
A high-resolution map of active promoters in the human genome. Nature (2005) 24.35
Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell (2010) 23.97
Capturing chromosome conformation. Science (2002) 23.93
Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature (2001) 21.55
Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet (2008) 18.28
TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res (2000) 15.70
An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol (2008) 13.96
Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res (2006) 13.32
ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet (2009) 13.12
An oestrogen-receptor-alpha-bound human chromatin interactome. Nature (2009) 12.16
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods (2008) 11.61
Looping and interaction between hypersensitive sites in the active beta-globin locus. Mol Cell (2002) 11.35
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol (2009) 11.28
Cofactor dynamics and sufficiency in estrogen receptor-regulated transcription. Cell (2000) 11.10
Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet (2006) 11.02
Estrogen receptor-alpha directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell (2003) 10.42
A census of human transcription factors: function, expression and evolution. Nat Rev Genet (2009) 9.19
Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet (2006) 8.99
Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res (2008) 8.89
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics (2009) 8.33
CTCF mediates interchromosomal colocalization between Igf2/H19 and Wsb1/Nf1. Science (2006) 7.68
Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences. Genome Res (2005) 7.09
Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes Dev (2002) 6.74
CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet (2011) 6.55
Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome. Genome Res (2006) 6.54
FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics (2008) 6.53
Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat Genet (2011) 5.97
Next-generation genomics: an integrative approach. Nat Rev Genet (2010) 5.88
Insights from genomic profiling of transcription factors. Nat Rev Genet (2009) 5.57
Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res (2006) 4.32
Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol (2011) 4.13
Myc dynamically and preferentially relocates to a transcription factory occupied by Igh. PLoS Biol (2007) 3.82
Structure and function of the interferon-beta enhanceosome. Cold Spring Harb Symp Quant Biol (1998) 3.81
High-throughput screening of chromatin immunoprecipitates using CpG-island microarrays. Methods Enzymol (2004) 3.76
Modeling ChIP sequencing in silico with applications. PLoS Comput Biol (2008) 3.48
CisModule: de novo discovery of cis-regulatory modules by hierarchical mixture modeling. Proc Natl Acad Sci U S A (2004) 3.37
Identification of unknown target genes of human transcription factors using chromatin immunoprecipitation. Methods (2002) 3.37
ZNF274 recruits the histone methyltransferase SETDB1 to the 3' ends of ZNF genes. PLoS One (2010) 3.15
Transcription factories: gene expression in unions? Nat Rev Genet (2009) 2.92
Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. Genome Res (2006) 2.82
Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nucleic Acids Res (2009) 2.74
Comparative analysis of the ternary complex factors Elk-1, SAP-1a and SAP-2 (ERP/NET). EMBO J (1995) 2.72
Dimerization specificity of Arabidopsis MADS domain homeotic proteins APETALA1, APETALA3, PISTILLATA, and AGAMOUS. Proc Natl Acad Sci U S A (1996) 2.68
Genomics tools for unraveling chromosome architecture. Nat Biotechnol (2010) 2.63
The enhanceosome. Curr Opin Struct Biol (2008) 2.56
A wave of nascent transcription on activated human genes. Proc Natl Acad Sci U S A (2009) 2.18
Detection of in vivo protein-DNA interactions using DamID in mammalian cells. Nat Protoc (2007) 2.05
Integrative model of genomic factors for determining binding site selection by estrogen receptor-α. Mol Syst Biol (2010) 2.04
Chromosome crosstalk in three dimensions. Nature (2009) 1.91
A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--a case study using E2F1. Genome Res (2006) 1.74
Intra- and inter-chromosomal interactions correlate with CTCF binding genome wide. Mol Syst Biol (2010) 1.59
W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data. Bioinformatics (2010) 1.57
cis-Regulatory control circuits in development. Dev Biol (2004) 1.54
PICS: probabilistic inference for ChIP-seq. Biometrics (2011) 1.37
Using ChIP-seq technology to generate high-resolution profiles of histone modifications. Methods Mol Biol (2011) 1.37
Characterizing the physical genome. Nat Genet (2002) 1.35
Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth. EMBO J (2011) 1.33
Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages. Nucleic Acids Res (2012) 1.32
Estrogen-mediated epigenetic repression of large chromosomal regions through DNA looping. Genome Res (2010) 1.18
Interactions of the Mcm1 MADS box protein with cofactors that regulate mating in yeast. Mol Cell Biol (2002) 1.09
Using ChIP-seq technology to identify targets of zinc finger transcription factors. Methods Mol Biol (2010) 1.06
ChIP-Seq using high-throughput DNA sequencing for genome-wide identification of transcription factor binding sites. Methods Enzymol (2010) 1.03
Systematic identification of conserved motif modules in the human genome. BMC Genomics (2010) 0.91
Thousands of cis-regulatory sequence combinations are shared by Arabidopsis and poplar. Plant Physiol (2011) 0.90
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell (2007) 30.22
The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol (2010) 13.99
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol (2010) 7.00
Suz12 binds to silenced regions of the genome in a cell-type-specific manner. Genome Res (2006) 6.75
Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes Dev (2002) 6.74
Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome. Genome Res (2006) 6.54
T-bet regulates the terminal maturation and homeostasis of NK and Valpha14i NKT cells. Immunity (2004) 6.43
Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27. Genes Dev (2004) 6.19
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res (2008) 4.08
Integrated epigenomic analyses of neuronal MeCP2 reveal a role for long-range interaction with active genes. Proc Natl Acad Sci U S A (2007) 4.00
Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy. Mol Cell (2009) 3.96
High-throughput screening of chromatin immunoprecipitates using CpG-island microarrays. Methods Enzymol (2004) 3.76
Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs. PLoS Genet (2007) 3.75
Identification of unknown target genes of human transcription factors using chromatin immunoprecipitation. Methods (2002) 3.37
Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A (2014) 3.35
ZNF274 recruits the histone methyltransferase SETDB1 to the 3' ends of ZNF genes. PLoS One (2010) 3.15
Characterizing transcription factor binding sites using formaldehyde crosslinking and immunoprecipitation. Methods (2002) 2.99
A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members. Genome Res (2007) 2.97
Comparison of sample preparation methods for ChIP-chip assays. Biotechniques (2006) 2.89
Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. Genome Res (2006) 2.82
Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nucleic Acids Res (2009) 2.74
Myc recruits P-TEFb to mediate the final step in the transcriptional activation of the cad promoter. J Biol Chem (2002) 2.68
Combinatorial analysis of transcription factor partners reveals recruitment of c-MYC to estrogen receptor-alpha responsive promoters. Mol Cell (2006) 2.48
Analysis of Myc bound loci identified by CpG island arrays shows that Max is essential for Myc-dependent repression. Curr Biol (2003) 2.47
Genome-scale ChIP-chip analysis using 10,000 human cells. Biotechniques (2007) 2.28
Identification of novel pRb binding sites using CpG microarrays suggests that E2F recruits pRb to specific genomic sites during S phase. Oncogene (2003) 2.22
Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3. Genome Biol (2012) 2.19
KAP1 protein: an enigmatic master regulator of the genome. J Biol Chem (2011) 2.15
Probing chromatin immunoprecipitates with CpG-island microarrays to identify genomic sites occupied by DNA-binding proteins. Methods Enzymol (2003) 2.12
E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites. Genome Res (2008) 2.07
E2F6 negatively regulates BRCA1 in human cancer cells without methylation of histone H3 on lysine 9. J Biol Chem (2003) 2.02
Loss of estrogen receptor signaling triggers epigenetic silencing of downstream targets in breast cancer. Cancer Res (2004) 1.97
CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome. Nucleic Acids Res (2005) 1.89
Identification of genes directly regulated by the oncogene ZNF217 using chromatin immunoprecipitation (ChIP)-chip assays. J Biol Chem (2007) 1.88
Selective regulation of lymphopoiesis and leukemogenesis by individual zinc fingers of Ikaros. Nat Immunol (2013) 1.88
Identification of the polycomb group protein SU(Z)12 as a potential molecular target for human cancer therapy. Mol Cancer Ther (2003) 1.84
A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--a case study using E2F1. Genome Res (2006) 1.74
Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263. J Biol Chem (2009) 1.71
DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nat Genet (2013) 1.64
The identification of E2F1-specific target genes. Proc Natl Acad Sci U S A (2002) 1.63
W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data. Bioinformatics (2010) 1.57
N-Myc regulates a widespread euchromatic program in the human genome partially independent of its role as a classical transcription factor. Cancer Res (2008) 1.52
DNA methylation of the Trip10 promoter accelerates mesenchymal stem cell lineage determination. Biochem Biophys Res Commun (2010) 1.52
Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches. Genome Res (2007) 1.50
Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells. Genome Res (2008) 1.45
W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data. Bioinformatics (2009) 1.42
Genomic approaches that aid in the identification of transcription factor target genes. Exp Biol Med (Maywood) (2004) 1.41
Epigenetic changes during disease progression in a murine model of human chronic lymphocytic leukemia. Proc Natl Acad Sci U S A (2009) 1.39
Functional analysis of KAP1 genomic recruitment. Mol Cell Biol (2011) 1.39
Using ChIP-seq technology to generate high-resolution profiles of histone modifications. Methods Mol Biol (2011) 1.37
High resolution detection and analysis of CpG dinucleotides methylation using MBD-Seq technology. PLoS One (2011) 1.35
Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes. PLoS One (2011) 1.34
5-azacytidine treatment reorganizes genomic histone modification patterns. Epigenetics (2010) 1.34
Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm. Genome Res (2013) 1.33
L3MBTL2 protein acts in concert with PcG protein-mediated monoubiquitination of H2A to establish a repressive chromatin structure. Mol Cell (2011) 1.32
Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages. Nucleic Acids Res (2012) 1.32
Genetic framework for GATA factor function in vascular biology. Proc Natl Acad Sci U S A (2011) 1.29
The transcription factor encyclopedia. Genome Biol (2012) 1.28
MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data. Nucleic Acids Res (2006) 1.28
OMGProm: a database of orthologous mammalian gene promoters. Bioinformatics (2004) 1.27
Cross-talk between site-specific transcription factors and DNA methylation states. J Biol Chem (2013) 1.24
Genome-wide analysis of transcription factor E2F1 mutant proteins reveals that N- and C-terminal protein interaction domains do not participate in targeting E2F1 to the human genome. J Biol Chem (2011) 1.18
MicroRNA-31 predicts the presence of lymph node metastases and survival in patients with lung adenocarcinoma. Clin Cancer Res (2013) 1.17
Targeted methylation of two tumor suppressor genes is sufficient to transform mesenchymal stem cells into cancer stem/initiating cells. Cancer Res (2011) 1.15
Autophagy driven by a master regulator of hematopoiesis. Mol Cell Biol (2011) 1.13
Analysis of the mechanisms mediating tumor-specific changes in gene expression in human liver tumors. Cancer Res (2008) 1.13
Epigenetic silencing mediated through activated PI3K/AKT signaling in breast cancer. Cancer Res (2011) 1.13
Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes. Genome Biol (2014) 1.12
Epigenetic modulation of miR-122 facilitates human embryonic stem cell self-renewal and hepatocellular carcinoma proliferation. PLoS One (2011) 1.11
Spark: a navigational paradigm for genomic data exploration. Genome Res (2012) 1.10
Amplification of distant estrogen response elements deregulates target genes associated with tamoxifen resistance in breast cancer. Cancer Cell (2013) 1.09
Using ChIP-seq technology to identify targets of zinc finger transcription factors. Methods Mol Biol (2010) 1.06
Three-tiered role of the pioneer factor GATA2 in promoting androgen-dependent gene expression in prostate cancer. Nucleic Acids Res (2014) 1.05
Recombinant antibodies to histone post-translational modifications. Nat Methods (2013) 1.05
The use of transient chromatin immunoprecipitation assays to test models for E2F1-specific transcriptional activation. J Biol Chem (2004) 1.05
Inference of hierarchical regulatory network of estrogen-dependent breast cancer through ChIP-based data. BMC Syst Biol (2010) 1.03
Genome-wide binding of the orphan nuclear receptor TR4 suggests its general role in fundamental biological processes. BMC Genomics (2010) 1.01
QChIPat: a quantitative method to identify distinct binding patterns for two biological ChIP-seq samples in different experimental conditions. BMC Genomics (2013) 0.98
Hierarchical modularity in ERα transcriptional network is associated with distinct functions and implicates clinical outcomes. Sci Rep (2012) 0.94
A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-alpha. Bioinformatics (2006) 0.94
ZBTB33 binds unmethylated regions of the genome associated with actively expressed genes. Epigenetics Chromatin (2013) 0.93
ChIP-seq defined genome-wide map of TGFβ/SMAD4 targets: implications with clinical outcome of ovarian cancer. PLoS One (2011) 0.92
Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors. Nucleic Acids Res (2013) 0.89
Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation. BMC Genomics (2013) 0.87
LOcating non-unique matched tags (LONUT) to improve the detection of the enriched regions for ChIP-seq data. PLoS One (2013) 0.87