Published in Nat Genet on February 04, 2007
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature (2008) 30.29
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
ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature (2009) 18.38
Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet (2008) 18.28
The accessible chromatin landscape of the human genome. Nature (2012) 16.86
A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol (2011) 16.53
Widespread transcription at neuronal activity-regulated enhancers. Nature (2010) 16.52
Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell (2008) 16.38
High-resolution mapping and characterization of open chromatin across the genome. Cell (2008) 15.93
Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A (2010) 15.13
FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell (2008) 14.18
A unique chromatin signature uncovers early developmental enhancers in humans. Nature (2010) 14.02
ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet (2009) 13.12
Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39
Integrative analysis of 111 reference human epigenomes. Nature (2015) 10.32
Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol (2010) 9.84
Initial impact of the sequencing of the human genome. Nature (2011) 9.18
Distinct factors control histone variant H3.3 localization at specific genomic regions. Cell (2010) 8.79
DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature (2011) 8.75
Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell (2010) 8.74
A map of the cis-regulatory sequences in the mouse genome. Nature (2012) 8.74
Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell (2009) 8.69
Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. Cell Stem Cell (2009) 8.62
Super-enhancers in the control of cell identity and disease. Cell (2013) 7.50
Charting histone modifications and the functional organization of mammalian genomes. Nat Rev Genet (2010) 7.39
Model-based analysis of two-color arrays (MA2C). Genome Biol (2007) 7.28
Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer. Cell (2009) 7.09
The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer. Nat Genet (2009) 6.99
Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature (2010) 6.87
Role of conserved non-coding DNA elements in the Foxp3 gene in regulatory T-cell fate. Nature (2010) 6.87
CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet (2011) 6.55
Transcriptional regulation of macrophage polarization: enabling diversity with identity. Nat Rev Immunol (2011) 6.34
Genomic views of distant-acting enhancers. Nature (2009) 6.27
A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling. Cell (2009) 6.26
9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response. Nature (2011) 6.25
Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature (2011) 6.10
A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol (2010) 6.01
Pioneer transcription factors: establishing competence for gene expression. Genes Dev (2011) 6.01
Nucleosome dynamics define transcriptional enhancers. Nat Genet (2010) 5.94
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
The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling. Nat Genet (2009) 5.65
Insights from genomic profiling of transcription factors. Nat Rev Genet (2009) 5.57
Histone methylation: a dynamic mark in health, disease and inheritance. Nat Rev Genet (2012) 5.42
Chromatin structure analyses identify miRNA promoters. Genes Dev (2008) 5.40
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res (2010) 5.40
Enhancer function: new insights into the regulation of tissue-specific gene expression. Nat Rev Genet (2011) 5.27
Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell (2011) 5.27
Functional and mechanistic diversity of distal transcription enhancers. Cell (2011) 5.22
Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals. Cell (2010) 5.22
ATP-dependent chromatin remodeling: genetics, genomics and mechanisms. Cell Res (2011) 4.91
The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet (2008) 4.91
A cis-regulatory map of the Drosophila genome. Nature (2011) 4.80
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. EMBO J (2010) 4.78
Transcriptional architecture and chromatin landscape of the core circadian clock in mammals. Science (2012) 4.77
DOT1L/KMT4 recruitment and H3K79 methylation are ubiquitously coupled with gene transcription in mammalian cells. Mol Cell Biol (2008) 4.56
Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming. Dev Cell (2010) 4.50
ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet (2010) 4.32
A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate. Nat Immunol (2010) 4.32
Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol (2007) 4.30
Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell (2012) 4.22
The GENCODE pseudogene resource. Genome Biol (2012) 4.18
Local DNA topography correlates with functional noncoding regions of the human genome. Science (2009) 4.18
Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding. Genome Res (2008) 4.11
Opposing regulation of the locus encoding IL-17 through direct, reciprocal actions of STAT3 and STAT5. Nat Immunol (2011) 3.91
Genome-wide views of chromatin structure. Annu Rev Biochem (2009) 3.89
Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res (2012) 3.80
Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs. PLoS Genet (2007) 3.75
seqMINER: an integrated ChIP-seq data interpretation platform. Nucleic Acids Res (2010) 3.74
Enhancer decommissioning by LSD1 during embryonic stem cell differentiation. Nature (2012) 3.67
Beta-catenin hits chromatin: regulation of Wnt target gene activation. Nat Rev Mol Cell Biol (2009) 3.67
Modification of enhancer chromatin: what, how, and why? Mol Cell (2013) 3.62
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol (2012) 3.61
The COMPASS family of histone H3K4 methylases: mechanisms of regulation in development and disease pathogenesis. Annu Rev Biochem (2012) 3.61
Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Res (2012) 3.61
Discovery and annotation of functional chromatin signatures in the human genome. PLoS Comput Biol (2009) 3.61
Functional enhancers at the gene-poor 8q24 cancer-linked locus. PLoS Genet (2009) 3.59
Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Genome Res (2011) 3.57
Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment. Cell (2014) 3.52
The RNA polymerase II core promoter - the gateway to transcription. Curr Opin Cell Biol (2008) 3.50
ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome. PLoS Comput Biol (2008) 3.46
Histone H3 lysine 4 trimethylation marks meiotic recombination initiation sites. EMBO J (2008) 3.40
8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC. Proc Natl Acad Sci U S A (2010) 3.37
Deconstructing repression: evolving models of co-repressor action. Nat Rev Genet (2010) 3.29
Global analysis of H3K4 methylation defines MLL family member targets and points to a role for MLL1-mediated H3K4 methylation in the regulation of transcriptional initiation by RNA polymerase II. Mol Cell Biol (2009) 3.26
Predictive chromatin signatures in the mammalian genome. Hum Mol Genet (2009) 3.25
Genomic sequence is highly predictive of local nucleosome depletion. PLoS Comput Biol (2007) 3.24
Genome-wide association of hypoxia-inducible factor (HIF)-1alpha and HIF-2alpha DNA binding with expression profiling of hypoxia-inducible transcripts. J Biol Chem (2009) 3.23
Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell (2011) 3.20
Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart. Proc Natl Acad Sci U S A (2011) 3.18
Reprogramming factor expression initiates widespread targeted chromatin remodeling. Cell Stem Cell (2011) 3.16
Role of nucleosomal occupancy in the epigenetic silencing of the MLH1 CpG island. Cancer Cell (2007) 3.15
H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome. Genome Res (2008) 3.09
Finding distal regulatory elements in the human genome. Curr Opin Genet Dev (2009) 3.02
Epigenetic modifications in pluripotent and differentiated cells. Nat Biotechnol (2010) 3.02
Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development. Nat Genet (2012) 2.94
Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity. Genome Res (2009) 2.87
Breast cancer risk-associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression. Nat Genet (2012) 2.86
A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
WebLogo: a sequence logo generator. Genome Res (2004) 59.58
Scalable molecular dynamics with NAMD. J Comput Chem (2005) 59.49
The diploid genome sequence of an Asian individual. Nature (2008) 46.29
A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A (2004) 44.81
Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (2002) 43.52
Human DNA methylomes at base resolution show widespread epigenomic differences. Nature (2009) 34.27
Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci U S A (2002) 25.47
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
An integrated semiconductor device enabling non-optical genome sequencing. Nature (2011) 20.85
A global map of p53 transcription-factor binding sites in the human genome. Cell (2006) 20.65
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
Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27
The accessible chromatin landscape of the human genome. Nature (2012) 16.86
Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell (2007) 16.66
High-resolution mapping and characterization of open chromatin across the genome. Cell (2008) 15.93
Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res (2009) 15.15
Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol (2005) 14.29
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
Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res (2006) 13.32
Mapping copy number variation by population-scale genome sequencing. Nature (2011) 12.55
Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. Nat Genet (2008) 12.51
Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39
piggyBac transposition reprograms fibroblasts to induced pluripotent stem cells. Nature (2009) 11.27
Sequencing of 50 human exomes reveals adaptation to high altitude. Science (2010) 11.27
The ASTRAL Compendium in 2004. Nucleic Acids Res (2004) 10.03
Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell (2010) 8.74
A map of the cis-regulatory sequences in the mouse genome. Nature (2012) 8.74
Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science (2008) 8.62
Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat Methods (2006) 8.52
A two-gene expression ratio predicts clinical outcome in breast cancer patients treated with tamoxifen. Cancer Cell (2004) 8.06
Automatic atom type and bond type perception in molecular mechanical calculations. J Mol Graph Model (2006) 7.93
Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas. Nat Genet (2012) 7.61
Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat Biotechnol (2009) 7.59
Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer (2005) 7.53
ZDOCK: an initial-stage protein-docking algorithm. Proteins (2003) 7.52
Oncogenic Kras maintains pancreatic tumors through regulation of anabolic glucose metabolism. Cell (2012) 7.36
A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells. Proc Natl Acad Sci U S A (2003) 7.30
Acute renal failure and sepsis. N Engl J Med (2004) 7.18
Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell (2012) 7.09
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol (2010) 7.08
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol (2010) 7.00
High-performance neuroprosthetic control by an individual with tetraplegia. Lancet (2012) 6.66
Genome-wide analysis of protein-DNA interactions. Annu Rev Genomics Hum Genet (2006) 6.47
Detection of functional DNA motifs via statistical over-representation. Nucleic Acids Res (2004) 6.31
9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response. Nature (2011) 6.25
DNase I sensitivity QTLs are a major determinant of human expression variation. Nature (2012) 6.17
Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res (2006) 5.99
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
Next-generation genomics: an integrative approach. Nat Rev Genet (2010) 5.88
The dog genome: survey sequencing and comparative analysis. Science (2003) 5.84
The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Res (2007) 5.67
New loci associated with kidney function and chronic kidney disease. Nat Genet (2010) 5.58
Antitumor activity of rapamycin in a Phase I trial for patients with recurrent PTEN-deficient glioblastoma. PLoS Med (2008) 5.54
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature (2008) 5.54
Predictive value for the Chinese population of the Framingham CHD risk assessment tool compared with the Chinese Multi-Provincial Cohort Study. JAMA (2004) 5.34
The oyster genome reveals stress adaptation and complexity of shell formation. Nature (2012) 5.30
Global mapping of c-Myc binding sites and target gene networks in human B cells. Proc Natl Acad Sci U S A (2006) 5.27
Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell (2011) 5.27
Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals. Cell (2010) 5.22
A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature (2013) 5.18
De novo mutations in histone-modifying genes in congenital heart disease. Nature (2013) 5.15