Published in Genome Biol on January 01, 2006
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 map of the cis-regulatory sequences in the mouse genome. Nature (2012) 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
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
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
Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells. Proc Natl Acad Sci U S A (2013) 2.71
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
ChIP-chip: data, model, and analysis. Biometrics (2007) 2.27
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
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
Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing. Nat Biotechnol (2013) 2.05
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
Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency. Cell Res (2011) 1.72
The transcriptional regulatory code of eukaryotic cells--insights from genome-wide analysis of chromatin organization and transcription factor binding. Curr Opin Cell Biol (2006) 1.71
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
Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine. Nat Protoc (2012) 1.66
Bayesian inference of spatial organizations of chromosomes. PLoS Comput Biol (2013) 1.66
Prediction of regulatory elements in mammalian genomes using chromatin signatures. BMC Bioinformatics (2008) 1.64
Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. Elife (2013) 1.64
Genome organization and long-range regulation of gene expression by enhancers. Curr Opin Cell Biol (2013) 1.63
Unraveling epigenetic regulation in embryonic stem cells. Cell Stem Cell (2008) 1.57
Transcription: Enhancers make non-coding RNA. Nature (2010) 1.54
PU.1 and C/EBP(alpha) synergistically program distinct response to NF-kappaB activation through establishing monocyte specific enhancers. Proc Natl Acad Sci U S A (2011) 1.30
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
beta-Catenin activates the growth factor endothelin-1 in colon cancer cells. Oncogene (2005) 1.21
Transcriptional regulation by Pol II(G) involving mediator and competitive interactions of Gdown1 and TFIIF with Pol II. Mol Cell (2012) 1.18
An integrated approach to identifying cis-regulatory modules in the human genome. PLoS One (2009) 1.16
Relative roles of genetic background and variation in PspA in the ability of antibodies to PspA to protect against capsular type 3 and 4 strains of Streptococcus pneumoniae. Infect Immun (2003) 1.15
Vaccine-induced human antibodies to PspA augment complement C3 deposition on Streptococcus pneumoniae. Microb Pathog (2007) 1.13
Positive inter-regulation between beta-catenin/T cell factor-4 signaling and endothelin-1 signaling potentiates proliferation and survival of prostate cancer cells. Mol Pharmacol (2005) 1.13
ChIP-chip for genome-wide analysis of protein binding in mammalian cells. Curr Protoc Mol Biol (2007) 1.11
CBX3 regulates efficient RNA processing genome-wide. Genome Res (2012) 1.10
Polycomb-like 3 promotes polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal. PLoS Genet (2012) 1.07
Regulation of DNA methylation turnover at LTR retrotransposons and imprinted loci by the histone methyltransferase Setdb1. Proc Natl Acad Sci U S A (2014) 1.04
Enhancers: multi-dimensional signal integrators. Transcription (2012) 1.02
Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing. Genome Biol (2010) 1.01
Developmental biology. Enhancing pluripotency and lineage specification. Science (2013) 0.99
Tet-mediated covalent labelling of 5-methylcytosine for its genome-wide detection and sequencing. Nat Commun (2013) 0.99
Genome-wide location analysis: insights on transcriptional regulation. Hum Mol Genet (2006) 0.96
Mnt-deficient mammary glands exhibit impaired involution and tumors with characteristics of myc overexpression. Cancer Res (2006) 0.94
Comparative annotation of functional regions in the human genome using epigenomic data. Nucleic Acids Res (2013) 0.94
Combined gene expression and DNA occupancy profiling identifies potential therapeutic targets of t(8;21) AML. Blood (2012) 0.92
p16(INK4a) -mediated suppression of telomerase in normal and malignant human breast cells. Aging Cell (2010) 0.88
Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual. Nucleic Acids Res (2011) 0.88
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Programmed Death-Ligand 1 Expression Is Common in Gastric Cancer Associated With Epstein-Barr Virus or Microsatellite Instability. Am J Surg Pathol (2016) 0.83
Mapping higher order structure of chromatin domains. Nat Genet (2011) 0.83
Histone acetyltransferase cofactor Trrap maintains self-renewal and restricts differentiation of embryonic stem cells. Stem Cells (2013) 0.83
Clinical observation on removal of small foreign bodies touching the optic nerve in the deep orbital region: a case series. Orbit (2014) 0.82
Global identification of transcriptional regulators of pluripotency and differentiation in embryonic stem cells. Nucleic Acids Res (2012) 0.80
Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells. Genome Res (2013) 0.79
STAR: an integrated solution to management and visualization of sequencing data. Bioinformatics (2013) 0.78
Corrigendum: Human body epigenome maps reveal noncanonical DNA methylation variation. Nature (2015) 0.77
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
SERPINB13 is a novel RUNX1 target gene. Biochem Biophys Res Commun (2011) 0.76
Effects of aminoguanidine on retinal apoptosis in mice with oxygen-induced retinopathy. Int J Ophthalmol (2013) 0.76
Comparative study of modified and conventional secondary hydroxyapatite orbital implantations. Int J Ophthalmol (2013) 0.75
Effects of minocycline on expression of bcl-2, bax in early retinal neuropathy of diabetes in rats. Int J Ophthalmol (2011) 0.75
Preliminary in vivo study of an intra-aortic impeller pump driven by an extracorporeal whirling magnet. Artif Organs (2002) 0.75
[In vivo and in vitro evaluation of inflow cannula of left ventricular assist]. Zhonghua Wai Ke Za Zhi (2003) 0.75