Published in Genome Res on September 14, 2010
Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO J (2011) 3.16
Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Mol Cell (2011) 2.77
H3K4 tri-methylation provides an epigenetic signature of active enhancers. EMBO J (2011) 2.38
ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity. Nucleic Acids Res (2011) 2.23
H2A.Z facilitates access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation. Cell Stem Cell (2012) 2.20
Gene induction and repression during terminal erythropoiesis are mediated by distinct epigenetic changes. Blood (2011) 1.43
Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells. Nucleic Acids Res (2011) 1.40
A misplaced lncRNA causes brachydactyly in humans. J Clin Invest (2012) 1.36
Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genes. Nat Genet (2015) 1.08
Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes. BMC Bioinformatics (2011) 1.04
Predicting expression: the complementary power of histone modification and transcription factor binding data. Epigenetics Chromatin (2014) 1.03
CHD3 protein recognizes and regulates methylated histone H3 lysines 4 and 27 over a subset of targets in the rice genome. Proc Natl Acad Sci U S A (2012) 1.02
Targeting H3K4 trimethylation in Huntington disease. Proc Natl Acad Sci U S A (2013) 0.98
Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features. BMC Genomics (2012) 0.96
Stage and gene specific signatures defined by histones H3K4me2 and H3K27me3 accompany mammalian retina maturation in vivo. PLoS One (2012) 0.93
Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements. BMC Biol (2011) 0.93
Predicting cell types and genetic variations contributing to disease by combining GWAS and epigenetic data. PLoS One (2013) 0.92
Sequential Monte Carlo multiple testing. Bioinformatics (2011) 0.90
Chromatin signature discovery via histone modification profile alignments. Nucleic Acids Res (2012) 0.89
Redistribution of H3K4me2 on neural tissue specific genes during mouse brain development. BMC Genomics (2012) 0.87
The DEK oncoprotein binds to highly and ubiquitously expressed genes with a dual role in their transcriptional regulation. Mol Cancer (2014) 0.86
Membrane-to-nucleus signaling links insulin-like growth factor-1- and stem cell factor-activated pathways. PLoS One (2013) 0.85
New insights from existing sequence data: generating breakthroughs without a pipette. Mol Cell (2013) 0.84
KMT2D regulates specific programs in heart development via histone H3 lysine 4 di-methylation. Development (2016) 0.83
GATA-1 genome-wide occupancy associates with distinct epigenetic profiles in mouse fetal liver erythropoiesis. Nucleic Acids Res (2013) 0.83
Computational study of associations between histone modification and protein-DNA binding in yeast genome by integrating diverse information. BMC Genomics (2011) 0.82
Balancing selection on a regulatory region exhibiting ancient variation that predates human-neandertal divergence. PLoS Genet (2013) 0.81
IL-23R is Epigenetically Regulated and Modulated by Chemotherapy in Non-Small Cell Lung Cancer. Front Oncol (2013) 0.79
Integrative genome-wide chromatin signature analysis using finite mixture models. BMC Genomics (2012) 0.78
Histone H2B Monoubiquitination Mediated by HISTONE MONOUBIQUITINATION1 and HISTONE MONOUBIQUITINATION2 Is Involved in Anther Development by Regulating Tapetum Degradation-Related Genes in Rice. Plant Physiol (2015) 0.78
Epigenetic regulation of glucose transporters in non-small cell lung cancer. Cancers (Basel) (2011) 0.78
The Chromatin Protein DUET/MMD1 Controls Expression of the Meiotic Gene TDM1 during Male Meiosis in Arabidopsis. PLoS Genet (2015) 0.78
Whole genome DNA methylation: beyond genes silencing. Oncotarget (2016) 0.78
HSFA2 orchestrates transcriptional dynamics after heat stress in Arabidopsis thaliana. Transcription (2016) 0.75
Identification of recurrent combinatorial patterns of chromatin modifications at promoters across various tissue types. BMC Bioinformatics (2016) 0.75
The KDM5 family is required for activation of pro-proliferative cell cycle genes during adipocyte differentiation. Nucleic Acids Res (2016) 0.75
Pax6 associates with H3K4-specific histone methyltransferases Mll1, Mll2, and Set1a and regulates H3K4 methylation at promoters and enhancers. Epigenetics Chromatin (2016) 0.75
Broad-Enrich: functional interpretation of large sets of broad genomic regions. Bioinformatics (2014) 0.75
Promoter H3K4 methylation dynamically reinforces activation-induced pathways in human CD4 T cells. Genes Immun (2016) 0.75
Muscle-relevant genes marked by stable H3K4me2/3 profiles and enriched MyoD binding during myogenic differentiation. PLoS One (2017) 0.75
Distinct functions of histone H3, lysine 4 methyltransferases in normal and malignant hematopoiesis. Curr Opin Hematol (2017) 0.75
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol (2004) 101.91
High-resolution profiling of histone methylations in the human genome. Cell (2007) 85.74
Chromatin modifications and their function. Cell (2007) 55.98
A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell (2006) 48.80
A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A (2004) 44.81
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet (2007) 32.41
Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature (2008) 30.29
The role of chromatin during transcription. Cell (2007) 26.48
Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature (2009) 24.41
A chromatin landmark and transcription initiation at most promoters in human cells. Cell (2007) 23.41
Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics (2002) 20.59
Genomic maps and comparative analysis of histone modifications in human and mouse. Cell (2005) 18.96
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 mammalian epigenome. Cell (2007) 18.13
Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet (2006) 17.19
More powerful procedures for multiple significance testing. Stat Med (1990) 17.12
High-resolution mapping and characterization of open chromatin across the genome. Cell (2008) 15.93
FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell (2008) 14.18
TM4 microarray software suite. Methods Enzymol (2006) 13.78
Nuclease hypersensitive sites in chromatin. Annu Rev Biochem (1988) 13.48
Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell (1999) 11.90
A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci U S A (2006) 10.63
Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet (2009) 8.11
Methylation of histone H3 Lys 4 in coding regions of active genes. Proc Natl Acad Sci U S A (2002) 7.67
Cellular memory and the histone code. Cell (2002) 7.30
Genomic views of distant-acting enhancers. Nature (2009) 6.27
Chromatin organization marks exon-intron structure. Nat Struct Mol Biol (2009) 5.90
The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Res (2007) 5.67
Nucleosome positioning as a determinant of exon recognition. Nat Struct Mol Biol (2009) 5.14
BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams. BMC Genomics (2008) 5.07
Remote control of gene transcription. Hum Mol Genet (2005) 4.80
Histone modification levels are predictive for gene expression. Proc Natl Acad Sci U S A (2010) 4.00
Nucleosomes are well positioned in exons and carry characteristic histone modifications. Genome Res (2009) 3.95
Biased chromatin signatures around polyadenylation sites and exons. Mol Cell (2009) 3.74
Discovery and annotation of functional chromatin signatures in the human genome. PLoS Comput Biol (2009) 3.61
Expression analysis of G Protein-Coupled Receptors in mouse macrophages. Immunome Res (2008) 3.54
Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites. Proc Natl Acad Sci U S A (2004) 3.41
Predictive chromatin signatures in the mammalian genome. Hum Mol Genet (2009) 3.25
Genome-wide pattern of TCF7L2/TCF4 chromatin occupancy in colorectal cancer cells. Mol Cell Biol (2008) 3.02
Analysis of interleukin-21-induced Prdm1 gene regulation reveals functional cooperation of STAT3 and IRF4 transcription factors. Immunity (2009) 2.89
The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation. Genes Dev (2010) 2.47
Characterization of human epigenomes. Curr Opin Genet Dev (2009) 2.17
Differential H3K4 methylation identifies developmentally poised hematopoietic genes. Dev Cell (2008) 1.89
Determination of enriched histone modifications in non-genic portions of the human genome. BMC Genomics (2009) 1.80
A glimpse into the epigenetic landscape of gene regulation. Curr Opin Genet Dev (2008) 1.41
Transcriptional features of genomic regulatory blocks. Genome Biol (2009) 1.37
Definition, conservation and epigenetics of housekeeping and tissue-enriched genes. BMC Genomics (2009) 1.30
Defining the chromatin signature of inducible genes in T cells. Genome Biol (2009) 1.15
Developmental mechanisms and cis-regulatory codes. Curr Opin Genet Dev (2006) 1.11
Duality of enhancer functioning mode revealed in a reduced TCR beta gene enhancer knockin mouse model. J Immunol (2009) 0.83
BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol (2012) 3.24
Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters. Nat Struct Mol Biol (2011) 2.79
H3K4 tri-methylation provides an epigenetic signature of active enhancers. EMBO J (2011) 2.38
Regulation of TCRbeta gene assembly by a promoter/enhancer holocomplex. Immunity (2006) 2.23
DNMT1-interacting RNAs block gene-specific DNA methylation. Nature (2013) 2.04
Genome-wide RNA polymerase II: not genes only! Trends Biochem Sci (2008) 2.02
Characterization of lysine 56 of histone H3 as an acetylation site in Saccharomyces cerevisiae. J Biol Chem (2005) 1.95
Essential function for SWI-SNF chromatin-remodeling complexes in the promoter-directed assembly of Tcrb genes. Nat Immunol (2007) 1.94
Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36. Nat Struct Mol Biol (2011) 1.85
CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters. Genome Res (2012) 1.65
Threonine-4 of mammalian RNA polymerase II CTD is targeted by Polo-like kinase 3 and required for transcriptional elongation. EMBO J (2012) 1.55
Uncleaved TFIIA is a substrate for taspase 1 and active in transcription. Mol Cell Biol (2006) 1.51
TLX homeodomain oncogenes mediate T cell maturation arrest in T-ALL via interaction with ETS1 and suppression of TCRα gene expression. Cancer Cell (2012) 1.36
Promoter activation by enhancer-dependent and -independent loading of activator and coactivator complexes. Mol Cell (2002) 1.31
Differential responses of immune cells to type I interferon contribute to host resistance to viral infection. Cell Host Microbe (2012) 1.12
Coronin-1A links cytoskeleton dynamics to TCR alpha beta-induced cell signaling. PLoS One (2008) 1.07
Coronin-1 expression in T lymphocytes: insights into protein function during T cell development and activation. Int Immunol (2004) 1.05
Divergent transcription is associated with promoters of transcriptional regulators. BMC Genomics (2013) 1.03
CoCAS: a ChIP-on-chip analysis suite. Bioinformatics (2009) 0.95
Membrane-cytoskeleton interactions during the formation of the immunological synapse and subsequent T-cell activation. Immunol Rev (2002) 0.95
Wdr12, a mouse gene encoding a novel WD-Repeat Protein with a notchless-like amino-terminal domain. Genomics (2002) 0.93
In vivo reinsertion of excised episomes by the V(D)J recombinase: a potential threat to genomic stability. PLoS Biol (2007) 0.92
Active STAT5 regulates T-bet and eomesodermin expression in CD8 T cells and imprints a T-bet-dependent Tc1 program with repressed IL-6/TGF-β1 signaling. J Immunol (2013) 0.89
Regulation of V(D)J recombination. Curr Opin Immunol (2006) 0.89
Assessing the efficiency and significance of Methylated DNA Immunoprecipitation (MeDIP) assays in using in vitro methylated genomic DNA. BMC Res Notes (2010) 0.88
Experimental assessment of the contribution of electrodynamic interactions to long-distance recruitment of biomolecular partners: Theoretical basis. Phys Rev E Stat Nonlin Soft Matter Phys (2012) 0.88
Assessing the role of the T cell receptor beta gene enhancer in regulating coding joint formation during V(D)J recombination. J Biol Chem (2003) 0.87
Epigenetic control of Tcrb gene rearrangement. Semin Immunol (2010) 0.87
Characterisation of genome-wide PLZF/RARA target genes. PLoS One (2011) 0.86
Extensive molecular mapping of TCRα/δ- and TCRβ-involved chromosomal translocations reveals distinct mechanisms of oncogene activation in T-ALL. Blood (2012) 0.86
Initiation of V(D)J recombination by Dbeta-associated recombination signal sequences: a critical control point in TCRbeta gene assembly. PLoS One (2009) 0.85
Methodological aspects of whole-genome bisulfite sequencing analysis. Brief Bioinform (2014) 0.84
C/EBPα is required for development of dendritic cell progenitors. Blood (2013) 0.83
Normal immune system development in mice lacking the Deltex-1 RING finger domain. Mol Cell Biol (2005) 0.83
Duality of enhancer functioning mode revealed in a reduced TCR beta gene enhancer knockin mouse model. J Immunol (2009) 0.83
Control of IL-2Ralpha gene expression: structural changes within the proximal enhancer/core promoter during T-cell development. Nucleic Acids Res (2002) 0.82
Epigenetic aspects of lymphocyte antigen receptor gene rearrangement or 'when stochasticity completes randomness'. Immunology (2013) 0.82
Restriction endonuclease accessibility as a determinant of altered chromatin structure. Methods Mol Biol (2004) 0.80
The gene signature in CCAAT-enhancer-binding protein α dysfunctional acute myeloid leukemia predicts responsiveness to histone deacetylase inhibitors. Haematologica (2013) 0.80
TCR beta allelic exclusion in dynamical models of V(D)J recombination based on allele independence. J Immunol (2010) 0.80
Reversal of microRNA-150 silencing disadvantages crizotinib-resistant NPM-ALK(+) cell growth. J Clin Invest (2015) 0.78
Molecular genetics at the T-cell receptor beta locus: insights into the regulation of V(D)J recombination. Adv Exp Med Biol (2009) 0.78
[Hypermethylation of CpG island in promoter region of MEIS1 gene and its expression in HOX11(+) acute T lymphoblastic leukemia]. Zhonghua Yi Xue Za Zhi (2013) 0.76
Epigenetic regulation of antigen receptor gene rearrangement. F1000 Biol Rep (2010) 0.76
Processing ChIP-chip data: from the scanner to the browser. Methods Mol Biol (2011) 0.75
Alpha beta T-cell development is not affected by inversion of TCR beta gene enhancer sequences: polar enhancement of gene expression regardless of enhancer orientation. Immunology (2003) 0.75
[Alpha/beta versus gamma/delta T cell development: a choice linked to the transcription factor Sox13]. Med Sci (Paris) (2007) 0.75
[Deciphering functional activity of TLX homeodomain oncogenes in T-ALL: a clue for a differentiating therapy?]. Med Sci (Paris) (2012) 0.75
Potassium permanganate as a probe to map DNA-protein interactions in vivo. J Biochem Biophys Methods (2004) 0.75
Expression profiling in mouse fetal thymus reveals clusters of coordinately expressed genes that mark individual stages of T-cell ontogeny. Immunogenetics (2002) 0.75