Published in Nature on February 12, 2009
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol (2010) 39.63
GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol (2010) 16.72
Widespread transcription at neuronal activity-regulated enhancers. Nature (2010) 16.52
Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A (2010) 15.13
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
lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature (2011) 11.31
Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell (2013) 9.55
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res (2009) 9.42
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
Super-enhancers in the control of cell identity and disease. Cell (2013) 7.50
Modular regulatory principles of large non-coding RNAs. Nature (2012) 7.42
Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science (2010) 7.41
Charting histone modifications and the functional organization of mammalian genomes. Nat Rev Genet (2010) 7.39
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
Most "dark matter" transcripts are associated with known genes. PLoS Biol (2010) 6.60
CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet (2011) 6.55
Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat Rev Genet (2011) 6.52
Genomic views of distant-acting enhancers. Nature (2009) 6.27
DNase I sensitivity QTLs are a major determinant of human expression variation. Nature (2012) 6.17
Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature (2011) 6.10
Pioneer transcription factors: establishing competence for gene expression. Genes Dev (2011) 6.01
Next-generation genomics: an integrative approach. Nat Rev Genet (2010) 5.88
Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat Genet (2011) 5.70
Insights from genomic profiling of transcription factors. Nat Rev Genet (2009) 5.57
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
Functional and mechanistic diversity of distal transcription enhancers. Cell (2011) 5.22
A validated regulatory network for Th17 cell specification. Cell (2012) 4.82
A cis-regulatory map of the Drosophila genome. Nature (2011) 4.80
Massively parallel functional dissection of mammalian enhancers in vivo. Nat Biotechnol (2012) 4.51
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
Reconstructing and reprogramming the tumor-propagating potential of glioblastoma stem-like cells. Cell (2014) 4.04
Opposing regulation of the locus encoding IL-17 through direct, reciprocal actions of STAT3 and STAT5. Nat Immunol (2011) 3.91
Combinatorial binding predicts spatio-temporal cis-regulatory activity. Nature (2009) 3.85
Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res (2012) 3.80
Principles for the post-GWAS functional characterization of cancer risk loci. Nat Genet (2011) 3.73
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
Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res (2013) 3.61
Functional enhancers at the gene-poor 8q24 cancer-linked locus. PLoS Genet (2009) 3.59
Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat Biotechnol (2015) 3.56
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
Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A (2014) 3.35
Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature (2011) 3.30
Deconstructing repression: evolving models of co-repressor action. Nat Rev Genet (2010) 3.29
Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart. Proc Natl Acad Sci U S A (2011) 3.18
Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell (2015) 3.10
Finding distal regulatory elements in the human genome. Curr Opin Genet Dev (2009) 3.02
Large-scale discovery of enhancers from human heart tissue. Nat Genet (2011) 2.70
Direct lineage conversions: unnatural but useful? Nat Biotechnol (2011) 2.69
ETV1 is a lineage survival factor that cooperates with KIT in gastrointestinal stromal tumours. Nature (2010) 2.65
Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence. Nat Rev Genet (2011) 2.60
DNA specificity determinants associate with distinct transcription factor functions. PLoS Genet (2009) 2.56
Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. Mol Cell (2013) 2.55
Lineage regulators direct BMP and Wnt pathways to cell-specific programs during differentiation and regeneration. Cell (2011) 2.53
Enhancers: the abundance and function of regulatory sequences beyond promoters. Dev Biol (2009) 2.50
Genome-wide remodeling of the epigenetic landscape during myogenic differentiation. Proc Natl Acad Sci U S A (2011) 2.48
Cell-specific determinants of peroxisome proliferator-activated receptor gamma function in adipocytes and macrophages. Mol Cell Biol (2010) 2.47
STATs shape the active enhancer landscape of T cell populations. Cell (2012) 2.45
HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data. BMC Bioinformatics (2010) 2.41
Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nat Genet (2013) 2.41
H3K4 tri-methylation provides an epigenetic signature of active enhancers. EMBO J (2011) 2.38
A high-resolution enhancer atlas of the developing telencephalon. Cell (2013) 2.34
Bcl-6 and NF-kappaB cistromes mediate opposing regulation of the innate immune response. Genes Dev (2010) 2.31
Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations. Nature (2013) 2.25
Sequence and chromatin determinants of cell-type-specific transcription factor binding. Genome Res (2012) 2.24
Propagation of adipogenic signals through an epigenomic transition state. Genes Dev (2010) 2.23
CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression. PLoS Genet (2010) 2.20
Networks of intergenic long-range enhancers and snpRNAs drive castration-resistant phenotype of prostate cancer and contribute to pathogenesis of multiple common human disorders. Cell Cycle (2011) 2.19
Topologically associating domains are stable units of replication-timing regulation. Nature (2014) 2.17
The FaceBase Consortium: a comprehensive program to facilitate craniofacial research. Dev Biol (2011) 2.16
Fine tuning of craniofacial morphology by distant-acting enhancers. Science (2013) 2.16
BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. Nature (2015) 2.15
Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. Genome Res (2010) 2.12
ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. Nucleic Acids Res (2012) 2.11
Dynamics of 5-hydroxymethylcytosine and chromatin marks in Mammalian neurogenesis. Cell Rep (2013) 2.10
Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization. Cell Res (2012) 2.09
Genomic views of STAT function in CD4+ T helper cell differentiation. Nat Rev Immunol (2011) 2.09
Transcriptional and epigenetic control of T helper cell specification: molecular mechanisms underlying commitment and plasticity. Annu Rev Immunol (2012) 2.06
Enhancer-associated H3K4 monomethylation by Trithorax-related, the Drosophila homolog of mammalian Mll3/Mll4. Genes Dev (2012) 2.04
Discriminative prediction of mammalian enhancers from DNA sequence. Genome Res (2011) 2.02
Sequentially acting Sox transcription factors in neural lineage development. Genes Dev (2011) 1.97
Analysis of variation at transcription factor binding sites in Drosophila and humans. Genome Biol (2012) 1.97
Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments. Nucleic Acids Res (2013) 1.96
The selection and function of cell type-specific enhancers. Nat Rev Mol Cell Biol (2015) 1.93
Integrated genetic and epigenetic analysis identifies haplotype-specific methylation in the FTO type 2 diabetes and obesity susceptibility locus. PLoS One (2010) 1.93
Looping back to leap forward: transcription enters a new era. Cell (2014) 1.93
Growth factor stimulation induces a distinct ER(alpha) cistrome underlying breast cancer endocrine resistance. Genes Dev (2010) 1.92
Target gene context influences the transcriptional requirement for the KAT3 family of CBP and p300 histone acetyltransferases. Epigenetics (2010) 1.92
An integrated ChIP-seq analysis platform with customizable workflows. BMC Bioinformatics (2011) 1.92
Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers. Genome Res (2011) 1.92
Annotating genes and genomes with DNA sequences extracted from biomedical articles. Bioinformatics (2011) 1.91
Enhancer and promoter interactions-long distance calls. Curr Opin Genet Dev (2011) 1.88
Genome-wide discovery of human heart enhancers. Genome Res (2010) 1.85
is-rSNP: a novel technique for in silico regulatory SNP detection. Bioinformatics (2010) 1.84
Genome-wide prediction of transcription factor binding sites using an integrated model. Genome Biol (2010) 1.84
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78
The sequence of the human genome. Science (2001) 101.55
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature (2007) 65.18
Prediction of complete gene structures in human genomic DNA. J Mol Biol (1997) 58.76
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res (2006) 48.10
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods (2007) 45.04
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res (2005) 44.08
Galaxy: a platform for interactive large-scale genome analysis. Genome Res (2005) 35.75
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet (2007) 32.41
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature (2002) 28.79
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
The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res (2007) 23.13
The transcriptional coactivators p300 and CBP are histone acetyltransferases. Cell (1996) 16.57
High-resolution mapping and characterization of open chromatin across the genome. Cell (2008) 15.93
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods (2008) 11.61
In vivo enhancer analysis of human conserved non-coding sequences. Nature (2006) 10.60
Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol (2004) 10.59
Scanning human gene deserts for long-range enhancers. Science (2003) 9.75
Nuclear protein CBP is a coactivator for the transcription factor CREB. Nature (1994) 9.37
Molecular cloning and functional analysis of the adenovirus E1A-associated 300-kD protein (p300) reveals a protein with properties of a transcriptional adaptor. Genes Dev (1994) 8.92
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature (2007) 7.91
Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Res (2008) 7.41
A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells. Proc Natl Acad Sci U S A (2003) 7.30
Transcriptional regulatory elements in the human genome. Annu Rev Genomics Hum Genet (2006) 7.18
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res (2007) 7.05
VISTA Enhancer Browser--a database of tissue-specific human enhancers. Nucleic Acids Res (2006) 7.04
Gene dosage-dependent embryonic development and proliferation defects in mice lacking the transcriptional integrator p300. Cell (1998) 6.73
Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity. Cell (2006) 6.49
Ordered recruitment of chromatin modifying and general transcription factors to the IFN-beta promoter. Cell (2000) 6.32
Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet (2007) 5.93
Genome-wide approaches to studying chromatin modifications. Nat Rev Genet (2008) 4.28
Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding. Genome Res (2008) 4.11
Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing. Nucleic Acids Res (2008) 4.08
Recruitment of CBP/p300 by the IFN beta enhanceosome is required for synergistic activation of transcription. Mol Cell (1998) 4.03
Close sequence comparisons are sufficient to identify human cis-regulatory elements. Genome Res (2006) 3.92
Ultraconservation identifies a small subset of extremely constrained developmental enhancers. Nat Genet (2008) 3.55
Transcription coactivator TRAP220 is required for PPAR gamma 2-stimulated adipogenesis. Nature (2002) 3.42
Interaction and functional collaboration of p300/CBP and bHLH proteins in muscle and B-cell differentiation. Genes Dev (1996) 3.24
The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res (2008) 3.04
A conserved retinoic acid response element required for early expression of the homeobox gene Hoxb-1. Nature (1994) 2.76
Predicting tissue-specific enhancers in the human genome. Genome Res (2007) 2.72
A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts. Genome Res (2005) 2.71
Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b. Genome Res (2007) 2.27
Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. Genome Res (2007) 2.16
A transgene containing lacZ inserted into the dystonia locus is expressed in neural tube. Nature (1988) 2.02
Identification of ancient remains through genomic sequencing. Genome Res (2008) 1.72
Qualifying the relationship between sequence conservation and molecular function. Genome Res (2008) 1.69
Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif. Genome Res (2008) 1.58
Identification of genes controlled by LMX1B in the developing mouse limb bud. Dev Dyn (2008) 1.25
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
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
Comparative metagenomics of microbial communities. Science (2005) 25.88
Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature (2009) 24.41
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
A high-resolution map of active promoters in the human genome. Nature (2005) 24.35
A global map of p53 transcription-factor binding sites in the human genome. Cell (2006) 20.65
A common allele on chromosome 9 associated with coronary heart disease. Science (2007) 20.37
International network of cancer genome projects. Nature (2010) 20.35
Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature (2004) 20.20
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 phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature (2009) 15.06
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
Population-based resequencing of ANGPTL4 uncovers variations that reduce triglycerides and increase HDL. Nat Genet (2007) 13.78
VISTA: computational tools for comparative genomics. Nucleic Acids Res (2004) 13.52
Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39
Most rare missense alleles are deleterious in humans: implications for complex disease and association studies. Am J Hum Genet (2007) 10.92
Genetic variation in PNPLA3 confers susceptibility to nonalcoholic fatty liver disease. Nat Genet (2008) 10.87
In vivo enhancer analysis of human conserved non-coding sequences. Nature (2006) 10.60
Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science (2003) 9.93
Scanning human gene deserts for long-range enhancers. Science (2003) 9.75
Dicer, Drosha, and outcomes in patients with ovarian cancer. N Engl J Med (2008) 8.77
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 complementary transposon tool kit for Drosophila melanogaster using P and piggyBac. Nat Genet (2004) 8.55
Insights into the phylogeny and coding potential of microbial dark matter. Nature (2013) 8.55
Sequencing and analysis of Neanderthal genomic DNA. Science (2006) 8.06
The amphioxus genome and the evolution of the chordate karyotype. Nature (2008) 8.03
Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res (2008) 8.01
Metagenomics: DNA sequencing of environmental samples. Nat Rev Genet (2005) 7.65
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature (2007) 7.42
rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res (2002) 7.33
Statistical analysis of real-time PCR data. BMC Bioinformatics (2006) 7.31
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
VISTA Enhancer Browser--a database of tissue-specific human enhancers. Nucleic Acids Res (2006) 7.04
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol (2010) 7.00
Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science (2011) 6.93
Genome-wide analysis of protein-DNA interactions. Annu Rev Genomics Hum Genet (2006) 6.47
Aldehyde dehydrogenase 1 is a marker for normal and malignant human colonic stem cells (SC) and tracks SC overpopulation during colon tumorigenesis. Cancer Res (2009) 6.43
Genomic views of distant-acting enhancers. Nature (2009) 6.27
9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response. Nature (2011) 6.25
Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection. Lancet (2003) 5.99
A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature (2006) 5.98
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
Whole-genome cartography of estrogen receptor alpha binding sites. PLoS Genet (2007) 5.85
Genomic minimalism in the early diverging intestinal parasite Giardia lamblia. Science (2007) 5.69
Medical sequencing at the extremes of human body mass. Am J Hum Genet (2007) 5.61
Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature (2006) 5.52
Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol (2008) 5.38
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
Rare loss-of-function mutations in ANGPTL family members contribute to plasma triglyceride levels in humans. J Clin Invest (2008) 5.05
Symbiosis insights through metagenomic analysis of a microbial consortium. Nature (2006) 5.04
Deletion of ultraconserved elements yields viable mice. PLoS Biol (2007) 4.81
A cis-regulatory map of the Drosophila genome. Nature (2011) 4.80
Gain-of-function SOS1 mutations cause a distinctive form of Noonan syndrome. Nat Genet (2006) 4.68
Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean. Nat Rev Microbiol (2010) 4.58
Massively parallel functional dissection of mammalian enhancers in vivo. Nat Biotechnol (2012) 4.51
A new HPV-DNA test for cervical-cancer screening in developing regions: a cross-sectional study of clinical accuracy in rural China. Lancet Oncol (2008) 4.43
Genome-wide experimental determination of barriers to horizontal gene transfer. Science (2007) 4.37
ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet (2010) 4.32
Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. PLoS Genet (2007) 4.25
An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol (2012) 4.15
Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J (2010) 4.15
Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers. Proc Natl Acad Sci U S A (2008) 4.13
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res (2008) 4.08