Published in PLoS Biol on April 19, 2011
An integrated encyclopedia of DNA elements in the human genome. Nature (2012) 64.73
An integrated map of genetic variation from 1,092 human genomes. Nature (2012) 59.82
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
Ensembl 2012. Nucleic Acids Res (2011) 14.55
The long-range interaction landscape of gene promoters. Nature (2012) 9.20
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13
A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell (2014) 8.79
A map of the cis-regulatory sequences in the mouse genome. Nature (2012) 8.74
Discovery and refinement of loci associated with lipid levels. Nat Genet (2013) 7.86
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods (2013) 7.06
Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat Rev Genet (2011) 6.52
Detecting differential usage of exons from RNA-seq data. Genome Res (2012) 6.34
DNase I sensitivity QTLs are a major determinant of human expression variation. Nature (2012) 6.17
Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat Genet (2011) 5.70
Obesity-associated variants within FTO form long-range functional connections with IRX3. Nature (2014) 5.61
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array. Nat Genet (2013) 5.58
Linking disease associations with regulatory information in the human genome. Genome Res (2012) 5.47
Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat Methods (2012) 4.89
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res (2012) 4.80
Massively parallel functional dissection of mammalian enhancers in vivo. Nat Biotechnol (2012) 4.51
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res (2011) 4.43
The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science (2013) 4.12
Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res (2012) 3.80
Chromatin marks identify critical cell types for fine mapping complex trait variants. Nat Genet (2012) 3.67
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
Pybedtools: a flexible Python library for manipulating genomic datasets and annotations. Bioinformatics (2011) 3.55
Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet (2014) 3.52
Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages. Cell (2012) 3.48
Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants. Proc Natl Acad Sci U S A (2013) 2.93
Metazoan promoters: emerging characteristics and insights into transcriptional regulation. Nat Rev Genet (2012) 2.92
Promiscuous RNA binding by Polycomb repressive complex 2. Nat Struct Mol Biol (2013) 2.91
Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism. Cell (2013) 2.87
Modeling gene expression using chromatin features in various cellular contexts. Genome Biol (2012) 2.76
The human mitochondrial transcriptome. Cell (2011) 2.70
Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations. Nat Genet (2015) 2.59
Circuitry and dynamics of human transcription factor regulatory networks. Cell (2012) 2.56
Bcl-6 directly represses the gene program of the glycolysis pathway. Nat Immunol (2014) 2.47
What fraction of the human genome is functional? Genome Res (2011) 2.46
Inferring direct DNA binding from ChIP-seq. Nucleic Acids Res (2012) 2.41
Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nat Genet (2013) 2.41
Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants. Nat Genet (2014) 2.38
Systematic evaluation of factors influencing ChIP-seq fidelity. Nat Methods (2012) 2.31
Identification of recurrent NAB2-STAT6 gene fusions in solitary fibrous tumor by integrative sequencing. Nat Genet (2013) 2.30
Sequence and chromatin determinants of cell-type-specific transcription factor binding. Genome Res (2012) 2.24
From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing. Genome Res (2013) 2.23
Single-cell chromatin accessibility reveals principles of regulatory variation. Nature (2015) 2.22
Controls of nucleosome positioning in the human genome. PLoS Genet (2012) 2.14
Functional analysis of transcription factor binding sites in human promoters. Genome Biol (2012) 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
A NOTCH1-driven MYC enhancer promotes T cell development, transformation and acute lymphoblastic leukemia. Nat Med (2014) 2.08
Transcription-dependent dynamic supercoiling is a short-range genomic force. Nat Struct Mol Biol (2013) 2.07
EWS-FLI1 utilizes divergent chromatin remodeling mechanisms to directly activate or repress enhancer elements in Ewing sarcoma. Cancer Cell (2014) 2.06
Epigenome-wide DNA methylation landscape of melanoma progression to brain metastasis reveals aberrations on homeobox D cluster associated with prognosis. Hum Mol Genet (2013) 1.95
System wide analyses have underestimated protein abundances and the importance of transcription in mammals. PeerJ (2014) 1.93
Kraken: a set of tools for quality control and analysis of high-throughput sequence data. Methods (2013) 1.92
Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming. Cell Stem Cell (2013) 1.91
Transcriptionally active chromatin recruits homologous recombination at DNA double-strand breaks. Nat Struct Mol Biol (2014) 1.89
Dense fine-mapping study identifies new susceptibility loci for primary biliary cirrhosis. Nat Genet (2012) 1.85
Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA. Nat Protoc (2012) 1.84
Data integration in the era of omics: current and future challenges. BMC Syst Biol (2014) 1.82
Reorganization of enhancer patterns in transition from naive to primed pluripotency. Cell Stem Cell (2014) 1.81
Analysis of alternative cleavage and polyadenylation by 3' region extraction and deep sequencing. Nat Methods (2012) 1.80
Variants at multiple loci implicated in both innate and adaptive immune responses are associated with Sjögren's syndrome. Nat Genet (2013) 1.79
Fine-mapping identifies multiple prostate cancer risk loci at 5p15, one of which associates with TERT expression. Hum Mol Genet (2013) 1.78
Tracking and coordinating an international curation effort for the CCDS Project. Database (Oxford) (2012) 1.78
Deep RNA sequencing reveals dynamic regulation of myocardial noncoding RNAs in failing human heart and remodeling with mechanical circulatory support. Circulation (2014) 1.76
DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes. Genome Biol (2013) 1.71
Asking for more. Nat Genet (2012) 1.70
5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Nat Protoc (2012) 1.70
A far downstream enhancer for murine Bcl11b controls its T-cell specific expression. Blood (2013) 1.69
The long noncoding RNAs NEAT1 and MALAT1 bind active chromatin sites. Mol Cell (2014) 1.68
PDGFR blockade is a rational and effective therapy for NPM-ALK-driven lymphomas. Nat Med (2012) 1.67
RFECS: a random-forest based algorithm for enhancer identification from chromatin state. PLoS Comput Biol (2013) 1.66
Genomic approaches towards finding cis-regulatory modules in animals. Nat Rev Genet (2012) 1.65
SETD2 loss-of-function promotes renal cancer branched evolution through replication stress and impaired DNA repair. Oncogene (2015) 1.65
A p53 enhancer region regulates target genes through chromatin conformations in cis and in trans. Genes Dev (2013) 1.62
diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates. PLoS One (2013) 1.58
Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia. Genome Biol (2013) 1.57
MicroRNA-driven developmental remodeling in the brain distinguishes humans from other primates. PLoS Biol (2011) 1.57
FunCoup 3.0: database of genome-wide functional coupling networks. Nucleic Acids Res (2013) 1.56
Rho-actin signaling to the MRTF coactivators dominates the immediate transcriptional response to serum in fibroblasts. Genes Dev (2014) 1.54
Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. Genome Res (2011) 1.53
Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks. Genome Res (2012) 1.47
Epigenetic priors for identifying active transcription factor binding sites. Bioinformatics (2011) 1.47
Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability. Genome Res (2013) 1.47
Disrupted auto-regulation of the spliceosomal gene SNRPB causes cerebro-costo-mandibular syndrome. Nat Commun (2014) 1.46
Joint association of genome-wide association study-identified susceptibility loci and dietary patterns in risk of renal cell carcinoma among non-Hispanic whites. Am J Epidemiol (2014) 1.46
Promoter-like epigenetic signatures in exons displaying cell type-specific splicing. Genome Biol (2015) 1.46
HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. Nucleic Acids Res (2012) 1.45
Transcriptional dynamics reveal critical roles for non-coding RNAs in the immediate-early response. PLoS Comput Biol (2015) 1.44
Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project. Nucleic Acids Res (2011) 1.43
5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation. Mol Cell (2014) 1.42
Loss of Cardio-Protective Effects at the ADAMTS7 Locus Due to Gene-Smoking Interactions. Circulation (2017) 1.41
DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements. Nat Genet (2013) 1.40
Long non-coding RNA modifies chromatin: epigenetic silencing by long non-coding RNAs. Bioessays (2011) 1.39
The genomic landscape of cohesin-associated chromatin interactions. Genome Res (2013) 1.36
NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data. BMC Bioinformatics (2013) 1.34
HLA typing from RNA-Seq sequence reads. Genome Med (2012) 1.34
Developing and implementing an institute-wide data sharing policy. Genome Med (2011) 1.32
Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
High-resolution profiling of histone methylations in the human genome. Cell (2007) 85.74
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Finding the missing heritability of complex diseases. Nature (2009) 67.95
Embryonic stem cell lines derived from human blastocysts. Science (1998) 65.53
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
RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77
Global variation in copy number in the human genome. Nature (2006) 57.50
Chromatin modifications and their function. Cell (2007) 55.98
Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A (2009) 54.68
A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell (2006) 48.80
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods (2007) 45.04
The language of covalent histone modifications. Nature (2000) 44.92
Finishing the euchromatic sequence of the human genome. Nature (2004) 41.40
The ENCODE (ENCyclopedia Of DNA Elements) Project. Science (2004) 38.24
Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer. Proc Natl Acad Sci U S A (1988) 35.13
DNA methylation patterns and epigenetic memory. Genes Dev (2002) 33.83
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet (2007) 32.41
Culture of human endothelial cells derived from umbilical veins. Identification by morphologic and immunologic criteria. J Clin Invest (1973) 31.28
DNAse footprinting: a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res (1978) 30.43
Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature (2008) 30.29
Control of developmental regulators by Polycomb in human embryonic stem cells. Cell (2006) 28.21
Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature (2006) 25.90
Capturing chromosome conformation. Science (2002) 23.93
Genomic maps and comparative analysis of histone modifications in human and mouse. Cell (2005) 18.96
Distribution and intensity of constraint in mammalian genomic sequence. Genome Res (2005) 18.85
The mammalian epigenome. Cell (2007) 18.13
Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet (2006) 17.19
Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell (2007) 16.66
The UCSC Genome Browser database: update 2010. Nucleic Acids Res (2009) 16.58
Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. Cancer Cell (2010) 16.12
Human chronic myelogenous leukemia cell-line with positive Philadelphia chromosome. Blood (1975) 15.95
High-resolution mapping and characterization of open chromatin across the genome. Cell (2008) 15.93
GENCODE: producing a reference annotation for ENCODE. Genome Biol (2006) 15.08
The 5' ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature (1980) 14.11
A vision for the future of genomics research. Nature (2003) 14.06
Nuclease hypersensitive sites in chromatin. Annu Rev Biochem (1988) 13.48
Human hepatocellular carcinoma cell lines secrete the major plasma proteins and hepatitis B surface antigen. Science (1980) 13.44
Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res (2006) 13.32
Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res (2009) 12.58
Prepublication data sharing. Nature (2009) 12.24
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol (2009) 11.28
Ensembl's 10th year. Nucleic Acids Res (2009) 10.82
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods (2009) 10.17
Genome-wide transcription and the implications for genomic organization. Nat Rev Genet (2007) 9.45
Variation in transcription factor binding among humans. Science (2010) 9.33
A census of human transcription factors: function, expression and evolution. Nat Rev Genet (2009) 9.19
Histone H3 lysine 4 methylation patterns in higher eukaryotic genes. Nat Cell Biol (2003) 8.82
Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci U S A (2003) 8.73
Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat Methods (2006) 8.52
Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res (2004) 8.35
Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat Genet (2003) 7.98
Dynamic changes in the human methylome during differentiation. Genome Res (2010) 7.96
FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res (2006) 7.72
Sequence census methods for functional genomics. Nat Methods (2007) 7.38
Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Res (2008) 7.35
Transcriptional regulatory elements in the human genome. Annu Rev Genomics Hum Genet (2006) 7.18
EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol (2006) 7.06
The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer. Nat Genet (2009) 6.99
A map of open chromatin in human pancreatic islets. Nat Genet (2010) 6.75
BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals. Nat Methods (2008) 6.51
A 200 base pair region at the 5' end of the chicken adult beta-globin gene is accessible to nuclease digestion. Cell (1981) 6.43
The expanding snoRNA world. Biochimie (2002) 6.10
Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer. Genome Res (2010) 6.03
ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res (2009) 5.98
Heritable individual-specific and allele-specific chromatin signatures in humans. Science (2010) 5.94
The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling. Nat Genet (2009) 5.65
Characterization of missing human genome sequences and copy-number polymorphic insertions. Nat Methods (2010) 5.44
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res (2010) 5.40
Genome-wide nucleotide-level mammalian ancestor reconstruction. Genome Res (2008) 5.12
Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains. Genome Res (2010) 5.08
Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. Proc Natl Acad Sci U S A (2000) 4.99
High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Res (2010) 4.69
Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res (2009) 4.47
Distinct localization of histone H3 acetylation and H3-K4 methylation to the transcription start sites in the human genome. Proc Natl Acad Sci U S A (2004) 4.39
RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. Nat Protoc (2006) 4.28
Local DNA topography correlates with functional noncoding regions of the human genome. Science (2009) 4.18
Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res (2009) 4.11
Multiple loci on 8q24 associated with prostate cancer susceptibility. Nat Genet (2009) 3.94
Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays. Methods (2002) 3.92
Functional enhancers at the gene-poor 8q24 cancer-linked locus. PLoS Genet (2009) 3.59
Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc Natl Acad Sci U S A (2004) 3.59
Mutation spectrum revealed by breakpoint sequencing of human germline CNVs. Nat Genet (2010) 3.52
DNase I hypersensitive sites in Drosophila chromatin occur at the 5' ends of regions of transcription. Proc Natl Acad Sci U S A (1981) 3.39
Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome. Proc Natl Acad Sci U S A (2007) 3.35
Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing. Proc Natl Acad Sci U S A (2010) 3.28
Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). Methods (2009) 3.16
DNA methylation and imprinting: why bother? Trends Genet (1997) 3.00
My5C: web tools for chromosome conformation capture studies. Nat Methods (2009) 2.96
PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics (2006) 2.85
Mapping accessible chromatin regions using Sono-Seq. Proc Natl Acad Sci U S A (2009) 2.83
The share of human genomic DNA under selection estimated from human-mouse genomic alignments. Cold Spring Harb Symp Quant Biol (2003) 2.83
Upregulation of c-MYC in cis through a large chromatin loop linked to a cancer risk-associated single-nucleotide polymorphism in colorectal cancer cells. Mol Cell Biol (2010) 2.80
Genomic antagonism between retinoic acid and estrogen signaling in breast cancer. Cell (2009) 2.76
Widely distributed noncoding purifying selection in the human genome. Proc Natl Acad Sci U S A (2007) 2.71
Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Res (2008) 2.60
Long-range chromosomal interactions and gene regulation. Mol Biosyst (2008) 2.56
A range of cancers is associated with the rs6983267 marker on chromosome 8. Cancer Res (2008) 2.43