Published in Genome Res on September 01, 2012
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Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res (2012) 3.80
Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Res (2012) 3.61
On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol (2013) 3.00
Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning. Nat Biotechnol (2015) 2.79
A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer. Nat Genet (2014) 2.72
Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer. Cell (2015) 2.39
Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res (2012) 2.32
Functional analysis of transcription factor binding sites in human promoters. Genome Biol (2012) 2.12
Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape. Cell Rep (2013) 2.03
Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments. Nucleic Acids Res (2013) 1.96
Predicting the human epigenome from DNA motifs. Nat Methods (2014) 1.88
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Exercise induces hippocampal BDNF through a PGC-1α/FNDC5 pathway. Cell Metab (2013) 1.76
Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes. Nat Methods (2014) 1.76
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Ancient transposable elements transformed the uterine regulatory landscape and transcriptome during the evolution of mammalian pregnancy. Cell Rep (2015) 1.65
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Swi/Snf chromatin remodeling/tumor suppressor complex establishes nucleosome occupancy at target promoters. Proc Natl Acad Sci U S A (2013) 1.60
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Comprehensive functional annotation of 77 prostate cancer risk loci. PLoS Genet (2014) 1.48
MYC: connecting selective transcriptional control to global RNA production. Nat Rev Cancer (2015) 1.47
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The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors. PLoS Genet (2016) 1.45
Recessive coding and regulatory mutations in FBLIM1 underlie the pathogenesis of chronic recurrent multifocal osteomyelitis (CRMO). PLoS One (2017) 1.44
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A brief review on the Human Encyclopedia of DNA Elements (ENCODE) project. Genomics Proteomics Bioinformatics (2013) 1.22
Distinct transcriptional regulatory modules underlie STAT3's cell type-independent and cell type-specific functions. Nucleic Acids Res (2013) 1.21
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Concise review: The Sox2-Oct4 connection: critical players in a much larger interdependent network integrated at multiple levels. Stem Cells (2013) 1.17
Repression of chimeric transcripts emanating from endogenous retrotransposons by a sequence-specific transcription factor. Genome Biol (2014) 1.17
Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features. Genome Res (2014) 1.13
Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape. Nucleic Acids Res (2014) 1.13
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Genome recognition by MYC. Cold Spring Harb Perspect Med (2014) 1.10
Mechanisms by which transcription factors gain access to target sequence elements in chromatin. Curr Opin Genet Dev (2012) 1.09
Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genes. Nat Genet (2015) 1.08
Widespread context dependency of microRNA-mediated regulation. Genome Res (2014) 1.08
RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells. PLoS One (2014) 1.07
Global analysis of Drosophila Cys₂-His₂ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants. Genome Res (2013) 1.07
A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana. Plant Cell (2014) 1.07
Promoter analysis reveals globally differential regulation of human long non-coding RNA and protein-coding genes. PLoS One (2014) 1.03
Transcription factor MITF and remodeller BRG1 define chromatin organisation at regulatory elements in melanoma cells. Elife (2015) 1.03
Genome-wide analysis of chromatin states reveals distinct mechanisms of sex-dependent gene regulation in male and female mouse liver. Mol Cell Biol (2013) 1.03
Topology of molecular interaction networks. BMC Syst Biol (2013) 1.03
An improved predictive recognition model for Cys(2)-His(2) zinc finger proteins. Nucleic Acids Res (2014) 1.02
PscanChIP: Finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments. Nucleic Acids Res (2013) 1.01
ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters. Nat Commun (2015) 1.01
Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamins. J Cell Biol (2015) 1.01
Targeting the Y/CCAAT box in cancer: YB-1 (YBX1) or NF-Y? Cell Death Differ (2013) 1.01
Fully automated high-throughput chromatin immunoprecipitation for ChIP-seq: identifying ChIP-quality p300 monoclonal antibodies. Sci Rep (2014) 0.99
Inferring regulatory element landscapes and transcription factor networks from cancer methylomes. Genome Biol (2015) 0.98
Decoding the human genome. Genome Res (2012) 0.97
Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility. Epigenetics Chromatin (2015) 0.97
A meta-analysis of Hodgkin lymphoma reveals 19p13.3 TCF3 as a novel susceptibility locus. Nat Commun (2014) 0.97
Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers. Genome Res (2013) 0.97
Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans. Hum Mol Genet (2015) 0.96
Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks. Genome Res (2016) 0.95
HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models. Nucleic Acids Res (2015) 0.95
Genome-wide kinetics of DNA excision repair in relation to chromatin state and mutagenesis. Proc Natl Acad Sci U S A (2016) 0.95
A widespread role of the motif environment in transcription factor binding across diverse protein families. Genome Res (2015) 0.94
ZBTB33 binds unmethylated regions of the genome associated with actively expressed genes. Epigenetics Chromatin (2013) 0.93
motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites. Bioinformatics (2015) 0.93
Transcription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell lines. BMC Genomics (2013) 0.93
A systematic survey of the Cys2His2 zinc finger DNA-binding landscape. Nucleic Acids Res (2015) 0.92
Base-resolution methylation patterns accurately predict transcription factor bindings in vivo. Nucleic Acids Res (2015) 0.92
GC-rich DNA elements enable replication origin activity in the methylotrophic yeast Pichia pastoris. PLoS Genet (2014) 0.91
Terminate and make a loop: regulation of transcriptional directionality. Trends Biochem Sci (2014) 0.91
Long non-coding RNA ANRIL regulates inflammatory responses as a novel component of NF-κB pathway. RNA Biol (2016) 0.91
Role of LRF/Pokemon in lineage fate decisions. Blood (2013) 0.90
Nucleosomes shape DNA polymorphism and divergence. PLoS Genet (2014) 0.90
i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly. Nucleic Acids Res (2015) 0.90
Epigenomics: the science of no-longer-junk DNA. Why study it in chronic kidney disease? Semin Nephrol (2013) 0.90
Identification of High-Impact cis-Regulatory Mutations Using Transcription Factor Specific Random Forest Models. PLoS Comput Biol (2015) 0.90
Integrative analysis of C. elegans modENCODE ChIP-seq data sets to infer gene regulatory interactions. Genome Res (2013) 0.89
Massively parallel cis-regulatory analysis in the mammalian central nervous system. Genome Res (2015) 0.89
A ChIP on the shoulder? Chromatin immunoprecipitation and validation strategies for ChIP antibodies. F1000Res (2015) 0.89
Next-generation sequencing and epigenomics research: a hammer in search of nails. Genomics Inform (2014) 0.89
Single-cell genome-wide studies give new insight into nongenetic cell-to-cell variability in animals. Histochem Cell Biol (2016) 0.88
Cell-type-specific enrichment of risk-associated regulatory elements at ovarian cancer susceptibility loci. Hum Mol Genet (2015) 0.88
Statistical significance of combinatorial regulations. Proc Natl Acad Sci U S A (2013) 0.88
SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps. PLoS Comput Biol (2015) 0.88
Site-specific programming of the host epithelial transcriptome by the gut microbiota. Genome Biol (2015) 0.88
Genomic Organization of Human Transcription Initiation Complexes. PLoS One (2016) 0.87
The Role of H3K4me3 in Transcriptional Regulation Is Altered in Huntington's Disease. PLoS One (2015) 0.87
New basal cell carcinoma susceptibility loci. Nat Commun (2015) 0.87
Inferring chromatin-bound protein complexes from genome-wide binding assays. Genome Res (2013) 0.87
Identification of the transcription factor ZEB1 as a central component of the adipogenic gene regulatory network. Elife (2014) 0.86
Machine learning and genome annotation: a match meant to be? Genome Biol (2013) 0.86
DELTA: A Distal Enhancer Locating Tool Based on AdaBoost Algorithm and Shape Features of Chromatin Modifications. PLoS One (2015) 0.86
Modeling the relationship of epigenetic modifications to transcription factor binding. Nucleic Acids Res (2015) 0.86
Systematic identification of transcriptional regulatory modules from protein-protein interaction networks. Nucleic Acids Res (2013) 0.86
High density methylation QTL analysis in human blood via next-generation sequencing of the methylated genomic DNA fraction. Genome Biol (2015) 0.85
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods (2007) 45.04
Circos: an information aesthetic for comparative genomics. Genome Res (2009) 40.02
TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res (2003) 29.26
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BioGRID: a general repository for interaction datasets. Nucleic Acids Res (2006) 22.41
Landscape of transcription in human cells. Nature (2012) 20.18
Genome-wide analysis of estrogen receptor binding sites. Nat Genet (2006) 18.63
The complex language of chromatin regulation during transcription. Nature (2007) 16.97
A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol (2011) 16.53
Chromosomal subunits in active genes have an altered conformation. Science (1976) 14.63
Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res (2009) 12.58
The biology of chromatin remodeling complexes. Annu Rev Biochem (2009) 10.02
Quantifying similarity between motifs. Genome Biol (2007) 9.27
Transcription regulation and animal diversity. Nature (2003) 9.22
Diversity and complexity in DNA recognition by transcription factors. Science (2009) 9.07
JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Res (2007) 8.79
Cohesins functionally associate with CTCF on mammalian chromosome arms. Cell (2008) 7.80
An expansive human regulatory lexicon encoded in transcription factor footprints. Nature (2012) 7.27
Transcriptional regulatory elements in the human genome. Annu Rev Genomics Hum Genet (2006) 7.18
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MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics (2011) 6.52
Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell (2011) 6.29
An atlas of combinatorial transcriptional regulation in mouse and man. Cell (2010) 6.24
Nucleosome dynamics define transcriptional enhancers. Nat Genet (2010) 5.94
Determinants of nucleosome organization in primary human cells. Nature (2011) 5.50
Nucleosome positioning signals in genomic DNA. Genome Res (2007) 4.99
The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet (2008) 4.91
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High-resolution nucleosome mapping reveals transcription-dependent promoter packaging. Genome Res (2009) 3.99
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ZNF274 recruits the histone methyltransferase SETDB1 to the 3' ends of ZNF genes. PLoS One (2010) 3.15
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Worldwide human relationships inferred from genome-wide patterns of variation. Science (2008) 22.44
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The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36
International network of cancer genome projects. Nature (2010) 20.35
A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature (2009) 18.39
Global identification of human transcribed sequences with genome tiling arrays. Science (2004) 17.85
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Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21
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A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (2003) 12.07
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PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol (2009) 11.28
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Ensembl's 10th year. Nucleic Acids Res (2009) 10.82
Mouse genomic variation and its effect on phenotypes and gene regulation. Nature (2011) 10.66
High-quality binary protein interaction map of the yeast interactome network. Science (2008) 10.65
Widespread parallel evolution in sticklebacks by repeated fixation of Ectodysplasin alleles. Science (2005) 10.46
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods (2009) 10.17
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
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Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science (2002) 9.43
Variation in transcription factor binding among humans. Science (2010) 9.33
Genomic analysis of regulatory network dynamics reveals large topological changes. Nature (2004) 9.32
Genome sequence of Aedes aegypti, a major arbovirus vector. Science (2007) 9.19
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res (2004) 9.18
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13
A high-resolution map of human evolutionary constraint using 29 mammals. Nature (2011) 8.67
Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science (2008) 8.62
The Reactome pathway knowledgebase. Nucleic Acids Res (2013) 8.56
Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat Methods (2006) 8.52
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell (2012) 8.41
Signals of recent positive selection in a worldwide sample of human populations. Genome Res (2009) 8.38
Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs. Nat Genet (2013) 8.02
Subcellular localization of the yeast proteome. Genes Dev (2002) 7.93
ZDOCK: an initial-stage protein-docking algorithm. Proteins (2003) 7.52
Global analysis of protein phosphorylation in yeast. Nature (2005) 7.46
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
The Ensembl core software libraries. Genome Res (2004) 7.30
The HGNC Database in 2008: a resource for the human genome. Nucleic Acids Res (2007) 7.29
Histone variant H2A.Z marks the 5' ends of both active and inactive genes in euchromatin. Cell (2005) 7.20
HTRA1 promoter polymorphism in wet age-related macular degeneration. Science (2006) 7.12
Performance comparison of exome DNA sequencing technologies. Nat Biotechnol (2011) 7.11
Divergence of transcription factor binding sites across related yeast species. Science (2007) 7.10
EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol (2006) 7.06
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res (2007) 7.05
A three-dimensional model of the yeast genome. Nature (2010) 7.01
CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res (2011) 6.97
The transcriptional activity of human Chromosome 22. Genes Dev (2003) 6.82
Population analysis of large copy number variants and hotspots of human genetic disease. Am J Hum Genet (2009) 6.79
Integrating biological data--the Distributed Annotation System. BMC Bioinformatics (2008) 6.56
The European Nucleotide Archive. Nucleic Acids Res (2010) 6.48
Dynamics of replication-independent histone turnover in budding yeast. Science (2007) 6.41