Published in Bioinformatics on September 10, 2008
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ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet (2009) 13.12
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics (2009) 8.33
A map of open chromatin in human pancreatic islets. Nat Genet (2010) 6.75
High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Res (2010) 4.69
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res (2011) 4.43
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ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions. Genome Biol (2011) 2.47
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Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res (2010) 2.29
CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression. PLoS Genet (2010) 2.20
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Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Res (2011) 2.07
Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data. PLoS Comput Biol (2011) 1.86
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Picking ChIP-seq peak detectors for analyzing chromatin modification experiments. Nucleic Acids Res (2012) 1.49
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Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis. Plant Cell (2012) 1.38
Alterations to chromatin in intestinal macrophages link IL-10 deficiency to inappropriate inflammatory responses. Eur J Immunol (2016) 1.38
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Drug-induced histone eviction from open chromatin contributes to the chemotherapeutic effects of doxorubicin. Nat Commun (2013) 1.31
De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis. Nucleic Acids Res (2010) 1.30
Close proximity to Igh is a contributing factor to AID-mediated translocations. Mol Cell (2012) 1.23
Using ChIP-chip and ChIP-seq to study the regulation of gene expression: genome-wide localization studies reveal widespread regulation of transcription elongation. Methods (2009) 1.23
Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection. PLoS Genet (2012) 1.22
High-resolution mapping of open chromatin in the rice genome. Genome Res (2011) 1.19
Integrative genomic analysis of human ribosomal DNA. Nucleic Acids Res (2011) 1.18
Uniform, optimal signal processing of mapped deep-sequencing data. Nat Biotechnol (2013) 1.17
Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity. Genome Biol (2012) 1.15
Genomic profiling of HMGN1 reveals an association with chromatin at regulatory regions. Mol Cell Biol (2010) 1.12
Replication fork polarity gradients revealed by megabase-sized U-shaped replication timing domains in human cell lines. PLoS Comput Biol (2012) 1.12
Maps of open chromatin highlight cell type-restricted patterns of regulatory sequence variation at hematological trait loci. Genome Res (2013) 1.10
Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state. Nat Commun (2015) 1.10
Chromatin accessibility data sets show bias due to sequence specificity of the DNase I enzyme. PLoS One (2013) 1.07
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Normalization of ChIP-seq data with control. BMC Bioinformatics (2012) 1.06
Chromatin accessibility: a window into the genome. Epigenetics Chromatin (2014) 1.06
Deciphering the code for retroviral integration target site selection. PLoS Comput Biol (2010) 1.06
Comparison of four ChIP-Seq analytical algorithms using rice endosperm H3K27 trimethylation profiling data. PLoS One (2011) 1.06
PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data. Bioinformatics (2014) 1.04
Genome-wide analysis of the relationships between DNaseI HS, histone modifications and gene expression reveals distinct modes of chromatin domains. Nucleic Acids Res (2011) 1.01
Epigenetics of human papillomaviruses. Virology (2013) 1.00
MACE: model based analysis of ChIP-exo. Nucleic Acids Res (2014) 0.99
The essential polysome-associated RNA-binding protein RBP42 targets mRNAs involved in Trypanosoma brucei energy metabolism. RNA (2012) 0.99
An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data. BMC Bioinformatics (2010) 0.98
Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum. Nat Neurosci (2015) 0.98
Statistical Analyses of Next Generation Sequence Data: A Partial Overview. J Proteomics Bioinform (2010) 0.98
Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers. Genome Res (2013) 0.97
Prediction of RNA Polymerase II recruitment, elongation and stalling from histone modification data. BMC Genomics (2011) 0.95
Profiling and identification of small rDNA-derived RNAs and their potential biological functions. PLoS One (2013) 0.94
VDA, a method of choosing a better algorithm with fewer validations. PLoS One (2011) 0.94
Lipid-induced epigenomic changes in human macrophages identify a coronary artery disease-associated variant that regulates PPAP2B Expression through Altered C/EBP-beta binding. PLoS Genet (2015) 0.94
Combining multiple ChIP-seq peak detection systems using combinatorial fusion. BMC Genomics (2012) 0.92
Mapping of genomic double-strand breaks by ligation of biotinylated oligonucleotides to forum domains: Analysis of the data obtained for human rDNA units. Genom Data (2014) 0.92
Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection. Nucleic Acids Res (2014) 0.92
On the value of intra-motif dependencies of human insulator protein CTCF. PLoS One (2014) 0.92
Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy. BMC Genomics (2013) 0.92
Genome accessibility is widely preserved and locally modulated during mitosis. Genome Res (2014) 0.91
ChIPseqR: analysis of ChIP-seq experiments. BMC Bioinformatics (2011) 0.91
A viral genome landscape of RNA polyadenylation from KSHV latent to lytic infection. PLoS Pathog (2013) 0.91
Current bioinformatic approaches to identify DNase I hypersensitive sites and genomic footprints from DNase-seq data. Front Genet (2012) 0.90
An enhancer polymorphism at the cardiomyocyte intercalated disc protein NOS1AP locus is a major regulator of the QT interval. Am J Hum Genet (2014) 0.90
H3K4me3 inversely correlates with DNA methylation at a large class of non-CpG-island-containing start sites. Genome Med (2012) 0.90
PeaKDEck: a kernel density estimator-based peak calling program for DNaseI-seq data. Bioinformatics (2014) 0.89
A short survey of computational analysis methods in analysing ChIP-seq data. Hum Genomics (2011) 0.89
A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function. Thorax (2011) 0.88
Transcription factor and chromatin features predict genes associated with eQTLs. Nucleic Acids Res (2012) 0.87
Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes. PLoS Genet (2012) 0.87
A comparison of peak callers used for DNase-Seq data. PLoS One (2014) 0.87
A varying threshold method for ChIP peak-calling using multiple sources of information. Bioinformatics (2010) 0.86
The transcription start site landscape of C. elegans. Genome Res (2013) 0.86
Discovery and characterization of human exonic transcriptional regulatory elements. PLoS One (2012) 0.86
Regulation of the boundaries of accessible chromatin. PLoS Genet (2013) 0.85
G9a/GLP-dependent H3K9me2 patterning alters chromatin structure at CpG islands in hematopoietic progenitors. Epigenetics Chromatin (2014) 0.85
A genome-wide analysis of open chromatin in human epididymis epithelial cells reveals candidate regulatory elements for genes coordinating epididymal function. Biol Reprod (2013) 0.85
Genetic landscape of open chromatin in yeast. PLoS Genet (2013) 0.85
Open chromatin profiling in mice livers reveals unique chromatin variations induced by high fat diet. J Biol Chem (2014) 0.85
Technical considerations for functional sequencing assays. Nat Immunol (2012) 0.85
A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data. Biol Direct (2014) 0.85
Processing and analyzing ChIP-seq data: from short reads to regulatory interactions. Brief Funct Genomics (2010) 0.84
Statistical Issues in the Analysis of ChIP-Seq and RNA-Seq Data. Genes (Basel) (2010) 0.83
Genome-wide nucleosome positioning is orchestrated by genomic regions associated with DNase I hypersensitivity in rice. PLoS Genet (2014) 0.83
Epigenetic landscape during osteoblastogenesis defines a differentiation-dependent Runx2 promoter region. Gene (2014) 0.83
Analysis of computational footprinting methods for DNase sequencing experiments. Nat Methods (2016) 0.82
Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite. BMC Syst Biol (2011) 0.82
Epigenetic methodologies for behavioral scientists. Horm Behav (2010) 0.82
Determinants of nucleosome positioning and their influence on plant gene expression. Genome Res (2015) 0.82
Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs. PLoS Comput Biol (2010) 0.81
Persistent Chromatin Modifications Induced by High Fat Diet. J Biol Chem (2016) 0.81
Comparative evaluation of DNase-seq footprint identification strategies. Front Genet (2014) 0.81
EMdeCODE: a novel algorithm capable of reading words of epigenetic code to predict enhancers and retroviral integration sites and to identify H3R2me1 as a distinctive mark of coding versus non-coding genes. Nucleic Acids Res (2012) 0.81
Allelic Imbalance in Regulation of ANRIL through Chromatin Interaction at 9p21 Endometriosis Risk Locus. PLoS Genet (2016) 0.81
LRH-1 controls proliferation in breast tumor cells by regulating CDKN1A gene expression. Oncogene (2014) 0.80
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Genome-wide mapping of in vivo protein-DNA interactions. Science (2007) 64.92
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods (2007) 45.04
High-resolution mapping and characterization of open chromatin across the genome. Cell (2008) 15.93
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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
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet (2007) 32.41
The UCSC Table Browser data retrieval tool. Nucleic Acids Res (2004) 25.12
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
The accessible chromatin landscape of the human genome. Nature (2012) 16.86
High-resolution mapping and characterization of open chromatin across the genome. Cell (2008) 15.93
Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res (2003) 11.12
DNase I sensitivity QTLs are a major determinant of human expression variation. Nature (2012) 6.17
Heritable individual-specific and allele-specific chromatin signatures in humans. Science (2010) 5.94
Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet (2007) 5.93
RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat Methods (2013) 4.85
High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Res (2010) 4.69
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res (2011) 4.43
An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol (2012) 4.15
Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res (2013) 3.61
DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. Cold Spring Harb Protoc (2010) 3.54
Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen arrays. Methods Enzymol (2006) 3.53
Comparative recombination rates in the rat, mouse, and human genomes. Genome Res (2004) 3.50
Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A (2014) 3.35
Synergistic and tunable human gene activation by combinations of synthetic transcription factors. Nat Methods (2013) 3.26
Epigenetic instability of cytokine and transcription factor gene loci underlies plasticity of the T helper 17 cell lineage. Immunity (2010) 3.24
The DNA sequence of human chromosome 7. Nature (2003) 3.18
The structure and evolution of centromeric transition regions within the human genome. Nature (2004) 2.78
Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis. PLoS Genet (2006) 2.62
Dissecting the regulatory architecture of gene expression QTLs. Genome Biol (2012) 2.51
Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer. Sci Transl Med (2013) 2.34
Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns. Genome Res (2009) 2.31
GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics (2013) 2.29
The DNA sequence and biology of human chromosome 19. Nature (2004) 2.29
Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature (2005) 2.27
Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci. Cell Metab (2010) 2.21
CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression. PLoS Genet (2010) 2.20
Modeling cancer progression via pathway dependencies. PLoS Comput Biol (2008) 2.12
Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Res (2011) 2.07
Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. Genome Res (2012) 1.99
Predicting cell-type-specific gene expression from regions of open chromatin. Genome Res (2012) 1.78
Genomic strategy for targeting therapy in castration-resistant prostate cancer. J Clin Oncol (2009) 1.75
Evidence for type II cells as cells of origin of K-Ras-induced distal lung adenocarcinoma. Proc Natl Acad Sci U S A (2012) 1.73
Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions. Genome Res (2013) 1.69
Interferon regulatory factors are transcriptional regulators of adipogenesis. Cell Metab (2008) 1.55
Site-specific silencing of regulatory elements as a mechanism of X inactivation. Cell (2012) 1.54
Analysis of complex disease association and linkage studies using the University of California Santa Cruz Genome Browser. Circ Cardiovasc Genet (2009) 1.53
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
Evidence of influence of genomic DNA sequence on human X chromosome inactivation. PLoS Comput Biol (2006) 1.52
Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles. Bioinformatics (2006) 1.49
Both noncoding and protein-coding RNAs contribute to gene expression evolution in the primate brain. Genome Biol Evol (2010) 1.45
Genome-wide sequence and functional analysis of early replicating DNA in normal human fibroblasts. BMC Genomics (2006) 1.39
Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU.1 and HMGA1. Cancer Res (2007) 1.34
Mapping regulatory elements by DNaseI hypersensitivity chip (DNase-Chip). Methods Mol Biol (2009) 1.33
Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects. Genome Res (2013) 1.31
Intronic enhancers coordinate epithelial-specific looping of the active CFTR locus. Proc Natl Acad Sci U S A (2009) 1.29
Predictive genes in adjacent normal tissue are preferentially altered by sCNV during tumorigenesis in liver cancer and may rate limiting. PLoS One (2011) 1.26
A complex intronic enhancer regulates expression of the CFTR gene by direct interaction with the promoter. J Cell Mol Med (2009) 1.23
Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection. PLoS Genet (2012) 1.22
Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets. Genome Res (2011) 1.20
Improving breast cancer survival analysis through competition-based multidimensional modeling. PLoS Comput Biol (2013) 1.20
High-resolution mapping of open chromatin in the rice genome. Genome Res (2011) 1.19
Modular utilization of distal cis-regulatory elements controls Ifng gene expression in T cells activated by distinct stimuli. Immunity (2010) 1.17
Distinct properties of cell-type-specific and shared transcription factor binding sites. Mol Cell (2013) 1.16
Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity. Genome Biol (2012) 1.15
Gene expression during normal and FSHD myogenesis. BMC Med Genomics (2011) 1.12
PERSONALIZED HYPOTHESIS TESTS FOR DETECTING MEDICATION RESPONSE IN PARKINSON DISEASE PATIENTS USING iPHONE SENSOR DATA. Pac Symp Biocomput (2016) 1.09
The hypersensitive glucocorticoid response specifically regulates period 1 and expression of circadian genes. Mol Cell Biol (2012) 1.06
A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity. Genome Res (2013) 1.05
MicroRNAs Classify Different Disease Behavior Phenotypes of Crohn's Disease and May Have Prognostic Utility. Inflamm Bowel Dis (2015) 1.00
Early de novo DNA methylation and prolonged demethylation in the muscle lineage. Epigenetics (2013) 1.00
Distant conserved sequences flanking endothelial-specific promoters contain tissue-specific DNase-hypersensitive sites and over-represented motifs. Hum Mol Genet (2006) 1.00
Genomic sweeping for hypermethylated genes. Bioinformatics (2006) 0.98
Allele-specific and heritable chromatin signatures in humans. Hum Mol Genet (2010) 0.96
High-resolution mapping studies of chromatin and gene regulatory elements. Epigenomics (2009) 0.91
H3K4me3 inversely correlates with DNA methylation at a large class of non-CpG-island-containing start sites. Genome Med (2012) 0.90
Integrating genetic association, genetics of gene expression, and single nucleotide polymorphism set analysis to identify susceptibility Loci for type 2 diabetes mellitus. Am J Epidemiol (2012) 0.89
A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function. Thorax (2011) 0.88
Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes. PLoS Genet (2012) 0.87
DNA methylation and differentiation: HOX genes in muscle cells. Epigenetics Chromatin (2013) 0.86
DNaseI hypersensitivity at gene-poor, FSH dystrophy-linked 4q35.2. Nucleic Acids Res (2009) 0.85
A genome-wide analysis of open chromatin in human epididymis epithelial cells reveals candidate regulatory elements for genes coordinating epididymal function. Biol Reprod (2013) 0.85
Impact of bioinformatic procedures in the development and translation of high-throughput molecular classifiers in oncology. Clin Cancer Res (2013) 0.84
A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins. BMC Bioinformatics (2010) 0.84
Discovering sequences with potential regulatory characteristics. Genomics (2008) 0.83