Published in PLoS Comput Biol on August 09, 2012
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods (2013) 7.06
ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat Rev Genet (2012) 3.23
Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape. Nat Biotechnol (2014) 2.70
Practical guidelines for the comprehensive analysis of ChIP-seq data. PLoS Comput Biol (2013) 1.81
Redeployment of Myc and E2f1-3 drives Rb-deficient cell cycles. Nat Cell Biol (2015) 1.61
Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons. Nat Neurosci (2014) 1.57
Expression of Terminal Effector Genes in Mammalian Neurons Is Maintained by a Dynamic Relay of Transient Enhancers. Neuron (2016) 1.37
High-throughput mapping of regulatory DNA. Nat Biotechnol (2016) 1.27
Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape. Cell (2016) 1.13
The role of chromatin insulators in nuclear architecture and genome function. Curr Opin Genet Dev (2013) 1.04
Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways. Elife (2014) 1.01
MACE: model based analysis of ChIP-exo. Nucleic Acids Res (2014) 0.99
An integrated model of multiple-condition ChIP-Seq data reveals predeterminants of Cdx2 binding. PLoS Comput Biol (2014) 0.99
Epigenomic landscapes of retinal rods and cones. Elife (2016) 0.95
Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes. Genome Biol (2013) 0.93
ETS1 is a genome-wide effector of RAS/ERK signaling in epithelial cells. Nucleic Acids Res (2014) 0.92
Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization. Cell (2017) 0.90
Identification of transcription factor binding sites from ChIP-seq data at high resolution. Bioinformatics (2013) 0.89
Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data. BMC Genomics (2014) 0.88
Motif signatures in stretch enhancers are enriched for disease-associated genetic variants. Epigenetics Chromatin (2015) 0.85
A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data. Biol Direct (2014) 0.85
Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction. Genome Res (2014) 0.84
Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment. BMC Genomics (2014) 0.83
Protein-DNA binding in high-resolution. Crit Rev Biochem Mol Biol (2015) 0.83
Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. Nat Commun (2014) 0.83
A new exhaustive method and strategy for finding motifs in ChIP-enriched regions. PLoS One (2014) 0.82
dPeak: high resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data. PLoS Comput Biol (2013) 0.81
Universal count correction for high-throughput sequencing. PLoS Comput Biol (2014) 0.80
Protection of CpG islands against de novo DNA methylation during oogenesis is associated with the recognition site of E2f1 and E2f2. Epigenetics Chromatin (2014) 0.80
Identification of cis-regulatory modules in promoters of human genes exploiting mutual positioning of transcription factors. Nucleic Acids Res (2013) 0.80
Identification of new branch points and unconventional introns in Saccharomyces cerevisiae. RNA (2016) 0.80
Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells. Front Genet (2016) 0.79
SPIB and BATF provide alternate determinants of IRF4 occupancy in diffuse large B-cell lymphoma linked to disease heterogeneity. Nucleic Acids Res (2014) 0.79
Elucidating MicroRNA Regulatory Networks Using Transcriptional, Post-transcriptional, and Histone Modification Measurements. Cell Rep (2015) 0.79
msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding. PLoS One (2015) 0.79
Detecting broad domains and narrow peaks in ChIP-seq data with hiddenDomains. BMC Bioinformatics (2016) 0.78
Genome-Wide Mapping and Interrogation of the Nmp4 Antianabolic Bone Axis. Mol Endocrinol (2015) 0.77
Defining bacterial regulons using ChIP-seq. Methods (2015) 0.77
Genome-Wide Mapping of Binding Sites Reveals Multiple Biological Functions of the Transcription Factor Cst6p in Saccharomyces cerevisiae. MBio (2016) 0.76
Bacterial regulon modeling and prediction based on systematic cis regulatory motif analyses. Sci Rep (2016) 0.76
Features that define the best ChIP-seq peak calling algorithms. Brief Bioinform (2016) 0.76
Genome-wide recruitment profiling of transcription factor Crz1 in response to high pH stress. BMC Genomics (2016) 0.75
CRCDA--Comprehensive resources for cancer NGS data analysis. Database (Oxford) (2015) 0.75
Wnt/Tcf1 pathway restricts embryonic stem cell cycle through activation of the Ink4/Arf locus. PLoS Genet (2017) 0.75
High resolution mapping of enhancer-promoter interactions. PLoS One (2015) 0.75
Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice. Sci Data (2016) 0.75
An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes. BMC Genomics (2016) 0.75
ChIP-BIT: Bayesian inference of target genes using a novel joint probabilistic model of ChIP-seq profiles. Nucleic Acids Res (2015) 0.75
Mocap: large-scale inference of transcription factor binding sites from chromatin accessibility. Nucleic Acids Res (2017) 0.75
Modular combinatorial binding among human trans-acting factors reveals direct and indirect factor binding. BMC Genomics (2017) 0.75
GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments. Nucleic Acids Res (2016) 0.75
Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1. Nucleic Acids Res (2016) 0.75
Differential chromatin profiles partially determine transcription factor binding. PLoS One (2017) 0.75
Mapping genome-wide transcription-factor binding sites using DAP-seq. Nat Protoc (2017) 0.75
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Model-based analysis of ChIP-Seq (MACS). Genome Biol (2008) 51.63
Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol (1994) 37.96
TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res (2003) 29.26
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell (2008) 28.29
JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res (2004) 19.32
ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature (2009) 18.38
Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A (2010) 15.13
Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol (2000) 14.30
An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol (2008) 13.96
ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet (2009) 13.12
Max: a helix-loop-helix zipper protein that forms a sequence-specific DNA-binding complex with Myc. Science (1991) 12.00
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods (2008) 11.61
An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat Biotechnol (2002) 10.23
Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res (2008) 8.89
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat Biotechnol (2006) 8.38
Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell (2011) 6.29
Direct conversion of mouse fibroblasts to hepatocyte-like cells by defined factors. Nature (2011) 5.84
Insights from genomic profiling of transcription factors. Nat Rev Genet (2009) 5.57
Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat Genet (2010) 5.26
Reciprocal transcriptional regulation of Pou5f1 and Sox2 via the Oct4/Sox2 complex in embryonic stem cells. Mol Cell Biol (2005) 4.54
Crystal structure of the heterodimeric bZIP transcription factor c-Fos-c-Jun bound to DNA. Nature (1995) 4.08
Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res (2008) 3.76
High-resolution computational models of genome binding events. Nat Biotechnol (2006) 3.74
An algorithm for finding signals of unknown length in DNA sequences. Bioinformatics (2001) 3.71
The transcription factor BATF controls the global regulators of class-switch recombination in both B cells and T cells. Nat Immunol (2011) 3.21
The nuclear receptor Nr5a2 can replace Oct4 in the reprogramming of murine somatic cells to pluripotent cells. Cell Stem Cell (2010) 2.89
Identification of a Ctcf cofactor, Yy1, for the X chromosome binary switch. Mol Cell (2007) 2.69
Practical strategies for discovering regulatory DNA sequence motifs. PLoS Comput Biol (2006) 2.53
DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies. PLoS Comput Biol (2007) 2.37
Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. Genome Res (2010) 2.12
The proto-oncogene c-myc in hematopoietic development and leukemogenesis. Oncogene (2002) 1.85
On the detection and refinement of transcription factor binding sites using ChIP-Seq data. Nucleic Acids Res (2010) 1.67
Deep and wide digging for binding motifs in ChIP-Seq data. Bioinformatics (2010) 1.61
Inferring transcription factor complexes from ChIP-seq data. Nucleic Acids Res (2011) 1.53
Informative priors based on transcription factor structural class improve de novo motif discovery. Bioinformatics (2006) 1.45
Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing. Nucleic Acids Res (2009) 1.45
PeakRanger: a cloud-enabled peak caller for ChIP-seq data. BMC Bioinformatics (2011) 1.44
Discovering homotypic binding events at high spatial resolution. Bioinformatics (2010) 1.33
Multiprotein-DNA complexes in transcriptional regulation. Annu Rev Biophys Biomol Struct (1999) 1.33
Regulation of collagen type I in vascular smooth muscle cells by competition between Nkx2.5 and deltaEF1/ZEB1. Mol Cell Biol (2004) 1.32
De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis. Nucleic Acids Res (2010) 1.30
A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information. Nucleic Acids Res (2012) 0.97
Cross-family interaction between the bHLHZip USF and bZip Fra1 proteins results in down-regulation of AP1 activity. Oncogene (1997) 0.90
ChIP-PaM: an algorithm to identify protein-DNA interaction using ChIP-Seq data. Theor Biol Med Model (2010) 0.88
Functional characterization of the promoter for the gene encoding human eosinophil peroxidase. J Biol Chem (1994) 0.82
Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (2002) 43.52
Core transcriptional regulatory circuitry in human embryonic stem cells. Cell (2005) 34.93
Control of developmental regulators by Polycomb in human embryonic stem cells. Cell (2006) 28.21
Transcriptional regulatory code of a eukaryotic genome. Nature (2004) 27.21
Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature (2006) 25.90
Genome-wide map of nucleosome acetylation and methylation in yeast. Cell (2005) 15.08
Control of pancreas and liver gene expression by HNF transcription factors. Science (2004) 12.05
An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics (2006) 11.13
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature (2007) 7.91
Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat Genet (2007) 6.92
Computational discovery of gene modules and regulatory networks. Nat Biotechnol (2003) 6.55
ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res (2007) 3.80
High-resolution computational models of genome binding events. Nat Biotechnol (2006) 3.74
Global position and recruitment of HATs and HDACs in the yeast genome. Mol Cell (2004) 3.74
Continuous representations of time-series gene expression data. J Comput Biol (2003) 3.32
Core transcriptional regulatory circuitry in human hepatocytes. Mol Syst Biol (2006) 3.15
Combining location and expression data for principled discovery of genetic regulatory network models. Pac Symp Biocomput (2002) 3.05
Genotype to phenotype: a complex problem. Science (2010) 2.92
A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data. Bioinformatics (2005) 2.52
Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast. Proc Natl Acad Sci U S A (2009) 2.36
Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex. PLoS Biol (2006) 2.17
Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes. Proc Natl Acad Sci U S A (2003) 2.10
Coordinated binding of NF-kappaB family members in the response of human cells to lipopolysaccharide. Proc Natl Acad Sci U S A (2006) 1.96
Global gene deletion analysis exploring yeast filamentous growth. Science (2012) 1.67
Control of transcription by cell size. PLoS Biol (2010) 1.61
K-ary clustering with optimal leaf ordering for gene expression data. Bioinformatics (2003) 1.53
Deconvolving cell cycle expression data with complementary information. Bioinformatics (2004) 1.51
Differentiated human stem cells resemble fetal, not adult, β cells. Proc Natl Acad Sci U S A (2014) 1.44
Global control of motor neuron topography mediated by the repressive actions of a single hox gene. Neuron (2010) 1.41
Synergistic binding of transcription factors to cell-specific enhancers programs motor neuron identity. Nat Neurosci (2013) 1.36
Discovering homotypic binding events at high spatial resolution. Bioinformatics (2010) 1.33
Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET. Genome Biol (2008) 1.29
Embryonic stem cell-based mapping of developmental transcriptional programs. Nat Methods (2011) 1.20
Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis. Genome Biol (2011) 1.19
Automated discovery of functional generality of human gene expression programs. PLoS Comput Biol (2007) 1.18
Combined analysis reveals a core set of cycling genes. Genome Biol (2007) 1.10
Rapid haplotype inference for nuclear families. Genome Biol (2010) 1.03
High-resolution genetic mapping with pooled sequencing. BMC Bioinformatics (2012) 1.01
Feed-forward regulation of a cell fate determinant by an RNA-binding protein generates asymmetry in yeast. Genetics (2010) 0.89
Large scale comparison of innate responses to viral and bacterial pathogens in mouse and macaque. PLoS One (2011) 0.87
Semi-supervised analysis of gene expression profiles for lineage-specific development in the Caenorhabditis elegans embryo. Bioinformatics (2006) 0.86
A Cdx4-Sall4 regulatory module controls the transition from mesoderm formation to embryonic hematopoiesis. Stem Cell Reports (2013) 0.86
ReadDB provides efficient storage for mapped short reads. BMC Bioinformatics (2011) 0.75
A multi-parametric flow cytometric assay to analyze DNA-protein interactions. Nucleic Acids Res (2012) 0.75
PHENOME-WIDE INTERACTION STUDY (PheWIS) IN AIDS CLINICAL TRIALS GROUP DATA (ACTG). Pac Symp Biocomput (2016) 0.75
Ruler arrays reveal haploid genomic structural variation. PLoS One (2012) 0.75