Identifying tissue-selective transcription factor binding sites in vertebrate promoters.

Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell (2007) 16.66

An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia. Nucleic Acids Res (2009) 2.69

Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression. Genome Res (2009) 2.64

DNA motifs in human and mouse proximal promoters predict tissue-specific expression. Proc Natl Acad Sci U S A (2006) 2.38

Sequence and chromatin determinants of cell-type-specific transcription factor binding. Genome Res (2012) 2.24

Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. Genome Res (2007) 2.16

A correlation with exon expression approach to identify cis-regulatory elements for tissue-specific alternative splicing. Nucleic Acids Res (2007) 1.94

Establishing glucose- and ABA-regulated transcription networks in Arabidopsis by microarray analysis and promoter classification using a Relevance Vector Machine. Genome Res (2006) 1.89

Computational prediction of methylation status in human genomic sequences. Proc Natl Acad Sci U S A (2006) 1.83

Predicting cell-type-specific gene expression from regions of open chromatin. Genome Res (2012) 1.78

Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1. Nucleic Acids Res (2009) 1.76

Genome-wide identification of PAX3-FKHR binding sites in rhabdomyosarcoma reveals candidate target genes important for development and cancer. Cancer Res (2010) 1.74

Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells. Blood (2009) 1.64

The promoters of human cell cycle genes integrate signals from two tumor suppressive pathways during cellular transformation. Mol Syst Biol (2005) 1.60

Interferon regulatory factors are transcriptional regulators of adipogenesis. Cell Metab (2008) 1.55

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

Discriminative motif discovery in DNA and protein sequences using the DEME algorithm. BMC Bioinformatics (2007) 1.52

Cis-regulatory modules in the mammalian liver: composition depends on strength of Foxa2 consensus site. Nucleic Acids Res (2008) 1.46

GADEM: a genetic algorithm guided formation of spaced dyads coupled with an EM algorithm for motif discovery. J Comput Biol (2009) 1.44

Site identification in high-throughput RNA-protein interaction data. Bioinformatics (2012) 1.43

Tissue-specific regulatory elements in mammalian promoters. Mol Syst Biol (2007) 1.41

Genome-wide mapping of boundary element-associated factor (BEAF) binding sites in Drosophila melanogaster links BEAF to transcription. Mol Cell Biol (2009) 1.40

Genome-wide mapping of SMAD target genes reveals the role of BMP signaling in embryonic stem cell fate determination. Genome Res (2009) 1.27

Genomic analyses of the RNA-binding protein Hu antigen R (HuR) identify a complex network of target genes and novel characteristics of its binding sites. J Biol Chem (2011) 1.24

Genomewide analysis of aryl hydrocarbon receptor binding targets reveals an extensive array of gene clusters that control morphogenetic and developmental programs. Environ Health Perspect (2009) 1.22

Identification of context-dependent motifs by contrasting ChIP binding data. Bioinformatics (2010) 1.19

A general approach for discriminative de novo motif discovery from high-throughput data. Nucleic Acids Res (2013) 1.18

A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data. PLoS One (2009) 1.13

De-novo discovery of differentially abundant transcription factor binding sites including their positional preference. PLoS Comput Biol (2011) 1.11

Activation of Bmp2-Smad1 signal and its regulation by coordinated alteration of H3K27 trimethylation in Ras-induced senescence. PLoS Genet (2011) 1.10

Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii. BMC Genomics (2010) 1.05

Extracting sequence features to predict protein-DNA interactions: a comparative study. Nucleic Acids Res (2008) 1.04

Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes. BMC Bioinformatics (2011) 1.04

Phylo-mLogo: an interactive and hierarchical multiple-logo visualization tool for alignment of many sequences. BMC Bioinformatics (2007) 0.99

Computational analyses of eukaryotic promoters. BMC Bioinformatics (2007) 0.99

DECOD: fast and accurate discriminative DNA motif finding. Bioinformatics (2011) 0.98

A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information. Nucleic Acids 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 widespread role of the motif environment in transcription factor binding across diverse protein families. Genome Res (2015) 0.94

Expression patterns of protein kinases correlate with gene architecture and evolutionary rates. PLoS One (2008) 0.88

Computational identification of tissue-specific alternative splicing elements in mouse genes from RNA-Seq. Nucleic Acids Res (2010) 0.87

Short sequence motifs, overrepresented in mammalian conserved non-coding sequences. BMC Genomics (2007) 0.87

Open chromatin profiling in mice livers reveals unique chromatin variations induced by high fat diet. J Biol Chem (2014) 0.85

A systems biology approach to transcription factor binding site prediction. PLoS One (2010) 0.85

CoMoDis: composite motif discovery in mammalian genomes. Nucleic Acids Res (2006) 0.83

AMD, an automated motif discovery tool using stepwise refinement of gapped consensuses. PLoS One (2011) 0.82

fdrMotif: identifying cis-elements by an EM algorithm coupled with false discovery rate control. Bioinformatics (2008) 0.82

Understanding variation in transcription factor binding by modeling transcription factor genome-epigenome interactions. PLoS Comput Biol (2013) 0.82

Discriminative motif optimization based on perceptron training. Bioinformatics (2013) 0.81

Computational challenges, tools, and resources for analyzing co- and post-transcriptional events in high throughput. Wiley Interdiscip Rev RNA (2014) 0.81

Genome-wide computational prediction and analysis of core promoter elements across plant monocots and dicots. PLoS One (2013) 0.81

The limits of de novo DNA motif discovery. PLoS One (2012) 0.79

Genome-wide signatures of transcription factor activity: connecting transcription factors, disease, and small molecules. PLoS Comput Biol (2013) 0.79

Models incorporating chromatin modification data identify functionally important p53 binding sites. Nucleic Acids Res (2013) 0.79

Extracting transcription factor binding sites from unaligned gene sequences with statistical models. BMC Bioinformatics (2008) 0.78

Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes. Nucleic Acids Res (2014) 0.78

A novel ab initio identification system of transcriptional regulation motifs in genome DNA sequences based on direct comparison scheme of signal/noise distributions. Nucleic Acids Res (2012) 0.78

An integrative computational approach to effectively guide experimental identification of regulatory elements in promoters. BMC Bioinformatics (2012) 0.77

Regulatory elements of Caenorhabditis elegans ribosomal protein genes. BMC Genomics (2012) 0.77

Bioinformatic identification of novel putative photoreceptor specific cis-elements. BMC Bioinformatics (2007) 0.77

Synchronization of cytoplasmic and transferred mitochondrial ribosomal protein gene expression in land plants is linked to Telo-box motif enrichment. BMC Evol Biol (2011) 0.77

Binding site discovery from nucleic acid sequences by discriminative learning of hidden Markov models. Nucleic Acids Res (2014) 0.76

Conserved elements associated with ribosomal genes and their trans-splice acceptor sites in Caenorhabditis elegans. Nucleic Acids Res (2010) 0.76

A novel, dynamic pattern-based analysis of NF-κB binding during the priming phase of liver regeneration reveals switch-like functional regulation of target genes. Front Physiol (2015) 0.76

Composing a Tumor Specific Bacterial Promoter. PLoS One (2016) 0.75

Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science (1993) 36.84

Sequence logos: a new way to display consensus sequences. Nucleic Acids Res (1990) 36.74

TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res (2003) 29.26

Expression of a single transfected cDNA converts fibroblasts to myoblasts. Cell (1987) 22.17

JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res (2004) 19.32

DNA binding sites: representation and discovery. Bioinformatics (2000) 16.01

An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat Biotechnol (2002) 10.23

Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet (2004) 9.96

Identification of consensus patterns in unaligned DNA sequences known to be functionally related. Comput Appl Biosci (1990) 6.16

Identification of regulatory regions which confer muscle-specific gene expression. J Mol Biol (1998) 6.13

Going the distance: a current view of enhancer action. Science (1998) 5.83

A predictive model for regulatory sequences directing liver-specific transcription. Genome Res (2001) 5.16

A compilation of composite regulatory elements affecting gene transcription in vertebrates. Nucleic Acids Res (1995) 4.93

Finding motifs using random projections. J Comput Biol (2002) 4.61

An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins (1990) 4.42

YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Res (2003) 3.71

The POU domain: versatility in transcriptional regulation by a flexible two-in-one DNA-binding domain. Genes Dev (1995) 2.97

The Eukaryotic Promoter Database EPD. Nucleic Acids Res (1998) 2.24

Modulation of hepatic gene expression by hepatocyte nuclear factor 1. Science (1997) 1.79

Mutation of hepatocyte nuclear factor-1beta inhibits Pkhd1 gene expression and produces renal cysts in mice. J Clin Invest (2004) 1.67

Discriminative motifs. J Comput Biol (2003) 1.24

FHX, a novel fork head factor with a dual DNA binding specificity. J Biol Chem (2000) 0.96

Dexamethasone stimulation of rat insulin-like growth factor binding protein-1 promoter activity involves multiple cis-elements. Mol Endocrinol (1996) 0.85

Identity between rat htf and human xbp-1 genes: determination of gene structure, target sequence, and transcription promotion function for HTF. Gene (2000) 0.83

Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics (2008) 39.08

ZOOM! Zillions of oligos mapped. Bioinformatics (2008) 29.78

Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet (2008) 18.28

Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell (2007) 16.66

ESEfinder: A web resource to identify exonic splicing enhancers. Nucleic Acids Res (2003) 12.81

The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes Dev (2002) 7.61

A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells. Proc Natl Acad Sci U S A (2003) 7.30

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol (2010) 7.00

Regulating gene expression through RNA nuclear retention. Cell (2005) 5.58

Network-based global inference of human disease genes. Mol Syst Biol (2008) 5.01

An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers. Hum Mol Genet (2006) 4.56

Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2. Genes Dev (2008) 4.24

Critical roles for Dicer in the female germline. Genes Dev (2007) 4.23

Large-scale structure of genomic methylation patterns. Genome Res (2005) 4.11

Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell (2013) 3.81

Updates to the RMAP short-read mapping software. Bioinformatics (2009) 3.18

A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression. EMBO J (2010) 3.18

High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Res (2009) 3.08

Direct coupling of the cell cycle and cell death machinery by E2F. Nat Cell Biol (2002) 3.00

A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers. Mol Syst Biol (2010) 2.92

Novel Foxo1-dependent transcriptional programs control T(reg) cell function. Nature (2012) 2.77

TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies. Nucleic Acids Res (2005) 2.73

An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia. Nucleic Acids Res (2009) 2.69

Similarity of position frequency matrices for transcription factor binding sites. Bioinformatics (2004) 2.51

Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucleic Acids Res (2003) 2.50

DNA motifs in human and mouse proximal promoters predict tissue-specific expression. Proc Natl Acad Sci U S A (2006) 2.38

Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. Genome Res (2007) 2.16

Whole exome sequencing to identify a novel gene (caveolin-1) associated with human pulmonary arterial hypertension. Circ Cardiovasc Genet (2012) 2.16

Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biol (2004) 2.12

Interacting models of cooperative gene regulation. Proc Natl Acad Sci U S A (2004) 2.09

Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing. Nucleic Acids Res (2006) 2.00

High-resolution human core-promoter prediction with CoreBoost_HM. Genome Res (2008) 1.88

Cell-type-based analysis of microRNA profiles in the mouse brain. Neuron (2012) 1.85

Computational prediction of methylation status in human genomic sequences. Proc Natl Acad Sci U S A (2006) 1.83

Identification of the human mature B cell miRNome. Immunity (2009) 1.82

Mining ChIP-chip data for transcription factor and cofactor binding sites. Bioinformatics (2005) 1.81

Adaptively inferring human transcriptional subnetworks. Mol Syst Biol (2006) 1.81

Determination of enriched histone modifications in non-genic portions of the human genome. BMC Genomics (2009) 1.80

Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes. Nucleic Acids Res (2005) 1.70

tRNA-derived microRNA modulates proliferation and the DNA damage response and is down-regulated in B cell lymphoma. Proc Natl Acad Sci U S A (2013) 1.66

ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes. Proc Natl Acad Sci U S A (2008) 1.65

BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. BMC Genomics (2013) 1.64

Genome-wide promoter extraction and analysis in human, mouse, and rat. Genome Biol (2005) 1.64

Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells. Blood (2009) 1.64

BCL6 suppression of BCL2 via Miz1 and its disruption in diffuse large B cell lymphoma. Proc Natl Acad Sci U S A (2009) 1.62

Interferon regulatory factors are transcriptional regulators of adipogenesis. Cell Metab (2008) 1.55

Neural potential of a stem cell population in the hair follicle. Cell Cycle (2007) 1.53

Hsa-miR-1246, hsa-miR-320a and hsa-miR-196b-5p inhibitors can reduce the cytotoxicity of Ebola virus glycoprotein in vitro. Sci China Life Sci (2014) 1.51

RNA landscape of evolution for optimal exon and intron discrimination. Proc Natl Acad Sci U S A (2008) 1.45

Development of the human cancer microRNA network. Silence (2010) 1.43

Poly A- transcripts expressed in HeLa cells. PLoS One (2008) 1.42

SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Bioinformatics (2011) 1.42

OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds. Nucleic Acids Res (2013) 1.41

Statistical significance of cis-regulatory modules. BMC Bioinformatics (2007) 1.41

Tissue-specific regulatory elements in mammalian promoters. Mol Syst Biol (2007) 1.41

Functional genomics as applied to mapping transcription regulatory networks. Curr Opin Microbiol (2002) 1.39

Profiling alternatively spliced mRNA isoforms for prostate cancer classification. BMC Bioinformatics (2006) 1.39

Predicting methylation status of CpG islands in the human brain. Bioinformatics (2006) 1.38

Regulation of the PDK4 isozyme by the Rb-E2F1 complex. J Biol Chem (2008) 1.38

Genome-wide prediction and analysis of function-specific transcription factor binding sites. In Silico Biol (2004) 1.35

Computing exact P-values for DNA motifs. Bioinformatics (2007) 1.33

A molecular signature predictive of indolent prostate cancer. Sci Transl Med (2013) 1.32

Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development. Genomics (2008) 1.31

H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence. Proc Natl Acad Sci U S A (2012) 1.28

Identification of tumor suppressors and oncogenes from genomic and epigenetic features in ovarian cancer. PLoS One (2011) 1.25

The transcription factor Foxo1 controls central-memory CD8+ T cell responses to infection. Immunity (2013) 1.23

A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome. Nucleic Acids Res (2006) 1.21

CD36-dependent regulation of muscle FoxO1 and PDK4 in the PPAR delta/beta-mediated adaptation to metabolic stress. J Biol Chem (2008) 1.16

DWE: discriminating word enumerator. Bioinformatics (2004) 1.15

DNA methylation data analysis and its application to cancer research. Epigenomics (2013) 1.14

Study of FoxA pioneer factor at silent genes reveals Rfx-repressed enhancer at Cdx2 and a potential indicator of esophageal adenocarcinoma development. PLoS Genet (2011) 1.14

Scanning the human genome at kilobase resolution. Genome Res (2008) 1.13

Dual-specificity splice sites function alternatively as 5' and 3' splice sites. Proc Natl Acad Sci U S A (2007) 1.10

Identification of synaptic targets of Drosophila pumilio. PLoS Comput Biol (2008) 1.10

ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor. Nucleic Acids Res (2011) 1.09

Boosting with stumps for predicting transcription start sites. Genome Biol (2007) 1.08

A new method for detecting human recombination hotspots and its applications to the HapMap ENCODE data. Am J Hum Genet (2006) 1.04

Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes. BMC Bioinformatics (2011) 1.04

Computational comparison of two mouse draft genomes and the human golden path. Genome Biol (2002) 1.01

Direct cloning of double-stranded RNAs from RNase protection analysis reveals processing patterns of C/D box snoRNAs and provides evidence for widespread antisense transcript expression. Nucleic Acids Res (2011) 1.01

Identification of novel androgen-regulated pathways and mRNA isoforms through genome-wide exon-specific profiling of the LNCaP transcriptome. PLoS One (2011) 1.00

Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells. Nucleic Acids Res (2013) 0.99

The transcriptome of human CD34+ hematopoietic stem-progenitor cells. Proc Natl Acad Sci U S A (2009) 0.98

Genome-wide localization of protein-DNA binding and histone modification by a Bayesian change-point method with ChIP-seq data. PLoS Comput Biol (2012) 0.98

The miR-424(322)/503 cluster orchestrates remodeling of the epithelium in the involuting mammary gland. Genes Dev (2014) 0.98

A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information. Nucleic Acids Res (2012) 0.97

Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells. BMC Bioinformatics (2008) 0.96

The mouse genome: experimental examination of gene predictions and transcriptional start sites. Genome Res (2004) 0.96

From worm to human: bioinformatics approaches to identify FOXO target genes. Mech Ageing Dev (2005) 0.95

Evolutionary impact of limited splicing fidelity in mammalian genes. Trends Genet (2007) 0.94

Functional mutation of SMAC/DIABLO, encoding a mitochondrial proapoptotic protein, causes human progressive hearing loss DFNA64. Am J Hum Genet (2011) 0.94

Histone methylation marks play important roles in predicting the methylation status of CpG islands. Biochem Biophys Res Commun (2008) 0.93

The effects of carbon dioxide and temperature on microRNA expression in Arabidopsis development. Nat Commun (2013) 0.93

Computational identification of active enhancers in model organisms. Genomics Proteomics Bioinformatics (2013) 0.92

Putative zinc finger protein binding sites are over-represented in the boundaries of methylation-resistant CpG islands in the human genome. PLoS One (2007) 0.90