Computational prediction of transcription-factor binding site locations.

Discovering motifs in ranked lists of DNA sequences. PLoS Comput Biol (2007) 4.40

Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res (2006) 4.32

MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes. BMC Bioinformatics (2005) 3.23

Regulatory polymorphisms underlying complex disease traits. J Mol Med (Berl) (2004) 3.22

DBD--taxonomically broad transcription factor predictions: new content and functionality. Nucleic Acids Res (2007) 3.18

Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proc Natl Acad Sci U S A (2006) 3.06

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

cisRED: a database system for genome-scale computational discovery of regulatory elements. Nucleic Acids Res (2006) 2.75

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

Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development. PLoS Genet (2011) 2.65

Systematic identification of mammalian regulatory motifs' target genes and functions. Nat Methods (2008) 2.58

Protein-DNA binding specificity predictions with structural models. Nucleic Acids Res (2005) 2.45

PReMod: a database of genome-wide mammalian cis-regulatory module predictions. Nucleic Acids Res (2006) 2.27

Glucocorticoid receptor-dependent gene regulatory networks. PLoS Genet (2005) 2.19

UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions. Nucleic Acids Res (2010) 2.16

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

Protein binding microarrays (PBMs) for rapid, high-throughput characterization of the sequence specificities of DNA binding proteins. Methods Mol Biol (2006) 2.00

A survey of motif discovery methods in an integrated framework. Biol Direct (2006) 1.94

Genome2D: a visualization tool for the rapid analysis of bacterial transcriptome data. Genome Biol (2004) 1.93

Computational identification of transcriptional regulatory elements in DNA sequence. Nucleic Acids Res (2006) 1.88

iRegulon: from a gene list to a gene regulatory network using large motif and track collections. PLoS Comput Biol (2014) 1.69

Searching for neuronal left/right asymmetry: genomewide analysis of nematode receptor-type guanylyl cyclases. Genetics (2006) 1.68

DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces. Nucleic Acids Res (2007) 1.68

Studies on DNA-binding selectivity of WRKY transcription factors lend structural clues into WRKY-domain function. Plant Mol Biol (2008) 1.65

A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements. Genome Res (2008) 1.60

Cis-regulatory variations: a study of SNPs around genes showing cis-linkage in segregating mouse populations. BMC Genomics (2006) 1.53

Design of compact, universal DNA microarrays for protein binding microarray experiments. J Comput Biol (2008) 1.45

The orientation of transcription factor binding site motifs in gene promoter regions: does it matter? BMC Genomics (2016) 1.41

Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry. Nucleic Acids Res (2007) 1.40

Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses. Genome Biol (2007) 1.38

MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes. Nucleic Acids Res (2006) 1.37

Modulefinder: a tool for computational discovery of cis regulatory modules. Pac Symp Biocomput (2005) 1.33

CisOrtho: a program pipeline for genome-wide identification of transcription factor target genes using phylogenetic footprinting. BMC Bioinformatics (2004) 1.30

Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data. BMC Bioinformatics (2006) 1.28

A generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1. BMC Genomics (2008) 1.23

An integrated approach to identifying cis-regulatory modules in the human genome. PLoS One (2009) 1.16

Using protein design algorithms to understand the molecular basis of disease caused by protein-DNA interactions: the Pax6 example. Nucleic Acids Res (2010) 1.16

The human genomic melting map. PLoS Comput Biol (2007) 1.14

Bounded search for de novo identification of degenerate cis-regulatory elements. BMC Bioinformatics (2006) 1.10

Protein-DNA binding: complexities and multi-protein codes. Nucleic Acids Res (2013) 1.09

Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis. BMC Plant Biol (2012) 1.08

Non-consensus GLI binding sites in Hedgehog target gene regulation. BMC Mol Biol (2010) 1.07

STIFDB2: an updated version of plant stress-responsive transcription factor database with additional stress signals, stress-responsive transcription factor binding sites and stress-responsive genes in Arabidopsis and rice. Plant Cell Physiol (2013) 1.04

Identifying regulatory elements in eukaryotic genomes. Brief Funct Genomic Proteomic (2009) 1.02

Conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sites. Genomics (2010) 1.02

Analysis of sequence specificities of DNA-binding proteins with protein binding microarrays. Methods Enzymol (2006) 1.02

Applying whole-genome studies of epigenetic regulation to study human disease. Cytogenet Genome Res (2006) 1.01

A comparative genomics approach to identifying the plasticity transcriptome. BMC Neurosci (2007) 1.00

A primer on regression methods for decoding cis-regulatory logic. PLoS Comput Biol (2009) 1.00

Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos. Nat Methods (2013) 1.00

WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences. BMC Bioinformatics (2007) 0.99

Scoring functions for transcription factor binding site prediction. BMC Bioinformatics (2005) 0.99

Discovering gapped binding sites of yeast transcription factors. Proc Natl Acad Sci U S A (2008) 0.98

Identification of human STAT5-dependent gene regulatory elements based on interspecies homology. J Biol Chem (2006) 0.95

STIF: Identification of stress-upregulated transcription factor binding sites in Arabidopsis thaliana. Bioinformation (2008) 0.94

Experimentally based contact energies decode interactions responsible for protein-DNA affinity and the role of molecular waters at the binding interface. Nucleic Acids Res (2009) 0.93

Prediction of mono- and di-nucleotide-specific DNA-binding sites in proteins using neural networks. BMC Struct Biol (2009) 0.93

Spurious transcription factor binding: non-functional or genetically redundant? Bioessays (2014) 0.92

Modeling the quantitative specificity of DNA-binding proteins from example binding sites. PLoS One (2009) 0.91

Integrating sequence, evolution and functional genomics in regulatory genomics. Genome Biol (2009) 0.90

Caenorhabditis elegans cisRED: a catalogue of conserved genomic elements. Nucleic Acids Res (2009) 0.89

A high-throughput percentage-of-binding strategy to measure binding energies in DNA-protein interactions: application to genome-scale site discovery. Nucleic Acids Res (2008) 0.89

Binding of nucleoid-associated protein fis to DNA is regulated by DNA breathing dynamics. PLoS Comput Biol (2013) 0.88

Predicting target DNA sequences of DNA-binding proteins based on unbound structures. PLoS One (2012) 0.88

In silico identification of NF-kappaB-regulated genes in pancreatic beta-cells. BMC Bioinformatics (2007) 0.87

Identification of conserved regulatory elements in mammalian promoter regions: a case study using the PCK1 promoter. Genomics Proteomics Bioinformatics (2008) 0.86

Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast. PLoS Comput Biol (2015) 0.84

Evolutionary Conserved Motif Finder (ECMFinder) for genome-wide identification of clustered YY1- and CTCF-binding sites. Nucleic Acids Res (2009) 0.83

Architecture of the sporulation-specific Cdc14 promoter from the oomycete Phytophthora infestans. Eukaryot Cell (2007) 0.83

DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices. BMC Bioinformatics (2009) 0.82

Benchmarks for flexible and rigid transcription factor-DNA docking. BMC Struct Biol (2011) 0.82

Nanopore sensing of individual transcription factors bound to DNA. Sci Rep (2015) 0.81

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

Unbiased proteomic analysis of proteins interacting with the HIV-1 5'LTR sequence: role of the transcription factor Meis. Nucleic Acids Res (2012) 0.80

RegNetB: predicting relevant regulator-gene relationships in localized prostate tumor samples. BMC Bioinformatics (2011) 0.80

CompMoby: comparative MobyDick for detection of cis-regulatory motifs. BMC Bioinformatics (2008) 0.80

A general integrative genomic feature transcription factor binding site prediction method applied to analysis of USF1 binding in cardiovascular disease. Hum Genomics (2009) 0.80

Prediction of a key role of motifs binding E2F and NR2F in down-regulation of numerous genes during the development of the mouse hippocampus. BMC Bioinformatics (2006) 0.79

An algorithm for identifying novel targets of transcription factor families: application to hypoxia-inducible factor 1 targets. Cancer Inform (2009) 0.79

NURBS: a database of experimental and predicted nuclear receptor binding sites of mouse. Bioinformatics (2012) 0.79

Biological code breaking in the 21st century. Mol Syst Biol (2006) 0.78

The FurA regulon in Anabaena sp. PCC 7120: in silico prediction and experimental validation of novel target genes. Nucleic Acids Res (2014) 0.78

Cis-regulatory programs in the development and evolution of vertebrate paired appendages. Semin Cell Dev Biol (2016) 0.78

Bayesian inference based modelling for gene transcriptional dynamics by integrating multiple source of knowledge. BMC Syst Biol (2012) 0.78

Advanced methods for the analysis of chromatin-associated proteins. Physiol Genomics (2014) 0.78

DBD2BS: connecting a DNA-binding protein with its binding sites. Nucleic Acids Res (2012) 0.77

Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites. BMC Bioinformatics (2012) 0.76

Using protein-binding microarrays to study transcription factor specificity: homologs, isoforms and complexes. Brief Funct Genomics (2014) 0.76

Using an ensemble of statistical metrics to quantify large sets of plant transcription factor binding sites. Plant Methods (2013) 0.76

Recent computational approaches to understand gene regulation: mining gene regulation in silico. Curr Genomics (2007) 0.76

PPARgene: A Database of Experimentally Verified and Computationally Predicted PPAR Target Genes. PPAR Res (2016) 0.75

Histone acetylation accompanied with promoter sequences displaying differential expression profiles of B-class MADS-box genes for phalaenopsis floral morphogenesis. PLoS One (2014) 0.75

Prediction and Validation of Transcription Factors Modulating the Expression of Sestrin3 Gene Using an Integrated Computational and Experimental Approach. PLoS One (2016) 0.75

DRUMS: Disk Repository with Update Management and Select option for high throughput sequencing data. BMC Bioinformatics (2014) 0.75

Integrating Multi-omics Data to Dissect Mechanisms of DNA repair Dysregulation in Breast Cancer. Sci Rep (2016) 0.75

The Construction of Regulatory Network for Insulin-Mediated Genes by Integrating Methods Based on Transcription Factor Binding Motifs and Gene Expression Variations. Genomics Inform (2015) 0.75

Identifying Cell Type-Specific Transcription Factors by Integrating ChIP-seq and eQTL Data-Application to Monocyte Gene Regulation. Gene Regul Syst Bio (2016) 0.75

Automated tools for comparative sequence analysis of genic regions using the GenePalette application. Dev Biol (2017) 0.75

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Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15

Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (2002) 43.52

Genome-wide location and function of DNA binding proteins. Science (2000) 31.25

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

Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature (2003) 29.16

Systematic determination of genetic network architecture. Nat Genet (1999) 25.45

Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature (2001) 21.55

MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res (1995) 21.22

Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science (2003) 16.49

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

Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol (2000) 14.30

A vision for the future of genomics research. Nature (2003) 14.06

Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol (1998) 13.99

Comparative analyses of multi-species sequences from targeted genomic regions. Nature (2003) 13.31

Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet (2001) 13.05

Genomics, gene expression and DNA arrays. Nature (2000) 11.48

Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science (2000) 10.14

E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints. Genes Dev (2002) 10.06

Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science (2003) 9.93

Transcription regulation and animal diversity. Nature (2003) 9.22

Regulatory element detection using correlation with expression. Nat Genet (2001) 8.92

Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci U S A (2002) 8.56

Human-mouse genome comparisons to locate regulatory sites. Nat Genet (2000) 8.08

Serial regulation of transcriptional regulators in the yeast cell cycle. Cell (2001) 7.99

Identifying regulatory networks by combinatorial analysis of promoter elements. Nat Genet (2001) 7.74

rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res (2002) 7.33

Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes Dev (2002) 6.74

Revealing modular organization in the yeast transcriptional network. Nat Genet (2002) 6.73

Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo. Proc Natl Acad Sci U S A (2001) 6.39

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

Evidence for stabilizing selection in a eukaryotic enhancer element. Nature (2000) 5.97

Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet (2000) 5.88

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Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res (2002) 4.83

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Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res (2001) 4.22

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Discovering regulatory elements in non-coding sequences by analysis of spaced dyads. Nucleic Acids Res (2000) 3.72

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