Published in Bioinformatics on October 01, 1999
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
rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res (2002) 7.33
Detection of functional DNA motifs via statistical over-representation. Nucleic Acids Res (2004) 6.31
Cluster-Buster: Finding dense clusters of motifs in DNA sequences. Nucleic Acids Res (2003) 3.99
Computational prediction of transcription-factor binding site locations. Genome Biol (2003) 3.39
Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucleic Acids Res (2003) 2.50
Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences. Nucleic Acids Res (2002) 2.30
Homotypic regulatory clusters in Drosophila. Genome Res (2003) 2.28
Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. Genome Res (2010) 2.12
Genome-wide co-occurrence of promoter elements reveals a cis-regulatory cassette of rRNA transcription motifs in Saccharomyces cerevisiae. Genome Res (2002) 2.04
A survey of motif discovery methods in an integrated framework. Biol Direct (2006) 1.94
TiProD: the Tissue-specific Promoter Database. Nucleic Acids Res (2006) 1.89
Computational identification of transcriptional regulatory elements in DNA sequence. Nucleic Acids Res (2006) 1.88
Identification of a novel cis-regulatory element involved in the heat shock response in Caenorhabditis elegans using microarray gene expression and computational methods. Genome Res (2002) 1.87
Predicting transcription factor synergism. Nucleic Acids Res (2002) 1.66
Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information. Nucleic Acids Res (2003) 1.60
Discovering functional transcription-factor combinations in the human cell cycle. Genome Res (2005) 1.53
SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation. Nucleic Acids Res (2004) 1.52
A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli. Genome Res (2004) 1.45
Statistical significance of cis-regulatory modules. BMC Bioinformatics (2007) 1.41
Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts. Genome Biol (2003) 1.40
Spatial and topological organization of DNA chains induced by gene co-localization. PLoS Comput Biol (2010) 1.21
Identification of sparsely distributed clusters of cis-regulatory elements in sets of co-expressed genes. Nucleic Acids Res (2004) 1.21
Opposing functions of the ETS factor family define Shh spatial expression in limb buds and underlie polydactyly. Dev Cell (2012) 1.16
Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data. Nucleic Acids Res (2009) 1.15
The Innate Immune Database (IIDB). BMC Immunol (2008) 1.11
MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs. Nucleic Acids Res (2008) 1.11
Identification of muscle-specific regulatory modules in Caenorhabditis elegans. Genome Res (2007) 1.07
Mapping yeast transcriptional networks. Genetics (2013) 1.06
Identifying regulatory elements in eukaryotic genomes. Brief Funct Genomic Proteomic (2009) 1.02
Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules. Algorithms Mol Biol (2007) 1.00
An improved distance measure between the expression profiles linking co-expression and co-regulation in mouse. BMC Bioinformatics (2006) 0.98
Flexible promoter architecture requirements for coactivator recruitment. BMC Mol Biol (2006) 0.96
Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level. Genome Biol (2002) 0.93
Marine organism cell biology and regulatory sequence discoveryin comparative functional genomics. Cytotechnology (2005) 0.92
Construction of predictive promoter models on the example of antibacterial response of human epithelial cells. Theor Biol Med Model (2005) 0.91
Integrating sequence, evolution and functional genomics in regulatory genomics. Genome Biol (2009) 0.90
Assessment of clusters of transcription factor binding sites in relationship to human promoter, CpG islands and gene expression. BMC Genomics (2004) 0.90
Comprehensive quantitative analyses of the effects of promoter sequence elements on mRNA transcription. Nucleic Acids Res (2003) 0.90
Genome-wide identification of new Wnt/beta-catenin target genes in the human genome using CART method. BMC Genomics (2010) 0.87
Statistical detection of cooperative transcription factors with similarity adjustment. Bioinformatics (2009) 0.87
Aberrant epigenetic changes and gene expression in cloned cattle dying around birth. BMC Dev Biol (2008) 0.85
A Fast Implementation of a Scan Statistic for Identifying Chromosomal Patterns of Genome Wide Association Studies. Comput Stat Data Anal (2009) 0.83
Increasing coverage of transcription factor position weight matrices through domain-level homology. PLoS One (2012) 0.82
Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes. BMC Genomics (2007) 0.79
Compo: composite motif discovery using discrete models. BMC Bioinformatics (2008) 0.79
Computational discovery of regulatory elements in a continuous expression space. Genome Biol (2012) 0.77
Recent computational approaches to understand gene regulation: mining gene regulation in silico. Curr Genomics (2007) 0.76
Quantitative perturbation-based analysis of gene expression predicts enhancer activity in early Drosophila embryo. Elife (2016) 0.76
Analysis of Co-Associated Transcription Factors via Ordered Adjacency Differences on Motif Distribution. Sci Rep (2017) 0.75
Discovery of Putative Herbicide Resistance Genes and Its Regulatory Network in Chickpea Using Transcriptome Sequencing. Front Plant Sci (2017) 0.75
Tandem machine learning for the identification of genes regulated by transcription factors. BMC Bioinformatics (2005) 0.75
A protein-protein interaction guided method for competitive transcription factor binding improves target predictions. Nucleic Acids Res (2009) 0.75