Published in Nucleic Acids Res on December 01, 2003
Global nucleosome occupancy in yeast. Genome Biol (2004) 5.49
CisModule: de novo discovery of cis-regulatory modules by hierarchical mixture modeling. Proc Natl Acad Sci U S A (2004) 3.37
Variable Selection in Nonparametric Varying-Coefficient Models for Analysis of Repeated Measurements. J Am Stat Assoc (2008) 2.50
Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues. Nucleic Acids Res (2006) 2.26
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
T-Reg Comparator: an analysis tool for the comparison of position weight matrices. Nucleic Acids Res (2005) 1.93
Statistical methods for identifying yeast cell cycle transcription factors. Proc Natl Acad Sci U S A (2005) 1.81
Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae. Nucleic Acids Res (2006) 1.65
The promoters of human cell cycle genes integrate signals from two tumor suppressive pathways during cellular transformation. Mol Syst Biol (2005) 1.60
Discovering functional transcription-factor combinations in the human cell cycle. Genome Res (2005) 1.53
Clustering of genes into regulons using integrated modeling-COGRIM. Genome Biol (2007) 1.48
Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics (2006) 1.47
On the relation between promoter divergence and gene expression evolution. Mol Syst Biol (2008) 1.43
Modelling the network of cell cycle transcription factors in the yeast Saccharomyces cerevisiae. BMC Bioinformatics (2006) 1.41
Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences. Bioinformatics (2008) 1.34
Extraction of transcription regulatory signals from genome-wide DNA-protein interaction data. Nucleic Acids Res (2005) 1.27
Systematic identification of yeast cell cycle transcription factors using multiple data sources. BMC Bioinformatics (2008) 1.25
Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data. Nucleic Acids Res (2009) 1.15
Periodic mRNA synthesis and degradation co-operate during cell cycle gene expression. Mol Syst Biol (2014) 1.10
Identifying cooperative transcriptional regulations using protein-protein interactions. Nucleic Acids Res (2005) 1.09
Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data. BMC Bioinformatics (2007) 1.09
Identification of regulatory targets of tissue-specific transcription factors: application to retina-specific gene regulation. Nucleic Acids Res (2005) 1.07
Dynamic modeling of cis-regulatory circuits and gene expression prediction via cross-gene identification. BMC Bioinformatics (2005) 1.05
Combinatorial control of gene expression by the three yeast repressors Mig1, Mig2 and Mig3. BMC Genomics (2008) 1.05
Prediction of synergistic transcription factors by function conservation. Genome Biol (2007) 1.01
A comprehensive performance evaluation on the prediction results of existing cooperative transcription factors identification algorithms. BMC Syst Biol (2014) 1.00
Inference of sparse combinatorial-control networks from gene-expression data: a message passing approach. BMC Bioinformatics (2010) 0.99
Systematic identification of cell cycle regulated transcription factors from microarray time series data. BMC Genomics (2008) 0.98
Uncovering transcriptional interactions via an adaptive fuzzy logic approach. BMC Bioinformatics (2009) 0.97
VARIABLE SELECTION AND ESTIMATION IN HIGH-DIMENSIONAL VARYING-COEFFICIENT MODELS. Stat Sin (2011) 0.94
Topological comparison of methods for predicting transcriptional cooperativity in yeast. BMC Genomics (2008) 0.92
Statistical significance of combinatorial regulations. Proc Natl Acad Sci U S A (2013) 0.88
TRRUST: a reference database of human transcriptional regulatory interactions. Sci Rep (2015) 0.87
Identifying cooperative transcription factors in yeast using multiple data sources. BMC Syst Biol (2014) 0.87
Simplified method to predict mutual interactions of human transcription factors based on their primary structure. PLoS One (2011) 0.86
PCTFPeval: a web tool for benchmarking newly developed algorithms for predicting cooperative transcription factor pairs in yeast. BMC Bioinformatics (2015) 0.86
A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription. BMC Genomics (2012) 0.85
Selection of thermodynamic models for combinatorial control of multiple transcription factors in early differentiation of embryonic stem cells. BMC Genomics (2008) 0.84
Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation. BMC Bioinformatics (2008) 0.84
Properly defining the targets of a transcription factor significantly improves the computational identification of cooperative transcription factor pairs in yeast. BMC Genomics (2015) 0.83
An ensemble learning approach to reverse-engineering transcriptional regulatory networks from time-series gene expression data. BMC Genomics (2009) 0.82
TREMOR--a tool for retrieving transcriptional modules by incorporating motif covariance. Nucleic Acids Res (2007) 0.82
Revealing cell cycle control by combining model-based detection of periodic expression with novel cis-regulatory descriptors. BMC Syst Biol (2007) 0.81
High-resolution analysis of condition-specific regulatory modules in Saccharomyces cerevisiae. Genome Biol (2008) 0.81
Profiling the transcription factor regulatory networks of human cell types. Nucleic Acids Res (2014) 0.80
Identification of cell cycle-related regulatory motifs using a kernel canonical correlation analysis. BMC Genomics (2009) 0.80
One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data. Nucleic Acids Res (2012) 0.79
Combinatorial Cis-regulation in Saccharomyces Species. G3 (Bethesda) (2016) 0.79
Computational structural analysis: multiple proteins bound to DNA. PLoS One (2008) 0.79
Embedding mRNA stability in correlation analysis of time-series gene expression data. PLoS Comput Biol (2008) 0.79
Deriving transcriptional programs and functional processes from gene expression databases. Bioinformatics (2012) 0.79
Robustness of transcriptional regulatory program influences gene expression variability. BMC Genomics (2009) 0.79
GBNet: deciphering regulatory rules in the co-regulated genes using a Gibbs sampler enhanced Bayesian network approach. BMC Bioinformatics (2008) 0.79
Loregic: a method to characterize the cooperative logic of regulatory factors. PLoS Comput Biol (2015) 0.77
CAGER: classification analysis of gene expression regulation using multiple information sources. BMC Bioinformatics (2005) 0.77
CoopTFD: a repository for predicted yeast cooperative transcription factor pairs. Database (Oxford) (2016) 0.77
JunD/AP1 regulatory network analysis during macrophage activation in a rat model of crescentic glomerulonephritis. BMC Syst Biol (2013) 0.76
Deciphering Cis-Regulatory Element Mediated Combinatorial Regulation in Rice under Blast Infected Condition. PLoS One (2015) 0.76
YCRD: Yeast Combinatorial Regulation Database. PLoS One (2016) 0.76
Functional and topological characterization of transcriptional cooperativity in yeast. BMC Res Notes (2012) 0.75
A novel statistical approach for identification of the master regulator transcription factor. BMC Bioinformatics (2017) 0.75
Detecting Cooperativity between Transcription Factors Based on Functional Coherence and Similarity of Their Target Gene Sets. PLoS One (2016) 0.75
PTRcombiner: mining combinatorial regulation of gene expression from post-transcriptional interaction maps. BMC Genomics (2014) 0.75
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell (1998) 62.20
Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (2002) 43.52
A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell (1998) 19.67
An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat Biotechnol (2002) 10.23
Regulatory element detection using correlation with expression. Nat Genet (2001) 8.92
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
A role for the transcription factors Mbp1 and Swi4 in progression from G1 to S phase. Science (1993) 6.37
Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature (2000) 4.52
Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev (2002) 3.27
Collaborative competition mechanism for gene activation in vivo. Mol Cell Biol (2003) 3.10
Forkhead-like transcription factors recruit Ndd1 to the chromatin of G2/M-specific promoters. Nature (2000) 2.74
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Forkhead transcription factors, Fkh1p and Fkh2p, collaborate with Mcm1p to control transcription required for M-phase. Curr Biol (2000) 2.31
Targeting the MEF2-like transcription factor Smp1 by the stress-activated Hog1 mitogen-activated protein kinase. Mol Cell Biol (2003) 2.23
Hir1p and Hir2p function as transcriptional corepressors to regulate histone gene transcription in the Saccharomyces cerevisiae cell cycle. Mol Cell Biol (1997) 2.11
Suppression of yeast RNA polymerase III mutations by FHL1, a gene coding for a fork head protein involved in rRNA processing. Mol Cell Biol (1994) 1.91
Overlapping and distinct roles of the duplicated yeast transcription factors Ace2p and Swi5p. Mol Microbiol (2001) 1.82
NDD1, a high-dosage suppressor of cdc28-1N, is essential for expression of a subset of late-S-phase-specific genes in Saccharomyces cerevisiae. Mol Cell Biol (1999) 1.75
The Skn7 response regulator of Saccharomyces cerevisiae interacts with Hsf1 in vivo and is required for the induction of heat shock genes by oxidative stress. Mol Biol Cell (2000) 1.69
Predicting transcription factor synergism. Nucleic Acids Res (2002) 1.66
Association of the cell cycle transcription factor Mbp1 with the Skn7 response regulator in budding yeast. Mol Biol Cell (1999) 1.53
Regulation of transcription at the Saccharomyces cerevisiae start transition by Stb1, a Swi6-binding protein. Mol Cell Biol (1999) 1.52
The yeast zinc finger regulators Pdr1p and Pdr3p control pleiotropic drug resistance (PDR) as homo- and heterodimers in vivo. Mol Microbiol (2002) 1.49
Genome-wide transcriptional analysis in S. cerevisiae by mini-array membrane hybridization. Yeast (1999) 1.41
Functional genomics as applied to mapping transcription regulatory networks. Curr Opin Microbiol (2002) 1.39
G1 transcription factors are differentially regulated in Saccharomyces cerevisiae by the Swi6-binding protein Stb1. Mol Cell Biol (2003) 1.27
Cell cycle transition under stress conditions controlled by vertebrate heat shock factors. EMBO J (2001) 1.20
A dominant allele of PDR1 alters transition metal resistance in yeast. J Biol Chem (2002) 1.02
Heat shock factor 1-mediated thermotolerance prevents cell death and results in G2/M cell cycle arrest. Cell Stress Chaperones (2001) 1.02
Cell cycle-dependent binding of yeast heat shock factor to nucleosomes. Mol Cell Biol (2000) 0.98
Swapping functional specificity of a MADS box protein: residues required for Arg80 regulation of arginine metabolism. Mol Cell Biol (2002) 0.94
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
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
DNA motifs in human and mouse proximal promoters predict tissue-specific expression. Proc Natl Acad Sci U S A (2006) 2.38
Identifying tissue-selective transcription factor binding sites in vertebrate promoters. Proc Natl Acad Sci U S A (2005) 2.36
Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. Genome Res (2007) 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
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
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
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
Tissue-specific regulatory elements in mammalian promoters. Mol Syst Biol (2007) 1.41
Statistical significance of cis-regulatory modules. BMC Bioinformatics (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
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
Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes. BMC Bioinformatics (2011) 1.04
A new method for detecting human recombination hotspots and its applications to the HapMap ENCODE data. Am J Hum Genet (2006) 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
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 transcriptome of human CD34+ hematopoietic stem-progenitor cells. Proc Natl Acad Sci U S A (2009) 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
Functional mutation of SMAC/DIABLO, encoding a mitochondrial proapoptotic protein, causes human progressive hearing loss DFNA64. Am J Hum Genet (2011) 0.94
Evolutionary impact of limited splicing fidelity in mammalian genes. Trends Genet (2007) 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
Predictive models of gene regulation: application of regression methods to microarray data. Methods Mol Biol (2007) 0.90
Evidence and characteristics of putative human alpha recombination hotspots. Hum Mol Genet (2004) 0.89
Pan-genome isolation of low abundance transcripts using SAGE tag. FEBS Lett (2006) 0.88
Gene set-based module discovery in the breast cancer transcriptome. BMC Bioinformatics (2009) 0.88
Correlated evolution of transcription factors and their binding sites. Bioinformatics (2011) 0.87
Computer software to find genes in plant genomic DNA. Methods Mol Biol (2003) 0.87
New fusion transcripts identified in normal karyotype acute myeloid leukemia. PLoS One (2012) 0.87
CDKN2A/p16 inactivation mechanisms and their relationship to smoke exposure and molecular features in non-small-cell lung cancer. J Thorac Oncol (2013) 0.86
OSCAR: one-class SVM for accurate recognition of cis-elements. Bioinformatics (2007) 0.86
Computational prediction of novel components of lung transcriptional networks. Bioinformatics (2006) 0.86
Heat shock protein 90beta1 is essential for polyunsaturated fatty acid-induced mitochondrial Ca2+ efflux. J Biol Chem (2008) 0.85
Major chromosomal breakpoint intervals in breast cancer co-localize with differentially methylated regions. Front Oncol (2012) 0.84
EpiRegNet: constructing epigenetic regulatory network from high throughput gene expression data for humans. Epigenetics (2011) 0.84
GFScan: a gene family search tool at genomic DNA level. Genome Res (2002) 0.84