Published in Mol Syst Biol on June 06, 2006
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet (2009) 6.02
Discovering motifs in ranked lists of DNA sequences. PLoS Comput Biol (2007) 4.40
Basal subtype and MAPK/ERK kinase (MEK)-phosphoinositide 3-kinase feedback signaling determine susceptibility of breast cancer cells to MEK inhibition. Cancer Res (2009) 3.14
ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells. Proc Natl Acad Sci U S A (2009) 2.96
Predicting tissue-specific enhancers in the human genome. Genome Res (2007) 2.72
Transcriptional regulatory circuits: predicting numbers from alphabets. Science (2009) 2.61
Reconstructing dynamic regulatory maps. Mol Syst Biol (2007) 2.36
A correlation with exon expression approach to identify cis-regulatory elements for tissue-specific alternative splicing. Nucleic Acids Res (2007) 1.94
Predicting cell-type-specific gene expression from regions of open chromatin. Genome Res (2012) 1.78
A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--a case study using E2F1. Genome Res (2006) 1.74
Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting. Genome Res (2012) 1.54
Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches. Genome Res (2007) 1.50
Deep resequencing of GWAS loci identifies rare variants in CARD9, IL23R and RNF186 that are associated with ulcerative colitis. PLoS Genet (2013) 1.34
A systems analysis of the chemosensitivity of breast cancer cells to the polyamine analogue PG-11047. BMC Med (2009) 1.22
Cis-regulatory code of stress-responsive transcription in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2011) 1.21
Dynamic CRM occupancy reflects a temporal map of developmental progression. Mol Syst Biol (2010) 1.13
Genome-wide in silico prediction of gene expression. Bioinformatics (2012) 1.00
A primer on regression methods for decoding cis-regulatory logic. PLoS Comput Biol (2009) 1.00
Computational analyses of eukaryotic promoters. BMC Bioinformatics (2007) 0.99
Functional genomic delineation of TLR-induced transcriptional networks. BMC Genomics (2007) 0.97
Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells. BMC Bioinformatics (2008) 0.96
PRISM offers a comprehensive genomic approach to transcription factor function prediction. Genome Res (2013) 0.94
Multilevel support vector regression analysis to identify condition-specific regulatory networks. Bioinformatics (2010) 0.93
Modeling the regulatory network of histone acetylation in Saccharomyces cerevisiae. Mol Syst Biol (2007) 0.90
BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors. BMC Bioinformatics (2009) 0.89
Identifying the genetic determinants of transcription factor activity. Mol Syst Biol (2010) 0.87
Transcription factor co-localization patterns affect human cell type-specific gene expression. BMC Genomics (2012) 0.81
Identification of direct target genes using joint sequence and expression likelihood with application to DAF-16. PLoS One (2008) 0.81
Revealing system-level correlations between aging and calorie restriction using a mouse transcriptome. Age (Dordr) (2009) 0.81
Predicting promoter activities of primary human DNA sequences. Nucleic Acids Res (2011) 0.81
A combinatorial approach to determine the context-dependent role in transcriptional and posttranscriptional regulation in Arabidopsis thaliana. BMC Syst Biol (2009) 0.80
Transcription factors expressed in olfactory bulb local progenitor cells revealed by genome-wide transcriptome profiling. Mol Cell Neurosci (2010) 0.76
In silico regulatory analysis for exploring human disease progression. Biol Direct (2008) 0.76
Integrative bioinformatics analysis of genomic and proteomic approaches to understand the transcriptional regulatory program in coronary artery disease pathways. PLoS One (2013) 0.76
Past Roadblocks and New Opportunities in Transcription Factor Network Mapping. Trends Genet (2016) 0.76
Promoting human promoters. Mol Syst Biol (2006) 0.75
Identification of condition-specific regulatory modules through multi-level motif and mRNA expression analysis. Int J Comput Biol Drug Des (2009) 0.75
Statistical significance for genomewide studies. Proc Natl Acad Sci U S A (2003) 88.64
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell (1998) 62.20
A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A (2004) 44.81
GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol (2003) 22.63
Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J Mol Biol (1987) 17.53
Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell (2002) 17.32
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics (1999) 14.36
Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol (2005) 14.29
Reverse engineering of regulatory networks in human B cells. Nat Genet (2005) 13.16
Control of pancreas and liver gene expression by HNF transcription factors. Science (2004) 12.05
An extensive network of coupling among gene expression machines. Nature (2002) 11.84
MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res (2003) 11.82
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
Transcription regulation and animal diversity. Nature (2003) 9.22
Regulatory element detection using correlation with expression. Nat Genet (2001) 8.92
Genomic strategies to identify mammalian regulatory sequences. Nat Rev Genet (2001) 5.78
Role for E2F in control of both DNA replication and mitotic functions as revealed from DNA microarray analysis. Mol Cell Biol (2001) 5.03
Integrating regulatory motif discovery and genome-wide expression analysis. Proc Natl Acad Sci U S A (2003) 4.74
Rb inactivation promotes genomic instability by uncoupling cell cycle progression from mitotic control. Nature (2004) 4.41
Cluster-Buster: Finding dense clusters of motifs in DNA sequences. Nucleic Acids Res (2003) 3.99
The enhanceosome and transcriptional synergy. Cell (1998) 3.93
Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells. Genome Res (2003) 3.79
Regulation of LEF-1/TCF transcription factors by Wnt and other signals. Curr Opin Cell Biol (1999) 3.52
Synexpression groups in eukaryotes. Nature (1999) 3.49
Direct coupling of the cell cycle and cell death machinery by E2F. Nat Cell Biol (2002) 3.00
CDC25A phosphatase is a target of E2F and is required for efficient E2F-induced S phase. Mol Cell Biol (1999) 2.84
TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies. Nucleic Acids Res (2005) 2.73
Similarity of position frequency matrices for transcription factor binding sites. Bioinformatics (2004) 2.51
Interacting models of cooperative gene regulation. Proc Natl Acad Sci U S A (2004) 2.09
TFDP1, CUL4A, and CDC16 identified as targets for amplification at 13q34 in hepatocellular carcinomas. Hepatology (2002) 2.05
Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation. Proc Natl Acad Sci U S A (2005) 1.86
Mining ChIP-chip data for transcription factor and cofactor binding sites. Bioinformatics (2005) 1.81
Identification of regulatory elements using a feature selection method. Bioinformatics (2002) 1.80
Aromatic hydrocarbon receptor interaction with the retinoblastoma protein potentiates repression of E2F-dependent transcription and cell cycle arrest. J Biol Chem (2000) 1.77
Genome-wide promoter extraction and analysis in human, mouse, and rat. Genome Biol (2005) 1.64
Discovering functional transcription-factor combinations in the human cell cycle. Genome Res (2005) 1.53
A sigmoidal transcriptional response: cooperativity, synergy and dosage effects. Biol Rev Camb Philos Soc (2003) 1.43
Genomic approaches that aid in the identification of transcription factor target genes. Exp Biol Med (Maywood) (2004) 1.41
Cell growth-regulated expression of mammalian MCM5 and MCM6 genes mediated by the transcription factor E2F. Oncogene (1999) 1.39
Expression of the AML-1 oncogene shortens the G(1) phase of the cell cycle. J Biol Chem (2000) 1.37
Identification of a novel cell cycle regulated gene, HURP, overexpressed in human hepatocellular carcinoma. Oncogene (2003) 1.36
p53-independent induction of Gadd45 by histone deacetylase inhibitor: coordinate regulation by transcription factors Oct-1 and NF-Y. Oncogene (2003) 1.29
The ubiquitous transcription factor Oct-1 and the liver-specific factor HNF-1 are both required to activate transcription of a hepatitis B virus promoter. Mol Cell Biol (1991) 1.26
The winged helix transcriptional activator HFH-3 is expressed in the distal tubules of embryonic and adult mouse kidney. J Biol Chem (1997) 1.25
Indirect and direct disruption of transcriptional regulation in cancer: E2F and AML-1. Crit Rev Eukaryot Gene Expr (1995) 1.13
Pharmacogenomic assessment of carboxylesterases 1 and 2. Genomics (2004) 1.09
Temporal control of cell cycle gene expression mediated by E2F transcription factors. Cell Cycle (2005) 1.03
Oct-1 and nuclear factor Y bind to the SURG-1 element to direct basal and gonadotropin-releasing hormone (GnRH)-stimulated mouse GnRH receptor gene transcription. Mol Endocrinol (2004) 0.93
Functional interaction between Oct-1 and retinoid X receptor. J Biol Chem (1999) 0.91
Regulation of the constitutive expression of the human CYP1A2 gene: cis elements and their interactions with proteins. Mol Pharmacol (1995) 0.87
Expression of protein-tyrosine phosphatases in the major insulin target tissues. FEBS Lett (1997) 0.86
Transcription factors and the down-regulation of G1/S boundary genes in human diploid fibroblasts during senescence. Front Biosci (1997) 0.86
Having it all? Stem cells, haematopoiesis and lymphopoiesis in adult human liver. Immunol Cell Biol (2002) 0.85
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
Rb inactivation promotes genomic instability by uncoupling cell cycle progression from mitotic control. Nature (2004) 4.41
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
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
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
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
β-Arrestin-1 links mitogenic sonic hedgehog signaling to the cell cycle exit machinery in neural precursors. Cell Cycle (2010) 1.46
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
FoxO1 stimulates fatty acid uptake and oxidation in muscle cells through CD36-dependent and -independent mechanisms. J Biol Chem (2005) 1.17
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
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
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
Predictive models of gene regulation: application of regression methods to microarray data. Methods Mol Biol (2007) 0.90
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
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
New fusion transcripts identified in normal karyotype acute myeloid leukemia. PLoS One (2012) 0.87
Computer software to find genes in plant genomic DNA. Methods Mol Biol (2003) 0.87
Computational prediction of novel components of lung transcriptional networks. Bioinformatics (2006) 0.86
OSCAR: one-class SVM for accurate recognition of cis-elements. Bioinformatics (2007) 0.86
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