Published in Genome Res on May 01, 2003
Detection of functional DNA motifs via statistical over-representation. Nucleic Acids Res (2004) 6.31
A cryptic sensor for HIV-1 activates antiviral innate immunity in dendritic cells. Nature (2010) 5.45
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Global and local architecture of the mammalian microRNA-transcription factor regulatory network. PLoS Comput Biol (2007) 4.31
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Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets. Genome Res (2008) 3.09
Dynamic regulatory network controlling TH17 cell differentiation. Nature (2013) 3.07
Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics. PLoS Comput Biol (2008) 3.02
Identification of functional modules using network topology and high-throughput data. BMC Syst Biol (2007) 3.00
Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nat Biotechnol (2009) 2.79
DNA motifs in human and mouse proximal promoters predict tissue-specific expression. Proc Natl Acad Sci U S A (2006) 2.38
Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data. BMC Bioinformatics (2010) 2.24
A genome-wide gene expression signature of environmental geography in leukocytes of Moroccan Amazighs. PLoS Genet (2008) 2.19
Evaluation of myc E-box phylogenetic footprints in glycolytic genes by chromatin immunoprecipitation assays. Mol Cell Biol (2004) 2.19
Human embryonic stem cell-derived test systems for developmental neurotoxicity: a transcriptomics approach. Arch Toxicol (2012) 2.17
Direct p53 transcriptional repression: in vivo analysis of CCAAT-containing G2/M promoters. Mol Cell Biol (2005) 2.13
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Expander: from expression microarrays to networks and functions. Nat Protoc (2010) 2.12
Modulation of the vitamin D3 response by cancer-associated mutant p53. Cancer Cell (2010) 1.95
Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification. Nucleic Acids Res (2004) 1.84
Adaptively inferring human transcriptional subnetworks. Mol Syst Biol (2006) 1.81
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Identification of plant promoter constituents by analysis of local distribution of short sequences. BMC Genomics (2007) 1.77
Gene networks and transcription factor motifs defining the differentiation of stem cells into hepatocyte-like cells. J Hepatol (2015) 1.74
A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--a case study using E2F1. Genome Res (2006) 1.74
The promoters of human cell cycle genes integrate signals from two tumor suppressive pathways during cellular transformation. Mol Syst Biol (2005) 1.60
Microarray-based analysis of ventilator-induced lung injury. Proc Am Thorac Soc (2007) 1.58
Transcriptional network analysis identifies BACH1 as a master regulator of breast cancer bone metastasis. J Biol Chem (2012) 1.58
Discovering functional transcription-factor combinations in the human cell cycle. Genome Res (2005) 1.53
Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells. Proc Natl Acad Sci U S A (2008) 1.53
Linking disease-associated genes to regulatory networks via promoter organization. Nucleic Acids Res (2005) 1.41
Wide-scale analysis of human functional transcription factor binding reveals a strong bias towards the transcription start site. PLoS One (2007) 1.40
The histone-like NF-Y is a bifunctional transcription factor. Mol Cell Biol (2008) 1.40
SP1 regulates the transcription of BMPR1A. J Surg Res (2011) 1.39
A balance between NF-Y and p53 governs the pro- and anti-apoptotic transcriptional response. Nucleic Acids Res (2008) 1.32
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Dissection of a DNA-damage-induced transcriptional network using a combination of microarrays, RNA interference and computational promoter analysis. Genome Biol (2005) 1.31
A catalog of stability-associated sequence elements in 3' UTRs of yeast mRNAs. Genome Biol (2005) 1.31
Nodule inception directly targets NF-Y subunit genes to regulate essential processes of root nodule development in Lotus japonicus. PLoS Genet (2013) 1.24
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Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis. Nucleic Acids Res (2007) 1.19
Increased microRNA activity in human cancers. PLoS One (2009) 1.18
MotifViz: an analysis and visualization tool for motif discovery. Nucleic Acids Res (2004) 1.16
Regulation of the transcription factor YY1 in mitosis through phosphorylation of its DNA-binding domain. Mol Biol Cell (2009) 1.16
Mechanisms of transcriptional repression of cell-cycle G2/M promoters by p63. Nucleic Acids Res (2006) 1.13
Allegro: analyzing expression and sequence in concert to discover regulatory programs. Nucleic Acids Res (2009) 1.11
Overexpression of transcription factor Sp1 leads to gene expression perturbations and cell cycle inhibition. PLoS One (2009) 1.09
Mapping of HNF4alpha target genes in intestinal epithelial cells. BMC Gastroenterol (2009) 1.08
New Onto-Tools: Promoter-Express, nsSNPCounter and Onto-Translate. Nucleic Acids Res (2006) 1.06
Posttranslational regulation of NF-YA modulates NF-Y transcriptional activity. Mol Biol Cell (2008) 1.06
NF-Y dependent epigenetic modifications discriminate between proliferating and postmitotic tissue. PLoS One (2008) 1.05
Novel regulators of the systemic response to lipopolysaccharide. Am J Respir Cell Mol Biol (2010) 1.04
Specific inhibition of NF-Y subunits triggers different cell proliferation defects. Nucleic Acids Res (2011) 1.04
Design principles of concentration-dependent transcriptome deviations in drug-exposed differentiating stem cells. Chem Res Toxicol (2014) 1.03
Targeting the Y/CCAAT box in cancer: YB-1 (YBX1) or NF-Y? Cell Death Differ (2013) 1.01
CUX1 and E2F1 regulate coordinated expression of the mitotic complex genes Ect2, MgcRacGAP, and MKLP1 in S phase. Mol Cell Biol (2008) 1.00
RhoJ regulates melanoma chemoresistance by suppressing pathways that sense DNA damage. Cancer Res (2012) 1.00
Functional characterization of variations on regulatory motifs. PLoS Genet (2008) 0.99
Relating protein adduction to gene expression changes: a systems approach. Mol Biosyst (2011) 0.99
Coordinated repression of cell cycle genes by KDM5A and E2F4 during differentiation. Proc Natl Acad Sci U S A (2012) 0.99
Reverse-engineering human regulatory networks. Wiley Interdiscip Rev Syst Biol Med (2012) 0.98
SHORT-ROOT and SCARECROW regulate leaf growth in Arabidopsis by stimulating S-phase progression of the cell cycle. Plant Physiol (2010) 0.98
In silico identification of transcriptional regulators associated with c-Myc. Nucleic Acids Res (2004) 0.98
Innate killing of Leishmania donovani by macrophages of the splenic marginal zone requires IRF-7. PLoS Pathog (2010) 0.98
Functional genomic delineation of TLR-induced transcriptional networks. BMC Genomics (2007) 0.97
Genome-wide prediction of transcriptional regulatory elements of human promoters using gene expression and promoter analysis data. BMC Bioinformatics (2006) 0.97
Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships. Nucleic Acids Res (2009) 0.96
Unraveling condition specific gene transcriptional regulatory networks in Saccharomyces cerevisiae. BMC Bioinformatics (2006) 0.95
Removal of AU bias from microarray mRNA expression data enhances computational identification of active microRNAs. PLoS Comput Biol (2008) 0.94
Retracted NF-Y substitutes H2A-H2B on active cell-cycle promoters: recruitment of CoREST-KDM1 and fine-tuning of H3 methylations. Nucleic Acids Res (2008) 0.94
REACTIN: regulatory activity inference of transcription factors underlying human diseases with application to breast cancer. BMC Genomics (2013) 0.91
An NF-Y-dependent switch of positive and negative histone methyl marks on CCAAT promoters. PLoS One (2008) 0.91
TEF-1 and C/EBPbeta are major p38alpha MAPK-regulated transcription factors in proliferating cardiomyocytes. Biochem J (2006) 0.89
Polo-like kinase 4 transcription is activated via CRE and NRF1 elements, repressed by DREAM through CDE/CHR sites and deregulated by HPV E7 protein. Nucleic Acids Res (2013) 0.89
Inferring biological functions and associated transcriptional regulators using gene set expression coherence analysis. BMC Bioinformatics (2007) 0.88
Genome-wide identification of new Wnt/beta-catenin target genes in the human genome using CART method. BMC Genomics (2010) 0.87
A new E6/P63 pathway, together with a strong E7/E2F mitotic pathway, modulates the transcriptome in cervical cancer cells. J Virol (2007) 0.87
In silico identification of NF-kappaB-regulated genes in pancreatic beta-cells. BMC Bioinformatics (2007) 0.87
Computational identification of transcriptional regulators in human endotoxemia. PLoS One (2011) 0.86
TaNF-YC11, one of the light-upregulated NF-YC members in Triticum aestivum, is co-regulated with photosynthesis-related genes. Funct Integr Genomics (2010) 0.86
HFR1 is crucial for transcriptome regulation in the cryptochrome 1-mediated early response to blue light in Arabidopsis thaliana. PLoS One (2008) 0.86
E2F2 and CREB cooperatively regulate transcriptional activity of cell cycle genes. Nucleic Acids Res (2013) 0.85
Computational detection of significant variation in binding affinity across two sets of sequences with application to the analysis of replication origins in yeast. BMC Bioinformatics (2008) 0.85
Using mouse genomics to understand idiopathic interstitial fibrosis. Proc Am Thorac Soc (2007) 0.85
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Transcriptional regulation by CHIP/LDB complexes. PLoS Genet (2010) 0.83
Transcriptional programs: modelling higher order structure in transcriptional control. BMC Bioinformatics (2009) 0.83
Identification of miR-27b as a novel signature from the mRNA profiles of adipose-derived mesenchymal stem cells involved in the tolerogenic response. PLoS One (2013) 0.83
Interplay among Drosophila transcription factors Ets21c, Fos and Ftz-F1 drives JNK-mediated tumor malignancy. Dis Model Mech (2015) 0.82
TREMOR--a tool for retrieving transcriptional modules by incorporating motif covariance. Nucleic Acids Res (2007) 0.82
Tissue-specific targeting of cell fate regulatory genes by E2f factors. Cell Death Differ (2015) 0.82
RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway. Nat Commun (2015) 0.82
Systems analysis of circadian time-dependent neuronal epidermal growth factor receptor signaling. Genome Biol (2006) 0.81
Expression profiling and biochemical analysis suggest stress response as a potential mechanism inhibiting proliferation of polyamine-depleted cells. J Biol Chem (2012) 0.81
Identification of primary transcriptional regulation of cell cycle-regulated genes upon DNA damage. Cell Cycle (2007) 0.81
Profiling of Discrete Gynecological Cancers Reveals Novel Transcriptional Modules and Common Features Shared by Other Cancer Types and Embryonic Stem Cells. PLoS One (2015) 0.80
Dissecting early differentially expressed genes in a mixture of differentiating embryonic stem cells. PLoS Comput Biol (2009) 0.80
Complex-based analysis of dysregulated cellular processes in cancer. BMC Syst Biol (2014) 0.80
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Beyond ATM: the protein kinase landscape of the DNA damage response. FEBS Lett (2011) 1.64
Activation of ATM depends on chromatin interactions occurring before induction of DNA damage. Nat Cell Biol (2008) 1.63
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DNA damage-induced phosphorylation of MdmX at serine 367 activates p53 by targeting MdmX for Mdm2-dependent degradation. Mol Cell Biol (2005) 1.56
The canine olfactory subgenome. Genomics (2004) 1.55
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Enhancing the prioritization of disease-causing genes through tissue specific protein interaction networks. PLoS Comput Biol (2012) 1.51
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ATM-dependent phosphorylation of ATF2 is required for the DNA damage response. Mol Cell (2005) 1.39
NetworkBLAST: comparative analysis of protein networks. Bioinformatics (2008) 1.37
Integrative analysis of genome-wide experiments in the context of a large high-throughput data compendium. Mol Syst Biol (2005) 1.36
Identifying functional modules using expression profiles and confidence-scored protein interactions. Bioinformatics (2009) 1.35
From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions. Mol Syst Biol (2008) 1.35
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Towards computational prediction of microRNA function and activity. Nucleic Acids Res (2010) 1.32
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Optimal function of the DNA repair enzyme TDP1 requires its phosphorylation by ATM and/or DNA-PK. EMBO J (2009) 1.32
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