Published in PLoS Comput Biol on April 29, 2010
HSF1 drives a transcriptional program distinct from heat shock to support highly malignant human cancers. Cell (2012) 2.94
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Genome-wide profiling of H3K56 acetylation and transcription factor binding sites in human adipocytes. PLoS One (2011) 1.34
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Cancer somatic mutations cluster in a subset of regulatory sites predicted from the ENCODE data. Mol Cancer (2016) 0.75
Transcriptional regulatory logic of the diurnal cycle in the mouse liver. PLoS Biol (2017) 0.75
Identifying novel transcription factors involved in the inflammatory response by using binding site motif scanning in genomic regions defined by histone acetylation. PLoS One (2017) 0.75
Simvastatin-induced sphingosine 1-phosphate receptor 1 expression is KLF2-dependent in human lung endothelial cells. Pulm Circ (2017) 0.75
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Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing. Nucleic Acids Res (2008) 4.08
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The role of cis-acting promoter elements in tissue-specific albumin gene expression. Science (1989) 2.86
Epigenetic reprogramming by adenovirus e1a. Science (2008) 2.38
Three microarray platforms: an analysis of their concordance in profiling gene expression. BMC Genomics (2005) 2.29
Acute physical stress elevates mouse period1 mRNA expression in mouse peripheral tissues via a glucocorticoid-responsive element. J Biol Chem (2005) 1.77
C/EBPalpha binds and activates the PU.1 distal enhancer to induce monocyte lineage commitment. Blood (2007) 1.52
The coactivator PGC-1 is involved in the regulation of the liver carnitine palmitoyltransferase I gene expression by cAMP in combination with HNF4 alpha and cAMP-response element-binding protein (CREB). J Biol Chem (2002) 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
A transcription factor affinity-based code for mammalian transcription initiation. Genome Res (2009) 1.23
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Predicting functionality of protein-DNA interactions by integrating diverse evidence. Bioinformatics (2009) 1.16
The role of C/EBP in nutrient and hormonal regulation of gene expression. Annu Rev Nutr (2001) 1.15
An enhancer 20 kilobases upstream of the human receptor activator of nuclear factor-kappaB ligand gene mediates dominant activation by 1,25-dihydroxyvitamin D3. Mol Endocrinol (2008) 1.08
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Trans-10, cis-12 conjugated linoleic acid activates the integrated stress response pathway in adipocytes. Physiol Genomics (2007) 0.98
Necdin and E2F4 are modulated by rosiglitazone therapy in diabetic human adipose and muscle tissue. Diabetes (2006) 0.98
Liver-specific and proliferation-induced deoxyribonuclease I hypersensitive sites in the mouse insulin-like growth factor binding protein-1 gene. Hepatology (1999) 0.95
Insulin and epidermal growth factor suppress basal glucose-6-phosphatase catalytic subunit gene transcription through overlapping but distinct mechanisms. Biochem J (2009) 0.81
Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (2002) 43.52
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Control of pancreas and liver gene expression by HNF transcription factors. Science (2004) 12.05
An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics (2006) 11.13
Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat Genet (2007) 6.92
Computational discovery of gene modules and regulatory networks. Nat Biotechnol (2003) 6.55
Foxp3 occupancy and regulation of key target genes during T-cell stimulation. Nature (2007) 5.81
High-resolution computational models of genome binding events. Nat Biotechnol (2006) 3.74
Core transcriptional regulatory circuitry in human hepatocytes. Mol Syst Biol (2006) 3.15
Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity. Nat Genet (2009) 3.06
Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis. Mol Cell (2009) 3.05
HSF1 drives a transcriptional program distinct from heat shock to support highly malignant human cancers. Cell (2012) 2.94
Practical strategies for discovering regulatory DNA sequence motifs. PLoS Comput Biol (2006) 2.53
A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data. Bioinformatics (2005) 2.52
Compounds from an unbiased chemical screen reverse both ER-to-Golgi trafficking defects and mitochondrial dysfunction in Parkinson's disease models. Dis Model Mech (2009) 2.16
Notch1 modulates timing of G1-S progression by inducing SKP2 transcription and p27 Kip1 degradation. J Exp Med (2005) 2.15
Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks. Sci Signal (2009) 2.04
Direct recruitment of polycomb repressive complex 1 to chromatin by core binding transcription factors. Mol Cell (2012) 1.71
Reduce in variation and improve efficiency of target volume delineation by a computer-assisted system using a deformable image registration approach. Int J Radiat Oncol Biol Phys (2007) 1.69
TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs. Bioinformatics (2005) 1.63
Antitumoral effect of a vaccination procedure with an autologous hemoderivative. Cancer Biol Ther (2003) 1.50
Unbiased, genome-wide in vivo mapping of transcriptional regulatory elements reveals sex differences in chromatin structure associated with sex-specific liver gene expression. Mol Cell Biol (2010) 1.45
Genome-wide profiling of H3K56 acetylation and transcription factor binding sites in human adipocytes. PLoS One (2011) 1.34
SOX2 co-occupies distal enhancer elements with distinct POU factors in ESCs and NPCs to specify cell state. PLoS Genet (2013) 1.32
Rethinking the use of radiation and chemotherapy after radical hysterectomy: a clinical-pathologic analysis of a Gynecologic Oncology Group/Southwest Oncology Group/Radiation Therapy Oncology Group trial. Gynecol Oncol (2005) 1.31
Extensive changes in DNA methylation are associated with expression of mutant huntingtin. Proc Natl Acad Sci U S A (2013) 1.28
ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data. Nucleic Acids Res (2011) 1.28
Large-scale discovery of ERK2 substrates identifies ERK-mediated transcriptional regulation by ETV3. Sci Signal (2011) 1.27
Genomic characterization of Wilms' tumor suppressor 1 targets in nephron progenitor cells during kidney development. Development (2010) 1.21
Brain and muscle Arnt-like protein-1 (BMAL1) controls circadian cell proliferation and susceptibility to UVB-induced DNA damage in the epidermis. Proc Natl Acad Sci U S A (2012) 1.19
SteinerNet: a web server for integrating 'omic' data to discover hidden components of response pathways. Nucleic Acids Res (2012) 1.11
Simultaneous reconstruction of multiple signaling pathways via the prize-collecting steiner forest problem. J Comput Biol (2013) 1.10
WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches. Nucleic Acids Res (2007) 1.07
Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signaling. PLoS Comput Biol (2013) 1.06
The small molecule, genistein, increases hepcidin expression in human hepatocytes. Hepatology (2013) 1.00
GRHL3/GET1 and trithorax group members collaborate to activate the epidermal progenitor differentiation program. PLoS Genet (2012) 0.99
SAMNet: a network-based approach to integrate multi-dimensional high throughput datasets. Integr Biol (Camb) (2012) 0.98
Targeting H3K4 trimethylation in Huntington disease. Proc Natl Acad Sci U S A (2013) 0.98
Poly-glutamine expanded huntingtin dramatically alters the genome wide binding of HSF1. J Huntingtons Dis (2012) 0.91
Evolution of DNA repair defects during malignant progression of low-grade gliomas after temozolomide treatment. Acta Neuropathol (2015) 0.90
The Ets transcription factor EHF as a regulator of cornea epithelial cell identity. J Biol Chem (2013) 0.85
Analysis of in vitro insulin-resistance models and their physiological relevance to in vivo diet-induced adipose insulin resistance. Cell Rep (2013) 0.85
Bmi1 promotes erythroid development through regulating ribosome biogenesis. Stem Cells (2015) 0.84
Insulin-induced enhancement of antitumoral response to methotrexate in breast cancer patients. Cancer Chemother Pharmacol (2003) 0.84
Recurrent pure mucinous carcinoma of the breast with mediastinal great vessel invasion: HER-2/neu confers aggressiveness. Am Surg (2008) 0.83
Isocitrate dehydrogenase mutations suppress STAT1 and CD8+ T cell accumulation in gliomas. J Clin Invest (2017) 0.82
Sequence analysis of chromatin immunoprecipitation data for transcription factors. Methods Mol Biol (2010) 0.81
Identification of telogen markers underscores that telogen is far from a quiescent hair cycle phase. J Invest Dermatol (2011) 0.81
Integrated network analyses for functional genomic studies in cancer. Semin Cancer Biol (2013) 0.80
N-Benzyl-3-sulfonamidopyrrolidines as novel inhibitors of cell division in E. coli. Bioorg Med Chem Lett (2007) 0.80
Sharing information to reconstruct patient-specific pathways in heterogeneous diseases. Pac Symp Biocomput (2014) 0.79
Serum markers variation consistent with autoschizis induced by ascorbic acid-menadione in patients with prostate cancer. Med Oncol (2003) 0.79
Swimming upstream: identifying proteomic signals that drive transcriptional changes using the interactome and multiple "-omics" datasets. Methods Cell Biol (2012) 0.79
Addition of an induction regimen of antiangiogenesis and antitumor immunity to standard chemotherapy improves survival in advanced malignancies. Med Oncol (2012) 0.76
Transcriptional regulation of epidermal barrier formation. Methods Mol Biol (2011) 0.75
Corrigendum: The genomic landscape of juvenile myelomonocytic leukemia. Nat Genet (2015) 0.75
Pathway-based network modeling finds hidden genes in shRNA screen for regulators of acute lymphoblastic leukemia. Integr Biol (Camb) (2016) 0.75
The role of endoscopy in nasogastric tube removal following esophageal surgery: a case report. Int J Surg (2007) 0.75