Published in Nucleic Acids Res on April 12, 2011
Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers. Genome Res (2013) 0.97
CCAT: Combinatorial Code Analysis Tool for transcriptional regulation. Nucleic Acids Res (2013) 0.86
TACO: a general-purpose tool for predicting cell-type-specific transcription factor dimers. BMC Genomics (2014) 0.85
MuMoD: a Bayesian approach to detect multiple modes of protein-DNA binding from genome-wide ChIP data. Nucleic Acids Res (2012) 0.83
Cofunctional Subpathways Were Regulated by Transcription Factor with Common Motif, Common Family, or Common Tissue. Biomed Res Int (2015) 0.75
Pluralistic and stochastic gene regulation: examples, models and consistent theory. Nucleic Acids Res (2016) 0.75
Subtypes of associated protein-DNA (Transcription Factor-Transcription Factor Binding Site) patterns. Nucleic Acids Res (2012) 0.75
Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science (1990) 35.96
TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res (2003) 29.26
JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res (2004) 19.32
DNA binding sites: representation and discovery. Bioinformatics (2000) 16.01
ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet (2009) 13.12
The Comprehensive Microbial Resource. Nucleic Acids Res (2001) 11.19
Diversity and complexity in DNA recognition by transcription factors. Science (2009) 9.07
BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac Symp Biocomput (2001) 8.65
A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J Mol Biol (1998) 7.75
ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics (2004) 7.21
Transcriptional regulation by cAMP and its receptor protein. Annu Rev Biochem (1993) 6.49
Regulatory sequence analysis tools. Nucleic Acids Res (2003) 5.72
Insights from genomic profiling of transcription factors. Nat Rev Genet (2009) 5.57
Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc Natl Acad Sci U S A (2001) 5.08
STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res (2007) 4.92
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. EMBO J (2010) 4.78
One nucleotide in a kappaB site can determine cofactor specificity for NF-kappaB dimers. Cell (2004) 4.53
DNA binding site sequence directs glucocorticoid receptor structure and activity. Science (2009) 4.48
enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res (2005) 4.03
Catabolite activator protein: DNA binding and transcription activation. Curr Opin Struct Biol (2004) 2.91
Finding composite regulatory patterns in DNA sequences. Bioinformatics (2002) 2.75
Inferring binding energies from selected binding sites. PLoS Comput Biol (2009) 2.66
Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays. Hum Mol Genet (2005) 2.56
DNA specificity determinants associate with distinct transcription factor functions. PLoS Genet (2009) 2.56
Practical strategies for discovering regulatory DNA sequence motifs. PLoS Comput Biol (2006) 2.53
Identifying target sites for cooperatively binding factors. Bioinformatics (2001) 2.31
Consensus DNA site for the Escherichia coli catabolite gene activator protein (CAP): CAP exhibits a 450-fold higher affinity for the consensus DNA site than for the E. coli lac DNA site. Nucleic Acids Res (1989) 2.24
E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites. Genome Res (2008) 2.07
Eukaryotic transcription factor binding sites--modeling and integrative search methods. Bioinformatics (2008) 1.84
Mining ChIP-chip data for transcription factor and cofactor binding sites. Bioinformatics (2005) 1.81
Combinatorial control of the bradykinin B2 receptor promoter by p53, CREB, KLF-4, and CBP: implications for terminal nephron differentiation. Am J Physiol Renal Physiol (2005) 1.70
A novel CRP-dependent regulon controls expression of competence genes in Haemophilus influenzae. J Mol Biol (2005) 1.57
Cis-regulatory modules in the mammalian liver: composition depends on strength of Foxa2 consensus site. Nucleic Acids Res (2008) 1.46
GADEM: a genetic algorithm guided formation of spaced dyads coupled with an EM algorithm for motif discovery. J Comput Biol (2009) 1.44
Computationally identifying novel NF-kappa B-regulated immune genes in the human genome. Genome Res (2003) 1.33
Non-canonical CRP sites control competence regulons in Escherichia coli and many other gamma-proteobacteria. Nucleic Acids Res (2006) 1.28
Regulation of competence development in Haemophilus influenzae. J Theor Biol (2000) 1.14
A kappaB sequence code for pathway-specific innate immune responses. EMBO J (2007) 1.01
Bipartite pattern discovery by entropy minimization-based multiple local alignment. Nucleic Acids Res (2004) 0.96
Enhanced position weight matrices using mixture models. Bioinformatics (2005) 0.94
Context-specific independence mixture modeling for positional weight matrices. Bioinformatics (2006) 0.93
Discovering sequence motifs. Methods Mol Biol (2008) 0.93
Sxy induces a CRP-S regulon in Escherichia coli. J Bacteriol (2009) 0.89
CRP binding and transcription activation at CRP-S sites. J Mol Biol (2008) 0.89
A single base difference between Pit-1 binding sites at the hGH promoter and locus control region specifies distinct Pit-1 conformations and functions. Mol Cell Biol (2006) 0.89
Flanking sequence composition differentially affects the binding and functional characteristics of glucocorticoid receptor homo- and heterodimers. Biochemistry (2006) 0.84
Gene-microarray analysis of multiple sclerosis lesions yields new targets validated in autoimmune encephalomyelitis. Nat Med (2002) 8.33
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature (2007) 7.91
Mesenchymal stem cell engraftment in lung is enhanced in response to bleomycin exposure and ameliorates its fibrotic effects. Proc Natl Acad Sci U S A (2003) 7.41
Acute exacerbations of idiopathic pulmonary fibrosis. Am J Respir Crit Care Med (2007) 6.71
STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res (2007) 4.92
miR-21 mediates fibrogenic activation of pulmonary fibroblasts and lung fibrosis. J Exp Med (2010) 4.71
From signatures to models: understanding cancer using microarrays. Nat Genet (2005) 4.29
enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res (2005) 4.03
Loss of integrin alpha(v)beta6-mediated TGF-beta activation causes Mmp12-dependent emphysema. Nature (2003) 4.02
Gene expression analysis reveals matrilysin as a key regulator of pulmonary fibrosis in mice and humans. Proc Natl Acad Sci U S A (2002) 4.00
Gene expression profiles distinguish idiopathic pulmonary fibrosis from hypersensitivity pneumonitis. Am J Respir Crit Care Med (2005) 3.72
Peripheral blood proteins predict mortality in idiopathic pulmonary fibrosis. Am J Respir Crit Care Med (2012) 3.42
Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis. Nat Genet (2013) 3.17
Up-regulation and profibrotic role of osteopontin in human idiopathic pulmonary fibrosis. PLoS Med (2005) 3.15
Inhibition and role of let-7d in idiopathic pulmonary fibrosis. Am J Respir Crit Care Med (2010) 3.02
Caveolin-1: a critical regulator of lung fibrosis in idiopathic pulmonary fibrosis. J Exp Med (2006) 2.92
MMP1 and MMP7 as potential peripheral blood biomarkers in idiopathic pulmonary fibrosis. PLoS Med (2008) 2.79
Human transcriptome subtraction by using short sequence tags to search for tumor viruses in conjunctival carcinoma. J Virol (2007) 2.68
Gene expression profiles of acute exacerbations of idiopathic pulmonary fibrosis. Am J Respir Crit Care Med (2009) 2.43
Comprehensive gene expression profiles reveal pathways related to the pathogenesis of chronic obstructive pulmonary disease. Proc Natl Acad Sci U S A (2004) 2.42
Idiopathic pulmonary fibrosis: aberrant recapitulation of developmental programs? PLoS Med (2008) 2.41
DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies. PLoS Comput Biol (2007) 2.37
WNT5A is a regulator of fibroblast proliferation and resistance to apoptosis. Am J Respir Cell Mol Biol (2009) 2.36
First-in-human trial of a STAT3 decoy oligonucleotide in head and neck tumors: implications for cancer therapy. Cancer Discov (2012) 2.31
Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data. PLoS One (2009) 2.29
Mesenchymal glioma stem cells are maintained by activated glycolytic metabolism involving aldehyde dehydrogenase 1A3. Proc Natl Acad Sci U S A (2013) 2.25
A novel genomic signature with translational significance for human idiopathic pulmonary fibrosis. Am J Respir Cell Mol Biol (2015) 2.21
Association between the MUC5B promoter polymorphism and survival in patients with idiopathic pulmonary fibrosis. JAMA (2013) 2.20
Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex. PLoS Biol (2006) 2.17
A role for the receptor for advanced glycation end products in idiopathic pulmonary fibrosis. Am J Pathol (2008) 2.17
Global expression profiling of fibroblast responses to transforming growth factor-beta1 reveals the induction of inhibitor of differentiation-1 and provides evidence of smooth muscle cell phenotypic switching. Am J Pathol (2003) 2.14
MicroRNAs in idiopathic pulmonary fibrosis. Transl Res (2011) 2.10
Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays. Bioinformatics (2004) 2.04
Genomewide RNA expression profiling in lung identifies distinct signatures in idiopathic pulmonary arterial hypertension and secondary pulmonary hypertension. Am J Physiol Heart Circ Physiol (2010) 2.03
Increased local expression of coagulation factor X contributes to the fibrotic response in human and murine lung injury. J Clin Invest (2009) 1.96
Accelerated variant of idiopathic pulmonary fibrosis: clinical behavior and gene expression pattern. PLoS One (2007) 1.88
Palliative care and location of death in decedents with idiopathic pulmonary fibrosis. Chest (2015) 1.85
Mapping and identification of essential gene functions on the X chromosome of Drosophila. EMBO Rep (2001) 1.83
Peripheral blood mononuclear cell gene expression profiles predict poor outcome in idiopathic pulmonary fibrosis. Sci Transl Med (2013) 1.81
A variant in the promoter of MUC5B and idiopathic pulmonary fibrosis. N Engl J Med (2011) 1.81
Patients with idiopathic pulmonary fibrosis with antibodies to heat shock protein 70 have poor prognoses. Am J Respir Crit Care Med (2013) 1.77
Human and porcine early kidney precursors as a new source for transplantation. Nat Med (2002) 1.73
Gene expression in relation to exhaled nitric oxide identifies novel asthma phenotypes with unique biomolecular pathways. Am J Respir Crit Care Med (2014) 1.69
Oxidative stress alters syndecan-1 distribution in lungs with pulmonary fibrosis. J Biol Chem (2008) 1.69
Comparison of normalization methods for CodeLink Bioarray data. BMC Bioinformatics (2005) 1.65
Relationship of DNA methylation and gene expression in idiopathic pulmonary fibrosis. Am J Respir Crit Care Med (2014) 1.63
mirConnX: condition-specific mRNA-microRNA network integrator. Nucleic Acids Res (2011) 1.62
Wnt coreceptor Lrp5 is a driver of idiopathic pulmonary fibrosis. Am J Respir Crit Care Med (2014) 1.61
Future directions in idiopathic pulmonary fibrosis research. An NHLBI workshop report. Am J Respir Crit Care Med (2014) 1.54
An R package suite for microarray meta-analysis in quality control, differentially expressed gene analysis and pathway enrichment detection. Bioinformatics (2012) 1.54
CD28 down-regulation on circulating CD4 T-cells is associated with poor prognoses of patients with idiopathic pulmonary fibrosis. PLoS One (2010) 1.53
miR-199a-5p Is upregulated during fibrogenic response to tissue injury and mediates TGFbeta-induced lung fibroblast activation by targeting caveolin-1. PLoS Genet (2013) 1.53
Blood transcriptional signatures of multiple sclerosis: unique gene expression of disease activity. Ann Neurol (2004) 1.48
Serum lysyl oxidase-like 2 levels and idiopathic pulmonary fibrosis disease progression. Eur Respir J (2013) 1.47
Gene expression profiling of target genes in ventilator-induced lung injury. Physiol Genomics (2006) 1.45
Global methylation patterns in idiopathic pulmonary fibrosis. PLoS One (2012) 1.44
Open-access biorepository for idiopathic pulmonary fibrosis. The way forward. Ann Am Thorac Soc (2014) 1.42
Mitogen-activated protein kinases regulate susceptibility to ventilator-induced lung injury. PLoS One (2008) 1.41
Cellular and humoral autoreactivity in idiopathic pulmonary fibrosis. J Immunol (2007) 1.39
ComiR: Combinatorial microRNA target prediction tool. Nucleic Acids Res (2013) 1.39
Multiple imprinted and stemness genes provide a link between normal and tumor progenitor cells of the developing human kidney. Cancer Res (2006) 1.39
MetaQC: objective quality control and inclusion/exclusion criteria for genomic meta-analysis. Nucleic Acids Res (2011) 1.35
Profibrotic role of miR-154 in pulmonary fibrosis. Am J Respir Cell Mol Biol (2012) 1.30
Improved detection of DNA motifs using a self-organized clustering of familial binding profiles. Bioinformatics (2005) 1.29
Molecular staging of epithelial maturation using secretory cell-specific genes as markers. Am J Respir Cell Mol Biol (2008) 1.28
The influence of radiographic phenotype and smoking status on peripheral blood biomarker patterns in chronic obstructive pulmonary disease. PLoS One (2009) 1.28
Matrix metalloproteinase 3 is a mediator of pulmonary fibrosis. Am J Pathol (2011) 1.27
Clara cells attenuate the inflammatory response through regulation of macrophage behavior. Am J Respir Cell Mol Biol (2009) 1.24
Approaching the degradome in idiopathic pulmonary fibrosis. Int J Biochem Cell Biol (2007) 1.24
Alignment and classification of time series gene expression in clinical studies. Bioinformatics (2008) 1.22
HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models. BMC Bioinformatics (2009) 1.16
The isolation and characterization of renal cancer initiating cells from human Wilms' tumour xenografts unveils new therapeutic targets. EMBO Mol Med (2012) 1.15
A functional and regulatory map of asthma. Am J Respir Cell Mol Biol (2007) 1.12
Combined analysis reveals a core set of cycling genes. Genome Biol (2007) 1.10
Biomarkers in idiopathic pulmonary fibrosis. Curr Opin Pulm Med (2012) 1.09
Transgelin is a direct target of TGF-beta/Smad3-dependent epithelial cell migration in lung fibrosis. FASEB J (2008) 1.09
Strategic plan for lung vascular research: An NHLBI-ORDR Workshop Report. Am J Respir Crit Care Med (2010) 1.09
Footer: a quantitative comparative genomics method for efficient recognition of cis-regulatory elements. Genome Res (2005) 1.09
Characterization and peripheral blood biomarker assessment of anti-Jo-1 antibody-positive interstitial lung disease. Arthritis Rheum (2009) 1.08
The pulmonary histopathologic manifestations of the anti-Jo-1 tRNA synthetase syndrome. Mod Pathol (2010) 1.08
Missing value imputation in high-dimensional phenomic data: imputable or not, and how? BMC Bioinformatics (2014) 1.06
Plasma B lymphocyte stimulator and B cell differentiation in idiopathic pulmonary fibrosis patients. J Immunol (2013) 1.05
FACS-assisted microarray profiling implicates novel genes and pathways in zebrafish gastrointestinal tract development. Gastroenterology (2009) 1.04
C-X-C motif chemokine 13 (CXCL13) is a prognostic biomarker of idiopathic pulmonary fibrosis. Am J Respir Crit Care Med (2014) 1.03
The HLA class II Allele DRB1*1501 is over-represented in patients with idiopathic pulmonary fibrosis. PLoS One (2011) 1.02
Targeting of Both the c-Met and EGFR Pathways Results in Additive Inhibition of Lung Tumorigenesis in Transgenic Mice. Cancers (Basel) (2010) 1.02
High throughput determination of TGFβ1/SMAD3 targets in A549 lung epithelial cells. PLoS One (2011) 1.02
Allele-specific transactivation of matrix metalloproteinase 7 by FOXA2 and correlation with plasma levels in idiopathic pulmonary fibrosis. Am J Physiol Lung Cell Mol Physiol (2012) 1.01
Systemic inhibition of NF-kappaB activation protects from silicosis. PLoS One (2009) 1.01
Inferring protein-DNA dependencies using motif alignments and mutual information. Bioinformatics (2007) 1.01
Reconstructing dynamic microRNA-regulated interaction networks. Proc Natl Acad Sci U S A (2013) 1.01
Towards systems biology of human pulmonary fibrosis. Proc Am Thorac Soc (2007) 1.00
Sil overexpression in lung cancer characterizes tumors with increased mitotic activity. Oncogene (2004) 1.00
FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting. Nucleic Acids Res (2005) 0.99
Impact of a disease-management program on symptom burden and health-related quality of life in patients with idiopathic pulmonary fibrosis and their care partners. Heart Lung (2009) 0.98
Analysis of microarray experiments for pulmonary fibrosis. Methods Mol Med (2005) 0.98