Published in Bioinformatics on July 01, 2007
Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell (2008) 3.96
Recognition models to predict DNA-binding specificities of homeodomain proteins. Bioinformatics (2012) 1.09
Covariation between homeodomain transcription factors and the shape of their DNA binding sites. Nucleic Acids Res (2013) 1.05
Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins. Nucleic Acids Res (2008) 1.04
Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes. Bioinformatics (2010) 0.98
Defining the plasticity of transcription factor binding sites by Deconstructing DNA consensus sequences: the PhoP-binding sites among gamma/enterobacteria. PLoS Comput Biol (2010) 0.93
Local gene regulation details a recognition code within the LacI transcriptional factor family. PLoS Comput Biol (2010) 0.86
Exploring the DNA-recognition potential of homeodomains. Genome Res (2012) 0.83
GntR Family of Bacterial Transcription Factors and Their DNA Binding Motifs: Structure, Positioning and Co-Evolution. PLoS One (2015) 0.82
Computational learning on specificity-determining residue-nucleotide interactions. Nucleic Acids Res (2015) 0.82
Identification of family-determining residues in PHD fingers. Nucleic Acids Res (2010) 0.81
Genetic analysis, structural modeling, and direct coupling analysis suggest a mechanism for phosphate signaling in Escherichia coli. BMC Genet (2015) 0.79
Assembly constraints drive co-evolution among ribosomal constituents. Nucleic Acids Res (2015) 0.78
Identification of Position-Specific Correlations between DNA-Binding Domains and Their Binding Sites. Application to the MerR Family of Transcription Factors. PLoS One (2016) 0.75
Subtypes of associated protein-DNA (Transcription Factor-Transcription Factor Binding Site) patterns. Nucleic Acids Res (2012) 0.75
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature (2007) 7.91
Novel signal transduction pathway utilized by extracellular HSP70: role of toll-like receptor (TLR) 2 and TLR4. J Biol Chem (2002) 6.16
STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res (2007) 4.92
enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res (2005) 4.03
Unphosphorylated STAT3 accumulates in response to IL-6 and activates transcription by binding to NFkappaB. Genes Dev (2007) 3.57
Inhibition and role of let-7d in idiopathic pulmonary fibrosis. Am J Respir Crit Care Med (2010) 3.02
Human transcriptome subtraction by using short sequence tags to search for tumor viruses in conjunctival carcinoma. J Virol (2007) 2.68
DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies. PLoS Comput Biol (2007) 2.37
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
Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex. PLoS Biol (2006) 2.17
Mapping and identification of essential gene functions on the X chromosome of Drosophila. EMBO Rep (2001) 1.83
The CCAAT/enhancer (C/EBP) family of basic-leucine zipper (bZIP) transcription factors is a multifaceted highly-regulated system for gene regulation. Cytokine (2011) 1.67
mirConnX: condition-specific mRNA-microRNA network integrator. Nucleic Acids Res (2011) 1.62
Nucleotide sequence of human monocyte interleukin 1 precursor cDNA. Proc. Natl. Acad. Sci. USA 1984. 81: 7907-7911. J Immunol (2007) 1.45
Interleukin 1 activates STAT3/nuclear factor-kappaB cross-talk via a unique TRAF6- and p65-dependent mechanism. J Biol Chem (2003) 1.45
Heat shock factor 1 represses transcription of the IL-1beta gene through physical interaction with the nuclear factor of interleukin 6. J Biol Chem (2002) 1.43
ComiR: Combinatorial microRNA target prediction tool. Nucleic Acids Res (2013) 1.39
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
Egr-1 mediates transcriptional repression of COL2A1 promoter activity by interleukin-1beta. J Biol Chem (2003) 1.22
TRAF6 activation of PI 3-kinase-dependent cytoskeletal changes is cooperative with Ras and is mediated by an interaction with cytoplasmic Src. J Cell Sci (2006) 1.21
Autocrine induction of the human pro-IL-1beta gene promoter by IL-1beta in monocytes. J Immunol (2002) 1.17
HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models. BMC Bioinformatics (2009) 1.16
Combined analysis reveals a core set of cycling genes. Genome Biol (2007) 1.10
Footer: a quantitative comparative genomics method for efficient recognition of cis-regulatory elements. Genome Res (2005) 1.09
High throughput determination of TGFβ1/SMAD3 targets in A549 lung epithelial cells. PLoS One (2011) 1.02
FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting. Nucleic Acids Res (2005) 0.99
Novel modeling of combinatorial miRNA targeting identifies SNP with potential role in bone density. PLoS Comput Biol (2012) 0.97
EGFR phosphorylation of DCBLD2 recruits TRAF6 and stimulates AKT-promoted tumorigenesis. J Clin Invest (2014) 0.97
The TATA-containing core promoter of the type II collagen gene (COL2A1) is the target of interferon-gamma-mediated inhibition in human chondrocytes: requirement for Stat1 alpha, Jak1 and Jak2. Biochem J (2003) 0.96
TRAF6 is autoinhibited by an intramolecular interaction which is counteracted by trans-ubiquitination. J Cell Biochem (2010) 0.94
Phosphorylation of IRF8 in a pre-associated complex with Spi-1/PU.1 and non-phosphorylated Stat1 is critical for LPS induction of the IL1B gene. Mol Immunol (2007) 0.94
The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus. Genome Biol (2009) 0.93
NF-IL6 and HSF1 have mutually antagonistic effects on transcription in monocytic cells. Biochem Biophys Res Commun (2002) 0.93
TRAF6 protein couples Toll-like receptor 4 signaling to Src family kinase activation and opening of paracellular pathway in human lung microvascular endothelia. J Biol Chem (2012) 0.90
Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome. Genome Biol (2007) 0.90
Overexpression of microRNA-1 promotes cardiomyocyte commitment from human cardiovascular progenitors via suppressing WNT and FGF signaling pathways. J Mol Cell Cardiol (2013) 0.90
A sequence alignment-independent method for protein classification. Appl Bioinformatics (2004) 0.90
Deregulation of common genes by c-Myc and its direct target, MT-MC1. Proc Natl Acad Sci U S A (2005) 0.89
Large scale comparison of innate responses to viral and bacterial pathogens in mouse and macaque. PLoS One (2011) 0.87
RNA deep sequencing reveals differential microRNA expression during development of sea urchin and sea star. PLoS One (2011) 0.86
Finding subtypes of transcription factor motif pairs with distinct regulatory roles. Nucleic Acids Res (2011) 0.85
Estrogen represses gene expression through reconfiguring chromatin structures. Nucleic Acids Res (2013) 0.85
Extracting biologically significant patterns from short time series gene expression data. BMC Bioinformatics (2009) 0.85
Expression of regulatory platelet microRNAs in patients with sickle cell disease. PLoS One (2013) 0.84
SOP3: a web-based tool for selection of oligonucleotide primers for single nucleotide polymorphism analysis by Pyrosequencing. Biotechniques (2005) 0.84
The IL17A and IL17F loci have divergent histone modifications and are differentially regulated by prostaglandin E2 in Th17 cells. Cytokine (2013) 0.83
Glucocorticoid inhibits the human pro-interleukin lbeta gene (ILIB) by decreasing DNA binding of transactivators to the signal-responsive enhancer. Mol Immunol (2005) 0.82
Conserved ETS domain arginines mediate DNA binding, nuclear localization, and a novel mode of bZIP interaction. J Biol Chem (2005) 0.81
T-ReCS: stable selection of dynamically formed groups of features with application to prediction of clinical outcomes. Pac Symp Biocomput (2015) 0.81
Self-organizing neural networks to support the discovery of DNA-binding motifs. Neural Netw (2006) 0.81
To bind or not to bind--FoxA1 determines estrogen receptor action in breast cancer progression. Breast Cancer Res (2012) 0.81
Electrostatic hot spot on DNA-binding domains mediates phosphate desolvation and the pre-organization of specificity determinant side chains. Nucleic Acids Res (2010) 0.80
Cloning and functional analysis of the mouse 5-lipoxygenase promoter. Am J Respir Cell Mol Biol (2002) 0.79
Distinct mechanisms for induction and tolerance regulate the immediate early genes encoding interleukin 1β and tumor necrosis factor α. PLoS One (2013) 0.78
Characterization of a cascade of protein interactions initiated at the IL-1 receptor. Biochem Biophys Res Commun (2003) 0.78
Spectral clustering strategies for heterogeneous disease expression data. Pac Symp Biocomput (2013) 0.78
Interleukin 1 (IL-1) induces the activation of Stat3. Adv Exp Med Biol (2003) 0.76
Dual regulatory role of human cytomegalovirus immediate-early protein in IL1B transcription is dependent upon Spi-1/PU.1. Biochem Biophys Res Commun (2002) 0.76
Inhibition of IL-1beta transcription by peptides derived from the hCMV IE2 transactivator. Mol Immunol (2008) 0.75
Web-based primer design software for genome-scale genotyping by pyrosequencing. Methods Mol Biol (2007) 0.75