Published in BMC Med Genomics on May 24, 2010
A network-based biomarker approach for molecular investigation and diagnosis of lung cancer. BMC Med Genomics (2011) 1.01
Expression, regulation, and function of atypical chemerin receptor CCRL2 on endothelial cells. J Immunol (2012) 0.96
Charting the NF-κB pathway interactome map. PLoS One (2012) 0.94
Cucurbitacin E exhibits anti-inflammatory effect in RAW 264.7 cells via suppression of NF-κB nuclear translocation. Inflamm Res (2013) 0.88
Glial and Neuroimmune Mechanisms as Critical Modulators of Drug Use and Abuse. Neuropsychopharmacology (2016) 0.81
On the crucial cerebellar wound healing-related pathways and their cross-talks after traumatic brain injury in Danio rerio. PLoS One (2014) 0.81
Time-course gene profiling and networks in demethylated retinoblastoma cell line. Oncotarget (2015) 0.80
Regulation of NF-κB activation through a novel PI-3K-independent and PKA/Akt-dependent pathway in human umbilical vein endothelial cells. PLoS One (2012) 0.80
Modelling biochemical networks with intrinsic time delays: a hybrid semi-parametric approach. BMC Syst Biol (2010) 0.77
The influence of tumour necrosis factor- α (TNF-α) on amyloid-β (Aβ)-degrading enzymes in vitro. Int J Mol Epidemiol Genet (2011) 0.77
Identification of Major Signaling Pathways in Prion Disease Progression Using Network Analysis. PLoS One (2015) 0.76
Anti-Inflammatory Activity of Triterpenes Isolated from Protium paniculatum Oil-Resins. Evid Based Complement Alternat Med (2015) 0.75
Dynamic network-based relevance score reveals essential proteins and functional modules in directed differentiation. Stem Cells Int (2015) 0.75
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature (2007) 144.95
Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res (2003) 103.76
KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res (1999) 40.62
BioGRID: a general repository for interaction datasets. Nucleic Acids Res (2006) 22.41
Human Protein Reference Database--2009 update. Nucleic Acids Res (2008) 21.25
STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res (2008) 20.62
American College of Rheumatology. Preliminary definition of improvement in rheumatoid arthritis. Arthritis Rheum (1995) 15.00
TAK1 is a ubiquitin-dependent kinase of MKK and IKK. Nature (2001) 11.84
Failure to regulate TNF-induced NF-kappaB and cell death responses in A20-deficient mice. Science (2000) 10.98
Signalling pathways of the TNF superfamily: a double-edged sword. Nat Rev Immunol (2003) 10.29
TLR signaling pathways. Semin Immunol (2004) 9.08
TRADD-TRAF2 and TRADD-FADD interactions define two distinct TNF receptor 1 signal transduction pathways. Cell (1996) 8.89
MyD88 is an adaptor protein in the hToll/IL-1 receptor family signaling pathways. Mol Cell (1998) 8.73
Involvement of toll-like receptors 2 and 4 in cellular activation by high mobility group box 1 protein. J Biol Chem (2003) 8.34
Activation of IKK by TNFalpha requires site-specific ubiquitination of RIP1 and polyubiquitin binding by NEMO. Mol Cell (2006) 7.32
TRAF6 deficiency results in osteopetrosis and defective interleukin-1, CD40, and LPS signaling. Genes Dev (1999) 6.93
Rheumatoid arthritis association at 6q23. Nat Genet (2007) 6.71
Essential function for the kinase TAK1 in innate and adaptive immune responses. Nat Immunol (2005) 6.13
TNF-dependent recruitment of the protein kinase RIP to the TNF receptor-1 signaling complex. Immunity (1996) 5.45
Coupling of a signal response domain in I kappa B alpha to multiple pathways for NF-kappa B activation. Mol Cell Biol (1995) 5.32
MyD88: an adapter that recruits IRAK to the IL-1 receptor complex. Immunity (1997) 5.23
Tumor necrosis factor and interleukin-1 in the serum of children with severe infectious purpura. N Engl J Med (1988) 4.69
Multiple polymorphisms in the TNFAIP3 region are independently associated with systemic lupus erythematosus. Nat Genet (2008) 4.33
HMGB1: endogenous danger signaling. Mol Med (2008) 4.02
Tumor necrosis factor: a pleiotropic cytokine and therapeutic target. Annu Rev Med (1994) 3.95
Distinct molecular mechanism for initiating TRAF6 signalling. Nature (2002) 3.82
Intracellular and extracellular roles of S100 proteins. Microsc Res Tech (2003) 3.70
Severe osteopetrosis, defective interleukin-1 signalling and lymph node organogenesis in TRAF6-deficient mice. Genes Cells (1999) 3.69
Site-specific Lys-63-linked tumor necrosis factor receptor-associated factor 6 auto-ubiquitination is a critical determinant of I kappa B kinase activation. J Biol Chem (2006) 3.51
High-mobility group box 1 (HMGB1) protein at the crossroads between innate and adaptive immunity. Immunol Rev (2007) 3.23
Alymphoplasia is caused by a point mutation in the mouse gene encoding Nf-kappa b-inducing kinase. Nat Genet (1999) 3.17
Defective lymphotoxin-beta receptor-induced NF-kappaB transcriptional activity in NIK-deficient mice. Science (2001) 3.11
Critical roles for interleukin 1 and tumor necrosis factor alpha in antibody-induced arthritis. J Exp Med (2002) 2.98
Toll4 (TLR4) expression in cardiac myocytes in normal and failing myocardium. J Clin Invest (1999) 2.94
The A20 zinc finger protein protects cells from tumor necrosis factor cytotoxicity. J Biol Chem (1992) 2.90
A comprehensive map of the toll-like receptor signaling network. Mol Syst Biol (2006) 2.89
A20: central gatekeeper in inflammation and immunity. J Biol Chem (2008) 2.83
Negative regulation of toll-like receptor-mediated signaling by Tollip. J Biol Chem (2001) 2.78
Mutant cells that do not respond to interleukin-1 (IL-1) reveal a novel role for IL-1 receptor-associated kinase. Mol Cell Biol (1999) 2.77
Molecular cloning and characterization of a second subunit of the interleukin 1 receptor complex. J Biol Chem (1995) 2.58
Critical roles of TRAF2 and TRAF5 in tumor necrosis factor-induced NF-kappa B activation and protection from cell death. J Biol Chem (2001) 2.50
Interleukin-1 (IL-1) receptor-associated kinase-dependent IL-1-induced signaling complexes phosphorylate TAK1 and TAB2 at the plasma membrane and activate TAK1 in the cytosol. Mol Cell Biol (2002) 2.47
Recruitment of TNF receptor 1 to lipid rafts is essential for TNFalpha-mediated NF-kappaB activation. Immunity (2003) 2.41
The essential role of MEKK3 in TNF-induced NF-kappaB activation. Nat Immunol (2001) 2.32
Summary and comparison of the signaling mechanisms of the Toll/interleukin-1 receptor family. Biochim Biophys Acta (2002) 2.26
TLR-4, IL-1R and TNF-R signaling to NF-kappaB: variations on a common theme. Cell Mol Life Sci (2008) 2.23
TRAF5, an activator of NF-kappaB and putative signal transducer for the lymphotoxin-beta receptor. J Biol Chem (1996) 2.23
A wave of nascent transcription on activated human genes. Proc Natl Acad Sci U S A (2009) 2.18
Impaired cytokine signaling in mice lacking the IL-1 receptor-associated kinase. J Immunol (1999) 2.11
IRAK1: a critical signaling mediator of innate immunity. Cell Signal (2007) 2.11
Transient IkappaB kinase activity mediates temporal NF-kappaB dynamics in response to a wide range of tumor necrosis factor-alpha doses. J Biol Chem (2005) 2.08
TRAF6, a molecular bridge spanning adaptive immunity, innate immunity and osteoimmunology. Bioessays (2003) 1.96
Mekk3 is essential for early embryonic cardiovascular development. Nat Genet (2000) 1.95
Endothelial atheroprotective and anti-inflammatory mechanisms. Ann N Y Acad Sci (2001) 1.66
The negative regulation of Toll-like receptor and associated pathways. Immunol Cell Biol (2007) 1.59
Positive and negative signaling components involved in TNFalpha-induced NF-kappaB activation. Cytokine (2008) 1.50
Potent anti-inflammatory effects of low-dose proteasome inhibition in the vascular system. J Mol Med (Berl) (2009) 1.49
Isolation and characterization of two novel A20-like proteins. Biochem J (2001) 1.49
Interleukin-1. Int J Biochem Cell Biol (1998) 1.44
Discovering functions and revealing mechanisms at molecular level from biological networks. Proteomics (2007) 1.29
TAK1 is recruited to the tumor necrosis factor-alpha (TNF-alpha) receptor 1 complex in a receptor-interacting protein (RIP)-dependent manner and cooperates with MEKK3 leading to NF-kappaB activation. J Biol Chem (2005) 1.28
Beyond tumor necrosis factor receptor: TRADD signaling in toll-like receptors. Proc Natl Acad Sci U S A (2008) 1.26
Integrated cellular network of transcription regulations and protein-protein interactions. BMC Syst Biol (2010) 1.20
Mechanism of TNFalpha-induced IL-1alpha, IL-1beta and IL-6 expression in human cardiac fibroblasts: effects of statins and thiazolidinediones. Cardiovasc Res (2007) 1.20
S100 chemokines mediate bookmarking of premetastatic niches. Nat Cell Biol (2006) 1.17
Global gene expression profiling unveils S100A8/A9 as candidate markers in H-ras-mediated human breast epithelial cell invasion. Mol Cancer Res (2008) 1.17
Systems biology of neutrophil differentiation and immune response. Curr Opin Immunol (2005) 1.14
Regulation of IRAK-4 kinase activity via autophosphorylation within its activation loop. Biochem Biophys Res Commun (2006) 1.05
On the attenuation and amplification of molecular noise in genetic regulatory networks. BMC Bioinformatics (2006) 1.04
Activation of p38, ERK1/2 and NIK pathways is required for IL-1beta and TNF-alpha-induced chemokine expression in human retinal pigment epithelial cells. Exp Eye Res (2001) 1.00
Toll-like receptors (TLRs) and immune disorders. J Infect Chemother (2006) 0.95
A systems biology approach to construct the gene regulatory network of systemic inflammation via microarray and databases mining. BMC Med Genomics (2008) 0.94
The coiled-coil domain of TRAF6 is essential for its auto-ubiquitination. Biochem Biophys Res Commun (2004) 0.91
A proteasome inhibitor reduces concurrent, sequential, and long-term IL-1 beta- and TNF-alpha-induced ECAM expression and adhesion. Am J Physiol Cell Physiol (2003) 0.90
Genome-wide analysis of host responses to the Pseudomonas aeruginosa type III secretion system yields synergistic effects. Cell Microbiol (2005) 0.87
TIR domain-containing adaptors regulate TLR signaling pathways. Adv Exp Med Biol (2005) 0.86
Dissecting innate immune responses with the tools of systems biology. Curr Opin Immunol (2005) 0.85
Location of pathogenic bacteria during persistent infections: insights from an analysis using game theory. PLoS One (2009) 0.83
Effect of selective proteasome inhibitors on TNF-induced activation of primary and transformed endothelial cells. Am J Physiol (1999) 0.83
Along a TNF-paved road from dead parasites in red cells to cerebral malaria, and beyond. Parasitology (2009) 0.76
Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics (2006) 1.47
Genome-wide transcription profiling of the early phase of biofilm formation by Candida albicans. Eukaryot Cell (2005) 1.46
Purification and characterization of enterovirus 71 viral particles produced from vero cells grown in a serum-free microcarrier bioreactor system. PLoS One (2011) 1.45
Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle. Bioinformatics (2004) 1.43
Complete mitochondrial genomes of Taenia multiceps, T. hydatigena and T. pisiformis: additional molecular markers for a tapeworm genus of human and animal health significance. BMC Genomics (2010) 1.43
Candida albicans Hap43 is a repressor induced under low-iron conditions and is essential for iron-responsive transcriptional regulation and virulence. Eukaryot Cell (2010) 1.42
A novel molecular signature identified by systems genetics approach predicts prognosis in oral squamous cell carcinoma. PLoS One (2011) 1.27
Identification of transcription factor cooperativity via stochastic system model. Bioinformatics (2006) 1.25
Heparin and calcium ions dramatically enhance antithrombin reactivity with factor IXa by generating new interaction exosites. Biochemistry (2003) 1.24
Combined use of MS-222 (tricaine) and isoflurane extends anesthesia time and minimizes cardiac rhythm side effects in adult zebrafish. Zebrafish (2010) 1.23
Integrated cellular network of transcription regulations and protein-protein interactions. BMC Syst Biol (2010) 1.20
Quantitative inference of dynamic regulatory pathways via microarray data. BMC Bioinformatics (2005) 1.20
A new measure of the robustness of biochemical networks. Bioinformatics (2005) 1.13
Thrombospondin type I domain containing 7A (THSD7A) mediates endothelial cell migration and tube formation. J Cell Physiol (2010) 1.12
Zebrafish as a model host for Candida albicans infection. Infect Immun (2010) 1.12
Heparin activates antithrombin anticoagulant function by generating new interaction sites (exosites) for blood clotting proteinases. Trends Cardiovasc Med (2002) 1.10
Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data. BMC Bioinformatics (2007) 1.09
Human antimicrobial peptide LL-37 inhibits adhesion of Candida albicans by interacting with yeast cell-wall carbohydrates. PLoS One (2011) 1.08
Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targets. BMC Syst Biol (2008) 1.07
Dynamic modeling of cis-regulatory circuits and gene expression prediction via cross-gene identification. BMC Bioinformatics (2005) 1.05
Thermosensitive liposomes entrapping iron oxide nanoparticles for controllable drug release. Nanotechnology (2009) 1.04
On the attenuation and amplification of molecular noise in genetic regulatory networks. BMC Bioinformatics (2006) 1.04
A network-based biomarker approach for molecular investigation and diagnosis of lung cancer. BMC Med Genomics (2011) 1.01
Adenylate kinase-4 is a marker of poor clinical outcomes that promotes metastasis of lung cancer by downregulating the transcription factor ATF3. Cancer Res (2012) 1.00
Inactivation of the phospholipase B gene PLB5 in wild-type Candida albicans reduces cell-associated phospholipase A2 activity and attenuates virulence. Int J Med Microbiol (2006) 0.99
Clinicopathological features and prognostic factors of gastric cancer patients aged 40 years or younger. J Surg Oncol (2012) 0.97
Robust H infinity-stabilization design in gene networks under stochastic molecular noises: fuzzy-interpolation approach. IEEE Trans Syst Man Cybern B Cybern (2008) 0.95
Dynamic transcript profiling of Candida albicans infection in zebrafish: a pathogen-host interaction study. PLoS One (2013) 0.94
A systems biology approach to construct the gene regulatory network of systemic inflammation via microarray and databases mining. BMC Med Genomics (2008) 0.94
Baculovirus transduction of mesenchymal stem cells triggers the toll-like receptor 3 pathway. J Virol (2009) 0.93
Global screening of potential Candida albicans biofilm-related transcription factors via network comparison. BMC Bioinformatics (2010) 0.93
Soluble THSD7A is an N-glycoprotein that promotes endothelial cell migration and tube formation in angiogenesis. PLoS One (2011) 0.90
Identifying functional mechanisms of gene and protein regulatory networks in response to a broader range of environmental stresses. Comp Funct Genomics (2010) 0.90
Zebrafish Thsd7a is a neural protein required for angiogenic patterning during development. Dev Dyn (2011) 0.89
Antiangiogenic antithrombin down-regulates the expression of the proangiogenic heparan sulfate proteoglycan, perlecan, in endothelial cells. Blood (2003) 0.88
Antiangiogenic antithrombin induces global changes in the gene expression profile of endothelial cells. Cancer Res (2006) 0.88
A small G protein Rhb1 and a GTPase-activating protein Tsc2 involved in nitrogen starvation-induced morphogenesis and cell wall integrity of Candida albicans. Fungal Genet Biol (2008) 0.88
LL37 and hBD-3 elevate the β-1,3-exoglucanase activity of Candida albicans Xog1p, resulting in reduced fungal adhesion to plastic. Biochem J (2012) 0.87
New measurement methods of network robustness and response ability via microarray data. PLoS One (2013) 0.86
YTRP: a repository for yeast transcriptional regulatory pathways. Database (Oxford) (2014) 0.85
A systematic approach to detecting transcription factors in response to environmental stresses. BMC Bioinformatics (2007) 0.85
Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data. Bioinform Biol Insights (2009) 0.85
Fabrication of an oriented Fc-fused lectin microarray through boronate formation. Angew Chem Int Ed Engl (2008) 0.85
Molecular epidemiology of integron-associated antimicrobial gene cassettes in the clinical isolates of Acinetobacter baumannii from northern Taiwan. Ann Lab Med (2013) 0.85
Interspecies protein-protein interaction network construction for characterization of host-pathogen interactions: a Candida albicans-zebrafish interaction study. BMC Syst Biol (2013) 0.85
Identification of infection- and defense-related genes via a dynamic host-pathogen interaction network using a Candida albicans-zebrafish infection model. J Innate Immun (2013) 0.84
Robust model matching design methodology for a stochastic synthetic gene network. Math Biosci (2011) 0.84
Treatment of Glucocorticoids Inhibited Early Immune Responses and Impaired Cardiac Repair in Adult Zebrafish. PLoS One (2013) 0.83
Robust synthetic gene network design via library-based search method. Bioinformatics (2011) 0.83
Serine protease PRSS23 is upregulated by estrogen receptor α and associated with proliferation of breast cancer cells. PLoS One (2012) 0.83
Expression of GOLM1 correlates with prognosis in human hepatocellular carcinoma. Ann Surg Oncol (2013) 0.83
Comparisons of robustness and sensitivity between cancer and normal cells by microarray data. Cancer Inform (2008) 0.83
Tumor-induced endothelial cell apoptosis: roles of NAD(P)H oxidase-derived reactive oxygen species. J Cell Physiol (2011) 0.82
Molecular epidemiology and antimicrobial resistance determinants of multidrug-resistant Acinetobacter baumannii in five proximal hospitals in Taiwan. Jpn J Infect Dis (2011) 0.82
Identification of network-based biomarkers of cardioembolic stroke using a systems biology approach with time series data. BMC Syst Biol (2015) 0.81
Construction and clarification of dynamic gene regulatory network of cancer cell cycle via microarray data. Cancer Inform (2007) 0.81
Diverse Hap43-independent functions of the Candida albicans CCAAT-binding complex. Eukaryot Cell (2013) 0.81
Responses of Candida albicans to the human antimicrobial peptide LL-37. J Microbiol (2014) 0.81
Stepwise orthogonal click chemistry toward fabrication of paclitaxel/galactose functionalized fluorescent nanoparticles for HepG2 cell targeting and delivery. Bioconjug Chem (2013) 0.81
Constructing gene regulatory networks for long term photosynthetic light acclimation in Arabidopsis thaliana. BMC Bioinformatics (2011) 0.81
PRSS23 is essential for the Snail-dependent endothelial-to-mesenchymal transition during valvulogenesis in zebrafish. Cardiovasc Res (2012) 0.81
[Study on the epidemiological characteristics of rubella from 1990-2006 in Shanghai]. Zhonghua Liu Xing Bing Xue Za Zhi (2007) 0.80
Trivalent galactosyl-functionalized mesoporous silica nanoparticles as a target-specific delivery system for boron neutron capture therapy. Nanoscale (2013) 0.80
Rhb1 regulates the expression of secreted aspartic protease 2 through the TOR signaling pathway in Candida albicans. Eukaryot Cell (2011) 0.80
Stochastic spatio-temporal dynamic model for gene/protein interaction network in early Drosophila development. Gene Regul Syst Bio (2009) 0.80
Chemoattraction of macrophages by secretory molecules derived from cells expressing the signal peptide of eosinophil cationic protein. BMC Syst Biol (2012) 0.80
Cysteine-rich protein 2 alters p130Cas localization and inhibits vascular smooth muscle cell migration. Cardiovasc Res (2013) 0.80
A novel method to identify cooperative functional modules: study of module coordination in the Saccharomyces cerevisiae cell cycle. BMC Bioinformatics (2011) 0.79
Characterizing the role of cell-wall β-1,3-exoglucanase Xog1p in Candida albicans adhesion by the human antimicrobial peptide LL-37. PLoS One (2011) 0.79
Fungicidal activity of a phospholipase-A2-derived synthetic peptide variant against Candida albicans. Rev Esp Quimioter (2007) 0.79
On the increase in network robustness and decrease in network response ability during the aging process: a systems biology approach via microarray data. IEEE/ACM Trans Comput Biol Bioinform (2013) 0.79
Reconstructing a network of stress-response regulators via dynamic system modeling of gene regulation. Gene Regul Syst Bio (2008) 0.79
Programmable cellular retention of nanoparticles by replacing the synergistic anion of transferrin. ACS Nano (2012) 0.78
Prediction of phenotype-associated genes via a cellular network approach: a Candida albicans infection case study. PLoS One (2012) 0.78
Quantitative characterization of nanoparticles in blood by transmission electron microscopy with a window-type microchip nanopipet. Anal Chem (2012) 0.78
Multiobjective H2/H∞ synthetic gene network design based on promoter libraries. Math Biosci (2011) 0.78
Robust model matching control of immune systems under environmental disturbances: dynamic game approach. J Theor Biol (2008) 0.78
Systematic Biological Filter Design with a Desired I/O Filtering Response Based on Promoter-RBS Libraries. IEEE/ACM Trans Comput Biol Bioinform (2015) 0.77
The protease-mediated nucleus shuttles of subnanometer gold quantum dots for real-time monitoring of apoptotic cell death. J Am Chem Soc (2010) 0.77
Multiple target drug cocktail design for attacking the core network markers of four cancers using ligand-based and structure-based virtual screening methods. BMC Med Genomics (2015) 0.77
Heat-activated sustaining nitric oxide release from zwitterionic diazeniumdiolate loaded in thermo-sensitive liposomes. Nitric Oxide (2010) 0.77
The role of TGF-β signaling and apoptosis in innate and adaptive immunity in zebrafish: a systems biology approach. BMC Syst Biol (2014) 0.77
Systematic approach to Escherichia coli cell population control using a genetic lysis circuit. BMC Syst Biol (2014) 0.77