AIMC Topic: Signal Transduction

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Network stratification analysis for identifying function-specific network layers.

Molecular bioSystems Feb 16, 2016
A major challenge of systems biology is to capture the rewiring of biological functions (e.g. signaling pathways) in a molecular network. To address this problem, we proposed a novel computational framework, namely network stratification analysis (Ne...
Disease Progression Gene Expression Profiling Liver Neoplasms Carcinoma, Hepatocellular Humans Neural Networks, Computer Algorithms Signal Transduction Cluster Analysis Models, Biological Gene Expression Regulation, Fungal Protein Interaction Maps Transcription, Genetic Gene Regulatory Networks Computational Biology Gene Expression Regulation, Neoplastic
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Detection of overlapping protein complexes in gene expression, phenotype and pathways of Saccharomyces cerevisiae using Prorank based Fuzzy algorithm.

Gene Jan 22, 2016
Proteins show their functional activity by interacting with other proteins and forms protein complexes since it is playing an important role in cellular organization and function. To understand the higher order protein organization, overlapping is an...
Computational Biology Signal Transduction Fuzzy Logic Cluster Analysis Multiprotein Complexes Algorithms Saccharomyces cerevisiae Phenotype Gene Expression Regulation, Fungal Protein Interaction Mapping Databases, Protein Fungal Proteins
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Learning a hierarchical representation of the yeast transcriptomic machinery using an autoencoder model.

BMC bioinformatics Jan 11, 2016
BACKGROUND: A living cell has a complex, hierarchically organized signaling system that encodes and assimilates diverse environmental and intracellular signals, and it further transmits signals that control cellular responses, including a tightly con...
Signal Transduction Models, Theoretical Transcription Factors Saccharomyces cerevisiae Neural Networks, Computer Computer Simulation Gene Expression Profiling Systems Biology Gene Expression Regulation, Fungal Saccharomyces cerevisiae Proteins
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Drug repositioning for non-small cell lung cancer by using machine learning algorithms and topological graph theory.

BMC bioinformatics Jan 11, 2016
BACKGROUND: Non-small cell lung cancer (NSCLC) is one of the leading causes of death globally, and research into NSCLC has been accumulating steadily over several years. Drug repositioning is the current trend in the pharmaceutical industry for ident...
Algorithms Drug Discovery Antineoplastic Agents Lung Neoplasms Gene Expression Regulation, Neoplastic Humans Machine Learning Signal Transduction Drug Repositioning Models, Theoretical Microarray Analysis Carcinoma, Non-Small-Cell Lung Neoplasm Proteins
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Hericium erinaceus Inhibits TNF-α-Induced Angiogenesis and ROS Generation through Suppression of MMP-9/NF-κB Signaling and Activation of Nrf2-Mediated Antioxidant Genes in Human EA.hy926 Endothelial Cells.

Oxidative medicine and cellular longevity Dec 28, 2015
Hericium erinaceus (HE) is an edible mushroom that has been shown to exhibit anticancer and anti-inflammatory activities. We investigated the antiangiogenic and antioxidant potentials of ethanol extracts of HE in human endothelial (EA.hy926) cells up...
NF-E2-Related Factor 2 Angiogenesis Inducing Agents Anti-Inflammatory Agents Humans Signal Transduction Matrix Metalloproteinase 9 Heme Oxygenase-1 Tumor Necrosis Factor-alpha Intercellular Adhesion Molecule-1 Glutathione Antioxidants Neovascularization, Pathologic Basidiomycota Inflammation Endothelial Cells Angiogenesis Inhibitors Reactive Oxygen Species NF-kappa B
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Sensitive and versatile electrogenerated chemiluminescence biosensing platform for protein kinase based on Ru(bpy)3(2+) functionalized gold nanoparticles mediated signal transduction.

Analytica chimica acta Dec 17, 2015
A novel, sensitive and versatile electrogenerated chemiluminescence biosensing platform is developed for monitoring activity and inhibition of protein kinase based on Ru(bpy)3(2+) functionalized gold nanoparticles (Ru(bpy)3(2+)-AuNPs) mediated signal...
Protein Kinases Microscopy, Atomic Force Ruthenium Compounds Signal Transduction Gold Metal Nanoparticles Luminescence Sensitivity and Specificity Biosensing Techniques
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Modulatory role of garlicin in migration and invasion of intrahepatic cholangiocarcinoma via PI3K/AKT pathway.

International journal of clinical and experimental pathology Nov 1, 2015
Increasing evidences have indicated the role of garlicin in inhibiting the progression of various tumors including glioma, pulmonary carcinoma and pancreatic carcinoma, via mediating cell apoptosis or cell cycle. The regulatory effect and related mol...
Phosphatidylinositol 3-Kinase Phosphoinositide-3 Kinase Inhibitors Cell Proliferation Signal Transduction Cell Movement Neoplasm Invasiveness Bile Duct Neoplasms Humans Dose-Response Relationship, Drug Allyl Compounds Disulfides Cell Line, Tumor Protein Kinase Inhibitors Antineoplastic Agents, Phytogenic Cholangiocarcinoma Phosphorylation Proto-Oncogene Proteins c-akt
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The transfer and transformation of collective network information in gene-matched networks.

Scientific reports Oct 9, 2015
Networks, such as the human society network, social and professional networks, and biological system networks, contain vast amounts of information. Information signals in networks are distributed over nodes and transmitted through intricately wired l...
Humans Neural Networks, Computer Algorithms Gene Regulatory Networks Models, Neurological Neurons Nerve Net Models, Genetic Signal Transduction
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PathwaysWeb: a gene pathways API with directional interactions, expanded gene ontology, and versioning.

Bioinformatics (Oxford, England) Sep 23, 2015
UNLABELLED: PathwaysWeb is a resource-based, well-documented web system that provides publicly available information on genes, biological pathways, Gene Ontology (GO) terms, gene-gene interaction networks (importantly, with the directionality of inte...
Signal Transduction Internet Information Storage and Retrieval Gene Ontology Algorithms Protein Interaction Maps Humans Databases, Factual Gene Regulatory Networks Mice Animals Computational Biology
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Machine Learning-based Classification of Diffuse Large B-cell Lymphoma Patients by Their Protein Expression Profiles.

Molecular & cellular proteomics : MCP Aug 26, 2015
Characterization of tumors at the molecular level has improved our knowledge of cancer causation and progression. Proteomic analysis of their signaling pathways promises to enhance our understanding of cancer aberrations at the functional level, but ...
Humans Lymphoma, Large B-Cell, Diffuse GTPase-Activating Proteins Cell Line, Tumor Neprilysin Gene Expression Regulation, Neoplastic Phosphoprotein Phosphatases Machine Learning Tissue Embedding Biomarkers, Tumor Tissue Fixation Proteomics Proteome Signal Transduction Neoplasm Proteins Principal Component Analysis Formaldehyde Apoptosis Regulatory Proteins Isotope Labeling
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