AIMC Topic: Signal Transduction

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Bioinformatics approach reveals systematic mechanism underlying lung adenocarcinoma.

Tumori May 21, 2015
BACKGROUND: The purpose of this work was to explore the systematic molecular mechanism of lung adenocarcinoma and gain a deeper insight into it.
Calcium Peroxisome Proliferator-Activated Receptors Protein Array Analysis Gene Ontology Adenocarcinoma of Lung Collagen Type X Receptor Cross-Talk Gene Expression Regulation, Neoplastic Membrane Proteins Signal Transduction Adenocarcinoma Software Gene Expression Profiling Lung Neoplasms Computational Biology Humans
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Entity linking for biomedical literature.

BMC medical informatics and decision making May 20, 2015
BACKGROUND: The Entity Linking (EL) task links entity mentions from an unstructured document to entities in a knowledge base. Although this problem is well-studied in news and social media, this problem has not received much attention in the life sci...
Semantics Signal Transduction Natural Language Processing Data Mining Medical Informatics
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MIMP: predicting the impact of mutations on kinase-substrate phosphorylation.

Nature methods May 4, 2015
Protein phosphorylation is important in cellular pathways and altered in disease. We developed MIMP (http://mimp.baderlab.org/), a machine learning method to predict the impact of missense single-nucleotide variants (SNVs) on kinase-substrate interac...
Amino Acid Sequence Substrate Specificity Mutation, Missense Phosphotransferases Software Polymorphism, Single Nucleotide Signal Transduction Phosphorylation Artificial Intelligence
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Toll-like receptor signaling in vertebrates: testing the integration of protein, complex, and pathway data in the protein ontology framework.

PloS one Apr 20, 2015
The Protein Ontology (PRO) provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation o...
Computational Biology Biological Ontologies Humans Chickens Protein Transport Signal Transduction Animals Molecular Sequence Annotation Evolution, Molecular Mice Toll-Like Receptors
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The potential of AOP networks for reproductive and developmental toxicity assay development.

Reproductive toxicology (Elmsford, N.Y.) Apr 15, 2015
Historically, the prediction of reproductive and developmental toxicity has largely relied on the use of animals. The adverse outcome pathway (AOP) framework forms a basis for the development of new non-animal test methods. It also provides biologica...
Humans Knowledge Bases Reproduction Embryonic Development Toxicity Tests Fetal Development Risk Assessment Gene Expression Regulation, Developmental Animal Testing Alternatives Gene Regulatory Networks Systems Integration Computer Simulation Signal Transduction Pregnancy Models, Biological Female Animals
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Functional annotation and biological interpretation of proteomics data.

Biochimica et biophysica acta Oct 31, 2014
Proteomics experiments often generate a vast amount of data. However, the simple identification and quantification of proteins from a cell proteome or subproteome is not sufficient for the full understanding of complex mechanisms occurring in the bio...
Computational Biology Proteomics Proteome Signal Transduction Humans Animals Protein Interaction Maps Protein Binding Databases, Protein Gene Ontology
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Inter-species pathway perturbation prediction via data-driven detection of functional homology.

Bioinformatics (Oxford, England) Aug 22, 2014
MOTIVATION: Experiments in animal models are often conducted to infer how humans will respond to stimuli by assuming that the same biological pathways will be affected in both organisms. The limitations of this assumption were tested in the IMPROVER ...
Translational Research, Biomedical Software Algorithms Phosphoproteins Cells, Cultured Rats Humans Gene Expression Regulation Species Specificity Cytokines Databases, Factual Signal Transduction Models, Animal Oligonucleotide Array Sequence Analysis Artificial Intelligence Animals Bronchi Gene Expression Profiling Epithelial Cells Systems Biology Phosphorylation
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Integrative exome sequencing and machine learning identify MICB and interferon pathway genes as contributors to SSc risk.

Annals of the rheumatic diseases Aug 1, 2025
OBJECTIVES: Systemic sclerosis (SSc) is a complex autoimmune disease with both known and unidentified genetic contributors. While genome-wide association studies (GWAS) have implicated multiple loci, many reside in noncoding regions. We aimed to iden...
Female Male Middle Aged Case-Control Studies White People Humans Scleroderma, Systemic Genome-Wide Association Study Exome Sequencing Machine Learning Interferons Genetic Predisposition to Disease Quantitative Trait Loci Polymorphism, Single Nucleotide Signal Transduction
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Integrating network pharmacology and experimental validation to advance psoriasis treatment: Multi-target mechanistic elucidation of medicinal herbs and natural compounds.

Autoimmunity reviews Jul 31, 2025
BACKGROUND: Psoriasis, a chronic immune-mediated inflammatory disease (IMID), presents significant therapeutic challenges, necessitating exploration of alternative treatments like medicinal herbs (MH) and natural compounds (NC). Network pharmacology ...
Biological Products Plants, Medicinal Network Pharmacology Humans Animals Signal Transduction Psoriasis
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Multi-omics identifies OSM-OSMR as a key receptor-ligand in the tumor environment of endometrial adenocarcinoma.

International immunopharmacology Jul 28, 2025
Endometrial adenocarcinoma carries a bleak prognosis, and the molecular markers that evaluate the progression of endometrial adenocarcinoma to advanced stages remain uncertain. Cell-cell communication plays a crucial role in the tumor microenvironmen...
Humans Oncostatin M Oncostatin M Receptor beta Subunit Multiomics Gene Expression Regulation, Neoplastic Prognosis Gene Expression Profiling Adenocarcinoma Cell Proliferation Transcriptome Mice, Nude Female Signal Transduction Cell Line, Tumor Ligands Tumor Microenvironment Mice Endometrial Neoplasms Animals
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