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References: Signaling Networks and Disease Modules

  1. Signal Transduction - Wikipedia - Comprehensive overview of cellular signaling pathways including receptor-mediated signaling, second messengers, kinase cascades, and how signaling networks are modeled as directed graphs.

  2. Network Pharmacology - Wikipedia - Describes the network-based approach to drug discovery that considers multi-target drug effects, polypharmacology, and drug combination strategies using protein interaction and disease networks.

  3. Cancer Systems Biology - Wikipedia - Explains how systems biology and network analysis approaches are applied to cancer research, covering oncogenic pathway networks, driver mutations, and network-based tumor classification.

  4. Network Medicine: Complex Systems in Human Disease and Therapeutics - Joseph Loscalzo - Harvard University Press - Foundational text on applying network science to medicine, covering disease modules, drug-target networks, comorbidity networks, and network-based drug repurposing.

  5. Systems Biology and Bioinformatics (2nd Edition) - Alireza Mashaghi - Cambridge University Press - Covers computational approaches to signaling network analysis including Boolean modeling, pathway enrichment, and network perturbation methods for understanding disease mechanisms.

  6. KEGG Disease Database - KEGG - Documentation for the KEGG disease database linking diseases to molecular networks, pathways, genes, and drugs, enabling network-based exploration of disease mechanisms.

  7. NDEx: Network Data Exchange - NDEx Project - Documentation for the open-source platform for sharing, storing, and publishing biological network models, supporting CX format and integration with Cytoscape for disease network analysis.

  8. Open Targets Platform - Open Targets - Guide to the drug target identification platform integrating genetics, genomics, transcriptomics, and network data to prioritize disease-gene associations for drug discovery.

  9. DisGeNET - DisGeNET - Documentation for the gene-disease association database, explaining evidence scores, data sources, and network analysis tools for exploring molecular mechanisms underlying human diseases.

  10. Drug Repurposing Hub - Broad Institute CLUE - Resource for computational drug repurposing using connectivity maps and network-based approaches, demonstrating how signaling network analysis identifies new therapeutic uses for existing drugs.