Understanding the modular structure of biological systems is essential for unraveling the complexity of life processes. This chapter explores the theory and practical applications of community detection in biological networks, including protein–protein interaction networks, gene regulatory networks, metabolic and signaling pathways, and more. By identifying clusters or communities of densely connected biological entities, researchers can uncover functional modules, predict unknown gene or protein functions, detect potential therapeutic targets, and understand system-level mechanisms and evolutionary processes. The chapter categorizes diverse biological networks, maps community detection applications to each, and presents methodologies and benefits in areas such as biomarker discovery, disease analysis, and drug development. It provides a comprehensive overview of how community detection enhances biological insight, contributing significantly to systems biology, precision medicine, and bioinformatics.
