Abstract
Since the turn of the last century, biological networks have been one of the most widely used mathematical models employed in systems biology to uncover complex relationships from raw omics data. In particular protein–protein interaction networks (PPINs) are often used to predict putative protein complexes and uncover the functional modular structure of the cell׳s proteomic machinery. In this survey we give an overview of density based algorithms for community detection in biological networks (mainly PPINs) which is a popular approach to network analysis, complementary to network clustering. We then touch on recent research direction involving biological data integration, network dynamization, and extensions to different types of biological networks.
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