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A disease is rarely a straightforward consequence of an abnormality in a single gene, but rather reflects the interplay of multiple molecular processes. The relationships among these processes are encoded in the interactome, a network that integrates all physical interactions within a cell, from protein-protein to regulatory protein–DNA and metabolic interactions. The documented propensity of disease-associated proteins to interact with each other suggests that they tend to cluster in the same neighborhood of the interactome, forming a disease module, a connected subgraph that contains all molecular determinants of a disease. The accurate identification of the corresponding disease module represents the first step toward a systematic understanding of the molecular mechanisms underlying a complex disease. Here, we present a network-based framework to identify the location of disease modules …