Active modules identification in multilayer intracellular networks

The network analysis has become a basic tool to gain insights on evolution and organization of living organisms in computational system biology. Since a group of genes may get involved into a biological process other than act alone, identifying modules from biological networks has been a central challenge to this field in the past decade. Several representative methods have been proposed to search such important modules using different intuitions while no unified framework exists yet, especially for multilayer networks, which can model gene expression dynamics and species conservation. This thesis provides a comprehensive study on active modules identification in multilayer intracellular networks, with the following main contributions: - An improvement on a heuristic method for identifying active modules from protein-protein interaction (PPI) networks. - A new objective of active modules to incorporate the topological structure and active property on the single layer and multilayer dynamic PPI network, and a convex optimization algorithm to solve it. - A new definition for active modules in single layer and multilayer gene co-expression networks and a novel algorithm which achieves the state-of-the-art performance. - A framework to conduct networks comparison via modules differentiation analysis, which can find condition-specific modules as well as conserved modules