MOTIVATION It has long been hypothesized that incorporating models of network noise as well as edge directions and known pathway information into the representation of protein-protein interaction (PPI) networks might improve their utility for functional inference. However, a simple way to do this has not been obvious. We find that diffusion state distance (DSD), our recent diffusion-based metri...

The increasing availability of biological networks (proteinprotein interaction graphs, metabolic and transcriptional networks, etc.) is offering new opportunities to analyze their topological properties and possibly gain new insights in their design principles. Here we concentrate on the problem of de novo identification of the building modules of networks, which we refer to as network modules....

This chapter introduces evolutionary analyses of protein interaction networks and of proteins as components of the networks. The authors show relationships between proteins in the networks and their evolutionary rates. For understanding protein-protein interaction (PPI) divergence, duplicated genes are often compared because they are derived from a common ancestral gene. In order to reveal evol...

Many evidences have demonstrated that protein complexes are overlapping and hierarchically organized in PPI networks. Meanwhile, the large size of PPI network wants complex detection methods have low time complexity. Up to now, few methods can identify overlapping and hierarchical protein complexes in a PPI network quickly. In this paper, a novel method, called MCSE, is proposed based on λ-modu...

How to identify protein complex is an important and challenging task in proteomics. It would make great contribution to our knowledge of molecular mechanism in cell life activities. However, the inherent organization and dynamic characteristic of cell system have rarely been incorporated into the existing algorithms for detecting protein complexes because of the limitation of protein-protein in...

prepulse inhibition (ppi), the objective measure of sensorimotor gating disturbance has being widely used in animal models of schizophrenia. dopaminergic direct and indirect agonists impair ppi. however, the profile of dopaminergic receptors involved in ppi impairment by dopamine agonists is not clear. by injecting shrna expressing plasmids against dopamine d2 receptor genes (drd2) in the nucle...

Prepulse Inhibition (PPI), the objective measure of sensorimotor gating disturbance has being widely used in animal models of schizophrenia. Dopaminergic direct and indirect agonists impair PPI. However, the profile of dopaminergic receptors involved in PPI impairment by dopamine agonists is not clear. By injecting shRNA expressing plasmids against dopamine D2 receptor genes (DRD2) in the nucle...

Almost every cellular process requires the interactions of pairs or larger complexes of proteins. High throughput protein-protein interaction (PPI) data have been generated using techniques such as the yeast two-hybrid systems, mass spectrometry method, and many more. Such data provide us with a new perspective to predict protein functions and to generate protein-protein interaction networks, a...

Recent advances in high-throughput laboratory techniques captured large-scale protein-protein interaction (PPI) data, making it possible to create a detailed map of protein interaction networks, and thus enable us to detect protein complexes from these PPI networks. However, most of the current state-of-the-art studies still have some problems, for instance, incapability of identifying overlapp...