Cliques (maximal complete subnets) in protein-protein interaction (PPI) network are an important resource used to analyze protein complexes and functional modules. Clique-based methods of predicting PPI complement the data defection from biological experiments. However, clique-based predicting methods only depend on the topology of network. The false-positive and false-negative interactions in ...

Methamphetamine (Meth) is recognized as one of the most important new distributedabused drug that causes severe damage to the different parts of the brain, especiallyhippocampus. Previous studies have demonstrated that Meth can induce apoptosis and celldeath in the brain. In this study, we evaluated the long-term effects of Meth abuse in theCA1 region of postmortem hippo...

Network medicine, the field of using biological networks to develop insight into disease and medicine, is a budding area of research where current efforts have been rewarded with only a middling level of success. Various network models have been proposed to help advise and direct medical research; this paper explores the possible utility of the ”interaction-interaction” (II) network model by ad...

BACKGROUND Experimental methods for the identification of essential proteins are always costly, time-consuming, and laborious. It is a challenging task to find protein essentiality only through experiments. With the development of high throughput technologies, a vast amount of protein-protein interactions are available, which enable the identification of essential proteins from the network leve...

Methamphetamine (Meth) is recognized as one of the most important new distributedabused drug that causes severe damage to the different parts of the brain, especiallyhippocampus. Previous studies have demonstrated that Meth can induce apoptosis and celldeath in the brain. In this study, we evaluated the long-term effects of Meth abuse in theCA1 region of postmortem hippo...

Protein complexes play an important role in cellular mechanism. Identification of protein complexes in protein-protein interaction (PPI) networks is the first step in understanding the organization and dynamics of cell function. Several high-throughput experimental techniques produce a large amount of protein interactions, which can be used to predict protein complexes in a PPI network. We have...

Performing global alignment between protein-protein interaction (PPI) networks of different organisms is important to infer knowledge about conservation across species. Known methods that perform this task operate symmetrically, that is to say, they do not assign a distinct role to the input PPI networks. However, in most cases, the input networks are indeed distinguishable on the basis of how ...

Protein-protein interaction (PPI) networks play an important role in studying the functional roles of proteins, including their association with diseases. However, protein interaction networks are not sufficient without the support of additional biological knowledge for proteins such as their molecular functions and biological processes. To complement and enrich PPI networks, we propose to expl...

Reconstruction of signaling pathways is crucial for understanding cellular mechanisms. A pathway is represented as a path of a signaling cascade involving a series of proteins to perform a particular function. Since a protein pair involved in signaling and response have a strong interaction, putative pathways can be detected from protein-protein interaction (PPI) networks. However, predicting d...