Protein-protein interactions (PPIs) are central to most biological processes. Although efforts have been devoted to the development of methodology for predicting PPIs and protein interaction networks, the application of most existing methods is limited because they need information about protein homology or the interaction marks of the protein partners. In the present work, we propose a method ...

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...

The reconstruction of protein-protein interaction (PPI) networks from high-throughput experimental data is one of the most challenging problems in bioinformatics. These biological networks have specific topologies defined by the functional and evolutionary relationships between the proteins and the physical limitations imposed on proteins interacting in the three-dimensional space. In this pape...

Empirical study of networks has enlightened our understanding of many application domains including the topology of biological systems. The Markov clustering algorithm (MCL), originally developed for clustering graphs, has been adopted to clustering protein-protein interaction (PPI) networks. MCL is also becoming an effective algorithm for the extraction of complexes from interaction networks. ...

Advances in modern technologies for measuring protein-protein interaction (PPI) has boosted research in PPI networks analysis and comparison. One of the challenging problems in comparative analysis of PPI networks is the comparison of networks across species for discovering conserved modules. Approaches for this task generally merge the considered networks into one new weighted graph, called al...

Proteins interact in complex protein-protein interaction (PPI) networks whose topological properties-such as scale-free topology, hierarchical modularity, and dissortativity-have suggested models of network evolution. Currently preferred models invoke preferential attachment or gene duplication and divergence to produce networks whose topology matches that observed for real PPIs, thus supportin...

Long-term (multiple-week or -month) release of small, water-soluble molecules from hydrogels remains a significant pharmaceutical challenge, which is typically overcome at the expense of more-complicated drug carrier designs. Such approaches are payload-specific and include covalent conjugation of drugs to base materials or incorporation of micro- and nanoparticles. As a simpler alternative, he...

Protein-Protein Interaction (PPI) networks contain valuable information for the isolation of groups of proteins that participate in the same biological function. Many proteins play different roles in the cell by taking part to several processes, but isolating the different processes in which a protein is involved is often a difficult task. In this paper we present a method based on a greedy loc...

Abstract* Introduction: Chronic morphine exposure can cause addiction and affect synaptic plasticity, but the underlying neural mechanisms of this phenomenon remain unknown. Herein we used electrophysiologic approaches in hippocampal CA1 area to examine the effect of chronic morphine administration on short-term plasticity. Methods: Experiments were carried out on hippocampal slices taken f...

BACKGROUND One of the crucial steps toward understanding the biological functions of a cellular system is to investigate protein-protein interaction (PPI) networks. As an increasing number of reliable PPIs become available, there is a growing need for discovering PPIs to reconstruct PPI networks of interesting organisms. Some interolog-based methods and homologous PPI families have been propose...