The increasing number of experimentally detected interactions between proteins makes it difficult for researchers to extract the interactions relevant for specific biological processes or diseases. This makes it necessary to accompany the large-scale detection of protein-protein interactions (PPIs) with strategies and tools to generate meaningful PPI subnetworks. To this end, we generated the H...

Protein-protein interaction (PPI) networks of many organisms share global topological features such as degree distribution, k-hop reachability, betweenness and closeness. Yet, some of these networks can differ significantly from the others in terms of local structures: e.g. the number of specific network motifs can vary significantly among PPI networks. Counting the number of network motifs pro...

The present study aimed to identify altered genes and pathways associated with four histotypes of ovarian cancer, according to the systematic tracking of dysregulated modules of reweighted protein‑protein interaction (PPI) networks. Firstly, the PPI network and gene expression data were initially integrated to infer and reweight normal ovarian and four types of ovarian cancer (endometrioid, ser...

Chronic obstructive pulmonary disease (COPD) is a multi-factor disease, which could be caused by many factors, including disturbances of metabolism and protein-protein interactions (PPIs). In this paper, a weighted COPD-related metabolic network and a weighted COPD-related PPI network were constructed base on COPD disease genes and functional information. Candidate genes in these weighted COPD-...

Successive whole genome duplications have recently been firmly established in all major eukaryote kingdoms. It is not clear, however, how such dramatic evolutionary process has contributed to shape the large scale topology of protein-protein interaction (PPI) networks. We propose and analytically solve a generic model of PPI network evolution under successive whole genome duplications. This dem...

Interactomes such as Protein interaction networks have many undiscovered links between entities. Experimental verification of every link in these networks is prohibitively expensive, and therefore computational methods to direct the search for possible links are of great value. The problem of finding undiscovered links in a network is also referred to as the link prediction problem. A popular a...

Protein-protein interactions (PPIs) are of biological interest for their active participation in coordinating a number of cellular processes in living organisms. This paper attempts to formulate PPIs as an optimization problem with an aim to independently maximize (a) the stability of a complex formed by two proteins predicted to be interacting, (b) the difference between their individual acces...

High-throughput experimental techniques have been producing more and more protein-protein interaction (PPI) data. The PPI network alignment greatly benefits the understanding of evolutionary relationship among species, helps identify conserved subnetworks, and provides extra information for functional annotations. Although a few methods have been developed for multiple PPI network alignment, th...

MOTIVATION High-throughput experimental techniques have produced a large amount of protein-protein interaction (PPI) data. The study of PPI networks, such as comparative analysis, shall benefit the understanding of life process and diseases at the molecular level. One way of comparative analysis is to align PPI networks to identify conserved or species-specific subnetwork motifs. A few methods ...