Mining Protein-Protein Interactions (PPIs) from the fast-growing biomedical literature resources has been proven as an effective approach for the identification of biological regulatory networks. This paper presents a novel method based on the idea of Interaction Relation Ontology (IRO), which specifies and organises words of various proteins interaction relationships. Our method is a two-stage...

UNLABELLED We describe an algorithm for global alignment of multiple protein-protein interaction (PPI) networks, the goal being to maximize the overall match across the input networks. The intuition behind our algorithm is that a protein in one PPI network is a good match for a protein in another network if the former's neighbors are good matches for the latter's neighbors. We encode this intui...

UNLABELLED Over the last few years, several computational techniques have been devised to recover protein complexes from the protein interaction (PPI) networks of organisms. These techniques model 'dense' subnetworks within PPI networks as complexes. However, our comprehensive evaluations revealed that these techniques fail to reconstruct many 'gold standard' complexes that are 'sparse' in the ...

Large-scale protein-protein interactions (PPIs) detected by yeast-two-hybrid (Y2H) systems are known to contain many false positives. The separation of credible interactions from background noise is still an unavoidable task. In the present study, we propose the relative reliability score for PPI as an intrinsic characteristic of global topology in the PPI networks. Our score is calculated as t...

Protein complex formed by a group of physical interacting proteins plays a crucial role in cell activities. Great effort has been made to computationally identify protein complexes from protein-protein interaction (PPI) network. However, the accuracy of the prediction is still far from being satisfactory, because the topological structures of protein complexes in the PPI network are too complic...

MOTIVATION Protein-protein interaction (PPI) extraction from published biological articles has attracted much attention because of the importance of protein interactions in biological processes. Despite significant progress, mining PPIs from literatures still rely heavily on time- and resource-consuming manual annotations. RESULTS In this study, we developed a novel methodology based on Bayes...

6 The increasing growth of data on protein-protein interaction (PPI) networks has boosted research 7 on their comparative analysis. In particular, recent studies proposed models and algorithms for 8 performing network alignment, that is, the comparison of networks across species for discovering 9 conserved functional complexes. In this paper, we present an algorithm for dividing PPI networks, 1...