The most common malignant neoplasm of the head and neck region is laryngeal cancerwhich presents a significant international health problem. The present study aims to screenpotential proteins related to laryngeal cancer by network analysis to further understandingdisease pathogenesis and biomarker discovery. Differentially expressed proteins were extractedfrom literatures of laryngeal cancer th...

Proteins are essential macromolecules of life that carry out most cellular processes. Since proteins aggregate to perform function, and since protein-protein interaction (PPI) networks model these aggregations, one would expect to uncover new biology from PPI network topology. Hence, using PPI networks to predict protein function and role of protein pathways in disease has received attention. A...

MOTIVATION Microarray-based gene expression data have been generated widely to study different biological processes and systems. Gene co-expression networks are often used to extract information about groups of genes that are 'functionally' related or co-regulated. However, the structural properties of such co-expression networks have not been rigorously studied and fully compared with known bi...

In information sharing networks, having a privacy preserving index (or PPI) is critically important for providing efficient search on access controlled content across distributed providers while preserving privacy. An understudied problem for PPI techniques is how to provide controllable privacy preservation, given the innate difference of privacy of the different content and providers. In this...

Revealing functional units in protein-protein interaction (PPI) networks are important for understanding cellular functional organization. Current algorithms for identifying functional units mainly focus on cohesive protein complexes which have more internal interactions than external interactions. Most of these approaches do not handle overlaps among complexes since they usually allow a protei...

MOTIVATION Much of the large-scale molecular data from living cells can be represented in terms of networks. Such networks occupy a central position in cellular systems biology. In the protein-protein interaction (PPI) network, nodes represent proteins and edges represent connections between them, based on experimental evidence. As PPI networks are rich and complex, a mathematical model is soug...

BACKGROUND Parkinson's Disease (PD) is one of the most prevailing neurodegenerative diseases. Improving diagnoses and treatments of this disease is essential, as currently there exists no cure for this disease. Microarray and proteomics data have revealed abnormal expression of several genes and proteins responsible for PD. Nevertheless, few studies have been reported involving PD-specific prot...

In emerging information networks, having a privacy preserving index (or PPI) is critically important for locating information of interest for data sharing across autonomous providers while preserving privacy. An understudied problem for PPI techniques is how to provide controllable privacy preservation, given the innate difference of privacy concerns regarding different data owners. In this pap...

In information sharing networks, having a privacy preserving index (or PPI) is critically important for providing efficient search on access controlled content across distributed providers while preserving privacy. An understudied problem for PPI techniques is how to provide controllable privacy preservation, given the innate difference of privacy of the different content and providers. In this...

Since cellular functionality is typically envisioned as having a hierarchical structure, we propose a framework to identify modules (or clusters) within protein-protein interaction (PPI) networks in this paper. Based on the within-module and between-module edges of subgraphs and degree distribution, we present a formal module definition in PPI networks. Using the new module definition, an effec...