With the increasing availability of high-throughput data, various computational methods have recently been developed for understanding the cell through protein-protein interaction (PPI) networks at a systems level. However, due to the incompleteness of the original PPI networks those efforts have been significantly hindered. In this paper, we propose a two stage method to predict underlying lin...

Intervertebral disc (IVD) degeneration is a pathological process, which may lead to lower back pain. The present study aimed to investigate the pathogenesis of IVD degeneration. GSE42611 was downloaded from Gene Expression Omnibus, including 4 nucleus pulposus samples isolated from degenerated IVDs and 4 nucleus pulposus samples separated from normal IVDs. The differentially expressed genes (DE...

MOTIVATION The increasing availability of large-scale protein-protein interaction (PPI) data has fueled the efforts to elucidate the building blocks and organization of cellular machinery. Previous studies have shown cross-species comparison to be an effective approach in uncovering functional modules in protein networks. This has in turn driven the research for new network alignment methods wi...

Pattern discovery in protein interaction networks can reveal crucial biological knowledge on the inner workings of cellular machinery. Although far from complete, extracting meaningful patterns from proteomic networks is a nontrivial task due to their size-complexity. This paper proposes a computational framework to efficiently discover topologically-similar patterns from large proteomic networ...

The ability to volitionally regulate emotions is critical to health and well-being. While patterns of neural activation during emotion regulation have been well characterized, patterns of connectivity between regions remain less explored. It is increasingly recognized that the human brain is organized into large-scale intrinsic connectivity networks (ICNs) whose interrelationships are altered i...