Cytoscape is open-source software for integration, visualization and analysis of biological
networks. It can be extended through Cytoscape plugins, enabling a broad community of …

Studying protein interaction networks of all proteins in an organism (“interactomes”) remains
one of the major challenges in modern biomedicine. Such information is crucial to …

With the elucidation of myriad anabolic and catabolic enzyme-catalyzed cellular pathways
crisscrossing each other, an obvious question arose: how could these networks operate with …

Understanding complex systems often requires a bottom-up analysis towards a systems
biology approach. The need to investigate a system, not only as individual components but …

Motivation Clustering analysis in a biological network is to group biological entities into
functional modules, thus providing valuable insight into the understanding of complex …

Studying the topology of a network is critical to inferring underlying dynamics such as
tolerance to failure, group behavior and spreading patterns. k-core decomposition is a well …

Protein-protein interaction (PPI) networks are viable tools to understand cell functions,
disease machinery, and drug design/repositioning. Interpreting a PPI, however, it is a …

Background Predicting protein complexes from protein-protein interaction data is becoming
a fundamental problem in computational biology. The identification and characterization of …

Abstract Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial
Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine …

Cellular processes are typically carried out by protein complexes and functional modules.
Identifying them plays an important role for our attempt to reveal principles of cellular …