title: Finding the shortest path with PesCa: a tool for network reconstruction.
abstract: Network analysis is of growing interest in several fields ranging from economics to biology. Several methods have been developed to investigate different properties of physical networks abstracted as graphs, including quantification of specific topological properties, contextual data enrichment, simulation of pathway dynamics and visual representation. In this context, the PesCa app for the Cytoscape network analysis environment is specifically designed to help researchers infer and manipulate networks based on the shortest path principle. PesCa offers different algorithms allowing network reconstruction and analysis starting from a list of genes, proteins and in general a set of interconnected nodes. The app is useful in the early stage of network analysis, i.e. to create networks or generate clusters based on shortest path computation, but can also help further investigations and, in general, it is suitable for every situation requiring the connection of a set of nodes that apparently do not share links, such as isolated nodes in sub-networks. Overall, the plugin enhances the ability of discovering interesting and not obvious relations between high dimensional sets of interacting objects.
authors: Center for Biomedical Computing, University of Verona, Verona, Italy.
authors: Giovanni
authors: G
authors: Scardoni
authors: Center for Biomedical Computing, University of Verona, Verona, Italy.
authors: Gabriele
authors: G
authors: Tosadori
authors: Birla Institute of Technology & Science, Goa, India.
authors: Sakshi
authors: S
authors: Pratap
authors: Department of Computer Science, University of Verona, Verona, Italy.
authors: Fausto
authors: F
authors: Spoto
authors: Department of Medicine, University of Verona, Verona, Italy.
authors: Carlo
authors: C
authors: Laudanna
keywords: biological networks; connect isolated node; cytoscape; pesca; protein protein interaction networks; shortest path