Description: The CBMC hosts a technological core facility based on four distinct technologies and including: ImageStream, Victor X5, BioFlux and RT-PCR. See the attached Excel file and link for a list of users and projects tacking advantage of the CBMC facility. ImageStream is now supported by Centro Grandi Attrezzature (CGA) of the University of Verona. The technologies are administrated by CBMC personnel and are accessible to university and external users upon request (contact dr. A. Montresor for ImageStream and Victors X and dr. L. Toffali for BioFlux). The CBMC also provides bioinformatics service for automatic quantitative analysis of underflow cell behavior and for static network analysis (contact dr. L. Toffali for cell behavior analysis and dr. G. Scardoni for network analysis).

Supervisors: Dr. Alberto Castellini, Prof. Carlo Laudanna, Dr. Giovanni Scardoni, Dr. Alessio Montresor, Dr. Lara Toffali.

Metabolomics in Panthetine pharmacology

Description: Panthetine is a CoA precursor shown to have high impact on autoimmune diseases, such MS, and on cell proliferation, including cancer. Its mechanism of action is, however, at present, unidentified. We exploited the Metabolom service for high throughput quantitate analysis of metabolic signatures in human leukocytes treated with Panthetine to unveil the metabolic process affected by Panthetine. The project is developed in conjunction with phosphonetwork analysis by exploiting the Kinexus service. The project takes advantage of MetScape, a metabolic network analysis tool for Cytoscape developed in collaboration with prof. Alla Karnosky (University of Michigan Medical School).

Supervisors: Dr. Gabriela Constantin.

Phosphonetwork analysis of B-chronic lymphocytic leukemia (B-CLL) Link   

Description: B-CLL is the most common adult leukemia in western countries. It is characterized by progressive accumulation of mature B-cells in primary and secondary lymphoid organs. B-CLL cells experience an environment-dependent unbalance between pro- and anti-apoptotic signaling mechanisms, along with alteration of chemokine-induced inside-out signaling leading to integrin activation and adhesion. The exact means by which B-CLL genetic alterations lead to leukemogenesis is still unclear and this hampers the possibility of reliable prognosis and affects the outcome of current treatments, which are still unsatisfactory. We are pursuing a deep characterization of signaling networks in BCLL cells by applying high throughput phospho-protein microarrays coupled to network topological analysis to identify network signatures of disease. The project is developed in collaborate with prof. F. Vinante and dr. A. Rigo, University of Verona.

Supervisors: Prof. Carlo Laudanna, Dr. Simone Zorzan, Dr. Giovanni Scardoni, Dr. Alessio Montresor.

Interference - Virtual experimental topological network analysis Link   

Description: A Cytoscape plugin to perform topological virtual knock-out experiments on biological networks. Interference allows computing the topological effect of node removal in complex networks. Applications span from pharmacology to proteomics and metabolomics.

Supervisors: Prof. Carlo Laudanna, Dr. Giovanni Scardoni.

HOMECAT for consensus homology mapping to integrate knowledge and functional genomic data Link   

Description: HOMECAT is a Cytoscape plugin allowing to identify orthologs with the consensus of several data sources, to conveniently convert identifiers and to directly map curated high-throughput data.

Supervisors: Dr. Simone Zorzan, Prof. Mario Rosario Buffelli.

Alzheimer Disease Pathological Processes Investigation By Systems Biology Approach Link   

Description: Systems Biology study of Alzheimer functional genomic data to gain new insights in the pathology and identify druggable targets.

Supervisors: Prof. Mario Rosario Buffelli.

Systems Biology of Survival and Axonal Regeneration of Central and Peripheral Nervous System Link   

Description: Investigation of neuronal survival and axonal regeneration processes of central and peripheral nervous system by high throughput phosphoproteomic approach.

Supervisors: Prof. Mario Rosario Buffelli.

MP solutions of Dynamical Inverse Problems Link   

Description: This project is aimed at discovering algorithms and developing software platforms for the identification of the best MP grammar explaining some given time series.

Supervisors: Prof. Vincenzo Manca, Dr. Luca Marchetti.

MP Modeling of Biological Dynamics Link   

Description: Discovery of MP grammars generating a given biological dynamics. Applications to cases of medical interest (gene expression networks, metabolic pathologies)

Supervisors: Prof. Vincenzo Manca, Dr. Luca Marchetti.

CentiScaPe: Centralities for Cytoscape Link   

Description: CentiScaPe is a Cytoscape plug-in for calculating network centralities with numerical and graphic output. Applications include analysis of signaling and metabololic networks, either indirect as well as direct.

Supervisors: Prof. Carlo Laudanna, Dr. Giovanni Scardoni.

Info-genomics Link   

Description: This is a very recent project concerning the development of a set of analytical indexes (based on information theory) able to describe in a concise way some key information held in DNA strings and genomes. These indexes could represent an innovative way to infer evolutionary relationships among biological species.

Supervisors: Prof. Vincenzo Manca, Dr. Giuditta Franco, Dr. Alberto Castellini.

Modularity in signaling networks regulating cell trafficking Link   

Description: Leukocyte trafficking is regulated by complex signaling networks triggered by chemoattractants and leading to very rapid integrin activation and cell recruitment. We have developed both experimental (trojan nanovectors) and computational tools (see Centiscape and Interference projects) to investigate the modular nature of intracellular molecular networks controlling cell trafficking.

Supervisors: Prof. Carlo Laudanna, Dr. Giovanni Scardoni, Dr. Gabriela Constantin, Dr. Alessio Montresor.

The MetaPlab project Link   

Description: This project involves the implementation of the MetaPlab virtual laboratory

Supervisors: Prof. Vincenzo Manca, Dr. Alberto Castellini, Dr. Luca Marchetti.