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BioPhys - Computational Biology

Componenti

Attività

Research Activities

The main goal of the BioPhys network  is  the study of problems and systems of Biological interest with the tools and ideas typical of theoretical physics. Our main focus is in Molecular Biology, a research context which has seen an impressive development in these last years  and is nowadays of central relevance, both for the deep scientific questions which it raises and for the large number of potential biomedical applications. In this framework, our research project is organized in three main directions:

1. Numerical simulations of systems of biological interest.  (protein folding, biomolecules aggregation, protein-protein interactions...)
2. Neural Networks and related systems. (Study of Brain connectivity, emergence of spatio-temporal patterns....)
3. Regulatory Networks  (Gene Regulatory Networks, Immune Networks, Chromatin organization....)

The common theme and the unifying setting of these research lines is the use of theoretical physics methods to model and analyse these problems. In particular methods borrowed from the statistical mechanics of disordered systems (Spin Glasses, Hopfield model...);  computational tools typical of the simulation of many-body physical systems (Montecarlo Simulations, Molecular Dynamics,...);  advanced mathematical tools (Graph theory, Network Theory, Stochastic Equations....)
The most relevant aspect of our research network is the strong interaction of all the units with biologist. All the problems that we address stem from precise biological questions to which we try to give quantitative and testable answers.  

Projects

2012-2015 "Grant di Ateneo" GeneRNet
"Computational and experimental approaches to identify and model biologically relevant Gene Regulatory Networks"

Prodotti della ricerca

1) Cantini, Laura; Medico, Enzo; Fortunato, Santo; Caselle, Michele
Detection of gene communities in multi-networks reveals cancer drivers
Scientific Reports (2015) Volume: 5 Article Number: 17386
http://hdl.handle.net/2318/1547072

2) Laura Cantini, Claudio Isella, Consalvo Petti, Gabriele Picco, Simone Chiola, Elisa Ficarra, Michele Caselle & Enzo Medico
"MicroRNA-mRNA interactions underlying colorectal cancer molecular subtypes"
Nature Communications (2015) Volume: 6 Article Number: 8878 .
http://hdl.handle.net/2318/1529830

3)  Matteo Osella, Carla Bosia, Davide Corà, Michele Caselle
"The Role of Incoherent MicroRNA-Mediated Feedforward Loops in Noise Buffering"
PLoS Comput Biol 2011 Mar 8; 7(3): e1001101
http://hdl.handle.net/2318/86735

4) Carla Bosia, Matteo Osella, Mariama El Baroudi, Davide Corà, Michele Caselle
"Gene autoregulation via intronic microRNAs and its functions."
BMC Syst Biol. 2012 Oct 10;6:131.
 http://hdl.handle.net/2318/130300

5) Boccignone G., Ferraro M. (2014)
Ecological Sampling of Gaze Shifts
IEEE Transactions on System Man and Cybernetics
vol. 44, pp. 266-279.
http://hdl.handle.net/2318/78528


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