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Logo Ateneo
   
Cazzaniga Paolo
E-mail: paolo dot cazzaniga at disco dot unimib dot it
Tel: 02 6448 7879
Address: viale Sarca 336, 20126 - Milano
Building: U14 Room: 1004


PhD Thesis title: Stochastic algorithms for biochemical processes

Curriculum Vitae:
Paolo Cazzaniga graduated "cum laude" in Computer Science from the University of Milano – Bicocca, Italy, in April 2005. The title of his Thesis is "Storage Devices Inside Membrane Systems", where he investigated membrane systems, a computational model of Natural Computing, whose aim is to abstract the way cells "compute"; in this work, he proposed a new variant of membrane systems able to store structured data.

From September 2005 to September 2006 he received a PreDoc scholarship from the University of Milano – Bicocca to work in the area of Systems Biology and Natural Computing. He mainly worked on the analysis and simulation of biochemical systems by means of stochastic algorithms implemented at the University of Milano – Bicocca lab.

Since November 2006 he is a Ph.D. student in Computer Science at the University of Milano – Bicocca. His research activity concerns the modeling and simulation of biological, chemical and ecological systems. He is mainly interested in stochastic methods: he is currently studying and analyzing the principal stochastic simulation algorithms, such as SSA, tau leaping, slow scale SSA, adaptive tau leaping.Moreover, he has introduced a novel method used to simulate multiple volumes systems, called tau-Dpp. He is also implementing different stochastic procedures exploiting parallel architectures (such as MPI) to perform faster simulations. The stochastic methods studied were applied to simulate, among others, the Ras/cAMP/PKA pathway in the yeast Saccharomyces cerevisiae.

Another research field in which he is involved is related to the use of evolutionary techniques to estimate the parameters of biological systems. In particular, he developed methods based on genetic algorithms and particle swarm optimizer to reconstruct the unknown parameters of the analyzed systems.

From January 2008 to July 2008 he spent a period at the University of Edinburgh, working under the supervision of Prof. Stephen Gilmore at the Laboratory for Foundations of Computer Science (LFCS).
 
 
List of publications

Journals

D. Besozzi, P. Cazzaniga, D. Pescini, G. Mauri.  A multivolume approach to stochastic modelling with membrane systems. Submitted
 
D. Besozzi, N. Busi, P. Cazzaniga, C. Ferretti, A. Leporati, G. Mauri, D. Pescini, C. Zandron.  (Tissue) P systems with cell polarity. Accepted

P. Cazzaniga, D. Pescini, D. Besozzi, G. Mauri, S. Colombo, E. Martegani.  Modeling and stochastic simulation of the Ras/cAMP/PKA pathway in the yeast Saccharomyces cerevisiae evidences a key regulatory function for intracellular guanine nucleotides pools. Journal of Biotechnology, 133, 3, 2008, 377-385

D. Besozzi, P. Cazzaniga, D. Pescini, G. Mauri.  Modelling metapopulations with stochastic membrane Systems. BioSystems, 91, 3, 2008, 499-514
 
M. Muskulus, D. Besozzi, R. Brijder, P. Cazzaniga, S. Houweling, D. Pescini, G. Rozenberg. Cycles and communicating classes in membrane systems and molecular dynamics. Theoretical Computer Science , Vol. 372, Issues 2-3, 15 March 2007, 242-266 (doi:10.1016/j.tcs.2006.11.027)
 
D. Besozzi, P. Cazzaniga, D. Pescini, G. Mauri.  Seasonal variance in P system models for metapopulations. Progress in Natural Science, Vol. 17, No. 4, 392-400, 2007
 
 
Proceedings of Conferences

P. Cazzaniga, D. Pescini, L. Vanneschi, D. Besozzi, G. Mauri.  A Comparison of Genetic Algorithms and Particle Swarm Optimization for Parameter Estimation in Stochastic Biochemical Systems, Proceedings of EvoBio 2009, LNCS 5483, 116-127, 2009

D. Pescini, P. Cazzaniga, C. Ferretti, G. Mauri.  Toward a wet implementation for tau-DPP. 9th International Workshop, WMC 2008 (D. Corne et al. eds.), LNCS 5391, 355-373, 2009

P. Cazzaniga, D. Pescini, D. Besozzi, G. Mauri.  Tau leaping stochastic simulation method in P systems. 7th International Workshop, WMC 2006 (H.J. Hoogeboom, G. Paun, G. Rozenberg, A. Salomaa, eds.), LNCS 4361, 298-313, 2006

 P. Cazzaniga, A. Leporati, G. Mauri, C. Zandron, P Systems with Memory, 6th International Workshop, WMC 2005, Vienna, Austria, July 18-21, 2005, Revised Selected and Invited Papers, (R. Freund, Gh. Paun, G. Rozenberg, A. Salomaa, eds.), Lecture Notes in Computer Science 3850, Springer-Verlag, 2006, 165-180
 
 
Other

D. Besozzi, P. Cazzaniga, M. Dugo, G. Mauri, D. Pescini. Stochastic modelling and parameter estimation of bacterial chemotaxis. Poster at Information Processes in Cells and Tissues (IPCAT), Ascona, Switzerland, April 2009

 E. Mosca, P. Cazzaniga, D. Pescini, G. Mauri, L. Milanesi. A stochastic, discrete model for the simulation of the action potential. Poster at Sysbiohealth Symposium 2008, Bologna, Italy, November 2008
 
D. Pescini, P. Cazzaniga, D. Besozzi, G. Mauri, S. Colombo, E. Martegani. Modeling and Simulations of the Ras signalling pathway in budding Yeast: Evidence for oscillatory regimes. Poster at ICSB 2008 - International Conference on Systems Biology, Goteborg, Sweden, August 2008

P. Cazzaniga, D. Pescini, D. Besozzi, G. Mauri, S. Colombo, E. Martegani. Stochastic Modeling and Simulations of the Ras/cAMP/PKA Pathway in budding Yeast. Poster at Sysbiohealth Symposium 2007, Milano, Italy, October 2007

E. Martegani, P. Cazzaniga, D. Pescini, D. Besozzi, S. Colombo, G. Mauri. Stochastic modeling of the Ras/cAMP signal transduction pathway in yeast. Poster at Computational Methods in Systems Biology (CMSB), Trento, Italy, October 2006
 
E. Martegani, R. Tisi, F. Belotti, S. Colombo, C. Paiardi, J. Winderickx, P. Cazzaniga, D. Besozzi, G. Mauri. Identification of an intracellular signalling complex for Ras/cAMP pathway in yeast: experimental evidences and modelling. Poster at ISSY 25 - 25th International Specialized Symposium on Yeasts, Hanasaari, Espoo, Finland, June 2006

P. Cazzaniga, D. Pescini, F.J. Romero-Campero, D. Besozzi, G. Mauri. Stochastic approaches in P systems for simulating biological systems. Proceedings of the Fourth Brainstorming Week on Membrane Computing, Volume I (M.A. Gutierrez-Naranjo, G. Paun, A. Riscos-Nunez, F.J. Romero-Campero, eds.), RGNC REPORT 02/2006, Fenix Editora, Sevilla, 145-165, 2006
 
M. Muskulus, S. Houweling, G. Rozenberg, D. Besozzi, P. Cazzaniga, D. Pescini, R. Brijder. Reaction cycles in membrane systems and molecular dynamics. Proceedings of the Fourth Brainstorming Week on Membrane Computing, Volume II (C. Graciani Diaz, G. Paun, A. Romero-Jimenez, F. Sancho-Caparrini, eds.), RGNC REPORT 03/2006, Fenix Editora, Sevilla, 185-208, 2006

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