July 24, 2017, Monday

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Cazzaniga Paolo

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

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

I received the doctoral degree in Computer Science from the University of Milano – Bicocca in February 2010. The title of my doctoral thesis is Stochastic algorithms for biochemical processes.
My research activity concerns the modeling and simulation of biological, chemical and ecological systems. I am mainly interested in stochastic methods: I am currently studying and analyzing the principal stochastic simulation algorithms, such as SSA, tau leaping, slow scale SSA, adaptive tau leaping, next reaction method, next subvolume method.
Moreover, I have introduced a novel method used to simulate multiple volumes systems, called tau-Dpp. I am also implementing different stochastic procedures exploiting parallel architectures (such as MPI, grid and CUDA) to perform faster simulations.
The stochastic methods studied were applied to simulate, among others, the Ras/cAMP/PKA pathway in the yeast Saccharomyces cerevisiae, the repressilator system, the bacterial chemotaxis and metapopulation systems.
Another research field in which I am involved is related to the use of evolutionary techniques to estimate the parameters of biological and chemical systems. In particular, I 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 I 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).



Publications

Journals

D. Pescini, P. Cazzaniga, D. Besozzi, G. Mauri, S. Colombo, E. Martegani. Simulation of the Ras/cAMP/PKA pathway in budding yeast highlights the establishment of stable oscillatory states. Biotechnology Advances, submitted

E. Mosca, I. Merelli, P. Cazzaniga, D. Pescini, G. Mauri, L. Milanesi. Grid computing for parameter sweep applications in systems biology models. International Journal of High Performance Computing Applications, accepted

D. Besozzi, N. Busi, P. Cazzaniga, C. Ferretti, A. Leporati, G. Mauri, D. Pescini, C. Zandron. (Tissue) P systems with cell polarity. Mathematical Structures in Computer Science, 19, 1141–1160, 2009

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, 377–385, 2008

D. Besozzi, P. Cazzaniga, D. Pescini, G. Mauri. Modelling metapopulations with stochastic membrane Systems. BioSystems, 91, 3, 499–514, 2008

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, 242–266, 2007 (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


Book Chapters

P. Cazzaniga, M. Gheorghe, N. Krasnogor, G. Mauri, D. Pescini, F.J. Romero-Campero. Probabilistic/stochastic models. In: The Oxford Handbook of Membrane Computing, (G. Paun, G. Rozenberg, A. Salomaa, eds.), pp. 455-474, Oxford University Press, 2009


Contributed Volumes

D. Besozzi, P. Cazzaniga, S. Cocolo, G. Mauri, D. Pescini. Modeling diffusion in a signal transduction pathway: the use of virtual volumes in P systems. International Journal of Foundations of Computer Science, Volume 22, Issue 1, 89–96, 2011

A. Leporati, D. Besozzi, P. Cazzaniga, D. Pescini, C. Ferretti. Computing with energy and chemical reactions. Natural Computing Series, Springer-Verlag, Volume 9, Number 2, 493–512, 2009

D. Besozzi, P. Cazzaniga, D. Pescini, G. Mauri. A multivolume approach to stochastic modelling with membrane systems. In: Algorithmic Bioprocesses, (A. Condon, D. Harel, J.N. Kok, A. Salomaa, E. Winfree, eds.), Natural Computing Series, Springer-Verlag, 519-542, 2009


Conference and Workshop Proceedings

E. Mosca, P. Cazzaniga, D. Pescini, G. Mauri, L. Milanesi. Modelling spatial heterogeneity and macromolecular crowding with membrane systems. Proceedings of CMC11 - Eleventh International Conference on Membrane Computing, 24-27 August 2010 - Jena, Germany, to appear in LNCS

D. Besozzi, P. Cazzaniga, G. Mauri, D. Pescini. BioSimWare: A P Systems–based Simulation Environment for Biological Systems. Proceedings of CMC11 - Eleventh International Conference on Membrane Computing, 24-27August 2010 - Jena, Germany, to appear in LNCS

D. Besozzi, P. Cazzaniga, D. Pescini, G. Mauri. An analysis on the influence of network topologies on local and global dynamics of metapopulation systems. Proceedings of the First Workshop on Applications of Membrane computing, Concurrency and Agent-based modelling in POPulation biology, EPCTS 33, 1–17, 2010

E. Mosca, P. Cazzaniga, D. Pescini, I. Merelli, G. Mauri, L. Milanesi. Stochastic simulations on a grid framework for parallel sweep applications in biological models. International Workshop on High Performance Computational Systems Biology, HiBi09, IEEE Computer Society, 0, 33-42, 2009

P. Cazzaniga, G. Mauri, L. Milanesi, E. Mosca, D. Pescini. A Novel Variant of P Systems for the Modelling and Simulation of Biochemical Systems. Proceedings of the 10th International Workshop on Membrane Computing, WMC 2009 (G. Paun, M.J. Perez-Jimenez, A. Riscos-Nunez, G. Rozenberg, A. Salomaa, eds.), LNCS 5957, 210–226, 2009

D. Besozzi, P. Cazzaniga, M. Dugo, D. Pescini, G. Mauri. A study on the combined interplay between stochastic fluctuations and the number of flagella in bacterial chemotaxis. Proceedings of CompMod2009 - 2nd International Workshop on Computational Models for Cell Processes (R.J. Back, I. Petre, E. de Vink, eds.), EPTCS 6, 47-62, 2009

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. First steps towards a wet implementation for tau-DPP. Proceedings of the 9th International Workshop on Membrane Computing, 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. Proceedings of the 7th International Workshop on Membrane Computing,  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. Proceedings of the 6th International Workshop on Membrane Computing, WMC 2005, Vienna, Austria, July 18-21, 2005, Revised Selected and Invited Papers, (R. Freund, Gh. Paun, G. Rozenberg, A. Salomaa, eds.), LNCS 3850,165-180, 2006

Contacts

Address

Dipartimento di Informatica, Sistemistica e Comunicazione (DISCo)

Università degli studi di Milano - Bicocca, Edificio U14 - Stanza 1004

Viale Sarca 336, 20126 - Milano, Italy

email: cazzaniga [at] disco [dot] unimib [dot] it

tel: +39 02 6448 7879



Links

Download BioSimWare here