Publications

Journal Papers

  1. P. Cazzaniga, C. Damiani, D. Besozzi, R. Colombo, M.S. Nobile, D. Gaglio, D. Pescini, S. Molinari, G. Mauri, L. Alberghina, M. Vanoni.
    Computational strategies for a system-level understanding of metabolism.
    Metabolites, Vol. 4, Issue 4, 1034-1087, 2014.
  2. M.S. Nobile, P. Cazzaniga, D. Besozzi, G. Mauri.
    GPU-accelerated simulations of mass-action kinetics models with cupSODA.
    The Journal of Supercomputing, Vol. 69, Issue 1, 17-24, 2014.
  3. P. Cazzaniga, M.S. Nobile, D. Besozzi, M. Bellini, G. Mauri.
    Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization.
    BioMed Research International (Special Issue "High-Performance Computing and Big Data in Omics-based Medicine"), Vol. 2014, Article ID 863298, 2014.
  4. M.S. Nobile, P. Cazzaniga, D. Besozzi, D. Pescini, G. Mauri.
    cuTauLeaping: a GPU-powered tau-leaping stochastic simulator for massive parallel analyses of biological systems.
    PLoS ONE 9(3): e91963, 2014.
  5. F. Amara, R. Colombo, P. Cazzaniga, D. Pescini, A. Csikász-Nagy, M. Muzi Falconi, D. Besozzi, P. Plevani.
    In vivo and in silico analysis of PCNA ubiquitylation in the activation of the Post Replication Repair pathway in S. cerevisiae.
    BMC Systems Biology 7:24, 2013.
  6. D. Besozzi, P. Cazzaniga, D. Pescini, G. Mauri, S. Colombo, E. Martegani.
    The role of feedback control mechanisms on the establishment of oscillatory regimes in the Ras/cAMP/PKA pathway in S. cerevisiae.
    EURASIP Journal on Bioinformatics and Systems Biology 2012:10, 2012.
  7. L. Corolli, F. Marini, C. Maj, D. Besozzi, G. Mauri.
    An excursion in reaction systems: from computer science to biology.
    Theoretical Computer Science, Vol. 454, 95–108, 2012.
  8. D. Pescini, P. Cazzaniga, D. Besozzi, G. Mauri, L. Amigoni, S. Colombo, E. Martegani.
    Simulation of the Ras/cAMP/PKA pathway in budding yeast highlights the establishment of stable oscillatory states.
    Biotechnology Advances, Vol. 30, Issue 1, 99–107, 2012.
  9. 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, Vol. 22, Issue 1, 89-96, 2011.
  10. A. Leporati, D. Besozzi, P. Cazzaniga, D. Pescini, C. Ferretti.
    Computing with energy and chemical reactions.
    Natural Computing, Vol. 9, No. 2, 493-512, 2010.
  11. 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, Vol.19, Issue 6, 1141-1160, 2009.
  12. 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, Vol. 133, Issue 3, 377-385, 2008.
  13. D. Besozzi, P. Cazzaniga, D. Pescini, G. Mauri.
    Modelling metapopulations with stochastic membrane systems.
    BioSystems, Vol. 91, Issue 3, 499-514, 2008.
  14. 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.
  15. 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, 242-266, 2007.
  16. D. Pescini, D. Besozzi, G. Mauri, C. Zandron.
    Dynamical probabilistic P systems.
    International Journal of Foundations of Computer Science, Vol. 17, No. 1, 183-204, 2006.
  17. D. Besozzi, E. Csuhaj-Varjú, G. Mauri, C. Zandron.
    On the power and size of extended gemmating P systems.
    Soft Computing, Vol. 9, No. 9, 650-656, 2005.
  18. D. Besozzi, G. Mauri, C. Zandron.
    Hierarchies of parallel rewriting P systems: A survey.
    New Generation Computing, Vol. 22, No. 4, 331-347, 2004.
  19. D. Besozzi, C. Ferretti, G. Mauri, C. Zandron.
    P Systems with deadlock.
    Biosystems, Vol. 70, No. 2, 95-105, 2003.
  20. D. Besozzi, G. Mauri, G. Păun, C. Zandron.
    Gemmating P systems: collapsing hierarchies.
    Theoretical Computer Science, Vol. 296, No. 2, 253-267, 2003.

Book Chapters

  1. M.S. Nobile, D. Cipolla, P. Cazzaniga, D. Besozzi.
    GPU-powered evolutionary design of mass-action based models of gene regulation.
    In: Evolutionary Computation in Gene Regulatory Network Research (H. Iba, N. Noman eds.), Wiley, in press.
  2. P. Cazzaniga, D. Besozzi, D. Pescini, G. Mauri.
    Molecular diffusion and compartmentalization in signal transduction pathways: an application of membrane systems to the study of bacterial chemotaxis.
    In: Applications of Membrane Computing in Systems and Synthetic Biology (M. Gheorghe, P. Frisco, M. Pérez-Jiménez eds.), Emergence, Complexity and Computation, Springer, Vol. 7, 65-96, 2014.
  3. D. Besozzi, I.I. Ardelean.
    Cell biology for Membrane Computing.
    In: The Oxford Handbook of Membrane Computing, (G. Păun, G. Rozenberg, A. Salomaa eds.), Oxford University Press, 2009.
  4. I.I. Ardelean, D. Besozzi, M.H. Garzon, G. Mauri, S. Roy.
    P system models for mechanosensitive channels.
    In: Applications of Membrane Computing, (G. Ciobanu, G. Păun, M.J. Pérez-Jiménez eds.), Springer-Verlag, Berlin, 2005.
  5. D. Besozzi, G. Mauri, C. Zandron.
    A survey of latest results on P systems with deadlock.
    In: Recent Results in Natural Computing, (M.J. Pérez-Jiménez, A. Romero-Jiménez, F. Sancho-Caparrini, eds.), University of Seville, 17-46, 2004.

Contributed Volumes

  1. D. Besozzi, P. Cazzaniga, D. Pescini, G. Mauri.
    A multi-volume approach to stochastic modeling 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 Proceedings

  1. A. Tangherloni, P. Cazzaniga, M.S. Nobile, D. Besozzi, G. Mauri.
    Deterministic simulations of large-scale models of cellular processes accelerated on Graphics Processing Units.
    Proceedings of CIBB 2015 - Twelfth International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, September 10-12, 2015, Naples, Italy. To appear.
  2. P. Cazzaniga, M.S. Nobile, D. Besozzi.
    The impact of particles initialization in PSO: parameter estimation as a case in point.
    Proceedings of 2015 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2015), Niagara Falls, Canada, August 12-15, 2015. To appear.
  3. M.S. Nobile, G. Pasi, P. Cazzaniga, D. Besozzi, R. Colombo, G. Mauri.
    Proactive particles in Swarm Optimization: A self-tuning algorithm based on Fuzzy Logic.
    2015 IEEE International Conference on Fuzzy Systems (FUZZ-IEEE 2015), Istanbul, Turkey, August 2-5, 2015. To appear.
  4. P. Cazzaniga, F. Ferrara, M.S. Nobile, D. Besozzi, G. Mauri.
    Parallelizing biochemical stochastic simulations: A comparison of GPUs and Intel Xeon Phi processors.
    Parallel Computing Technologies (Proceedings of 13th International Conference, PaCT 2015) (V. Malyshkin, ed.), LNCS 9251, 363-374, 2015.
  5. M.S. Nobile, A.G. Citrolo, P. Cazzaniga, D. Besozzi, G. Mauri.
    A memetic hybrid method for the Molecular Distance Geometry Problem with incomplete information.
    2014 IEEE Congress on Evolutionary Computation (CEC 2014), 1014-1021, 2014.
  6. M. Bellini, D. Besozzi, P. Cazzaniga, G. Mauri, M.S. Nobile.
    Simulation and analysis of the blood coagulation cascade accelerated on GPU.
    22nd Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP), 2014. IEEE Computer Society Conference Publishing Services (CPS), 590-593, 2014.
  7. D. Besozzi, G. Caravagna, P. Cazzaniga, M.S. Nobile, D. Pescini, A. Re.
    GPU-powered simulation methodologies for biological systems.
    Proceedings of Wivace 2013 - Italian Workshop on Artificial Life and Evolutionary Computation (A. Graudenzi, G. Caravagna, G. Mauri and M. Antoniotti, eds.), EPTCS 130, 87–91, 2013.
  8. D. Besozzi.
    Computational methods in Systems Biology: case studies and biological insights. (Invited contribution)
    Proceedings of the 4th International Workshop on Computational Models for Cell Processes (I. Petre, ed.), EPTCS 116, 3-10, 2013.
  9. M.S. Nobile, D. Besozzi, P. Cazzaniga, G. Mauri.
    The foundation of Evolutionary Petri Nets.
    Proceedings of the 4th International Workshop on Biological Processes & Petri Nets (BioPPN 2013), a satellite event of PETRI NETS 2013 (G. Balbo and M. Heiner, eds.), CEUR Workshop Proceedings Vol. 988, 60-74, 2013.
  10. M.S. Nobile, D. Besozzi, P. Cazzaniga, D. Pescini, G. Mauri.
    Reverse engineering of kinetic reaction networks by means of Cartesian Genetic Programming and Particle Swarm Optimization.
    IEEE Congress on Evolutionary Computation (CEC 2013), 1594-1601, 2013.
  11. M.S. Nobile, D. Besozzi, P. Cazzaniga, G. Mauri, D. Pescini.
    cupSODA: a CUDA-powered simulator of mass-action kinetics.
    Proceedings of 12th International Conference on Parallel Computing Technologies (PaCT 2013) (V. Malyshkin, ed.), LNCS 7979, 344-357, 2013.
  12. M.S. Nobile, D. Besozzi, P. Cazzaniga, G. Mauri, D. Pescini.
    Estimating reaction constants in stochastic biological systems with a multi-swarm PSO running on GPUs.
    Proceedings of the fourteenth International Conference on Genetic and Evolutionary Computation Conference Companion. ACM New York, NY, USA, GECCO Companion '12, 1421-1422, 2012.
  13. M.S. Nobile, D. Besozzi, P. Cazzaniga, G. Mauri, D. Pescini.
    A GPU-based multi-swarm PSO method for parameter estimation in stochastic biological systems exploiting discrete-time target series.
    Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics (M. Giacobini, L. Vanneschi, W.S. Bush, eds.), LNCS 7246, 74-85, 2012.
  14. D. Besozzi, P. Cazzaniga, D. Pescini, G. Mauri, S. Colombo, E. Martegani.
    Investigating oscillatory regimes in the Ras/cAMP/PKA pathway in S. cerevisiae: the role of feedback control mechanisms.
    Eigth International Workshop on Computational Systems Biology, WCSB 2011, June 6-8, 2011, Zürich, Switzerland, (H. Koeppl, J. Acimovic, J. Kesseli, T. Mäki-Marttunen, A. Larjo, O. Yli-Harja, eds.), TICSP Series #57, 33-36, 2011.
  15. D. Besozzi, P. Cazzaniga, G. Mauri, D. Pescini.
    BioSimWare: a software for the modeling, simulation and analysis of biological systems.
    Membrane Computing, 11th International Conference, CMC 2010, Jena, Germany, August 24-27, 2010. Revised Selected Papers, (M. Gheorghe, T. Hinze, G. Păun, G. Rozenberg, A. Salomaa, eds.), LNCS 6501, 119-143, 2010.
  16. D. Besozzi, P. Cazzaniga, D. Pescini, G. Mauri.
    An analysis on the influence of network topologies on local and global dynamics of metapopulation systems.
    Applications of Membrane Computing, Concurrency and Agent-based Modelling in Population Biology (AMCA-POP 2010) (P. Milazzo, M.J. Pérez-Jiménez, eds.), EPTCS 33, 1–17, 2010.
  17. 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.
  18. D. Besozzi, P. Cazzaniga, G.Mauri, D. Pescini, L. Vanneschi.
    A comparison of genetic algorithms and particle swarm optimization for parameter estimation in stochastic biochemical systems.
    EvoBIO 2009, (C. Pizzuti, M.D. Ritchie, M. Giacobini, eds.), LNCS 5483, 116–127, 2009.
  19. D. Besozzi, G. Mauri, D. Pescini, C. Zandron.
    Membrane systems in Systems Biology.
    WODES 2008. 9th International Workshop on Discrete Event Systems, (B. Lennartson, M. Fabian, K. Akesson, A. Giua, R. Kumar, eds.), IEEE Press, 275-280, 2008.
  20. P. Cazzaniga, D. Pescini, D. Besozzi, G. Mauri.
    Tau leaping stochastic simulation method in P systems.
    Membrane Computing, 7th International Workshop (WMC 2006), (H.J. Hoogeboom, G. Păun, G. Rozenberg, A. Salomaa, eds.), LNCS 4361, 298-313, 2006.
  21. D. Besozzi, G. Rozenberg.
    Formalizing spherical membrane structures and membrane proteins populations.(Invited contribution)
    Membrane Computing, 7th International Workshop (WMC 2006), (H.J. Hoogeboom, G. Păun, G. Rozenberg, A. Salomaa, eds.), LNCS 4361, 18-41, 2006.
  22. D. Pescini, D. Besozzi, C. Zandron, G. Mauri.
    Analysis and simulation of dynamics in probabilistic P systems.
    DNA Computing, 11th International Workshop on DNA Computing (DNA11), (N. Pierce, A. Carbone, eds.), LNCS 3892, 236-247, 2006.
  23. D. Pescini, D. Besozzi, G. Mauri.
    Investigating local evolutions in dynamical probabilistic P systems.
    Proceedings of 7th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing (SYNASC'05), IEEE Computer Press, 440-447, 2005.
  24. D. Besozzi, G. Ciobanu.
    A P system description of the sodium-potassium pump.
    Proceedings of 5th Membrane Computing International Workshop (WMC04), (G. Mauri, G. Păun, M.J. Pérez-Jiménez, G. Rozenberg, A. Salomaa, eds.), LNCS 3365, 210-223, 2005.
  25. D. Besozzi, G. Mauri, G. Vaszil, C. Zandron.
    Collapsing hierarchies of parallel rewriting P systems without target conflicts.
    Proceedings of Membrane Computing International Workshop (WMC03), (C. Martín-Vide, G. Mauri, G. Păun, G. Rozenberg, A. Salomaa, eds.), LNCS 2933, 55-69, 2004.
  26. D. Besozzi, G. Mauri, C. Zandron.
    Deadlock decidability in partial parallel P systems.
    Proceedings of 9th International Workshop on DNA Based Computers, (J. Chen, J. Reif, eds.), LNCS 2943, 55-60, 2004.
  27. D. Besozzi, G. Mauri, C. Zandron.
    Parallel rewriting P systems without target conflicts.
    Proceedings of Membrane Computing International Workshop (WMC-CdeA2002), (G. Păun, G. Rozenberg, A. Salomaa, C. Zandron, eds.), LNCS 2597, 119-133, 2003.
  28. D. Besozzi, C. Ferretti, G. Mauri, C. Zandron.
    Parallel rewriting P systems with deadlock.
    Proceedings of 8th International Workshop on DNA Based Computers, (M. Hagiya, A. Ohuchi, eds.), LNCS 2568, 302-314, 2003.
  29. D. Besozzi, C. Zandron, G. Mauri, N. Sabadini.
    P systems with gemmation of mobile membranes.
    Proceedings of ICTCS01, (A. Restivo, S. Ronchi Della Rocca, L. Roversi, eds.), LNCS 2202, 136-153, 2001.

Posters and abstracts

  1. P. Cazzaniga, M.S. Nobile, D. Besozzi, A.G. Citrolo, A. Tangherloni, A. Donizetti, G. Mauri.
    Towards a GPU-powered toolbox for the computational analysis of biological systems.
    Twelfth Annual Meeting of the Bioinformatics Italian Society (BITS 2015), June 3-5, 2015, Milan, Italy.
  2. M.S. Nobile, L.A. Harris, E. Shockley, J.C. Pino, P. Cazzaniga, D. Besozzi, C.F. Lopez, G. Mauri.
    GPU computing for accelerated analyses of a large-scale model of cell fate in cancer cells.
    Twelfth Annual Meeting of the Bioinformatics Italian Society (BITS 2015), June 3-5, 2015, Milan, Italy.
  3. N. Frik, M.S. Nobile, D. Besozzi, T. LaBean.
    Useful disorder: Engineering self-assembly and randomized neuromimetic networks for sensing and computation.
    12th Annual Conference on Foundations of Nanoscience: Self-assembled architectures and devices (FNANO15), Snowbird, Utah, USA, April 13-16, 2015.
  4. M.S. Nobile, L.A. Harris, E. Shockley, P. Cazzaniga, D. Besozzi, C.F. Lopez, G. Mauri.
    GPU-powered sensitivity analysis of a large-scale model of death cell signaling and proliferation in cancer cells.
    Third Annual Winter q-bio Meeting, Maui, Hawaii, February 17-20, 2015.
  5. M.S. Nobile, P. Cazzaniga, D. Besozzi, D. Cipolla, G. Mauri.
    Towards an integrated toolbox for GPU-powered computational analysis of complex biological systems.
    Third Annual Winter q-bio Meeting, Maui, Hawaii, February 17-20, 2015.
  6. D. Besozzi, M.S. Nobile, P. Cazzaniga, D. Cipolla, G. Mauri.
    From the inference of molecular structures to the analysis of emergent cellular dynamics: accelerating the computational study of biological systems with GPUs.
    Proceedings of the NETTAB 2014 Workshop: from Structural Bioinformatics to Integrative Systems Biology, Torino, Italy, October 15-17, 2014.
  7. D. Besozzi, P. Cazzaniga, R. Colombo, G. Mauri, M.S. Nobile, D. Pescini.
    Accelerating the computational analysis of biological systems by means of Graphics Processing Units.
    ICSB 2013 - 14th International Conference on Systems Biology, Copenhagen, Denmark, August 30 - September 3, 2013.
  8. D. Besozzi, R. Colombo, P. Cazzaniga, M.S. Nobile, D. Pescini, G. Mauri.
    A GPU-powered computational analysis of PCNA ubiquitylation processes involved in UV-induced DNA lesions bypass.
    ICSB 2013 - 14th International Conference on Systems Biology, Copenhagen, Denmark, August 30 - September 3, 2013.
  9. P. Cazzaniga, R. Colombo, M.S. Nobile, D. Pescini, G. Mauri, D. Besozzi.
    GPU-powered sensitivity analysis and parameter estimation of a reaction-based model of the Post Replication Repair pathway in yeast.
    WCSB 2013 - 10th International Workshop on Computational Systems Biology, Tampere, Finland, June 10-12, 2013.
  10. F. Amara, R. Colombo, F. Spadaro, D. Besozzi, M. Muzi-Falconi, P. Plevani.
    PCNA ubiquitylation as the wet readout of a Post-Replication Repair computational model.
    Ubiquitin and ubiquitin-like modifiers: from functional modules to Systems Biology, Cavtat (Dubrovnik), Croatia, September 21-25, 2011.
  11. P. Cazzaniga, D. Besozzi, D. Pescini, G. Mauri, S. Colombo, E. Martegani.
    The role of Ras modulators and feedback control mechanisms on the establishment of oscillations in the Ras/cAMP/PKA pathway in S. cerevisiae.
    ICSB2011 - 12th International Conference on Systems Biology, Heidelberg/Mannheim, August 28 - September 1, 2011.
  12. P. Cazzaniga, D. Pescini, D. Besozzi, G. Mauri, S. Colombo, E. Martegani.
    Simulation of the Ras/cAMP/PKA pathway in budding yeast evidences the presence of stable oscillatory states.
    IBS2010 - 14th International Biotechnology Symposium and Exhibition, Biotechnology for the Sustainability of Human Society, Rimini, Italy, September 14-18, 2010.
    (Abstract in: Journal of Biotechnology, Vol. 150, Suppl.1, 545, 2010.)
  13. D. Besozzi, P. Cazzaniga, A. Devecchi, P. Landini, D. Pescini.
    An in silico investigation of different regulation mechanisms of the bacterial second messenger c-di-GMP.
    IBS2010 - 14th International Biotechnology Symposium and Exhibition, Biotechnology for the Sustainability of Human Society, Rimini, Italy, September 14-18, 2010.
    (Abstract in: Journal of Biotechnology, Vol. 150, Suppl.1, 546, 2010.)
  14. D. Besozzi, P. Cazzaniga, D. Pescini, G. Mauri.
    BioSimWare: a simulation environment for stochastic modeling of complex biological systems.
    IBS2010 - 14th International Biotechnology Symposium and Exhibition, Biotechnology for the Sustainability of Human Society, Rimini, Italy, September 14-18, 2010.
    (Abstract in: Journal of Biotechnology, Vol. 150, Suppl.1, 519-520, 2010.)
  15. F. Amara, D. Besozzi, R. Colombo, I. Mura, M. Muzi-Falconi, P. Plevani.
    Post-Replication Repair (PRR) in Saccharomyces cerevisiae: a Systems Biology approach.
    The interface between the ubiquitin family and the DNA damage response, Red Island, Rovinj, Croatia, September 1-5, 2010.
  16. D. Besozzi, P. Cazzaniga, G. Mauri, D. Pescini.
    Effects of stochastic fluctuations on the coordination of flagella in bacterial chemotaxis.
    Fourth Annual q-bio Conference on Cellular Information Processing, Santa Fe, New Mexico, August 11-14, 2010.
  17. P. Cazzaniga, D. Pescini, D. Scotti, D. Besozzi, G. Mauri, S. Colombo, E. Martegani.
    Simulation of the Ras/cAMP/PKA pathway in budding yeast evidences the presence of stable oscillatory states.
    SysBioHealth 2009, Milano, Italy, November 25-27, 2009.
  18. D. Besozzi, P. Cazzaniga, M. Dugo, G. Mauri, D. Pescini.
    Stochastic modelling and parameter estimation of bacterial chemotaxis.
    Information Processing in Cells and Tissues (IPCAT 2009), Ascona, Switzerland, April 5-9, 2009.
  19. F. Amara, D. Besozzi, A. Csikasz-Nagy, S. Riva, M. Muzi Falconi, P. Plevani.
    Analyzing the Saccharomyces cerevisiae Post Replication Repair pathway through a Systems Biology approach.
    Systems level understanding of DNA damage responses, Egmond aan Zee, The Netherlands, March 30 - April 1, 2009.
  20. 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.
    9th International Conference on Systems Biology (ICSB2008), Göteborg, Sweden, August 22-28, 2008.
  21. E. Martegani, P. Cazzaniga, D. Besozzi, S. Colombo, G. Mauri.
    Stochastic modeling and simulations of the Ras/cAMP/PKA pathway in budding yeast.
    SysBioHealth 2007, Milano, Italy, October 16-19, 2007.
  22. E. Martegani, P. Cazzaniga, D. Besozzi, S. Colombo, G. Mauri.
    Stochastic modeling of the Ras/cAMP signal transduction pathway in yeast.
    International Conference on Computational Methods in Systems Biology (CMSB2006), Trento, Italy, October 2006.
  23. 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.
    25th International Specialized Symposium on Yeasts (ISSY 25), Hanasaari, Espoo, Finland, June 2006.

Technical Reports

  1. 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 4th Brainstorming Week on Membrane Computing, Volume II (C. Graciani Diaz, G. Păun, A. Romero-Jiménez, F. Sancho-Caparrini, eds.), RGNC REPORT 03/2006, Fenix Editora, Sevilla, 185-208, 2006.
  2. P. Cazzaniga, D. Pescini, F.J. Romero-Campero, D. Besozzi, G. Mauri.
    Stochastic approaches in P systems for simulating biological systems.
    Proceedings of the 4th Brainstorming Week on Membrane Computing, Volume I (M.A. Gutiérrez-Naranjo, G. Păun, A. Riscos-Nùñez, F.J. Romero-Campero, eds.), RGNC REPORT 02/2006, Fenix Editora, Sevilla, 145-165, 2006.
  3. D. Besozzi, N. Busi, G. Franco, R. Freund, G. Păun.
    Two universality results for (mem)brane systems.
    Proceedings of the 4th Brainstorming Week on Membrane Computing, Volume I (M.A. Gutiérrez-Naranjo, G. Păun, A. Riscos-Nùñez, F.J. Romero-Campero, eds.), RGNC REPORT 02/2006, Fenix Editora, Sevilla, 49-62, 2006.
  4. I.I. Ardelean, D. Besozzi.
    Some notes on the interplay between P systems and chemotaxis in Bacteria.
    Proceedings of the 4th Brainstorming Week on Membrane Computing, Volume I (M.A. Gutiérrez-Naranjo, G. Păun, A. Riscos-Nùñez, F.J. Romero-Campero, eds.), RGNC REPORT 02/2006, Fenix Editora, Sevilla, 41-48, 2006.
  5. I.I. Ardelean, D. Besozzi.
    On modeling ion fluxes across biological membranes with P systems.
    Proceedings of the 3rd Brainstorming Week on Membrane Computing, (M.A. Gutiérrez-Naranjo, A. Riscos-Nùñez, F.J. Romero-Campero, D. Sburlan, eds.), RGNC REPORT 01/2005, 35-42, 2005.

Other Works

  1. S. Aguzzoli, I.I. Ardelean, D. Besozzi, B. Gerla, C. Manara.
    P systems under uncertainty: the case of transmembrane proteins.
    Proceedings of Brainstorming Workshop on Uncertainty in Membrane Computing, Palma de Mallorca, 8-10 Novembre 2004, Departament de Matemàtiques i Informàtica, Universitat de les Illes Balears, ISBN 84-7632-897-4, 107-117, 2004.
  2. S. Aguzzoli, D. Besozzi, B. Gerla, C. Manara.
    P systems with vague boundaries: the t-norm approach.
    Proceedings of Brainstorming Workshop on Uncertainty in Membrane Computing, Palma de Mallorca, 8-10 Novembre 2004, Departament de Matem àtiques i Inform àtica, Universitat de les Illes Balears, ISBN 84-7632-897-4, 97-105, 2004.

Submitted Papers (under review)