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Logo Ateneo
   
Nobile Marco Salvatore
foto Marco Nobile
Ph.D. of the XXVII cycle
Room 1046 building U14, viale Sarca 336, 20126 Milano (Italy)
E-mail address: nobile AT disco DOT unimib DOT it
Research areas: Soft Computing; High-performance Computing; Systems and Synthetic Biology; Bio-Inspired, Natural and Neuromorphic Computation; Structural Computational Biology

Ph.D. thesis: Evolutionary Inference of Biological Systems Accelerated on Graphics Processing Units

Advisor: Professor Giancarlo Mauri

Journal papers

Conference proceedings

Tutorials

Book chapters

  • Cazzaniga P., Nobile M.S., Tangherloni A., Besozzi D.: Accelerating stochastic simulations of mechanistic models of biological systems: Advantages and issues in the parallelization on Graphics Processing Units. In Quantitative Biology: Computational Methods and Examples, Brian Munsky, William Hlavacek, Lev Tsimring (Eds.), (2015, in preparation)
  • Nobile M.S., Cipolla D., Besozzi D., Cazzaniga P.: GPU-powered evolutionary design of mass-action based models of gene regulation. In Evolutionary Computation in Gene Regulatory Network Research, Hitoshi Iba, Nasimul Noman (Eds.), John Wiley & Sons, 2016

Posters and abstracts

  • Rizza M., Nobile M.S., Masoli S., D’angelo E., Antoniotti M.: Automatic calibration of cerebellar stellate neuronal models using Swarm Intelligence, International Conference on Systems Biology (ICSB 2016), Barcelona, Spain
  • Nobile M.S., Cazzaniga P., Tangherloni A., Spolaor S., Besozzi D., Mauri G.: High-performance computing in Systems Biology: accelerating the simulation and analysis of large and complex biological systems, International Conference on Systems Biology (ICSB 2016), Barcelona, Spain
  • Tangherloni A., Capitoli G., Cazzaniga P., Nobile M.S., Besozzi D., Mauri G.: Deterministic simulations of large-scale models of biochemical reaction networks accelerated on Graphics Processing Units, International Conference on Systems Biology (ICSB 2016), Barcelona, Spain
  • Rizza M., Nobile M.S.:Automatic calibration of cerebellar stellate neuronal models using Swarm Intelligence, Second International Meeting of the Milan Center for Neuroscience (NeuroMi 2016), Milano, Italy
  • Mauri G., Nobile M.S., Cazzaniga P., Besozzi D.: High-performance computing in Systems Biology: accelerating the simulation and analysis of large and complex biological systems, Proceedings of SysMod SIG 2016 meeting, Orlando, Florida (USA)
  • Frik N., Nobile M.S., Besozzi D., LaBean T.: Useful disorder: engineering self-assembly and randomized neuromimetic networks for sensing and computation, Proceedings of the 12th Conference on Foundations of Nanoscience: Self-Assembled Architectures and Devices (FNANO 2015), Snowbird Cliff Lodge, Snowbird, Utah (USA)
  • Cazzaniga P., Nobile M.S., Besozzi D., Citrolo A.G., Tangherloni A., Donizetti A. and Mauri G.: Towards a GPU-powered toolbox for the computational analysis of biological systems, BITS Annual Meeting 2015, Milano (Italy)
  • Nobile M.S., Harris L., Shockley E., Pino J., Cazzaniga P., Besozzi D., Lopez C.F., Mauri G.: GPU computing for accelerated analyses of a large-scale model of cell fate in cancer cells, BITS Annual Meeting 2015, Milano (Italy)
  • Nobile M.S., Cazzaniga P., Besozzi D., Cipolla D., Mauri G.: Towards an integrated toolbox for GPU-powered computational analysis of complex biological systems, 2015 Winter Q-Bio Meeting, Maui, Hawai'i (USA)
  • Nobile M.S., Harris L., Shockley E., Cazzaniga P., Besozzi D., Lopez C.F., Mauri G.: GPU-powered sensitivity analysis of a large-scale model of death cell signaling and proliferation in cancer cells, 2015 Winter Q-Bio Meeting, Maui, Hawai'i (USA)
  • Besozzi D., Nobile M.S., Cazzaniga P., Cipolla D., Mauri G.: 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), pp. 88–90, 2014
  • Bellini M., Besozzi D., Cazzaniga P., Mauri G., Nobile M.S.: Simulation and analysis of the blood coagulation cascade accelerated on GPU, Proceedings of 22nd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing (PDP 2014), Torino (Italy), pp. 590–593, 2014
  • Caravagna G., Cazzaniga P., Nobile M. S., Pescini D., Re A.: Enhancing simulation of chemical reactions at mesoscales, BITS 2014 - 11th Annual Meeting of the Bioinformatics Italian Society February 26-28, 2014, Rome, (Italy), 2014
  • Besozzi D., Caravagna G., Cazzaniga P., Nobile M. S., Pescini D., Re A.: GPU-powered simulation methodologies for biological systems, In A. Graudenzi, G. Caravagna, G. Mauri, M. Antoniotti (Eds.): Wivace 2013 Italian Workshop on Artificial Life and Evolutionary Computation, EPTCS, pp. 93–97, 2013
  • Besozzi D., Cazzaniga P., Colombo R., Mauri G., Nobile M. S., Pescini D.: Accelerating the computational analysis of biological systems by means of Graphics Processing Units, ICSB 2013 - 14th International Conference on Systems Biology, Copenhagen (Denmark), 2013
  • Besozzi D., Colombo R., Cazzaniga P., Nobile M. S., Pescini D., Mauri G.: 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), 2013
  • Cazzaniga P., Colombo R., Nobile M.S., Pescini D., Mauri G., Besozzi D.: GPU-powered sensitivity analysis and parameter estimation of a reaction-based model of the post replication repair pathway in yeast, Proceedings of the 10th International Workshop on Computational Systems Biology (WCSB 2013), Tampere (Finland), p. 109, 2013
  • Nobile M.S., Besozzi D., Cazzaniga P., Mauri G., Pescini D.: 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

Teaching

  • "1st SYSBIO.IT School on Computational Systems Biology": lectures on advanced biochemical modeling and simulation, high-performance computing, parameter estimation
    SYSBIO.IT Centre of Systems Biology
  • "Laboratory of Informatics"
    Undergraduate course in Physics, University of Milano-Bicocca
  • "Computational Biology" (2014-2015): lectures on GPGPU programming and GPU-powered biochemical simulation (deterministic, stochastic, hybrid, fine- and coarse-grained)
    Postgraduate course in Computer Science, University of Milano-Bicocca
  • "Systems Biology" (2014-2015): lectures on stochastic biochemical simulation (exact, approximate, hybrid) and estimation of kinetic parameters by means of local and global optimization techniques
    Postgraduate course in Molecular Biotechnologies and Bioinformatics, University of Milano
  • "Bioinformatics Methods": lectures on GPGPU programming and GPU-powered methodologies for bioinformatics and systems biology
    Postgraduate course in Industrial Biotechnology, University of Milano-Bicocca
  • "Computational Biology": lectures on GPGPU programming and GPU-powered biochemical simulation (deterministic, stochastic, hybrid, fine- and coarse-grained)
    Postgraduate course in Computer Science, University of Milano-Bicocca
  • "Soft Computing" (2012-2013): lectures on particle swarm optimization and applications
    Postgraduate course in Computer Science, University of Milano-Bicocca
  • "Laboratory of Informatics and Mathematics"
    Undergraduate course in Mathematics, University of Milan-Bicocca
  • "Systems Biology" (2012-2013): lectures on estimation of kinetic parameters exploiting local (gradient descent, Levenberg-Marquardt) and global optimization techniques (simulated annealing, genetic algorithms, particle swarm optimization, covariance matrix adaptation evolution strategy)
    Postgraduate course in Molecular Biotechnologies and Bioinformatics, University of Milano
  • "Algorithms and Data Structures": tutoring activity
    Undergraduate course in Computer Science, University of Milano-Bicocca
  • "Laboratory of Algorithms and Operations Research"
    Undergraduate course in Computer Science, University of Milano-Bicocca
  • "Soft Computing" (2011-2012): lectures on particle swarm optimization and applications
    Postgraduate course in Computer Science, University of Milano-Bicocca
  • "Systems Biology" (2011-2012): lectures on parameter estimation and genetic programming
    Postgraduate course in Molecular Biotechnologies and Bioinformatics, University of Milano

  
Approfondimenti

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redazioneweb@disco.unimib.it - ultimo aggiornamento di questa pagina 26/09/2016