

Ph.D. of the XXVII cycle
Room 1046 building U14, viale Sarca 336, 20126 Milano (Italy)
Email address: nobile AT disco DOT unimib DOT it
Journal papers
 Harris L.A., Nobile M.S., Pino J.C., Lubbock A.L.R., Besozzi D., Mauri G., Cazzaniga P., Lopez C.F.: GPUpowered model analysis with PySB/cupSODA. Bioinformatics, (in press, 2017)
 Nobile M.S., Porreca A.E., Spolaor S., Manzoni L., Cazzaniga P., Mauri G., Besozzi D.: Efficient simulation of reaction systems on Graphics Processing Units. Fundamenta Informaticae (accepted, 2017)
 Tangherloni A., Nobile M.S., Besozzi D., Mauri G., Cazzaniga P.: LASSIE: Simulating largescale models of biochemical systems on GPUs. BMC Bioinformatics, 18(1):246, 2017
 Nobile M.S., Cazzaniga P., Tangherloni A., Besozzi D.: Graphics Processing Units in Bioinformatics, Computational Biology and Systems Biology. Briefings in Bioinformatics, 2016
 Tangherloni A., Nobile M.S., Cazzaniga P., Besozzi D., Mauri G.: Gillespie’s Stochastic Simulation Algorithm on MIC coprocessors. Journal of Supercomputing, 73(2):676–686, 2017
 Cazzaniga P., Damiani C., Besozzi D., Colombo R., Nobile M.S., Gaglio D., Pescini D., Molinari S., Mauri G., Alberghina L., Vanoni M.: Computational strategies for a systemlevel understanding of metabolism. Metabolites, 4(4):1034–1087, 2014
 Nobile M.S., Cazzaniga P., Besozzi D., Pescini D., Mauri G.: cuTauLeaping: a GPUpowered tauleaping stochastic
simulator for massive parallel analyses of biological systems. PLoS ONE, 9(3):e91963, 2014
 Cazzaniga P., Nobile M.S., Besozzi D., Bellini M., Mauri G.: Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization. BioMed Research International, vol. 2014, Article ID 863298, 2014
 Nobile M.S., Cazzaniga P., Besozzi D., Mauri G.: GPUaccelerated simulations of massaction kinetics models with cupSODA. Journal of Supercomputing, 69(1):17–24, 2014
 Bellini M., Besozzi D., Cazzaniga P., Mauri G., Nobile M.S.: Modeling and simulation of the blood coagulation cascade. ECS Journal, 37(7):10–23, 10341087, 2014
Conference proceedings
 Spolaor S., Tangherloni A., Rundo L., Nobile M.S., Cazzaniga P.: Reboot strategies in Particle Swarm Optimization and their impact on parameter estimation of biochemical systems, IEEE International Conference on Computational Intelligence and Bioinformatics (CIBCB 2017), Manchester, UK (accepted)
 Nobile M.S., Mauri G.: Accelerated analysis of biological parameters space using GPUs, 14th International Conference on Parallel Computing Technologies (PaCT 2017), Nizhni Novgorod, Russia (accepted)
 Tangherloni A., Rundo L., Nobile M.S.: Proactive Particles in Swarm Optimization: a settingsfree algorithm for realparameter single objective optimization problems, Proceedings of the 2017 IEEE Congress on Evolutionary Computation (CEC 2017), Donostia S. Sebastian (Spain), 2017
 Ramazzotti D., Nobile M.S., Cazzaniga P., Mauri G., Antoniotti M.: Parallel implementation of efficient search schemes for the inference of cancer progression models, Proceedings of IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology, Chiang Mai (Thailand), 2016
 Tangherloni A., Nobile M.S., Cazzaniga P.: GPUpowered Bat Algorithm for the parameter estimation of biochemical kinetic values, Proceedings of IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology, Chiang Mai (Thailand), 2016
 Cumbo F., Nobile M.S., Damiani C., Colombo R., Mauri G., Cazzaniga P.: COSYS: Computational Systems Biology infrastructure, Proceedings of the 13th International Conference on Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB2016), Stirling (UK), 2016
 Re A., Caravagna G., Pescini D., Nobile M.S., Cazzaniga P.: Approximate simulation of chemical reaction systems with micro, meso and macroscales, Proceedings of the 13th International Conference on Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB2016), Stirling (UK), 2016
 Nobile M.S., Tangherloni A., Besozzi D., Cazzaniga P.: GPUpowered and settingsfree parameter estimation of biochemical systems, Proceedings of the IEEE World Congress on Computational Intelligence 2016, Vancouver (Canada), 2016
 Tangherloni A., Cazzaniga P., Nobile M.S., Besozzi D., Mauri G.: Deterministic simulations of largescale models of cellular processes accelerated on Graphics Processing Units, 12th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB2015), Naples (Italy), 2015
 Cazzaniga P., Nobile M.S., Besozzi D.: The impact of particles initialization in PSO: parameter estimation as a case in point, 2015 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, August 1215, Niagara Falls, (Canada), 2015
 Nobile M.S., Iba H.: A double swarm methodology for parameter estimation in oscillating gene regulatory networks, Proceedings of the 2015 IEEE Congress on Evolutionary Computation (CEC2015). S. Obayashi, C. Poloni, T. Murata (Eds.). Sendai (Japan), pp. 2376–2383, 2015
 Nobile M.S., Pasi G., Cazzaniga P., Besozzi D., Colombo R., Mauri G.: Proactive particles in swarm optimization: a selftuning algorithm based on fuzzy logic, Proceedings of the 2015 IEEE International Conference on Fuzzy Systems (FUZZIEEE 2015), Istanbul (Turkey), pp. 1–8, 2015
 Cazzaniga P., Ferrara F., Nobile M.S., Besozzi D., Mauri G.: Parallelizing biochemical stochastic simulations: a comparison of GPUs and Intel Xeon Phi coprocessors, Proceedings of the 13th International Conference on Parallel Computing Technologies (PaCT 2015), Petrozavodsk (Russia). V. Malyshkin (Ed.). Lecture Notes in Computer Science. Vol. 9251, pp. 363–374, 2015
 Nobile M.S., Citrolo A.G., Cazzaniga P., Besozzi D., Mauri G.,: A memetic hybrid method for the molecular distance
geometry problem with incomplete information, Proceedings of the 2014 IEEE Congress on Evolutionary Computation (CEC2014), Beijing (China), pp. 1014–1021, 2014
 Nobile M.S.: Evolutionary inference of biochemical interaction networks accelerated on Graphics Processing Units, Proceedings of the 11th International Conference on High Performance Computing & Simulation 2013 (HPCS 2013), Helsinki (Finland), pp. 668–670, 2013
 Nobile M.S., Besozzi D., Cazzaniga P., Mauri G.: 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
 Nobile M.S., Besozzi D., Cazzaniga P., Mauri G., Pescini D.: Reverse engineering of kinetic reaction networks by means of cartesian genetic programming and particle swarm optimization, Proceedings of the 2013 IEEE Congress on Evolutionary Computation (CEC2013), Cancun (Mexico). Luis Gerardo de la Fraga (Ed.). Vol. 1, pp. 1594–1601, 2013
 Nobile M.S., Besozzi D., Cazzaniga P., Mauri G., Pescini D.: cupSODA: a CUDApowered simulator of massaction kinetics, In 12th International Conference on Parallel Computing Technologies (PaCT), Saint Petersburg (Russia), Proceedings. V. Malyshkin (Ed.). Lecture Notes in Computer Science. Vol. 7979, pp. 344–357, 2013
 Nobile M.S., Besozzi D., Cazzaniga P., Mauri G., Pescini D.: A GPUbased multiswarm PSO method for parameter estimation in stochastic biological systems exploiting discretetime target series. In 10th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Computational Biology, EvoBIO 2012, Malaga (Spain), Proceedings. Mario Giacobini, Leonardo Vanneschi, and William Bush (Eds.). Lecture Notes in Computer Science. Vol. 7264, pp. 74–85, 2012
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.: GPUpowered evolutionary design of massaction 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.: Highperformance 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 largescale 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.: Highperformance 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 selfassembly and randomized
neuromimetic networks for sensing and computation, Proceedings of the 12th Conference on Foundations of Nanoscience: SelfAssembled 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 GPUpowered 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 largescale 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 GPUpowered computational analysis of complex biological systems, 2015 Winter QBio Meeting, Maui, Hawai'i (USA)
 Nobile M.S., Harris L., Shockley E., Cazzaniga P., Besozzi D., Lopez C.F., Mauri G.: GPUpowered sensitivity analysis of a largescale model of death cell signaling and proliferation in cancer cells, 2015 Winter QBio 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 NetworkBased 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 2628, 2014, Rome, (Italy), 2014
 Besozzi D., Caravagna G., Cazzaniga P., Nobile M. S., Pescini D., Re A.: GPUpowered 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 GPUpowered computational analysis of PCNA ubiquitylation processes involved in UVinduced 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.: GPUpowered sensitivity analysis and parameter estimation of a reactionbased 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 multiswarm 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
Academic Year 20162017
 "Computational Systems Biology": lectures on parameter estimation (local and global search) and highperformance computing for life sciences
Postgraduate course in Biotechnology, University of MilanoBicocca
 "Laboratory of Informatics"
Undergraduate course in Physics, University of MilanoBicocca
 "Laboratory of Informatics"
Undergraduate course in Biotechnology, University of MilanoBicocca
Academic Year 20152016
 "1st SYSBIO.IT School on Computational Systems Biology": lectures on advanced biochemical modeling and simulation, highperformance computing, parameter estimation
SYSBIO.IT Centre of Systems Biology
 "Laboratory of Informatics"
Undergraduate course in Physics, University of MilanoBicocca
Academic Year 20142015
 "Computational Biology": lectures on GPGPU programming and GPUpowered biochemical simulation (deterministic, stochastic, hybrid, fine and coarsegrained)
Postgraduate course in Computer Science, University of MilanoBicocca
 "Systems Biology": 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 GPUpowered methodologies for bioinformatics and systems biology
Postgraduate course in Industrial Biotechnology, University of MilanoBicocca
 "Computational Biology": lectures on GPGPU programming and GPUpowered biochemical simulation (deterministic, stochastic, hybrid, fine and coarsegrained)
Postgraduate course in Computer Science, University of MilanoBicocca
Academic Year 20122013
 "Soft Computing": lectures on particle swarm optimization and applications
Postgraduate course in Computer Science, University of MilanoBicocca
 "Laboratory of Informatics and Mathematics"
Undergraduate course in Mathematics, University of MilanBicocca
 "Systems Biology": lectures on estimation of kinetic parameters exploiting local (gradient descent, LevenbergMarquardt) 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 MilanoBicocca
 "Laboratory of Algorithms and Operations Research"
Undergraduate course in Computer Science, University of MilanoBicocca
Academic Year 20112012
 "Soft Computing": lectures on particle swarm optimization and applications
Postgraduate course in Computer Science, University of MilanoBicocca
 "Systems Biology": lectures on parameter estimation and genetic programming
Postgraduate course in Molecular Biotechnologies and Bioinformatics, University of Milano
 Further readings  About me
My main research interest is Soft Computing in many forms: Evolutionary Computation (EC), Swarm Intelligence (SI), Fuzzy Logic (FL). I extensively exploited creative combinations of such techniques to create fully automatic tools able to tackle complex problems in Systems Biology, Synthetic Biology and Computational Structural Biology.
For instance, I created methods for the parameter estimation of biochemical models which combine SI and FL.
By integrating EC and SI, I designed methods for the reverse engineering of biochemical systems and the inference of protein structures according to partial data.
EC and SI methods provide powerful means to tackle hard computational problems; however, both methodologies rely on populations of candidate solutions, so that they require the execution of multiple simulations of the biological system under investigation, which is a computationally demanding activity.
For this reason, I also work on the optimization and acceleration of deterministic, stochastic and hybrid simulation algorithms, also including the spatial component.
In particular, I largely rely on highperformance parallel coprocessors like GPUs and MICs, to leverage the relevant computational power offered by new generation accelerators.
 My personal page on the BIMIB (Bioinformatics, Natural Calculus, and Systems Biology) website
 I am part of a research unit in the SYSBIO Centre for Systems Biology, working on in silico simulations and analysis
 My profile on Google Scholar
 My profile in the Genetic Programming Bibliography
 My LinkedIn profile
 My profile on ResearchGate
 My profile on Academia.edu
 My ORCID profile
 Associations
I am member of the Workgroup "HPCenabled Modelling for Life Sciences" in the context of the "HighPerformance Modelling and Simulation for Big Data Applications" COST Action
I am senior member of the Italian Society of Biochemistry and Molecular Biology. I belong to the group "Computational and Systems Biology"  GITHUB repository
Follow @aresio
