Publications

Nobile M.S., Vlachou T., Spolaor S., Bossi D., Cazzaniga P., Lanfrancone L., Mauri G., Pelicci P.G., Besozzi D.: Modeling cell proliferation in human acute myeloid leukemia xenografts, Bioinformatics, 2019 (in press)

Rundo L., Tangherloni A., Nobile M.S., Militello C., Besozzi D., Mauri G., Cazzaniga P.: MedGA: A Novel Evolutionary Method for Medical Image Enhancement, Expert Systems with Applications, 119: 387–399, 2019

Ramazzotti D., Nobile M.S., Antoniotti M., Graudenzi A.: Efficient computational strategies to learn the structure of probabilistic graphical models of cumulative phenomena, Journal of Computational Science, 30:1–10, 2019

Nobile M.S., Cazzaniga P., Besozzi D., Mauri G.: ginSODA: massive parallel integration of stiff ODE systems on GPUs, Journal of Supercomputing, 2019 (in press)

Tangherloni A., Spolaor S., Rundo L., Nobile M.S., Cazzaniga P., Mauri G., Liò P., Merelli I., Besozzi D.: GenHap: A novel computational method based on genetic algorithms for haplotype assembly, BMC Bioinformatics, 2019 (in press)

Nobile M.S., Pasi G., Cazzaniga P., Besozzi D., Colombo R., Mauri G.: Fuzzy Self-Tuning PSO: a settings-free algorithm for global optimization, Swarm and Evolutionary Computation, 39:70–85, 2018

Harris L.A., Nobile M.S., Pino J.C., Lubbock A.L.R., Besozzi D., Mauri G., Cazzaniga P., Lopez C.F.: GPU-powered model analysis with PySB/cupSODA, Bioinformatics, 33(21):3492–3494, 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, 154:307–321, 2017

Tangherloni A., Nobile M.S., Cazzaniga P., Besozzi D., Mauri G.: LASSIE: Simulating large-scale 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, 18(5):870–885, 2017

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 system-level understanding of metabolism, Metabolites, 4(4):1034–1087, 2014

Nobile M.S., Cazzaniga P., Besozzi D., Pescini D., Mauri G.: cuTauLeaping: a GPU-powered tau-leaping 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.: GPU-accelerated simulations of mass-action 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 and analysis of the blood coagulation cascade accelerated on GPU, ECS Journal, 37(7):10–23, 2014



Tangherloni A., Spolaor S., Rundo L., Nobile M.S., Cazzaniga P., Mauri G., Liò P., Besozzi D., Merelli I.: GenHap: evolutionary computation for genotype assembly, 15th International Conference on Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB 2018), Lisbon, Portugal, 2018

Totis N., Tangherloni A., Beccuti M., Cazzaniga P., Nobile M.S., Besozzi D., Pennisi M., Pappalardo F.: GPU powered parameter estimation of a large-scale kinetic metabolic network, 15th International Conference on Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB 2018), Lisbon, Portugal, 2018

Damiani C., Pescini D., Nobile M.S.: Global sensitivity analysis of constraint-based metabolic models, Accepted to the 15th International Conference on Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB 2018), Lisbon, Portugal, 2018

Tangherloni A., Rundo L., Spolaor S., Nobile M.S., Merelli I., Besozzi D., Mauri G., Cazzaniga P., Lio P.: High Performance Computing for Haplotyping: Models and Platforms, 24th International European Conference on Parallel and Distributed Computing (Euro-Par 2018), Lecture Notes on Computer Science vol. 11339, pp. 650–661, 2018

Beccuti M., Cazzaniga P., Pennisi M., Besozzi D., Nobile M.S., Pernice S., Russo G., Tangherloni A., Pappalardo F.: GPU accelerated analysis of Treg-Teff cross regulation in relapsing-remitting multiple sclerosis, 24th International European Conference on Parallel and Distributed Computing (Euro-Par 2018), Lecture Notes on Computer Science vol. 11339, pp. 626–637, 2018

Tangherloni A., Rundo L., Spolaor S., Cazzaniga P., and Nobile M.S.: GPU-powered multi-swarm parameter estimation of biological systems: a master-slave approach, Proceedings of the 26th Euromicro International Conference on Parallel, Distributed and Network-based Processing (PDP2018), Cambridge (United Kingdom), 2018

Rundo L., Han C., Zhang J., Hataya R., Nagano Y., Militello C., Ferretti C., Nobile M.S., Tangherloni A., Gilardi M. C., Vitabile S., Nakayama H., Mauri G.: CNN-based prostate zonal segmentation on T2-weighted MR images: a cross-dataset study, Italian Workshop on Neural Networks (WIRN 2018), Vietri sul Mare (Italy), 2018

Ramazzotti D., Nobile M.S., Antoniotti M., Graudenzi A.: Structural learning of probabilistic graphical models of cumulative phenomena, Proceedings of the 18th International Conference, Wuxi (China), 2018

Nobile M.S., Tangherloni A., Rundo L., Spolaor S., Besozzi D., Mauri G., Cazzaniga P.: Computational Intelligence for Parameter Estimation of Biochemical Systems, Proceedings of IEEE World Congress on Computational Intelligence (WCCI 2018), Rio de Janeiro (Brasil), 2018

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, Proceedings of the IEEE International Conference on Computational Intelligence and Bioinformatics (CIBCB 2017), Manchester (United Kingdom), 2017

Nobile M.S., Mauri G.: Accelerated analysis of biological parameters space using GPUs, 14th International Conference on Parallel Computing Technologies (PaCT 2017), Lecture Notes in Computer Science vol. 10421, Nizhni Novgorod (Russia), 2017

Tangherloni A., Rundo L., Nobile M.S.: Proactive Particles in Swarm Optimization: a settings-free algorithm for real-parameter single objective optimization problems, Proceedings of the 2017 IEEE Congress on Evolutionary Computation (CEC 2017), Donostia S. Sebastian (Spain), 2017

Spolaor S., Tangherloni A., Rundo L., Cazzaniga P., Nobile M.S.: Estimation of Kinetic Reaction Constants: Exploiting Reboot Strategies to Improve PSO’s Performance, Proceedings of the 14th International Computational Intelligence methods for Bioinformatics and Biostatistics, Cagliari (Italy), Lecture Notes on Computer Science 10834, 92:102, 2019

Tangherloni A., Nobile M.S., Cazzaniga P.: GPU-powered Bat Algorithm for the parameter estimation of biochemical kinetic values, Proceedings of the IEEE Conference on Computational Intelligence for Bioinformatics and Computational Biology (CIBCB 2016), Chiang Mai (Thailand), 2016

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 the IEEE Conference on Computational Intelligence for Bioinformatics and Computational Biology (CIBCB 2016), Chiang Mai (Thailand), 2016

Cumbo F., Nobile M.S., Damiani C., Colombo R., Mauri G., Cazzaniga P.: COSYS: A Computational Infrastructure for Systems Biology, Proceedings of the 13th International Conference on Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB 2016), Lecture Notes in Computer Science vol. 10477, pp. 82–92, Stirling (United Kingdom), 2017

Nobile M.S., Tangherloni A., Besozzi D., Cazzaniga P.: GPU-powered and settings-free parameter estimation of biochemical systems, Proceedings of the 2016 IEEE Congress on Evolutionary Computation (CEC 2016), Vancouver (Canada), 2016

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 (CEC 2015). 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 self-tuning algorithm based on fuzzy logic, Proceedings of the IEEE International Conference on Fuzzy Systems (FUZZ-IEEE 2015), Istanbul (Turkey), pp. 1–8, 2015

Cazzaniga P., Nobile M.S., Besozzi D.: The impact of particles initialization in PSO: parameter estimation as a case in point, Proceedings of the 2015 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2015), August 12-15, Niagara Falls (Canada), pp. 1–8, 2015

Tangherloni A., Cazzaniga P., Nobile M.S., Besozzi D., Mauri G.: Deterministic simulations of large-scale models of cellular processes accelerated on graphics processing units, Proceedings of the 12th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB 2015), Naples (Italy), 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

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

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 (CEC 2014), Beijing (China), pp. 1014–1021, 2014

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 Conference on Evolutionary Computation (CEC 2013), Cancun (Mexico), Vol. 1, pp. 1594–1601, 2013

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.), Milano (Italy), CEUR Workshop Proceedings, Vol. 988, pp. 60–74, 2013

Besozzi D., Caravagna G., Cazzaniga P., Nobile M. S., Pescini D., Re A.: GPU-powered simulation methodologies for biological systems, Wivace 2013 Italian Workshop on Artificial Life and Evolutionary Computation, A. Graudenzi, G. Caravagna, G. Mauri, M. Antoniotti (Eds.), EPTCS 130, Milano (Italy), 2013, pp. 87–91

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, pp. 1421–1422, 2012

Nobile M.S., Besozzi D., Cazzaniga P., Mauri G., Pescini D.: A GPU-based multi-swarm PSO method for parameter estimation in stochastic biological systems exploiting discrete-time target series, In 10th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Computational Biology, EvoBIO 2012, Malaga (Spain), Proceedings. M. Giacobini, L. Vanneschi, and W. Bush (Ed.). Lecture Notes in Computer Science. Vol. 7264, pp. 74–85, 2012

Spolaor S., Gribaudo M., Iacono M., Kadavy T., Komínková Oplatková Z., Mauri G., Pllana S., Senkerik R., Stojanovic N., Turunen E., Viktorin A., Vitabile S., Zamuda A., Nobile M.S.: Towards Human Cell Simulation. In “cHiPSEt – High Performance Modeling and Simulation for Big Data Applications”. J. Kołodziej and H. González-Vélez (editors). Lecture Notes in Computer Science 11400. Springer. Pages 1–29, 2019 (in press)

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 (editors). The MIT press. Pages 423–440, 2018

Nobile M.S., Cipolla D., Cazzaniga P., Besozzi D.: GPU-powered evolutionary design of mass-action based models of gene regulation. In “Evolutionary Computation in Gene Regulatory Network Research”, 1st edition. Hitoshi Iba, Nasimul Noman (editors). John Wiley & Sons. Pages 118–150, 2016

(Recent) abstracts and posters

Nobile M.S., Vlauchu T., Spolaor S., Bossi D., Cazzaniga P., Lanfrancone L., Besozzi D., Pelicci P.G., Mauri G.: A cell proliferation model of human acute myeloid leukemia xenograft. ISMB 2018, July 2018, Chicago, IL, USA

Besozzi D., Nobile M.S., Cazzaniga P., Spolaor S., Mauri G.: Dealing with cellular heterogeneity and lack of quantitative parameters in dynamical modeling of biological systems: a fuzzy logic based approach. CSHL Meeting “Cellular Dynamics & Models”, April 2017, New York, USA