Publications

Marco Beccuti's publications:

All
Journals
Lecture Notes
Proceedings
Book Chapters

[2021]

E. G. Amparore, M. Beccuti, P. Castagno, G. Franceschinis, M. Pennisi and S. Pernice. Multiformalism modeling and simulation of immune system mechanisms. Proceeding of IEEE Int. Conference on Bioinformatics and Biomedicine (BIMB'21), pages 3259-3266, Houston, United States, 9-12 December 2021.
N. Licheri, E. Amparore, V. Bonnici, R. Giugno, M. Beccuti. An entropy heuristic to optimize decision diagrams for index-driven search in biological graph databases. 30th ACM Int. Conference on Information and Knowledge Management (CIKM2021), Queensland, Australia, 1-5 November 2021. CEUR Workshop Proceedings, 2021, 3052.
L. Alessandri, M. L. Ratto, S.G. Contaldo, M. Beccuti, F. Cordero, M. Arigoni, and R. A. Calogero. Sparsely connected autoencoders: A multi‐purpose tool for single cell omics analysis. Int. Journal of Molecular Sciences, Volume 22, Issue 23, Article number 12755, December 2021.
M. Beccuti, P. Castagno, G. Franceschinis, M. Pennisi, and S. Pernice. A Petri Net Formalism to Study Systems at Different Scales Exploiting Agent-Based and Stochastic Simulations. Proceeding of 17th European Performance Engineering Workshop (EPEW21), Volume 13104 LNCS, pp. 22 - 43, Tsukuba, Japan December 9-14 (2021).
N. Licheri, V. Bonnici, M. Beccuti, R. Giugno. GRAPES-DD: exploiting decision diagrams for index-driven search in biological graph databases. BMC Bioinformatics, Volume 22, Issue 1, Article number 209 (2021).
L. Alessandri, F. Cordero, M. Beccuti, N. Licheri, M. Arigoni, M. Olivero, M.F. Di Renzo, A. Sapino, R.A. Calogero. Sparsely-connected autoencoder (SCA) for single cell RNAseq data mining. Systems Biology and Applications, Volume 7, Issue 1, Article number: 1 (2021).
M. Beccuti, V. Bonnici, R. Giugno, MODIMO: Workshop on Multi-Omics Data Integration for Modelling Biological Systems30th ACM Int. Conference on Information and Knowledge Management (CIKM 2021), Queensland, Australia, 1-5 November 2021.
V. Nosi, L. Alessandri, M. Milan, M. Arigoni, S. Benvenuti, D. Cacchiarelli, M. Cesana, S. Riccardo, L. Di Filippo, F. Cordero, M. Beccuti, P. M. Comoglio, R. Calogero. MET Exon 14 Skipping: A Case Study for the Detection of Genetic Variants in Cancer Driver Genes by Deep Learning. Int. Journal of Molecular Sciences, Volume 22, Issue 8, Article number 4217 (2021).
E. Genuardi, G. Romano, M. Beccuti, B. Alessandria, D. Mannina, C. Califano, D. Rota Scalabrini, S. Cortelazzo, M. Ladetto, S. Ferrero, R.A. Calogero, F. Cordero. Application of the Euro Clonality next-generation sequencing-based marker screening approach to detect immunoglobulin heavy chain rearrangements in mantle cell lymphoma patients: first data from the Fondazione Italiana Linfomi MCL0208 trial. British Journal of Haematology, 18 May 2021.
G. Ferrero, N. Licheri, M. De Bortoli, R.A. Calogero, M. Beccuti, F. Cordero. Computational Analysis of circRNA Expression Data. Chapter in book RNA Bioinformatics in series Methods in Molecular Biology. Editor E. Picardi. Ed. Springer Science. 2021.
L. Alessandrì, F. Cordero, M. Beccuti, M. Arigoni, R .A. Calogero. Computational Analysis of Single-Cell RNA-Seq Data Chapter in book RNA Bioinformatics in series Methods in Molecular Biology. Editor E. Picardi. Ed. Springer Science. 2021.

[2020]
S. Pernice, M. Beccuti, G. Romano, M. Pennisi, A. Maglione, S. Cutrupi, F. Pappalardo, L. Capra, G. Franceschinis, M. De Pierro, G. Balbo, F.Cordero and R. Calogero. Multiple Sclerosis disease: a computational approach for investigating its drug interactions. Proceeding of 16th Int. Conference Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB 2019), volume 12313 LNBI, pp. 299-308, Bergamo, Italy, September 4-6, 2019.

S. Pernice, L. Follia, A. Maglione, M. Pennisi, F. Pappalardo, F. Novelli, M. Clerico, Marco Beccuti, F. Cordero, S. Rolla. Computational modeling of the immune response in multiple sclerosis using epimod framework. BMC Bioinformatics, Volume 21, Article number: 550 (2020).

S. Pernice, P. Castagno, L. Marcotulli, M. M. Maule, L. Richiardi, G. Moirano, M. Sereno, F. Cordero and Marco Beccuti. Impacts of reopening strategies for COVID-19 epidemic: a modeling study in Piedmont region. BMC Infectious Diseases, Volume 20, Article number: 798 (2020).

P. Castagno, S. Pernice, G. Ghetti, M. Povero, L. Pradelli, D. Paolotti, G. Balbo, Matteo Sereno and Marco Beccuti. A computational framework for modeling and studying pertussis epidemiology and vaccination. BMC Bioinformatics, Volume 21, 16 September 2020, Page 344.

N. Totis, A. Tangherloni, M. Beccuti, P. Cazzaniga, M. Nobile, D. Besozzi, M. Pennisi and F. Pappalardo. Efficient and Settings-Free Calibration of Detailed Kinetic Metabolic Models with Enzyme Isoforms Characterization. In 15th Int. Conference Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB 2018), Caparica, Portugal, September 6-8, 2018.

G. Ferrero, N. Licheri, L.C. Tarrero, C. De Intinis, V. Miano, R.A. Calogero, F. Cordero, M. De Bortoli, and M. Beccuti. Docker4circ: A framework for the reproducible characterization of circRNAs from RNA-seq data. International Journal of Molecular Sciences, Volume 21, Issue 1, 1 January 2020, Article number 293.

[2019]

S. Pernice, G. Romano, G. Russo, M. Beccuti, M. Pennisi, and F. Pappalardo. Exploiting Stochastic Petri Net formalism to capture the Relapsing Remitting Multiple Sclerosis variability under Daclizumab administration. In 3rd Int. Workshop on Computational Methods for the Immune System Function (CMISF 2019), San Diego, USA, November 2019.

L. Capra, M. Beccuti, M. De Pierro, L. Follia, G. Franceschinis and S. Pernice. A Tool for the Automatic Derivation of Symbolic ODE from Symmetric Net Models In 27th IEEE Int. Symposium on the Modeling, Analysis, and Simulation of Computer and Telecommunication Systems (MASCOTS19), Rennes, France, October 22-25, 2019, Article number 8843193, Pages 36-48.

S. Pernice, M. Pennisi, G. Romano, A. Maglione, S. Cutrupi, F. Pappalardo, G. Balbo, M. Beccuti, F. Cordero and R.A. Calogero. A computational approach based on the Colored Petri Net formalism for studying Multiple Sclerosis. BMC Bioinformatics, Volume 20, 10 December 2019, Article number 623.

S. Pernice, L. Follia, G. Balbo, L. Milanesi, G. Sartini, N. Totis, P. Lio I. Merelli, F. Cordero and M. Beccuti. Integrating Petri nets and Flux Balance methods in computationalbiology models: a methodological and computational practice. Fundamenta Informaticae, Volume 171, Issue 1-4, 2019, Pages 367-392.

L. Alessandrì, F. Cordero, M. Beccuti, M. Arigoni, M. Olivero, G. Romano, S. Rabellino, N. Licheri, G. De Libero, L. Pace, R.A. Calogero. rCASC: reproducible classification analysis of single-cell sequencing data. Gigascience, Volume 8, Issue 9, September 2019.

S. Pernice, M. Beccuti, P. Do', M. Pennisi, and F. Pappalardo. Estimating Daclizumab effects in Multiple Sclerosis using Stochastic Symmetric Nets. In 2nd Int. Workshop on Computational Methods for the Immune System Function (CMISF 2018), December 3 - 6, 2018, Madrid, Spain, Article number 8621259, Pages 1393-1400.

L. Follia, G. Ferrero, G. Mandili, M. Beccuti, D. Giordano, R. Spadi, M. A. Satolli, A. Evangelista, H. Katayama, W. Hong, A. A. Momin, M. Capello, S. M. Hanash, F. Novelli and F.Cordero. Integrative analysis of novel metabolic subtypes in pancreatic cancer fosters new prognostic biomarkers. Frontiers in Oncology, Volume 9, Issue FEB, 2019, Article number 115.

M. Beccuti, P. Cazzaniga, M. Pennisi, D. Besozzi, M. S. Nobile, S. Pernice, G. Russo, A. Tangherloni and F. Pappalardo. GPU accelerated analysis of Treg-Teff cross regulation in relapsing-remitting multiple sclerosis. In 24th International European Conference on Parallel and Distributed Computing (Euro-Par 2018),vol. 11339 of Spring LNCS, pp. 626-637, August 29-31, 2018, Turin, Italy,

[2018]

F. Kordon, H. Garavel, L.M. Hillah, E. Paviot-Adet, L. Jezequel, F. Hulin-Hubard, E. Amparore, M. Beccuti, B. Berthomieu, H. Evrard, P.G. Jensen, D. Le Botlan, T. Liebke, J. Meijer, J. Srba, Y. Thierry-Mieg, J. van de Pol and K. Wolf. MCC’2017 - The Seventh Model Checking Contest. In LNCS Transactions on Petri Nets and Other Models of Concurrency (ToPNoC), vol. 11090, Pages 181-209, 2018.

M. Beccuti, L. Capra, M. De Pierro, G. Franceschinis and S. Pernice. Deriving Symbolic Ordinary Differential Equations from Stochastic Symmetric Nets without unfolding. In 15th European Performance Engineering Workshop (EPEW 2018), Spring LNCS, pp. 30-45, Octobre 29-30, 2018, Paris, France.

E. G. Amparore, S. Donatelli, M. Beccuti G. Garbi and A. Miner. Decision Diagrams for Petri nets: a comparison of variable ordering algorithms. In LNCS Transactions on Petri Nets and Other Models of Concurrency (ToPNoC), vol. 11090, pp. 73-92, 2018.

N. Kulkarni, L. Alessandrì, R. Panero, M. Arigoni, M. Olivero, F. Cordero, M. Beccuti and R. A. Calogero. Reproducible Bioinformatics Project: A community for reproducible bioinformatics analysis pipelines. BMC Bioinformatics, Volume 19, Issue 10, pages 211-219, October 2018.

E. G. Amparore, M. Beccuti, M. Botta, S. Donatelli, F. Tango. Adaptive Artificial Co-pilot as Enabler for Autonomous Vehicles and Intelligent Transportation Systems. Proceeding of 10th International Workshop on Agents in Traffic and Transportation (ATT 2018), CEUR Workshop Proceedings, Volume 2129, pp. 70-77, Stockholm, Sweden, July 14, 2018.

L. Coscujuela Tarrero, G. Ferrero, V. Miano, C. De Intinis, L. Ricci, M. Arigoni, F. Riccardo, L. Annaratone, I. Castellano, R.A. Calogero, M. Beccuti, F. Cordero and M. De Bortoli. Luminal breast cancer specific circular RNAs uncovered by a novel tool for data analysis. Oncotarget, Volume 9, Issue 18, 2018, Pages 14580-14596, Impact Journals.

P. Mozgunov, M. Beccuti, A. Horvath, T. Jaki, R. Sirovich, E. Bibbona. A review of the deterministic and diffusion approximations for stochastic chemical reaction networks. Reaction Kinetics, Mechanisms and Catalysis, Volume 123, Issue 2, 1 April 2018, Pages 289-312, Springer Press.

M. Beccuti, F. Cordero M. Arigoni, R. Panero, E. G. Amparore, S. Donatelli and R. A. Calogero. SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer. Bioinformatics, Volume 34, Issue 5, 1 March 2018, Pages 871-872. Oxford University Press.

[2017]

G. Chiavassa, C. Fornari, R. Sirovich, M. Pennisi, M. Beccuti and F. Cordero. A mathematical model to study breast cancer growth. In IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2017), pages 1438-1445 Kansas City, MO, USA, November 13 - 16, 2017.

M. Beccuti, E. Genuardi, G. Romano, L. Monitillo, D. Barbero, M. Boccadoro, M. Ladetto, R. A. Calogero, S. Ferrero and F. Cordero. HashClone: a new tool to quantify the minimal residual disease in B-cell lymphoma from deep sequencing data. BMC Bioinformatics Volume 18, Issue 1, 23 November 2017.

E. G. Amparore, M. Beccuti, S. Donatelli. Gradient-based variable ordering of Decision Diagrams for systems with structural units. In 15th International Symposium on Automated Technology for Verification and Analysi (ATVA'17), Spring LNCS, Pages 184-200, October 3-6, 2017, Pune, India.

P. Ballarini, M. Beccuti, E. Bibbona, A. Horváth, R. Sirovich and J. Sproston. Analysis of Timed Properties Using the Jump-Diffusion Approximation. In 14th European Performance Engineering Workshop (EPEW' 17), Spring LNCS, pp. 69-84, September 7-8, 2017, Berlin, Germany.

E. G. Amparore, S. Donatelli, M. Beccuti, G. Garbi and A. Miner M. Decision diagrams for Petri nets: which variable ordering? International Workshop on Petri Nets and Software Engineering (PNSE 2017), CEUR Workshop Proceedings, pp 31-51, Zaragoza, Spain, June 26-27, 2017.

G. Ferrero, V. Miano, M. Beccuti, G. Balbo, M De Bortoli and F. Cordero. Dissecting the genomic activity of a transcriptional regulator by the integrative analysis of omics data. Scientific Reports, Volume 7, Article number: 8564 (2017). doi:10.1038/s41598-017-08754-9.

F. Martina, M. Beccuti, G. Balbo, F. Cordero. A New Features Selection Method to Improve Classification Performances in Imbalanced Data Sets. PLoS ONE 12(8):e0177475. Public Library of Science. 14 Aug. 2017. doi:10.1371/journal.pone.0177475.

N. Totis, L. Follia, F. Cordero, C. Riganti, F. Novelli, G. Balbo and M. Beccuti. Overcoming the lack of kinetic information in biochemical reactions networks. ACM SIGMETRICS Performance Evaluation Review. Volume 44 Issue 4, March 2017, Pages 91-102. ACM New York, NY, USA

[2016]

P. Catarsi , F. Cordero, G. Ferrero, M. Beccuti, V. Poletto, E. Bonetti, L. Villani, M. Massa, G. Fois, R. Campanelli, U. Magrini, V. Rosti, G. Barosi. Deregulated Genes in Hematopoietic Stem Cells Isolated from Spleen of Patients with Myelofibrosis Blood, 128(22), 4279. 2016. (Extended abstract)

N. Totis, M. Beccuti, F. Cordero, L. Follia, C. Riganti, F. Novelli and G. Balbo. Dealing with indetermination in biochemical networks. International Workshop of the Italian group on Quantitative Methods in Informatics (InfQ 2016), ACM digital library, October 24-25, Taormina, Italy.

G. Miglio, A. D. Sabatino, E. Veglia, M. T. Giraudo, M. Beccuti, F. Cordero. A computational analysis of S-(2-succino)cysteine sites in proteins. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Elsevier Press Volume 1864, Issue 2, February 2016, Pages 211-218.

E. G. Amparore, G. Balbo, M. Beccuti, S. Donatelli and G. Franceschinis 30 years of GreatSPN. Principles of Performance and Reliability Modeling and Evaluation. Editors Lance Fiondella and Antonio Puliafito. Ed. Springer Series in Reliability Engineering 2016.

[2015]

M. Munoz-Amatriain, S. Lonardi, M. Luo, ..., M. Beccuti, et al. Sequencing of 15,622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. The Plant Journal, Ed. Wiley-Blackwell, Volume 84(1), 2015, Pages 216-227.

A. Angius, G. Balbo, M. Beccuti, E. Bibbona, A. Horvath, R. Sirovich. Approximate analysis of biological systems by hybrid switching jump diffusion. Theoretical Computer Science, Elsevier Press., Volume 587, July 2015, Pages 49-72.

C. Fornari, G. Balbo, S.M. Halawani, O. Ba-Rukab, A.R. Ahmad, R. A. Calogero, F. Cordero and M. Beccuti. A versatile mathematical work-flow to explore how Cancer Stem Cell fate influences tumor progression. BMC Systems Biology, Volume 9, Issue 3:S1, June 2015.

M. Carrara, J. Lum, F. Cordero, M. Beccuti, S. Donatelli, R.A. Calogero, F. Zolezzi. Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis. BMC Bioinformatics, Volume 16, Issue 9:S2, June 2015.

E. Medico, M. Russo, G. Picco, C. Cancelliere, E. Valtorta, G. Corti, M. Buscarino, C. Isella, S. Lamba, B. Martinoglio, S. Veronese, S. Siena, A. Sarote-Bianchi, M. Beccuti, M. Mottolese, M. Linnebacher, F. Cordero, F. Di Nicolantonio, A. Bardelli. The molecular landscape of colorectal cancer cell lines unveils clinically actionable targets. Nature Communications, Volume 6, Article number 7002, April 2015.

M. Beccuti, C. Fornari, G. Franceschinis, S. M. Halawani, O. Barukab, A. Ahmad, G. Balbo. From Symmetric Nets to Differential Equations exploiting Model Symmetries. Computer Journal, Oxford University Press., Volume 58, Issue 1, Jan.2015, Pages 23-39.

M. Beccuti, E. G. Amparore, S. Donatelli, P. Buchholz, D. Scheftelowitsch and G. Franceschinis. Markov Decision Petri Nets with Uncertainty. Proceedings of 12th European Workshop on Performance Engineering (EPEW'15), Spring LNCS, 31 August and 1 September, 2015, pages 177-192, Madrid, Spain.

D. Duma, F. Cordero,M. Beccuti, G. Ciardo, T. J. Close and S. Lonardi. Scrible: Ultra-Accurate Error-Correction of Pooled Sequenced Reads. Proceedings of 15th Workshop on Algorithms in Bioinformatics (WABI'15), Spring LNCS, September 10-12, 2015, pages 162-174, USA, Atlanta.

M. Beccuti, G. Franceschinis and Jeremy Sproston. Modeling and verification of distributed systems using Markov decision processes. Chapter in book. Quantitative Assessments of Distributed Systems: Methodologies and Techniques. Editors Dario Bruneo e Salvatore Distefano. Ed. Wiley. 2015.

[2014]

M. Beccuti, M. Carrara, F. Cordero, F. Lazzarato, S. Donatelli, F. Nadalin, A. Policriti and R.A. Calogero. Chimera: a Bioconductor package for secondary analysis of fusion products. Bioinformatics, Oxford University Press., Volume 30, Issue 24, Dec.2014, Pages 3556-3557

M. Beccuti, G. Franceschinis, D. Codetta-Raiteri and S. Haddad. Computing Optimal Repair Strategies by means of NdRFT Modelling and Analysis. Computer Journal, Oxford University Press., Volume 57, Issue 12, Dec.2014, Pages 1870-1892.

C. Fornari, M. Beccuti, S. Lanzardo, L. Conti, G. Balbo, F. Cavallo, R.A. Calogero, F. Cordero. A mathematical-biological joint effort to investigate the tumor-initiating ability of cancer stem cells. PLoS ONE 9(9):e106193, Public Library of Science, Sept.2014.

M. Beccuti, E. Bibbona, A. Horvath, R. Sirovich, A. Angius and G. Balbo. Analysis of Petri Net models through Stochastic Differential Equation. Proceedings of International Conference on application and theory of Petri nets and other models of concurrency (ICATPN'14), volume 8489 of Spring LNCS, June 23-27, 2014, pages 273-293, Tunis, Tunisia.

E. G. Amparore, M. Beccuti and S. Donatelli. (Stochastic) model checking in GreatSPN. Proceedings of International Conference on application and theory of Petri nets and other models of concurrency (ICATPN'14), volume 8489 of Spring LNCS, June 23-27, 2014, pages 354-363, Tunis, Tunisia.

E. G. Amparore, M. Beccuti, S. Collina, F. De Simone, S. Donatelli and F. Tango. Cognitive Systems in Intelligent Vehicles. A new Frontier for Autonomous Driving. Proceedings of 11th International Conference on Informatics in Control, Automation and Robotics (ICINCO'14), pages 817-822, Vienna, Austria, 1-3 September, 2014.

M. Beccuti, S. Chiaradonna, F. Di Giandomenico, S. Donatelli, G. Dondossola, G. Franceschinis. Model-based evaluation of the impact of attacks to the telecommunication service of the electrical grid. Chapter 84 in book. Cyber Behavior: Concepts, Methodologies, Tools, and Applications Editors Bologna S. and Theron P., Ed. IGI Global. 2014

[2013]

M. Beccuti, M. Carrara, F. Cordero, S. Donatelli, R.A. Calogero. The structure of state of art gene fusion-finder algorithms. International Journal of of OA Bioinformatics, Volume 1(1), 2013.

S. Lonardi, D Duma, M. Alpert, F. Cordero, M. Beccuti, P. R. Bhat, Y. Wu, G. Ciardo, B. Alsaihati, Y. Ma, S. Wanamaker, J.Resnik, M. Luo, T. J. Close. Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space. PLOS Computational Biology, Volume 9(4), 2013.

M. Carrara, M. Beccuti, F. Lazzarato, F. Cordero, R. A. Calogero, S. Donatelli and F. Cavallo. State of art fusion-finder algorithms sensitivity and specificity. International Journal of Biomedicine and Biotechnology, Volume 2013, Number 16, (2013), Pages 1-6.

M. Carrara, M. Beccuti, F. Cavallo, S. Donatelli, F. Lazzarato, F. Cordero, and R. Calogero. State of art fusion-finder algorithms are suitable to detect Transcription-Induced Chimeras in normal tissues? BMC Bioinformatics, Volume 14, Suppl. 6, 2013.

F. Cordero, M. Beccuti, C. Fornari, S. Lanzardo, L. Conti, F. Cavallo, G. Balbo and R. Calogero. Multi-level model for the investigation of oncoantigen-driven vaccination effect. BMC Bioinformatics, Volume 14, Suppl. 6, 2013.

E. G. Amparore, P. Ballarini, M. Beccuti, S. Donatelli and G. Franceschinis. Expressing and computing passage time measures of GSPN models with HASL. Proceedings of International Conference on application and theory of Petri nets and other models of concurrency (ICATPN'13), volume 7929 of Spring LNCS, pages 110-119, June 24-28, 2013, Milano, Italy.

E. G. Amparore, B. Barbot, M. Beccuti, S. Donatelli and G. Franceschinis. Simulation-based Verification of Hybrid Automata Stochastic Logic Formulas for Stochastic Symmetric Net models. Proceedings of ACM SIGSIM Conference on Principles of Advanced Discrete Simulation (PADS'13), pages 253-264 , Montreal, Canada, 19-22 May, 2013.

M. Beccuti, S. Chiaradonna, F. Di Giandomenico, S. Donatelli, G. Dondossola, G. Franceschinis. A model based approach for the evaluation of cyber attacks to the electrical grid. Chapter 14 in book. Model-Based Evaluation of the Impact of Attacks to the Telecommunication Service of the Electrical Grid. Editors Sandro Bologna and Paul Theron. IGI Global, 2013.

[2012]

K.F. Mayer, R. Waugh, P. Langridge, T.J. Close, ..., M. Beccuti, et al. A physical, genetic and functional sequence assembly of the barley genome. Nature, Volume 491, Page 711-716. November 2012.

F. Cordero, M. Beccuti, S. Donatelli, R.A. Calogero. Disclosing the nature of computational tools for the analysis of Next Generation Sequencing data. International Journal of Current Topics in Medicinal Chemistry, Volume 12, 24 Issues, 2012.

M. Beccuti, S. Chiaradonna, F. Di Giandomenico, S. Donatelli, G. Dondossola, G. Franceschinis. Quantification of Dependencies between Electrical and Information Infrastructures. International Journal of Critical Infrastructure Protection, Volume 5, Issue 1, March 2012, Pages 14-27. Ed. Elsevier.

F. Cordero, M. Beccuti, M. Arigoni, S. Donatelli, R.A. Calogero. Optimizing a Massive Parallel Sequencing Workflow for Quantitative miRNA Expression Analysis. PLoS ONE, Public Library of Science. 20 Feb 2012. doi:10.1371/journal.pone.0031630

M. Beccuti and G. Franceschinis Efficient simulation of Stochastic Well-Formed Nets through symmetry exploitation. Proceedings of Winter Simulation Conference (WSC'12), pages 296-296, Berlin, Germany, 9-12 December, 2012.

M. Beccuti, A. Bobbio, G. Franceschinis and R. Terruggia. A new symbolic approach for network reliability analysis. Proceedings of 42nd Annual IEEE/IFIP International Conference on Dependable Systems and Networks (DSN'12), Boston, Massachusetts, USA, 25-28 June, 2012.

[2011]

M. Beccuti, S. Haddad, G. Franceschinis. MDWNsolver: a framework to design and solve Markov Decision Petri Nets. International Journal of Performability Engineering, Volume 7, Issue 5, September 2011, Pages 417-428. Ed. RAMS Consultants.

S. Baarir, M. Beccuti, C. Dutheillet, G. Franceschinis, S. Haddad. Lumping partially symmetrical stochastic models. Performance Evaluation, Volume 68, Issue 1, January 2011, Pages 21-44.

E. G. Amparore, M. Beccuti, S. Donatelli and G. Franceschinis. Probe Automata for Passage Time Specification. Proceedings of 8th International Conference on Quantitative Evaluation of SysTems (QEST'11), pages 101-110, Aachen, Germany, 5-8 September 2011. IEEE Computer Society Press.

M. Beccuti, A. Horvart, A. Horvath, M. De Pierro and K. Farkas A Mean Field Based Methodology for Modeling Mobility in Ad Hoc Networks. Proceedings of the 73rd International Conference on IEE Vehicular Technology Conference (VTC2011-Spring), Budapest, Hungary, May 2011.

G. Balbo, M. Beccuti, M. De Pierro and G. Franceschinis. Computing First Passage Time Distributions in Stochastic Well-Formed Nets. Proceeding of 2nd International Conference on Performance Engineering (ICPE'11 - WOSP and SIPEW joint), pages 7-18 Karlsruhe, Germany, March 2011.

[2010]

G. Balbo, M. Beccuti, M. De Pierro and G. Franceschinis. First Passage Time Computation in Tagged GSPNs with Queue Places. Computer Journal, Oxford University Press., Volume 54, Issue 5, May 2010, Pages 653-673.

M. Beccuti, V. Fragnelli, G. Franceschinis and S. Villa. Dynamic simulations of kidney exchanges. International Conference on Operations research (OR2010), Springer LNCS, pages 439-445 September 1-3, 2010, Munich, Germany.

G. Balbo, M. Beccuti, M. De Pierro and G. Franceschinis. On the importance of token scheduling policies in Stochastic Petri nets. Proceedings of the International Conference on Operations research (OR2010), Springer LNCS, pages 181-187 September 1-3, 2010, Munich, Germany.

J. Babar, M. Beccuti, S. Donatelli, and A. Miner. GreatSPN Enhanced with Decision Diagram Data Structures. In 31st International Conference on application and theory of Petri nets and other models of concurrency (ICATPN'10), volume 6128 of Springer LNCS, pages 308-317. June 21-25, 2010, Braga, Portugal.

[2009]

S. Baarir, M. Beccuti, D. Cerotti, M. De Pierro, S. Donatelli and G. Franceschinis. The GreatSPN Tool: Recent Enhancements. ACM Performance Evaluation Review, Volume 36, Issue 4, September 2009, Pages 4-9.

M. Beccuti, A. Bottrighi, G. Franceschinis, S. Montani and P. Terenziani. Modeling clinical guidelines through Petri Nets. In 12th International Conference on Artificial Intelligence in Medicine (AIME'09), volume 5651 of Springer LNCS, pages 61-70. July 18-22, 2009, Verona, Italy.

S. Baarir, M. Beccuti, C. Dutheillet and G. Franceschinis. From partially to fully lumped Markov chains in Stochastic Well Formed Petri Nets. Proceeding of the 4th International Conference on Performance Evaluation, Methodologies and Tools (VALUETOOLS'09), Pisa, Italy, ACM Digital Library, October 2009.

M. Beccuti, D. Codetta-Raiteri and G. Franceschinis. Multiple abstraction levels in performance analysis of WSN monitoring systems. Proceeding of the 1st International Workshop on Performance Methodologies and Tools for Wireless Sensor Networks (WSNPerf-VALUETOOLS'09), Pisa, Italy, ACM Digital Library, October 2009.

M. Beccuti, D. Codetta-Raiteri, G. Franceschinis and S. Haddad. Parametric NdRFT for the derivation of optimal repair strategies. Proceeding of the 39th International Conference on Dependable Systems and Networks (DSN'09), pages 399-408, Estoril, Lisbon, Portugal, 29 June-2 July 2009. IEEE Computer Society Press.

M. Beccuti, G. Franceschinis, S. Donatelli, S. Chiaradonna, F. Di Giandomenico, P. Lollini, G. Dondossola and F. Garrone. Quantification of Dependencies in Electrical and Information Infrastructures: the CRUTIAL approach. Proceedings of the 4th International Conference on Critical Infrastructures (CRIS'09), pages 1-8, Linkoping, Sweden, 28-30 April 2009. IEEE Computer Society Press.

[2008]

M. Beccuti, G. Franceschinis, M. Kaaniche and K. Kanoun. Multi-level dependability modeling of interdependencies between the Electricity and Information Infrastructures. In 3rd International Workshop on Critical Information Infrastructures Security (CRITIS'08), volume 5508 of Springer LNCS, pages 48-59. October 13-15, 2008, Rome, Italy.

M. Beccuti, G. Franceschinis, M. Kaaniche and K. Kanoun. Multi-level dependability modeling of interdependencies between the Electricity and Information Infrastructures. Proceedings of 3rd International Workshop on Critical Information Inftrastructures Security (CRITIS'08), pages 109-124, Roma, Italy, October 2008.

M. Beccuti, D. Codetta-Raiteri, G. Franceschinis and S. Haddad. Non deterministic Repairable Fault Trees for computing optimal repair strategy. Proceeding of 3rd International Conference on Performance Evaluation, Methodologies and Tools (VALUETOOLS'08), Athens, Greece, ACM Digital Library, October 2008.

S. Baarir, M. Beccuti, G. Franceschinis. New solvers for asymmetric systems in GreatSPN. Proceeding of 5th International Conference on the Quantitative Evaluation of SysTems (QEST'08), pages 235-236, St.Malo, France, 14-17 September 2008. IEEE Computer Society Press.

M. Beccuti, D. Codetta-Raiter, G. Franceschinis, and S. Haddad. A framework to design and solve Markov Decision Well-formed Net models. Proceeding of 4th International Conference on Quantitative Evaluation of SysTems (QEST'07), Edinburgh, Scotland, 16-19 September 2007. IEEE Computer Society Press.

[2007]

M. Beccuti, G. Franceschinis, and S. Haddad. Markov Decision Petri Net and Markov Decision Well-Formed Net Formalisms. In 28th International Conference on application and theory of Petri nets and other models of concurrency (ICATPN'07), volume 4546 of Springer LNCS, pages 43-62. June 25-29, 2007, Siedlce, Poland.

[2006]

M. Beccuti, S. Baarir, G. Franceschinis, J-M. Ilie. Efficient lumpability check in partially symmetric systems. Proceeding of 3rd International Conference on Quantitative Evaluation of Systems (QEST'06), Riverside, CA, USA, September 2006. IEEE Soc. Press.

[2004]

J.-M. Ilie, S. Baarir, M. Beccuti, C. Delamare, S. Donatelli, C. Dutheillet, G. Franceschinis, R. Gaeta, P. Moreaux. Extended SWN Solvers in GreatSPN. Proceeding of 1st International Conference on Quantitative Evaluation of Systems (QEST04), Enschede, Netherlands. September 2004. IEEE Soc. Press: 324-325.

Publications in refereed international journals

L. Alessandri, M. L. Ratto, S.G. Contaldo, M. Beccuti, F. Cordero, M. Arigoni, and R. A. Calogero. Sparsely connected autoencoders: A multi‐purpose tool for single cell omics analysis. Int. Journal of Molecular Sciences, Volume 22, Issue 23, Article number 12755, December 2021..

N. Licheri, V. Bonnici, M. Beccuti, R. Giugno. GRAPES-DD: exploiting decision diagrams for index-driven search in biological graph databases. BMC Bioinformatics, Volume 22, Issue 1, Article number 209 (2021).

V. Nosi, L. Alessandri, M. Milan, M. Arigoni, S. Benvenuti, D. Cacchiarelli, M. Cesana, S. Riccardo, L. Di Filippo, F. Cordero, M. Beccuti P. M. Comoglio, R. Calogero.MET Exon 14 Skipping: A Case Study for the Detection of Genetic Variants in Cancer Driver Genes by Deep Learning. Int. Journal of Molecular Sciences, Volume 22, Issue 8, Article number 4217 (2021).

L. Alessandri, F. Cordero, M. Beccuti, N. Licheri, M. Arigoni, M. Olivero, M.F. Di Renzo, A. Sapino, R.A. Calogero. Sparsely-connected autoencoder (SCA) for single cell RNAseq data mining. Systems Biology and Applications, Volume 7, Issue 1, Article number: 1 (2021). 2019.

E. Genuardi, G. Romano, M. Beccuti, B. Alessandria, D. Mannina, C. Califano, D. Rota Scalabrini, S. Cortelazzo, M. Ladetto, S. Ferrero, R.A. Calogero, F. Cordero. Application of the Euro Clonality next-generation sequencing-based marker screening approach to detect immunoglobulin heavy chain rearrangements in mantle cell lymphoma patients: first data from the Fondazione Italiana Linfomi MCL0208 trial. British Journal of Haematology, 18 May 2021.

S. Pernice, L. Follia, A. Maglione, M. Pennisi, F. Pappalardo, F. Novelli, M. Clerico, Marco Beccuti, F. Cordero, S. Rolla. Computational modeling of the immune response in multiple sclerosis using epimod framework. BMC Bioinformatics, Volume 21, Article number: 550 (2020).

S. Pernice, P. Castagno, L. Marcotulli, M. M. Maule, L. Richiardi, G. Moirano, M. Sereno, F. Cordero and Marco Beccuti. Impacts of reopening strategies for COVID-19 epidemic: a modeling study in Piedmont region. BMC Infectious Diseases, Volume 20, Article number: 798 (2020).

P. Castagno, S. Pernice, G. Ghetti, M. Povero, L. Pradelli, D. Paolotti, G. Balbo, Matteo Sereno, Marco Beccuti. A computational framework for modeling and studying pertussis epidemiology and vaccination. BMC Bioinformatics, Volume 21, 16 September 2020, Page 344.

G. Ferrero, N. Licheri, L.C. Tarrero, C. De Intinis, V. Miano, R.A. Calogero, F. Cordero, M. De Bortoli, and M. Beccuti. Docker4circ: A framework for the reproducible characterization of circRNAs from RNA-seq data. International Journal of Molecular Sciences, Volume 21, Issue 1, 1 January 2020, Article number 293.

S. Pernice, M. Pennisi, G. Romano, A. Maglione, S. Cutrupi, F. Pappalardo; G. Balbo; M. Beccuti, F. Cordero and R.A. Calogero. A computational approach based on the Colored Petri Net formalism for studying Multiple Sclerosis. BMC Bioinformatics, Volume 20, 10 December 2019, Article number 623.

S. Pernice, L. Follia, G. Balbo, L. Milanesi, G. Sartini, N. Totis, P. Lio I. Merelli, F. Cordero and M. Beccuti. Integrating Petri nets and Flux Balance methods in computationalbiology models: a methodological and computational practice. Fundamenta Informaticae, Volume 171, Issue 1-4, 2019, Pages 367-392.

L. Alessandrì, F. Cordero, M. Beccuti, M. Arigoni, M. Olivero, G. Romano, S. Rabellino, N. Licheri, G. De Libero, L. Pace, R.A. Calogero. rCASC: reproducible classification analysis of single-cell sequencing data. Gigascience, Volume 8, Issue 9, September 2019.

L. Follia, G. Ferrero, G. Mandili, M. Beccuti, D. Giordano, R. Spadi, M. A. Satolli, A. Evangelista, H. Katayama, W. Hong, A. A. Momin, M. Capello, S. M. Hanash, F. Novelli and F.Cordero. Integrative analysis of novel metabolic subtypes in pancreatic cancer fosters new prognostic biomarkers. Frontiers in Oncology Volume 9, Issue FEB, 2019, Article number 115.

N. Kulkarni, L. Alessandrì, R. Panero, M. Arigoni, M. Olivero, F. Cordero, M. Beccuti and R. A. Calogero. Reproducible Bioinformatics Project: A community for reproducible bioinformatics analysis pipelines. BMC Bioinformatics, Volume 19, Issue 10, pages 211-219, October 2018.

L. Coscujuela Tarrero, G. Ferrero, V. Miano, C. De Intinis, L. Ricci, M. Arigoni, F. Riccardo, L. Annaratone, I. Castellano, R.A. Calogero, M. Beccuti, F. Cordero and M. De Bortoli. Luminal breast cancer specific circular RNAs uncovered by a novel tool for data analysis. Oncotarget, Volume 9, Issue 18, 2018, Pages 14580-14596, Impact Journals.

Pavel Mozgunov, M. Beccuti, Andras Horvath, Thomas Jaki, Roberta Sirovich, Enrico Bibbona. A review of the deterministic and diffusion approximations for stochastic chemical reaction networks. Reaction Kinetics, Mechanisms and Catalysis, Volume 123, Issue 2, 1 April 2018, Pages 289-312, Springer Press.

M. Beccuti, F. Cordero M. Arigoni, R. Panero, E. G. Amparore, S. Donatelli and R. A. Calogero. SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer. Bioinformatics, Volume 34, Issue 5, 1 March 2018, Pages 871-872. Oxford University Press.

M. Beccuti, E. Genuardi, G. Romano, L. Monitillo, D. Barbero, M. Boccadoro, M. Ladetto, R. A. Calogero, S. Ferrero and F. Cordero. HashClone: a new tool to quantify the minimal residual disease in B-cell lymphoma from deep sequencing data. BMC Bioinformatics Volume 18, Issue 1, 23 November 2017..

G. Ferrero, V. Miano, M. Beccuti, G. Balbo, M De Bortoli and F. Cordero. Dissecting the genomic activity of a transcriptional regulator by the integrative analysis of omics data. Scientific Reports, Volume 7, Article number: 8564 (2017). doi:10.1038/s41598-017-08754-9.

F. Martina, M. Beccuti, G. Balbo, F. Cordero. A New Features Selection Method to Improve Classification Performances in Imbalanced Data Sets. PLoS ONE 12(8):e0177475. Public Library of Science. 14 Aug. 2017. doi:10.1371/journal.pone.0177475.

N. Totis, L. Follia, F. Cordero, C. Riganti, F. Novelli, G. Balbo and M. Beccuti. Overcoming the lack of kinetic information in biochemical reactions networks. ACM SIGMETRICS Performance Evaluation Review. Volume 44 Issue 4, March 2017, Pages 91-102. ACM New York, NY, USA

E. G. Amparore, G. Balbo, M. Beccuti, S. Donatelli and G. Franceschinis 30 years of GreatSPN. Principles of Performance and Reliability Modeling and Evaluation. Editors Lance Fiondella and Antonio Puliafito. Ed. Springer Series in Reliability Engineering 2016.

P. Catarsi , F. Cordero, G. Ferrero, M. Beccuti, V. Poletto, E. Bonetti, L. Villani, M. Massa, G. Fois, R. Campanelli, U. Magrini, V. Rosti, G. Barosi. Deregulated Genes in Hematopoietic Stem Cells Isolated from Spleen of Patients with Myelofibrosis Blood, 128(22), 4279. 2016. (Extended abstract)

G. Miglio, A. D. Sabatino, E. Veglia, M. T. Giraudo, M. Beccuti, F. Cordero. A computational analysis of S-(2-succino)cysteine sites in proteins. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Elsevier Press Volume 1864, Issue 2, February 2016, Pages 211-218.

M. Munoz-Amatriain, S. Lonardi, M. Luo, ..., M. Beccuti, et al. Sequencing of 15,622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. The Plant Journal, Ed. Wiley-Blackwell, Volume 84(1), 2015, Pages 216-227.

A. Angius, G. Balbo, M. Beccuti, E. Bibbona, A. Horvath, R. Sirovich. Approximate analysis of biological systems by hybrid switching jump diffusion. Theoretical Computer Science, Elsevier Press., Volume 587, July 2015, Pages 49-72.

C. Fornari, G. Balbo, S.M. Halawani, O. Ba-Rukab, A.R. Ahmad, R. A. Calogero, F. Cordero and M. Beccuti. A versatile mathematical work-flow to explore how Cancer Stem Cell fate influences tumor progression. BMC Systems Biology, Volume 9, Issue 3:S1, June 2015.

M. Carrara, J. Lum, F. Cordero, M. Beccuti, S. Donatelli, R.A. Calogero, F. Zolezzi. Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis. BMC Bioinformatics, Volume 16, Issue 9:S2, June 2015.

E. Medico, M. Russo, G. Picco, C. Cancelliere, E. Valtorta, G. Corti, M. Buscarino, C. Isella, S. Lamba, B. Martinoglio, S. Veronese, S. Siena, A. Sarote-Bianchi, M. Beccuti, M. Mottolese, M. Linnebacher, F. Cordero, F. Di Nicolantonio, A. Bardelli. The molecular landscape of colorectal cancer cell lines unveils clinically actionable targets. Nature Communications, Volume 6, Article number 7002, April 2015.

M. Beccuti, C. Fornari, G. Franceschinis, S. M. Halawani, O. Barukab, A. Ahmad, G. Balbo. From Symmetric Nets to Differential Equations exploiting Model Symmetries. Computer Journal, Oxford University Press., Volume 58, Issue 1, Jan.2015, Pages 23-39.

M. Beccuti, M. Carrara, F. Cordero, F. Lazzarato, S. Donatelli, F. Nadalin, A. Policriti and R.A. Calogero. Chimera: a Bioconductor package for secondary analysis of fusion products. Bioinformatics, Oxford University Press., Volume 30, Issue 24, Dec.2014, Pages 3556-3557

M. Beccuti, G. Franceschinis, D. Codetta-Raiteri and S. Haddad. Computing Optimal Repair Strategies by means of NdRFT Modelling and Analysis. Computer Journal, Oxford University Press., Volume 57, Issue 12, Dec.2014, Pages 1870-1892.

C. Fornari, M. Beccuti, S. Lanzardo, L. Conti, G. Balbo, F. Cavallo, R.A. Calogero, F. Cordero. A mathematical-biological joint effort to investigate the tumor-initiating ability of cancer stem cells. PLoS ONE 9(9):e106193, Public Library of Science, Sept.2014.

M. Beccuti, M. Carrara, F. Cordero, S. Donatelli, R.A. Calogero. The structure of state of art gene fusion-finder algorithms. International Journal of of OA Bioinformatics, Volume 1(1), 2013.

S. Lonardi, D Duma, M. Alpert, F. Cordero, M. Beccuti, P. R. Bhat, Y. Wu, G. Ciardo, B. Alsaihati, Y. Ma, S. Wanamaker, J.Resnik, M. Luo, T. J. Close. Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space. PLOS Computational Biology, Volume 9(4), 2013.

M. Carrara, M. Beccuti, F. Lazzarato, F. Cordero, R. A. Calogero, S. Donatelli and F. Cavallo. State of art fusion-finder algorithms sensitivity and specificity. International Journal of Biomedicine and Biotechnology, Volume 2013, Number 16, (2013), Pages 1-6.

M. Carrara, M. Beccuti, F. Cavallo, S. Donatelli, F. Lazzarato, F. Cordero, and R. Calogero. State of art fusion-finder algorithms are suitable to detect Transcription-Induced Chimeras in normal tissues? BMC Bioinformatics, Volume 14, Suppl. 6, 2013.

F. Cordero, M. Beccuti, C. Fornari, S. Lanzardo, L. Conti, F. Cavallo, G. Balbo and R. Calogero. Multi-level model for the investigation of oncoantigen-driven vaccination effect. BMC Bioinformatics, Volume 14, Suppl. 6, 2013.

K.F. Mayer, R. Waugh, P. Langridge, T.J. Close, ..., M. Beccuti, et al. A physical, genetic and functional sequence assembly of the barley genome. Nature, Volume 491, Page 711-716. November 2012.

F. Cordero, M. Beccuti, S. Donatelli, R.A. Calogero. Disclosing the nature of computational tools for the analysis of Next Generation Sequencing data. International Journal of Current Topics in Medicinal Chemistry, Volume 12, 24 Issues, 2012.

M. Beccuti, S. Chiaradonna, F. Di Giandomenico, S. Donatelli, G. Dondossola, G. Franceschinis. Quantification of Dependencies between Electrical and Information Infrastructures. International Journal of Critical Infrastructure Protection, Volume 5, Issue 1, March 2012, Pages 14-27. Ed. Elsevier.

F. Cordero, M. Beccuti, M. Arigoni, S. Donatelli, R.A. Calogero. Optimizing a Massive Parallel Sequencing Workflow for Quantitative miRNA Expression Analysis. PLoS ONE, Public Library of Science. 20 Feb 2012. doi:10.1371/journal.pone.0031630

M. Beccuti, S. Haddad, G. Franceschinis. MDWNsolver: a framework to design and solve Markov Decision Petri Nets. International Journal of Performability Engineering, Volume 7, Issue 5, September 2011, Pages 417-428. Ed. RAMS Consultants.

S. Baarir, M. Beccuti, C. Dutheillet, G. Franceschinis, S. Haddad. Lumping partially symmetrical stochastic models. Performance Evaluation, Volume 68, Issue 1, January 2011, Pages 21-44.

G. Balbo, M. Beccuti, M. De Pierro and G. Franceschinis. First Passage Time Computation in Tagged GSPNs with Queue Places. Computer Journal, Oxford University Press., Volume 54, Issue 5, May 2010, Pages 653-673.

S. Baarir, M. Beccuti, D. Cerotti, M. De Pierro, S. Donatelli and G. Franceschinis. The GreatSPN Tool: Recent Enhancements. ACM Performance Evaluation Review, Volume 36, Issue 4, September 2009, Pages 4-9.

Publications in lecture notes

M. Beccuti, P. Castagno, G. Franceschinis, M. Pennisi, and S. Pernice. A Petri Net Formalism to Study Systems at Different Scales Exploiting Agent-Based and Stochastic Simulations. Proceeding of 17th European Performance Engineering Workshop (EPEW21), Volume 13104 LNCS, pp. 22 - 43, Tsukuba, Japan December 9-14 (2021).

S. Pernice, M. Beccuti, G. Romano, M. Pennisi, A. Maglione, S. Cutrupi, F. Pappalardo, L. Capra, G. Franceschinis, M. De Pierro, G. Balbo, F.Cordero and R. Calogero. Multiple Sclerosis disease: a computational approach for investigating its drug interactions. Proceeding of 16th Int. Conference Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB 2019), volume 12313 LNBI, pp. 299-308, Bergamo, Italy, September 4-6, 2019.

N. Totis, A. Tangherloni, M. Beccuti, P. Cazzaniga, M. Nobile, D. Besozzi, M. Pennisi and F. Pappalardo. Efficient and Settings-Free Calibration of Detailed Kinetic Metabolic Models with Enzyme Isoforms Characterization. In 15th Int. Conference Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB 2018), Caparica, Portugal, September 6-8, 2018.

M. Beccuti, P. Cazzaniga, M. Pennisi, D. Besozzi, M. S. Nobile, S. Pernice, G. Russo, A. Tangherloni and F. Pappalardo. GPU accelerated analysis of Treg-Teff cross regulation in relapsing-remitting multiple sclerosis. In 24th International European Conference on Parallel and Distributed Computing (Euro-Par 2018),vol. 11339 of Spring LNCS, pp. 626-637, August 29-31, 2018, Turin, Italy,

F. Kordon, H. Garavel, L.M. Hillah, E. Paviot-Adet, L. Jezequel, F. Hulin-Hubard, E. Amparore, M. Beccuti, B. Berthomieu, H. Evrard, P.G. Jensen, D. Le Botlan, T. Liebke, J. Meijer, J. Srba, Y. Thierry-Mieg, J. van de Pol and K. Wolf. MCC’2017 - The Seventh Model Checking Contest. In LNCS Transactions on Petri Nets and Other Models of Concurrency (ToPNoC), vol. 11090, Pages 181-209, 2018.

M. Beccuti, L. Capra, M. De Pierro, G. Franceschinis and S. Pernice. Deriving Symbolic Ordinary Differential Equations from Stochastic Symmetric Nets without unfolding. In 15th European Performance Engineering Workshop (EPEW 2018), Spring LNCS, pp. 30-45, Octobre 29-30, 2018, Paris, France.

E. G. Amparore, S. Donatelli, M. Beccuti G. Garbi and A. Miner. Decision Diagrams for Petri nets: a comparison of variable ordering algorithms. In LNCS Transactions on Petri Nets and Other Models of Concurrency (ToPNoC), vol. 11090, pp. 73-92, 2018.

E. G. Amparore, M. Beccuti, S. Donatelli. Gradient-based variable ordering of Decision Diagrams for systems with structural units. In 15th International Symposium on Automated Technology for Verification and Analysi (ATVA'17), Spring LNCS, Pages 184-200, October 3-6, 2017, Pune, India.

P. Ballarini, M. Beccuti, E. Bibbona, A. Horváth, R. Sirovich and J. Sproston. Analysis of Timed Properties Using the Jump-Diffusion Approximation. In 14th European Performance Engineering Workshop (EPEW'17), Spring LNCS, pp. 69-84, September 7-8, 2017, Berlin, Germany.

M. Beccuti, E. G. Amparore, S. Donatelli, P. Buchholz, D. Scheftelowitsch and G. Franceschinis. Markov Decision Petri Nets with Uncertainty. Proceedings of 12th European Workshop on Performance Engineering (EPEW'15), Spring LNCS, 31 August and 1 September, 2015, pages 177-192, Madrid, Spain.

D. Duma, F. Cordero,M. Beccuti, G. Ciardo, T. J. Close and S. Lonardi. Scrible: Ultra-Accurate Error-Correction of Pooled Sequenced Reads. Proceedings of 15th Workshop on Algorithms in Bioinformatics (WABI'15), Spring LNCS, September 10-12, 2015, pages 162-174, USA, Atlanta.

M. Beccuti, E. Bibbona, A. Horvath, R. Sirovich, A. Angius and G. Balbo. Analysis of Petri Net models through Stochastic Differential Equation. Proceedings of International Conference on application and theory of Petri nets and other models of concurrency (ICATPN'14), volume 8489 of Spring LNCS, June 23-27, 2014, pages 273-293, Tunis, Tunisia.

E. G. Amparore, M. Beccuti and S. Donatelli. (Stochastic) model checking in GreatSPN. Proceedings of International Conference on application and theory of Petri nets and other models of concurrency (ICATPN'14), volume 8489 of Spring LNCS, June 23-27, 2014, pages 354-363, Tunis, Tunisia.

E. G. Amparore, P. Ballarini, M. Beccuti, S. Donatelli and G. Franceschinis. Expressing and computing passage time measures of GSPN models with HASL. Proceedings of International Conference on application and theory of Petri nets and other models of concurrency (ICATPN'13), volume 7929 of Spring LNCS, pages 110-119, June 24-28, 2013, Milano, Italy.

G. Balbo, M. Beccuti, M. De Pierro and G. Franceschinis. On the importance of token scheduling policies in Stochastic Petri nets. Proceedings of the International Conference on Operations research (OR2010), Springer LNCS, pages 181-187 September 1-3, 2010, Munich, Germany.

M. Beccuti, V. Fragnelli, G. Franceschinis and S. Villa. Dynamic simulations of kidney exchanges. International Conference on Operations research (OR2010), Springer LNCS, pages 439-445 September 1-3, 2010, Munich, Germany.

J. Babar, M. Beccuti, S. Donatelli, and A. Miner. GreatSPN Enhanced with Decision Diagram Data Structures. In 31st International Conference on application and theory of Petri nets and other models of concurrency (ICATPN'10), volume 6128 of Springer LNCS, pages 308-317. June 21-25, 2010, Braga, Portugal.

M. Beccuti, A. Bottrighi, G. Franceschinis, S. Montani and P. Terenziani. Modeling clinical guidelines through Petri Nets. In 12th International Conference on Artificial Intelligence in Medicine (AIME'09), volume 5651 of Springer LNCS, pages 61-70. July 18-22, 2009, Verona, Italy.

M. Beccuti, G. Franceschinis, M. Kaaniche and K. Kanoun. Multi-level dependability modeling of interdependencies between the Electricity and Information Infrastructures. In 3rd International Workshop on Critical Information Infrastructures Security (CRITIS'08), volume 5508 of Springer LNCS, pages 48-59. October 13-15, 2008, Rome, Italy.

M. Beccuti, G. Franceschinis, and S. Haddad. Markov Decision Petri Net and Markov Decision Well-Formed Net Formalisms. In 28th International Conference on application and theory of Petri nets and other models of concurrency (ICATPN'07), volume 4546 of Springer LNCS, pages 43-62. June 25-29, 2007, Siedlce, Poland.

Publications in refereed conferences

E. G. Amparore, M. Beccuti, P. Castagno, G. Franceschinis, M. Pennisi and S. Pernice. Multiformalism modeling and simulation of immune system mechanisms. Proceeding of IEEE Int. Conference on Bioinformatics and Biomedicine (BIMB'21), pages 3259-3266, Houston, United States, 9-12 December 2021.

N. Licheri, E. Amparore, V. Bonnici, R. Giugno, M. Beccuti. An entropy heuristic to optimize decision diagrams for index-driven search in biological graph databases. 30th ACM Int. Conference on Information and Knowledge Management (CIKM2021), Queensland, Australia, 1-5 November 2021. CEUR Workshop Proceedings, 2021, 3052.

M. Beccuti, V. Bonnici, R. Giugno, MODIMO: Workshop on Multi-Omics Data Integration for Modelling Biological Systems30th ACM Int. Conference on Information and Knowledge Management (CIKM 2021), Queensland, Australia, 1-5 November 2021,

S. Pernice, G. Romano, G. Russo, M. Beccuti, M. Pennisi, and F. Pappalardo. Exploiting Stochastic Petri Net formalism to capture the Relapsing Remitting Multiple Sclerosis variability under Daclizumab administration. In 3rd Int. Workshop on Computational Methods for the Immune System Function (CMISF 2019), San Diego, USA, November 2019.

L. Capra, M. Beccuti, M. De Pierro, L. Follia, G. Franceschinis and S. Pernice A Tool for the Automatic Derivation of Symbolic ODE from Symmetric Net Models In 27th IEEE Int. Symposium on the Modeling, Analysis, and Simulation of Computer and Telecommunication Systems (MASCOTS19), Rennes, France, October 22-25, 2019, Article number 8843193, Pages 36-48.

S. Pernice, M. Beccuti, P. Do', M. Pennisi, and F. Pappalardo. Estimating Daclizumab effects in Multiple Sclerosis using Stochastic Symmetric Nets. In 2nd Int. Workshop on Computational Methods for the Immune System Function (CMISF 2018), December 3 - 6, 2018, Madrid, Spain, Article number 8621259, Pages 1393-1400.

E. G. Amparore, M. Beccuti, M. Botta, S. Donatelli, F. Tango. Adaptive Artificial Co-pilot as Enabler for Autonomous Vehicles and Intelligent Transportation Systems. Proceeding of 10th International Workshop on Agents in Traffic and Transportation (ATT 2018), CEUR Workshop Proceedings, Volume 2129, pp. 70-77, Stockholm, Sweden, July 14, 2018.

G. Chiavassa, C. Fornari, R. Sirovich, M. Pennisi, M. Beccuti and F. Cordero. A mathematical model to study breast cancer growth. In IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2017), pages 1438-1445 Kansas City, MO, USA, November 13 - 16, 2017.

E. G. Amparore, S. Donatelli, M. Beccuti, G. Garbi and A. Miner M. Decision diagrams for Petri nets: which variable ordering? International Workshop on Petri Nets and Software Engineering (PNSE 2017), ,CEUR Workshop Proceedings, pp 31-51, Zaragoza, Spain, June 26-27, 2017.

N. Totis, M. Beccuti, F. Cordero, L. Follia, C. Riganti, F. Novelli and G. Balbo. Dealing with indetermination in biochemical networks. International Workshop of the Italian group on Quantitative Methods in Informatics (InfQ 2016), ACM digital library, October 24-25, Taormina, Italy.

E. G. Amparore, M. Beccuti, S. Collina, F. De Simone, S. Donatelli and F. Tango. Cognitive Systems in Intelligent Vehicles. A new Frontier for Autonomous Driving. Proceedings of 11th International Conference on Informatics in Control, Automation and Robotics (ICINCO'14), pages 817-822, Vienna, Austria, 1-3 September, 2014.

E. G. Amparore, B. Barbot, M. Beccuti, S. Donatelli and G. Franceschinis. Simulation-based Verification of Hybrid Automata Stochastic Logic Formulas for Stochastic Symmetric Net models. Proceedings of ACM SIGSIM Conference on Principles of Advanced Discrete Simulation (PADS'13), pages 253-264 , Montreal, Canada, 19-22 May, 2013.

M. Beccuti and G. Franceschinis Efficient simulation of Stochastic Well-Formed Nets through symmetry exploitation. Proceedings of Winter Simulation Conference (WSC'12), pages 296-296, Berlin, Germany, 9-12 December, 2012.

M. Beccuti, A. Bobbio, G. Franceschinis and R. Terruggia. A new symbolic approach for network reliability analysis. Proceedings of 42nd Annual IEEE/IFIP International Conference on Dependable Systems and Networks (DSN'12), Boston, Massachusetts, USA, 25-28 June, 2012.

E. G. Amparore, M. Beccuti, S. Donatelli and G. Franceschinis. Probe Automata for Passage Time Specification. Proceedings of 8th International Conference on Quantitative Evaluation of SysTems (QEST'11), pages 101-110, Aachen, Germany, 5-8 September 2011. IEEE Computer Society Press.

M. Beccuti, A. Horvart, A. Horvath, M. De Pierro and K. Farkas A Mean Field Based Methodology for Modeling Mobility in Ad Hoc Networks. Proceedings of the 73rd International Conference on IEE Vehicular Technology Conference (VTC2011-Spring), Budapest, Hungary, May 2011.

G. Balbo, M. Beccuti, M. De Pierro and G. Franceschinis. Computing First Passage Time Distributions in Stochastic Well-Formed Nets. Proceeding of 2nd International Conference on Performance Engineering (ICPE'11 - WOSP and SIPEW joint), pages 7-18 Karlsruhe, Germany, March 2011.

S. Baarir, M. Beccuti, C. Dutheillet and G. Franceschinis. From partially to fully lumped Markov chains in Stochastic Well Formed Petri Nets. Proceeding of the 4th International Conference on Performance Evaluation, Methodologies and Tools (VALUETOOLS'09), Pisa, Italy, ACM Digital Library, October 2009.

M. Beccuti, D. Codetta-Raiteri and G. Franceschinis. Multiple abstraction levels in performance analysis of WSN monitoring systems. Proceeding of the 1st International Workshop on Performance Methodologies and Tools for Wireless Sensor Networks (WSNPerf-VALUETOOLS'09), Pisa, Italy, ACM Digital Library, October 2009.

M. Beccuti, D. Codetta-Raiteri, G. Franceschinis and S. Haddad. Parametric NdRFT for the derivation of optimal repair strategies. Proceeding of the 39th International Conference on Dependable Systems and Networks (DSN'09), pages 399-408, Estoril, Lisbon, Portugal, 29 June-2 July 2009. IEEE Computer Society Press.

M. Beccuti, G. Franceschinis, S. Donatelli, S. Chiaradonna, F. Di Giandomenico, P. Lollini, G. Dondossola and F. Garrone. Quantification of Dependencies in Electrical and Information Infrastructures: the CRUTIAL approach. Proceedings of the 4th International Conference on Critical Infrastructures (CRIS'09), pages 1-8, Linkoping, Sweden, 28-30 April 2009. IEEE Computer Society Press.

M. Beccuti, G. Franceschinis, M. Kaaniche and K. Kanoun. Multi-level dependability modeling of interdependencies between the Electricity and Information Infrastructures. Proceedings of 3rd International Workshop on Critical Information Inftrastructures Security (CRITIS'08), pages 109-124, Roma, Italy, October 2008.

M. Beccuti, D. Codetta-Raiteri, G. Franceschinis and S. Haddad. Non deterministic Repairable Fault Trees for computing optimal repair strategy. Proceeding of 3rd International Conference on Performance Evaluation, Methodologies and Tools (VALUETOOLS'08), Athens, Greece, ACM Digital Library, October 2008.

S. Baarir, M. Beccuti, G. Franceschinis. New solvers for asymmetric systems in GreatSPN. Proceeding of 5th International Conference on the Quantitative Evaluation of SysTems (QEST'08), pages 235-236, St.Malo, France, 14-17 September 2008. IEEE Computer Society Press.

M. Beccuti, D. Codetta-Raiter, G. Franceschinis, and S. Haddad. A framework to design and solve Markov Decision Well-formed Net models. Proceeding of 4th International Conference on Quantitative Evaluation of SysTems (QEST'07), Edinburgh, Scotland, 16-19 September 2007. IEEE Computer Society Press.

M. Beccuti, S. Baarir, G. Franceschinis, J-M. Ilie. Efficient lumpability check in partially symmetric systems. Proceeding of 3rd International Conference on Quantitative Evaluation of Systems (QEST'06), Riverside, CA, USA, September 2006. IEEE Soc. Press.

J.-M. Ilie, S. Baarir, M. Beccuti, C. Delamare, S. Donatelli, C. Dutheillet, G. Franceschinis, R. Gaeta, P. Moreaux. Extended SWN Solvers in GreatSPN. Proceeding of 1st International Conference on Quantitative Evaluation of Systems (QEST04), Enschede, Netherlands. September 2004. IEEE Soc. Press: 324-325.

Publications in book chapters

G. Ferrero, N. Licheri, M. De Bortoli, R.A. Calogero, M. Beccuti, F. Cordero. Computational Analysis of circRNA Expression Data. Chapter in book RNA Bioinformatics in series Methods in Molecular Biology. Editor E. Picardi. Ed. Springer Science. 2021.

L. Alessandrì, F. Cordero, M. Beccuti, M. Arigoni, R .A. Calogero. Computational Analysis of Single-Cell RNA-Seq Data Chapter in book RNA Bioinformatics in series Methods in Molecular Biology. Editor E. Picardi. Ed. Springer Science. 2021.

M. Beccuti, S. Chiaradonna, F. Di Giandomenico, S. Donatelli, G. Dondossola, G. Franceschinis. Model-based evaluation of the impact of attacks to the telecommunication service of the electrical grid. Chapter 84 in book. Cyber Behavior: Concepts, Methodologies, Tools, and Applications Editors Bologna S. and Theron P., Ed. IGI Global. 2014

M. Beccuti, G. Franceschinis and Jeremy Sproston. Modeling and verification of distributed systems using Markov decision processes. Chapter in book. Quantitative Assessments of Distributed Systems: Methodologies and Techniques. Editors Dario Bruneo e Salvatore Distefano. Ed. Wiley. 2015.

M. Beccuti, S. Chiaradonna, F. Di Giandomenico, S. Donatelli, G. Dondossola, G. Franceschinis. A model based approach for the evaluation of cyber attacks to the electrical grid. Chapter 14 in book. Model-Based Evaluation of the Impact of Attacks to the Telecommunication Service of the Electrical Grid. Editors Sandro Bologna and Paul Theron. IGI Global, 2013.

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