Extended SWN Solvers in GreatSPN. - Jean-Michel Ilié; Souheib Baarir; Marco Beccuti; Clément Delamare; Susanna Donatelli; Claude Dutheillet; Giuliana Franceschinis; Rossano Gaeta; Patrice Moreaux (QEST, 2004)

Efficient lumpability check in partially symmetric systems. - Marco Beccuti; Giuliana Franceschinis; Souheib Baarir; Jean-Michel Ilié (QEST, 2006)

Markov Decision Petri Net and Markov Decision Well-Formed Net Formalisms. - Marco Beccuti; Giuliana Franceschinis; Serge Haddad (ICATPN, 2007)

A framework to design and solve Markov Decision Well-formed Net models. - Marco Beccuti; Daniele Codetta Raiteri; Giuliana Franceschinis; Serge Haddad (QEST, 2007)

Multi-level Dependability Modeling of Interdependencies between the Electricity and Information Infrastructures. - Marco Beccuti; Giuliana Franceschinis; Mohamed Kaâniche; Karama Kanoun (CRITIS, 2008)

New Solvers for Asymmetric Systems in GreatSPN. - Souheib Baarir; Marco Beccuti; Giuliana Franceschinis (QEST, 2008)

Non deterministic repairable fault trees for computing optimal repair strategy. - Marco Beccuti; Daniele Codetta Raiteri; Giuliana Franceschinis; Serge Haddad (VALUETOOLS, 2008)

Modeling Clinical Guidelines through Petri Nets. - Marco Beccuti; Alessio Bottrighi; Giuliana Franceschinis; Stefania Montani; Paolo Terenziani (AIME, 2009)

Parametric NdRFT for the derivation of optimal repair strategies. - Marco Beccuti; Giuliana Franceschinis; Daniele Codetta Raiteri; Serge Haddad (DSN, 2009)

From partially to fully lumped Markov chains in stochastic well formed Petri nets. - Souheib Baarir; Marco Beccuti; Claude Dutheillet; Giuliana Franceschinis (VALUETOOLS, 2009)

Multiple abstraction levels in performance analysis of WSN monitoring systems. - Marco Beccuti; Daniele Codetta Raiteri; Giuliana Franceschinis (VALUETOOLS, 2009)

The GreatSPN tool: recent enhancements. - Souheib Baarir; Marco Beccuti; Davide Cerotti; Massimiliano De Pierro; Susanna Donatelli; Giuliana Franceschinis (SIGMETRICS Perform. Evaluation Rev., 2009)

GreatSPN Enhanced with Decision Diagram Data Structures. - Junaid Babar; Marco Beccuti; Susanna Donatelli; Andrew S. Miner (Petri Nets, 2010)

Stochastic Petri Nets Sensitivity to Token Scheduling Policies. - Gianfranco Balbo; Marco Beccuti; Massimiliano De Pierro; Giuliana Franceschinis (OR, 2010)

Dynamic Simulations of Kidney Exchanges. - Marco Beccuti; V. Fragnelli; Giuliana Franceschinis; S. Villa (OR, 2010)

Probe Automata for Passage Time Specification. - Elvio Gilberto Amparore; Marco Beccuti; Susanna Donatelli; Giuliana Franceschinis (QEST, 2011)

A Mean Field Based Methodology for Modeling Mobility in Ad Hoc Networks. - Marco Beccuti; Massimiliano De Pierro; András Horváth; Ádám Horváth; Károly Farkas (VTC Spring, 2011)

Computing first passage time distributions in stochastic well-formed nets. - Gianfranco Balbo; Marco Beccuti; Massimiliano De Pierro; Giuliana Franceschinis (ICPE, 2011)

First Passage Time Computation in Tagged GSPNs with Queue Places. - Gianfranco Balbo; Marco Beccuti; Massimiliano De Pierro; Giuliana Franceschinis (Comput. J., 2011)

Barcoding-free BAC Pooling Enables Combinatorial Selective Sequencing of the Barley Gene Space - Stefano Lonardi; Denisa Duma; Matthew Alpert; Francesca Cordero; Marco Beccuti; Prasanna Bhat; Yonghui Wu; Gianfranco Ciardo; Burair Alsaihati; Yaqin Ma; Steve Wanamaker; Josh Resnik; et al. (CoRR, 2011)

Lumping partially symmetrical stochastic models. - Souheib Baarir; Marco Beccuti; Claude Dutheillet; Giuliana Franceschinis; Serge Haddad (Perform. Evaluation, 2011)

A new symbolic approach for network reliability analysis. - Marco Beccuti; Andrea Bobbio; Giuliana Franceschinis; Roberta Terruggia (DSN, 2012)

Efficient simulation of stochastic well-formed nets through symmetry exploitation. - Marco Beccuti; Giuliana Franceschinis (WSC, 2012)

Quantification of dependencies between electrical and information infrastructures. - Marco Beccuti; Silvano Chiaradonna; Felicita Di Giandomenico; Susanna Donatelli; Giovanna Dondossola; Giuliana Franceschinis (Int. J. Crit. Infrastructure Prot., 2012)

Expressing and Computing Passage Time Measures of GSPN Models with HASL. - Elvio Gilberto Amparore; Paolo Ballarini; Marco Beccuti; Susanna Donatelli; Giuliana Franceschinis (Petri Nets, 2013)

Simulation-based verification of hybrid automata stochastic logic formulas for stochastic symmetric nets. - Elvio Gilberto Amparore; Benoît Barbot; Marco Beccuti; Susanna Donatelli; Giuliana Franceschinis (SIGSIM-PADS, 2013)

State of art fusion-finder algorithms are suitable to detect transcription-induced chimeras in normal tissues? - Matteo Carrara; Marco Beccuti; Federica Cavallo; Susanna Donatelli; Fulvio Lazzarato; Francesca Cordero; Raffaele A. Calogero (BMC Bioinform., 2013)

Multi-level model for the investigation of oncoantigen-driven vaccination effect. - Francesca Cordero; Marco Beccuti; Chiara Fornari; Stefania Lanzardo; Laura Conti; Federica Cavallo; Gianfranco Balbo; Raffaele A. Calogero (BMC Bioinform., 2013)

Model Checking Contest @ Petri Nets, Report on the 2013 edition. - Fabrice Kordon; Alban Linard; Marco Beccuti; Didier Buchs; Lukasz Fronc; Lom-Messan Hillah; Francis Hulin-Hubard; Fabrice Legond-Aubry; Niels Lohmann; Alexis Marechal; Emmanuel Paviot-Adet; Franck Pommereau; et al. (CoRR, 2013)

Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space. - Stefano Lonardi; Denisa Duma; Matthew Alpert; Francesca Cordero; Marco Beccuti; Prasanna R. Bhat; Yonghui Wu; Gianfranco Ciardo; Burair Alsaihati; Yaqin Ma; Steve Wanamaker; Josh Resnik; et al. (PLoS Comput. Biol., 2013)

(Stochastic) Model Checking in GreatSPN. - Elvio Gilberto Amparore; Marco Beccuti; Susanna Donatelli (Petri Nets, 2014)

Mathematical models on cancer progression. - Marco Beccuti (BioPPN@Petri Nets, 2014)

Analysis of Petri Net Models through Stochastic Differential Equations. - Marco Beccuti; Enrico Bibbona; András Horváth; Roberta Sirovich; Alessio Angius; Gianfranco Balbo (Petri Nets, 2014)

Cognitive Systems in Intelligent Vehicles - A New Frontier for Autonomous Driving. - Elvio Gilberto Amparore; Marco Beccuti; Simona Collina; Flavia De Simone; Susanna Donatelli; Fabio Tango (ICINCO (2), 2014)

Chimera: a Bioconductor package for secondary analysis of fusion products. - Marco Beccuti; Matteo Carrara; Francesca Cordero; Fulvio Lazzarato; Susanna Donatelli; Francesca Nadalin; Alberto Policriti; Raffaele A. Calogero (Bioinform., 2014)

Computing Optimal Repair Strategies by Means of NdRFT Modeling and Analysis. - Marco Beccuti; Giuliana Franceschinis; Daniele Codetta Raiteri; Serge Haddad (Comput. J., 2014)

Markov Decision Petri Nets with Uncertainty. - Marco Beccuti; Elvio Gilberto Amparore; Susanna Donatelli; Dimitri Scheftelowitsch; Peter Buchholz 001; Giuliana Franceschinis (EPEW, 2015)

Scrible: Ultra-Accurate Error-Correction of Pooled Sequenced Reads. - Denise Duma; Francesca Cordero; Marco Beccuti; Gianfranco Ciardo; Timothy J. Close; Stefano Lonardi (WABI, 2015)

Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis. - Matteo Carrara; Josephine Lum; Francesca Cordero; Marco Beccuti; Michael Poidinger; Susanna Donatelli; Raffaele A. Calogero; Francesca Zolezzi (BMC Bioinform., 2015)

A versatile mathematical work-flow to explore how Cancer Stem Cell fate influences tumor progression. - Chiara Fornari; Gianfranco Balbo; Sami M. Halawani; Omar M. Ba-Rukab; Ab Rahman Ahmad; Raffaele A. Calogero; Francesca Cordero; Marco Beccuti (BMC Syst. Biol., 2015)

From Symmetric Nets to Differential Equations exploiting Model Symmetries. - Marco Beccuti; Chiara Fornari; Giuliana Franceschinis; Sami M. Halawani; Omar M. Ba-Rukab; Ab Rahman Ahmad; Gianfranco Balbo (Comput. J., 2015)

Approximate analysis of biological systems by hybrid switching jump diffusion. - Alessio Angius; Gianfranco Balbo; Marco Beccuti; Enrico Bibbona; András Horváth; Roberta Sirovich (Theor. Comput. Sci., 2015)

Dealing with indetermination in biochemical networks. - Niccoló Totis; Marco Beccuti; Francesca Cordero; Laura Follia; Chiara Riganti; Francesco Novelli (VALUETOOLS, 2016)

Decision Diagrams for Petri Nets: Which Variable Ordering? - Elvio Gilberto Amparore; Susanna Donatelli; Marco Beccuti; Giulio Garbi; Andrew S. Miner (PNSE @ Petri Nets, 2017)

Gradient-Based Variable Ordering of Decision Diagrams for Systems with Structural Units. - Elvio Gilberto Amparore; Marco Beccuti; Susanna Donatelli (ATVA, 2017)

A mathematical model to study breast cancer growth. - Giorgia Chivassa; Chiara Fornari; Roberta Sirovich; Marzio Pennisi; Marco Beccuti; Francesca Cordero (BIBM, 2017)

Analysis of Timed Properties Using the Jump-Diffusion Approximation. - Paolo Ballarini; Marco Beccuti; Enrico Bibbona; András Horváth; Roberta Sirovich; Jeremy Sproston (EPEW, 2017)

HashClone: a new tool to quantify the minimal residual disease in B-cell lymphoma from deep sequencing data. - Marco Beccuti; Elisa Genuardi; Greta Romano; Luigia Monitillo; Daniela Barbero; Mario Boccadoro; Marco Ladetto; Raffaele A. Calogero; Simone Ferrero; Francesca Cordero (BMC Bioinform., 2017)

Overcoming the lack of kinetic information in biochemical reactions networks. - Niccoló Totis; Laura Follia; Chiara Riganti; Francesco Novelli; Francesca Cordero; Marco Beccuti (SIGMETRICS Perform. Evaluation Rev., 2017)

Estimating Daclizumab effects in Multiple Sclerosis using Stochastic Symmetric Nets. - Simone Pernice; Marco Beccuti; Pietro Do'; Marzio Pennisi; Francesco Pappalardo 001 (BIBM, 2018)

Efficient and Settings-Free Calibration of Detailed Kinetic Metabolic Models with Enzyme Isoforms Characterization. - Niccoló Totis; Andrea Tangherloni; Marco Beccuti; Paolo Cazzaniga; Marco S. Nobile; Daniela Besozzi; Marzio Pennisi; Francesco Pappalardo 001 (CIBB, 2018)

Deriving Symbolic Ordinary Differential Equations from Stochastic Symmetric Nets Without Unfolding. - Marco Beccuti; Lorenzo Capra; Massimiliano De Pierro; Giuliana Franceschinis; Simone Pernice (EPEW, 2018)

GPU Accelerated Analysis of Treg-Teff Cross Regulation in Relapsing-Remitting Multiple Sclerosis. - Marco Beccuti; Paolo Cazzaniga; Marzio Pennisi; Daniela Besozzi; Marco S. Nobile; Simone Pernice; Giulia Russo; Andrea Tangherloni; Francesco Pappalardo 001 (Euro-Par Workshops, 2018)

Adaptive Artificial Co-pilot as Enabler for Autonomous Vehicles and Intelligent Transportation Systems. - Elvio Gilberto Amparore; Marco Beccuti; Marco Botta; Susanna Donatelli; Fabio Tango (ATT@IJCAI, 2018)

SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer. - Marco Beccuti; Francesca Cordero; Maddalena Arigoni; Riccardo Panero; Elvio Gilberto Amparore; Susanna Donatelli; Raffaele A. Calogero (Bioinform., 2018)

Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines. - Neha Kulkarni; Luca Alessandrì; Riccardo Panero; Maddalena Arigoni; Martina Olivero; Giulio Ferrero; Francesca Cordero; Marco Beccuti; Raffaele A. Calogero (BMC Bioinform., 2018)

Decision Diagrams for Petri Nets: A Comparison of Variable Ordering Algorithms. - Elvio Gilberto Amparore; Susanna Donatelli; Marco Beccuti; Giulio Garbi; Andrew S. Miner (Trans. Petri Nets Other Model. Concurr., 2018)

MCC'2017 - The Seventh Model Checking Contest. - Fabrice Kordon; Hubert Garavel; Lom-Messan Hillah; Emmanuel Paviot-Adet; Loïg Jezequel; Francis Hulin-Hubard; Elvio Gilberto Amparore; Marco Beccuti; Bernard Berthomieu; Hugues Evrard; Peter Gjøl Jensen; Didier Le Botlan; et al. (Trans. Petri Nets Other Model. Concurr., 2018)

Exploiting Stochastic Petri Net formalism to capture the Relapsing Remitting Multiple Sclerosis variability under Daclizumab administration. - Simone Pernice; Greta Romano; Giulia Russo; Marco Beccuti; Marzio Pennisi; Francesco Pappalardo 001 (BIBM, 2019)

Multiple Sclerosis Disease: A Computational Approach for Investigating Its Drug Interactions. - Simone Pernice; Marco Beccuti; Greta Romano; Marzio Pennisi; Alessandro Maglione; Santina Cutrupi; Francesco Pappalardo 001; Lorenzo Capra; Giuliana Franceschinis; Massimiliano De Pierro; Gianfranco Balbo; Francesca Cordero; et al. (CIBB, 2019)

A Tool for the Automatic Derivation of Symbolic ODE from Symmetric Net Models. - Marco Beccuti; Lorenzo Capra; Massimiliano De Pierro; Giuliana Franceschinis; Laura Follia; Simone Pernice (MASCOTS, 2019)

A computational approach based on the colored Petri net formalism for studying multiple sclerosis. - Simone Pernice; Marzio Pennisi; Greta Romano; Alessandro Maglione; Santina Cutrupi; Francesco Pappalardo 001; Gianfranco Balbo; Marco Beccuti; Francesca Cordero; Raffaele A. Calogero (BMC Bioinform., 2019)

A computational framework for modeling and studying pertussis epidemiology and vaccination. - Paolo Castagno; Simone Pernice; Gianni Ghetti; Massimiliano Povero; Lorenzo Pradelli; Daniela Paolotti; Gianfranco Balbo; Matteo Sereno; Marco Beccuti (BMC Bioinform., 2020)

Computational modeling of the immune response in multiple sclerosis using epimod framework. - Simone Pernice; Laura Follia; Alessandro Maglione; Marzio Pennisi; Francesco Pappalardo 001; Francesco Novelli; Marinella Clerico; Marco Beccuti; Francesca Cordero; Simona Rolla (BMC Bioinform., 2020)

Integrating Petri Nets and Flux Balance Methods in Computational Biology Models: a Methodological and Computational Practice. - Simone Pernice; Laura Follia; Gianfranco Balbo; Luciano Milanesi; Giulia Sartini; Niccoló Totis; Pietro Lió; Ivan Merelli; Francesca Cordero; Marco Beccuti (Fundam. Informaticae, 2020)

Multiformalism modeling and simulation of immune system mechanisms. - Elvio Gilberto Amparore; Marco Beccuti; Paolo Castagno; Giuliana Franceschinis; Marzio Pennisi; Simone Pernice (BIBM, 2021)

MODIMO: Workshop on Multi-Omics Data Integration for Modelling Biological Systems. - Marco Beccuti; Vincenzo Bonnici; Rosalba Giugno (CIKM, 2021)

An Entropy Heuristic to Optimize Decision Diagrams for Index-driven Search in Biological Graph Databases. - Nicola Licheri; Elvio Amparone; Vincenzo Bonnici; Rosalba Giugno; Marco Beccuti (CIKM Workshops, 2021)

A Petri Net Formalism to Study Systems at Different Scales Exploiting Agent-Based and Stochastic Simulations. - Marco Beccuti; Paolo Castagno; Giuliana Franceschinis; Marzio Pennisi; Simone Pernice (EPEW, 2021)

GRAPES-DD: exploiting decision diagrams for index-driven search in biological graph databases. - Nicola Licheri; Vincenzo Bonnici; Marco Beccuti; Rosalba Giugno (BMC Bioinform., 2021)

An Agent-Based Model to Support Infection Control Strategies at School. - Daniele Baccega; Simone Pernice; Pietro Terna; Paolo Castagno; Giovenale Moirano; Lorenzo Richiardi; Matteo Sereno; Sergio Rabellino; Milena Maria Maule; Marco Beccuti (J. Artif. Soc. Soc. Simul., 2022)

OmniReprodubileCellAnalysis: a comprehensive toolbox for the analysis of cellular biology data. - Dora Tortarolo; Simone Pernice; Fabiana Clapero; Donatella Valdembri; Guido Serini; Federica Riccardo; Lidia Tarone; Chiara Enrico Bena; Carla Bosia; Sandro Gepiro Contaldo; Marco Beccuti; Marzio Pennisi; et al. (BIBM, 2023)

Synergy Between Mechanistic Modelling and Ensemble Feature Selection Approaches to Explore Multiscale Biological Heterogeneity. - Riccardo Aucello; Nicola Licheri; Elena Rosso; Giulio Ferrero; Sandro Gepiro Contaldo; Simone Pernice; Pietro Lió; Francesca Cordero; Marco Beccuti (CIBB, 2023)

Living Along COVID-19: Assessing Contention Policies Through Agent-Based Models. - Daniele Baccega; Simone Pernice; Paolo Castagno; Matteo Sereno; Marco Beccuti (CIBB, 2023)

Stochastic Modeling and Dosage Optimization of a Cancer Vaccine Exploiting the EpiMod Framework. - Marco Beccuti; Giuliana Franceschinis; Marzio Pennisi; Simone Pernice; Irene Terrone (CIBB, 2023)

Extension of the GreatMod Modeling Framework to Simulate Non-Markovian Processes with General-Distributed Events. - Irene Terrone; Daniela Volpatto; Simone Pernice; Elvio G. Amparore; Roberta Sirovich; Francesca Cordero; Marco Beccuti (CIBB, 2023)

MODIMO: Workshop on Multi-Omics Data Integration for Modelling Biological Systems. - Simone Avesani; Vincenzo Bonnici; Simone Pernice; Marco Beccuti; Rosalba Giugno (CIKM, 2023)

ICT Infrastructure Supporting the Italian Research Infrastructure on Microbial Resources MIRRI-IT. - Marco Beccuti; Antonio d'Acierno; Simone Donetti; Sandro Gepiro Contaldo; Paolo Romano 001; Giovanna Cristina Varese (CoRDI, 2023)

Artificial intelligence methods for biomedical imaging and omics data. - Carlo Alberto Barbano; Marco Beccuti; Francesca Cordero; Desislav Nikolaev Ivanov; Nicola Licheri; Simone Pernice; Alberto Presta; Riccardo Renzulli; Marco Grangetto (Ital-IA, 2023)

CONNECTOR, fitting and clustering of longitudinal data to reveal a new risk stratification system. - Simone Pernice; Roberta Sirovich; Elena Grassi; Marco Viviani 002; Martina Ferri; Francesco Sassi; Luca Alessandrì; Dora Tortarolo; Raffaele A. Calogero; Livio Trusolino; Andrea Bertotti; Marco Beccuti; et al. (Bioinform., 2023)

A new computational workflow to guide personalized drug therapy. - Simone Pernice; Alessandro Maglione; Dora Tortarolo; Roberta Sirovich; Marinella Clerico; Simona Rolla; Marco Beccuti; Francesca Cordero (J. Biomed. Informatics, 2023)

PHeP: TrustAlert Open-Source Platform for Enhancing Predictive Healthcare with Deep Learning. - Sandro Gepiro Contaldo; Emanuele Pietropaolo; Lorenzo Bosio; Simone Pernice; Irene Terrone; Daniele Baccega; Yuting Wang; Rahul Kumar Sahoo; Giuseppe Rizzo 002; Alessia Visconti; Paola Berchialla; Marco Beccuti (CIBB, 2024)

Functional Data Analysis and Clustering of Haematological Parameters in SARS-CoV-2 Patients. - Daniela Volpatto; Marco Frattarola; Simone Pernice; Francesca Cordero; Marco Beccuti; Giulio Mengozzi; Stefano De Angelis; Roberta Sirovich (CIBB, 2024)

From Compositional Petri Net Modeling to Macro and Micro Simulation by Means of Stochastic Simulation and Agent-Based Models. - Elvio Gilberto Amparore; Marco Beccuti; Paolo Castagno; Simone Pernice; Giuliana Franceschinis; Marzio Pennisi (ACM Trans. Model. Perform. Evaluation Comput. Syst., 2024)

CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications. - Simone Alessandri; Maria L. Ratto; Sergio Rabellino; Gabriele Piacenti; Sandro Gepiro Contaldo; Simone Pernice; Marco Beccuti; Raffaele A. Calogero; Luca Alessandrì (BMC Bioinform., 2024)

Epidemic Modelling Frameworks for Studying Infectious Disease Dynamics. - Daniele Baccega; Marco Beccuti; Simone Pernice; Irene Terrone (ICHI, 2025)