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

ParallNormal: An Efficient Variant Calling Pipeline for Unmatched Sequencing Data. - Laura Follia; Fabio Tordini; Simone Pernice; Greta Romano; Giulia Beatrice Piaggeschi; Giulio Ferrero (PDP, 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)

MethylFASTQ: A Tool Simulating Bisulfite Sequencing Data. - Giulia Beatrice Piaggeschi; Nicola Licheri; Greta Romano; Simone Pernice; Laura Follia; Giulio Ferrero (PDP, 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)

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)

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)

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)

Exploiting GPU computing for effective Agent-Based simulation: initial experiments. - Marzio Pennisi; Giuliana Franceschinis; Daniele Baccega; Simone Pernice; Irene Terrone (PDP, 2025)