Junior researcher (RTDa)
My current research activities focus mainly on the development and analysis of simulation algorithms and mathematical models applied to various fields, ranging from computational epidemiology to the modelling of complex biological systems. Another area of research is dedicated to the analysis of longitudinal data, typically characterised by a small and irregular number of observations over time.
- Junior researcher (RTDa), Computer Science department, University of Turin
- Postdoctoral researcher, Computer Science department, University of Turin
- PhD in Computer Science, University of Turin
- Master of Science in Mathematics, University of Turin
Forge4Flame: An intuitive dashboard for designing GPU agent-based models to simulate infectious disease spread
Baccega, Daniele; Terrone, Irene; Heywood, Peter; Chisholm, Robert; Richmond, Paul; Contaldo, Sandro Gepiro; Bosio, Lorenzo; Pernice, Simone; Beccuti, Marco
Simulation Modelling Practice and Theory (2025-12-01)
UnifiedGreatMod: A new holistic modelling paradigm for studying biological systems on a complete and harmonious scale
Aucello, Riccardo; Pernice, Simone; Tortarolo, Dora; Calogero, Raffaele A.; Herrera-Rincon, Celia; Ronchi, Giulia; Geuna, Stefano; Cordero, Francesca; Lió, Pietro; Beccuti, Marco
Bioinformatics (2025-03-01)
Dynamic Resources Management for Exascale in ADMIRE Framework
Carretero, Jesus; Singh, David E.; Fernandez-Muñoz, Javier; Sedona, Rocco; Pernice, Simone; Cantalupo, Barbara; Aldinucci, Marco; Torquati, Massimo; Tarraf, Ahmad; Jeannot, Emmanuel; Wolf, Felix
Procedia Computer Science (2025-01-01)
A Simulation-Based Framework to Reduce I/O Contention in HPC
Pernice, Simone; Tarraf, Ahmad; Besnard, Jean Baptiste; Cantalupo, Barbara; Cascajo, Alberto; Singh, David E.; Wolf, Felix; Carretero, Jesus; Shende, Sameer; Aldinucci, Marco
Proceedings 2025 IEEE International Parallel and Distributed Processing Symposium Workshops Ipdpsw 2025 (2025-01-01)
Epidemic Modelling Frameworks for Studying Infectious Disease Dynamics
Baccega, Daniele; Beccuti, Marco; Pernice, Simone; Terrone, Irene
Proceedings 2025 IEEE 13th International Conference on Healthcare Informatics Ichi 2025 (2025-01-01)
Living Along COVID-19: Assessing Contention Policies Through Agent-Based Models
Baccega, Daniele; Pernice, Simone; Castagno, Paolo; Sereno, Matteo; Beccuti, Marco
Lecture Notes in Computer Science (2025-01-01)
Synergy Between Mechanistic Modelling and Ensemble Feature Selection Approaches to Explore Multiscale Biological Heterogeneity
Aucello, Riccardo; Licheri, Nicola; Rosso, Elena; Ferrero, Giulio; Contaldo, Sandro Gepiro; Pernice, Simone; Lió, Pietro; Cordero, Francesca; Beccuti, Marco
Lecture Notes in Computer Science (2025-01-01)
Functional Data Analysis and Clustering of Haematological Parameters in SARS-CoV-2 Patients
Volpatto, Daniela; Frattarola, Marco; Pernice, Simone; Cordero, Francesca; Beccuti, Marco; Mengozzi, Giulio; De Angelis, Stefano; Sirovich, Roberta
Lecture Notes in Computer Science (2025-01-01)
Stochastic Modeling and Dosage Optimization of a Cancer Vaccine Exploiting the EpiMod Framework
Beccuti, Marco; Franceschinis, Giuliana; Pennisi, Marzio; Pernice, Simone; Terrone, Irene
Lecture Notes in Computer Science (2025-01-01)
Extension of the GreatMod Modeling Framework to Simulate Non-Markovian Processes with General-Distributed Events
Terrone, Irene; Volpatto, Daniela; Pernice, Simone; Amparore, Elvio; Sirovich, Roberta; Cordero, Francesca; Beccuti, Marco
Lecture Notes in Computer Science (2025-01-01)
PHeP: TrustAlert Open-Source Platform for Enhancing Predictive Healthcare with Deep Learning
Contaldo, Sandro Gepiro; Pietropaolo, Emanuele; Bosio, Lorenzo; Pernice, Simone; Terrone, Irene; Baccega, Daniele; Wang, Yuting; Sahoo, Rahul Kumar; Rizzo, Giuseppe; Visconti, Alessia; Berchialla, Paola; Beccuti, Marco
Lecture Notes in Computer Science (2025-01-01)
Exploiting GPU computing for effective Agent-Based simulation: initial experiments
Pennisi, Marzio; Franceschinis, Giuliana; Baccega, Daniele; Pernice, Simone; Terrone, Irene
Proceedings 33rd Euromicro International Conference on Parallel Distributed and Network Based Processing Pdp 2025 (2025-01-01)
CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications
Alessandri, Simone; Ratto, Maria L.; Rabellino, Sergio; Piacenti, Gabriele; Contaldo, Sandro Gepiro; Pernice, Simone; Beccuti, Marco; Calogero, Raffaele A.; Alessandri, Luca
BMC Bioinformatics (2024-12-01)
Synchronies and asynchronies in the development of COVID-19 pandemic in Italy
Giraudo, Maria Teresa; Falcone, Manuele; Cislaghi, Cesare; Cordero, Francesca; Pernice, Simone; Sirovich, Roberta
Epidemiologia E Prevenzione (2024-05-01)
A new computational workflow to guide personalized drug therapy
Pernice, Simone; Maglione, Alessandro; Tortarolo, Dora; Sirovich, Roberta; Clerico, Marinella; Rolla, Simona; Beccuti, Marco; Cordero, Francesca
Journal of Biomedical Informatics (2023-12-01)
From Compositional Petri Net Modeling to Macro and Micro Simulation by Means of Stochastic Simulation and Agent-Based Models
Amparore, Elvio; Beccuti, Marco; Castagno, Paolo; Pernice, Simone; Franceschinis, Giuliana; Pennisi, Marzio
ACM Transactions on Modeling and Performance Evaluation of Computing Systems (2023-10-25)
MODIMO: Workshop on Multi-Omics Data Integration for Modelling Biological Systems
Avesani, Simone; Bonnici, Vincenzo; Pernice, Simone; Beccuti, Marco; Giugno, Rosalba
International Conference on Information and Knowledge Management Proceedings (2023-10-21)
CONNECTOR, fitting and clustering of longitudinal data to reveal a new risk stratification system
Pernice, Simone; Sirovich, Roberta; Grassi, Elena; Viviani, Marco; Ferri, Martina; Sassi, Francesco; Alessandrì, Luca; Tortarolo, Dora; Calogero, Raffaele A.; Trusolino, Livio; Bertotti, Andrea; Beccuti, Marco; Olivero, Martina; Cordero, Francesca
Bioinformatics (2023-05-01)
How the Competition for Cysteine May Promote Infection of SARS-CoV-2 by Triggering Oxidative Stress
Vernone, Annamaria; Bergandi, Loredana; Pernice, Simone; Pescarmona, Gianpiero; Silvagno, Francesca
Antioxidants (2023-02-01)
OmniReprodubileCellAnalysis: a comprehensive toolbox for the analysis of cellular biology data
Tortarolo, Dora; Pernice, Simone; Clapero, Fabiana; Valdembri, Donatella; Serini, Guido; Riccardo, Federica; Tarone, Lidia; Bena, Chiara Enrico; Bosia, Carla; Contaldo, Sandro Gepiro; Beccuti, Marco; Pennisi, Marzio; Cordero, Francesca
Proceedings 2023 2023 IEEE International Conference on Bioinformatics and Biomedicine Bibm 2023 (2023-01-01)
Artificial intelligence methods for biomedical imaging and omics data
Barbano, Carlo Alberto; Beccuti, Marco; Cordero, Francesca; Ivanov, Desislav Nikolaev; Licheri, Nicola; Pernice, Simone; Presta, Alberto; Renzulli, Riccardo; Grangetto, Marco
Ceur Workshop Proceedings (2023-01-01)
An Agent-Based Model to Support Infection Control Strategies at School
Baccega, Daniele; Pernice, Simone; Terna, Pietro; Castagno, Paolo; Moirano, Giovenale; Richiardi, Lorenzo; Sereno, Matteo; Rabellino, Sergio; Maule, Milena Maria; Beccuti, Marco
JASSS (2022-01-01)
Multiformalism modeling and simulation of immune system mechanisms
Amparore, Elvio Gilberto; Beccuti, Marco; Castagno, Paolo; Franceschinis, Giuliana; Pennisi, Marzio; Pernice, Simone
Proceedings 2021 IEEE International Conference on Bioinformatics and Biomedicine Bibm 2021 (2021-01-01)
A Petri Net Formalism to Study Systems at Different Scales Exploiting Agent-Based and Stochastic Simulations
Beccuti, M.; Castagno, P.; Franceschinis, G.; Pennisi, M.; Pernice, S.
Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics (2021-01-01)
Computational modeling of the immune response in multiple sclerosis using epimod framework
Pernice, Simone; Follia, Laura; Maglione, Alessandro; Pennisi, Marzio; Pappalardo, Francesco; Novelli, Francesco; Clerico, Marinella; Beccuti, Marco; Cordero, Francesca; Rolla, Simona
BMC Bioinformatics (2020-12-01)
Impacts of reopening strategies for COVID-19 epidemic: a modeling study in Piedmont region
Pernice, Simone; Castagno, Paolo; Marcotulli, Linda; Maule, Milena Maria; Richiardi, Lorenzo; Moirano, Giovenale; Sereno, Matteo; Cordero, Francesca; Beccuti, Marco
BMC Infectious Diseases (2020-12-01)
A computational framework for modeling and studying pertussis epidemiology and vaccination
Castagno, Paolo; Pernice, Simone; Ghetti, Gianni; Povero, Massimiliano; Pradelli, Lorenzo; Paolotti, Daniela; Balbo, Gianfranco; Sereno, Matteo; Beccuti, Marco
BMC Bioinformatics (2020-09-16)
Multiple sclerosis disease: A computational approach for investigating its drug interactions
Pernice, Simone; Beccuti, Marco; Romano, Greta; Pennisi, Marzio; Maglione, Alessandro; Cutrupi, Santina; Pappalardo, Francesco; Capra, Lorenzo; Franceschinis, Giuliana; De Pierro, Massimiliano; Balbo, Gianfranco; Cordero, Francesca; Calogero, Raffaele
Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics (2020-01-01)
A computational approach based on the colored Petri net formalism for studying multiple sclerosis
Pernice, Simone; Pennisi, Marzio; Romano, Greta; Maglione, Alessandro; Cutrupi, Santina; Pappalardo, Francesco; Balbo, Gianfranco; Beccuti, Marco; Cordero, Francesca; Calogero, Raffaele A.
BMC Bioinformatics (2019-12-10)
Exploiting Stochastic Petri Net formalism to capture the Relapsing Remitting Multiple Sclerosis variability under Daclizumab administration
Pernice, Simone; Romano, Greta; Russo, Giulia; Beccuti, Marco; Pennisi, Marzio; Pappalardo, Francesco
Proceedings 2019 IEEE International Conference on Bioinformatics and Biomedicine Bibm 2019 (2019-11-01)
A tool for the automatic derivation of symbolic ode from symmetric net models
Beccuti, Marco; Capra, Lorenzo; De Pierro, Massimiliano; Franceschinis, Giuliana; Follia, Laura; Pernice, Simone
Proceedings IEEE Computer Society S Annual International Symposium on Modeling Analysis and Simulation of Computer and Telecommunications Systems Mascots (2019-10-01)
MethylFASTQ: A Tool Simulating Bisulfite Sequencing Data
Piaggeschi, Giulia; Licheri, Nicola; Romano, Greta; Pernice, Simone; Follia, Laura; Ferrero, Giulio
Proceedings 27th Euromicro International Conference on Parallel Distributed and Network Based Processing Pdp 2019 (2019-03-19)
Estimating Daclizumab effects in Multiple Sclerosis using Stochastic Symmetric Nets
Pernice, Simone; Beccuti, Marco; Do, Pietro; Pennisi, Marzio; Pappalardo, Francesco
Proceedings 2018 IEEE International Conference on Bioinformatics and Biomedicine Bibm 2018 (2019-01-21)
Integrating Petri Nets and Flux Balance Methods in Computational Biology Models: A Methodological and Computational Practice
Pernice, Simone; Follia, Laura; Balbo, Gianfranco; Milanesi, Luciano; Sartini, Giulia; Totis, Niccoló; Lió, Pietro; Merelli, Ivan; Cordero, Francesca; Beccuti, Marco
Fundamenta Informaticae (2019-01-01)
GPU accelerated analysis of treg-teff cross regulation in relapsing-remitting multiple sclerosis
Beccuti, Marco; Cazzaniga, Paolo; Pennisi, Marzio; Besozzi, Daniela; Nobile, Marco S.; Pernice, Simone; Russo, Giulia; Tangherloni, Andrea; Pappalardo, Francesco
Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics (2019-01-01)
ParallNormal: An Efficient Variant Calling Pipeline for Unmatched Sequencing Data
Follia, Laura; Tordini, Fabio; Pernice, Simone; Romano, Greta; Piaggeschi, Giulia Beatrice; Ferrero, Giulio
Proceedings 26th Euromicro International Conference on Parallel Distributed and Network Based Processing Pdp 2018 (2018-06-06)
Deriving Symbolic Ordinary Differential Equations from Stochastic Symmetric Nets Without Unfolding
Beccuti, Marco; Capra, Lorenzo; De Pierro, Massimiliano; Franceschinis, Giuliana; Pernice, Simone
Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics (2018-01-01)