A Genetic Algorithm for Shortest Path Motion Problem in Three Dimensions. - Marzio Pennisi; Francesco Pappalardo 001; Alfredo Motta; Alessandro Cincotti (ICIC (2), 2007)

Towards a Personalized Schedule with Triplex Vaccine. - Francesco Pappalardo 001; Santo Motta; Pierluigi Lollini; Emilio Mastriani; Marzio Pennisi (WILF, 2007)

Optimal vaccination schedules using simulated annealing. - Marzio Pennisi; Roberto Catanuto; Francesco Pappalardo 001; Santo Motta (Bioinform., 2008)

The ImmunoGrid Simulator: How to Use It. - Francesco Pappalardo 001; Mark D. Halling-Brown; Marzio Pennisi; Ferdinando Chiacchio; Clare Sansom; Adrian J. Shepherd; David S. Moss; Santo Motta; Vladimir Brusic (CIBB, 2009)

HAMFAST: Fast Hamming Distance Computation. - Francesco Pappalardo 001; Cristiano Calonaci; Marzio Pennisi; Emilio Mastriani; Santo Motta (CSIE (1), 2009)

Agent Based Modeling of Lung Metastasis-Immune System Competition. - Marzio Pennisi; Francesco Pappalardo 001; Santo Motta (ICARIS, 2009)

Agent Based Modeling of Atherosclerosis: A Concrete Help in Personalized Treatments. - Francesco Pappalardo 001; Alessandro Cincotti; Alfredo Motta; Marzio Pennisi (ICIC (2), 2009)

ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization. - Francesco Pappalardo 001; Mark D. Halling-Brown; Nicolas Rapin; Ping Zhang 008; Davide Alemani; Andrew P. J. Emerson; Paola Paci; Patrice Duroux; Marzio Pennisi; Arianna Palladini; Olivo Miotto; Daniel Churchill; et al. (Briefings Bioinform., 2009)

Simulated Annealing and Optimal Protocols. - Marzio Pennisi; Roberto Catanuto; Francesco Pappalardo 001; Santo Motta; Emilio Mastriani; Alessandro Cincotti (J. Circuits Syst. Comput., 2009)

Universal immune system simulator framework (UISS). - Francesco Pappalardo 001; Marzio Pennisi; Santo Motta (BCB, 2010)

GRIDUISS - A Grid Based Universal Immune System Simulator Framework. - Francesco Pappalardo 001; Marzio Pennisi; Ferdinando Chiacchio; Alessandro Cincotti; Santo Motta (ICIC (1), 2010)

Cancer Immunoprevention: What Can We Learn from in Silico Models? - Francesco Pappalardo 001; Marzio Pennisi; Alessandro Cincotti; Ferdinando Chiacchio; Santo Motta; Pierluigi Lollini (ICIC (3), 2010)

Modeling the competition between lung metastases and the immune system using agents. - Marzio Pennisi; Francesco Pappalardo 001; Arianna Palladini; Giordano Nicoletti; Patrizia Nanni; Pierluigi Lollini; Santo Motta (BMC Bioinform., 2010)

Predicting Long-Term Vaccine Efficacy against Metastases Using Agents. - Marzio Pennisi; Dario Motta; Alessandro Cincotti; Francesco Pappalardo 001 (ICIC (3), 2011)

Mathematical modeling of the immune system recognition to mammary carcinoma antigen. - Carlo Bianca; Ferdinando Chiacchio; Francesco Pappalardo 001; Marzio Pennisi (BMC Bioinform., 2012)

A Mathematical Model of Immune-System-Melanoma Competition. - Marzio Pennisi (Comput. Math. Methods Medicine, 2012)

iAtheroSim: atherosclerosis process simulator on smart devices. - Francesco Pappalardo 001; Marzio Pennisi; Ferdinando Chiacchio; Salvatore Musumeci; Santo Motta (BCB, 2013)

Agent based modeling of Treg-Teff cross regulation in relapsing-remitting multiple sclerosis. - Marzio Pennisi; Abdul Mateen Rajput; Luca Toldo; Francesco Pappalardo 001 (BMC Bioinform., 2013)

Relapsing-remitting multiple scleroris and the role of vitamin D: an agent based model. - Francesco Pappalardo 001; Marzio Pennisi; Abdul Mateen Rajput; Ferdinando Chiacchio; Santo Motta (BCB, 2014)

OntoFast: Construct Ontology Rapidly. - Abdul Mateen Rajput; Marzio Pennisi; Santo Motta; Francesco Pappalardo 001 (KESW, 2014)

Induction of T-cell memory by a dendritic cell vaccine: a computational model. - Francesco Pappalardo 001; Marzio Pennisi; Alessia Ricupito; Francesco Topputo; Matteo Bellone (Bioinform., 2014)

Computational modeling of the expansion of human cord blood CD133+ hematopoietic stem/progenitor cells with different cytokine combinations. - Francesca Gullo; Mark van der Garde; Giulia Russo; Marzio Pennisi; Santo Motta; Francesco Pappalardo 001; Suzanne Watt (Bioinform., 2015)

A computational model to predict the immune system activation by citrus-derived vaccine adjuvants. - Francesco Pappalardo 001; Epifanio Fichera; Nicoletta Paparone; Alessandro Lombardo; Marzio Pennisi; Giulia Russo; Marco Leotta; Alessandro Pedretti; Francesco De Fiore; Santo Motta (Bioinform., 2016)

A methodological approach for using high-level Petri Nets to model the immune system response. - Marzio Pennisi; Salvatore Cavalieri; Santo Motta; Francesco Pappalardo 001 (BMC Bioinform., 2016)

SHyFTA, a Stochastic Hybrid Fault Tree Automaton for the modelling and simulation of dynamic reliability problems. - Ferdinando Chiacchio; Diego D'Urso; Lucio Compagno; Marzio Pennisi; Francesco Pappalardo 001; Gabriele Manno (Expert Syst. Appl., 2016)

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

Optimization and analisys of vaccination schedules using simulated annealing and agent based models. - Marzio Pennisi; Juan A. Sanchez-Lantaron; Pedro A. Reche; Giulia Russo; Francesco Pappalardo 001 (BIBM, 2017)

Introducing scale factor adjustments on agent-based simulations of the immune system. - Juan A. Sanchez-Lantaron; Pedro A. Reche; Marzio Pennisi; Giulia Russo; Francesco Pappalardo 001 (BIBM, 2017)

2DIs: A SBML Compliant Web Platform for the Design and Modeling of Immune System Interactions. - Marzio Pennisi; Giulia Russo; Giuseppe Sgroi; Giuseppe Parasiliti; Francesco Pappalardo 001 (ICIC (2), 2017)

Modeling PI3K/PDK1/Akt and MAPK Signaling Pathways Using Continuous Petri Nets. - Giulia Russo; Marzio Pennisi; Roberta Boscarino; Francesco Pappalardo 001 (ICIC (2), 2017)

Combining agent based-models and virtual screening techniques to predict the best citrus-derived vaccine adjuvants against human papilloma virus. - Marzio Pennisi; Giulia Russo; Silvia Ravalli; Francesco Pappalardo 001 (BMC Bioinform., 2017)

An agent based modeling approach for the analysis of tuberculosis - immune system dynamics. - Francesco Pappalardo 001; Giulia Russo; Marzio Pennisi; Giuseppe Sgroi; Giuseppe Alessandro Parasiliti Palumbo; Santo Motta; Epifanio Fichera (BIBM, 2018)

Agent based modeling of relapsing multiple sclerosis: a possible approach to predict treatment outcome. - Francesco Pappalardo 001; Giulia Russo; Marzio Pennisi; Giuseppe Sgroi; Giuseppe Alessandro Parasiliti Palumbo; Santo Motta; Davide Maimone; Ferdinando Chiacchio (BIBM, 2018)

Parallel Pair-Wise Interaction for Multi-Agent Immune Systems Modelling. - Mozhgan K. Chimeh; Peter Heywood; Marzio Pennisi; Francesco Pappalardo 001; Paul Richmond (BIBM, 2018)

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)

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)

BIOESOnet: A Tool for the Generation of Personalized Human Metabolic Pathways from 23andMe Exome Data. - Marzio Pennisi; Gabriele Forzano; Giulia Russo; Barbara Tomasello; Marco Favetta; Marcella Renis; Francesco Pappalardo 001 (ICIC (2), 2018)

Combining Parallel Genetic Algorithms and Machine Learning to Improve the Research of Optimal Vaccination Protocols. - Marzio Pennisi; Giulia Russo; Francesco Pappalardo 001 (PDP, 2018)

Continuous Petri Nets and microRNA Analysis in Melanoma. - Giulia Russo; Marzio Pennisi; Roberta Boscarino; Francesco Pappalardo 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

A MapReduce tool for in-depth analysis of KEGG pathways: identification and visualization of therapeutic target candidates. - Giuseppe Alessandro Parasiliti Palumbo; Pietro Biondi; Giuseppe Sgroi; Marzio Pennisi; Giulia Russo; Francesco Pappalardo 001 (BIBM, 2019)

Generation of digital patients for the simulation of tuberculosis with UISS-TB. - Marzio Pennisi; Miguel A. Juárez; Giulia Russo; Marco Viceconti; Francesco Pappalardo 001 (BIBM, 2019)

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)

Evaluation of the efficacy of RUTI and ID93/GLA-SE vaccines in tuberculosis treatment: in silico trial through UISS-TB simulator. - Giulia Russo; Francesco Pappalardo 001; Miguel A. Juárez; Marzio Pennisi; Pere-Joan Cardona; Rhea Coler; Epifanio Fichera; Marco Viceconti (BIBM, 2019)

Gene expression and pathway bioinformatics analysis detect a potential predictive value of MAP3K8 in thyroid cancer progression. - Valentina Di Salvatore; Fiorenza Gianì; Giulia Russo; Marzio Pennisi; Pasqualino Malandrino; Francesco Frasca; Francesco Pappalardo 001 (BIBM, 2019)

In Silico Evaluation of Daclizumab and Vitamin D Effects in Multiple Sclerosis Using Agent Based Models. - Marzio Pennisi; Giulia Russo; Giuseppe Sgroi; Giuseppe Alessandro Parasiliti Palumbo; Francesco Pappalardo 001 (CIBB, 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 MapReduce Based Tool for the Analysis and Discovery of Novel Therapeutic Targets. - Giuseppe Parasiliti; Marzio Pennisi; Pietro Biondi; Giuseppe Sgroi; Giulia Russo; Christian Napoli 001; Francesco Pappalardo 001 (PDP, 2019)

Computational modeling reveals MAP3K8 as mediator of resistance to vemurafenib in thyroid cancer stem cells. - Fiorenza Gianì; Giulia Russo; Marzio Pennisi; Laura Sciacca; Francesco Frasca; Francesco Pappalardo 001 (Bioinform., 2019)

EpiMethEx: a tool for large-scale integrated analysis in methylation hotspots linked to genetic regulation. - Saverio Candido; Giuseppe Alessandro Parasiliti Palumbo; Marzio Pennisi; Giulia Russo; Giuseppe Sgroi; Valentina Di Salvatore; Massimo Libra; Francesco Pappalardo 001 (BMC Bioinform., 2019)

Parallelisation strategies for agent based simulation of immune systems. - Mozhgan Kabiri Chimeh; Peter Heywood; Marzio Pennisi; Francesco Pappalardo 001; Paul Richmond (BMC Bioinform., 2019)

Predicting the artificial immunity induced by RUTI® vaccine against tuberculosis using universal immune system simulator (UISS). - Marzio Pennisi; Giulia Russo; Giuseppe Sgroi; Angela Bonaccorso; Giuseppe Alessandro Parasiliti Palumbo; Epifanio Fichera; Dipendra Kumar Mitra; Kenneth B. Walker; Pere-Joan Cardona; Merce Amat; Marco Viceconti; Francesco Pappalardo 001 (BMC Bioinform., 2019)

POSITION PAPER: Credibility of In Silico Trial Technologies: A Theoretical Framing. - Marco Viceconti; Miguel A. Juárez; Cristina Curreli; Marzio Pennisi; Giulia Russo; Francesco Pappalardo 001 (CoRR, 2019)

Computational Immunogenetics. - Marta Gomez-Perosanz; Giulia Russo; Jose Luis Sanchez-Trincado Lopez; Marzio Pennisi; Pedro A. Reche; Adrian J. Shepherd; Francesco Pappalardo 001 (Encyclopedia of Bioinformatics and Computational Biology (2), 2019)

Toward computational modelling on immune system function. - Francesco Pappalardo 001; Marzio Pennisi; Pedro A. Reche; Giulia Russo (BMC Bioinform., 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)

Verify: a toolbox for deterministic verification of computational models. - Giuseppe Alessandro Parasiliti Palumbo; Giulia Russo; Giuseppe Sgroi; Marco Viceconti; Marzio Pennisi; Cristina Curreli; Francesco Pappalardo 001 (BIBM, 2020)

Evaluation of the predictive capability of PETAL tool: a retrospective study on potential tyrosine kinases drug resistance targets. - Giuseppe Sgroi; Marzio Pennisi; Giulia Russo; Francesco Pappalardo 001; Giuseppe Alessandro Parasiliti Palumbo (BIBM, 2020)

Generation of digital patients for the simulation of tuberculosis with UISS-TB. - Miguel A. Juárez; Marzio Pennisi; Giulia Russo; Dimitrios Kiagias; Cristina Curreli; Marco Viceconti; Francesco Pappalardo 001 (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)

In silico trial to test COVID-19 candidate vaccines: a case study with UISS platform. - Giulia Russo; Marzio Pennisi; Epifanio Fichera; Santo Motta; Giuseppina Raciti; Marco Viceconti; Francesco Pappalardo 001 (BMC Bioinform., 2020)

Moving forward through the in silico modeling of tuberculosis: a further step with UISS-TB. - Giulia Russo; Giuseppe Sgroi; Giuseppe Alessandro Parasiliti Palumbo; Marzio Pennisi; Miguel A. Juárez; Pere-Joan Cardona; Santo Motta; Kenneth B. Walker; Epifanio Fichera; Marco Viceconti; Francesco Pappalardo 001 (BMC Bioinform., 2020)

In Silico Trial to test COVID-19 candidate vaccines: a case study with UISS platform. - Giulia Russo; Marzio Pennisi; Marco Viceconti; Francesco Pappalardo 001 (CoRR, 2020)

Credibility of In Silico Trial Technologies - A Theoretical Framing. - Marco Viceconti; Miguel A. Juárez; Cristina Curreli; Marzio Pennisi; Giulia Russo; Francesco Pappalardo 001 (IEEE J. Biomed. Health Informatics, 2020)

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

Multi-scale Agent-based Models in Immunology. A Short Review. - Marzio Pennisi (CIKM Workshops, 2021)

A Preliminary Analysis of Hospitalized Covid-19 Patients in Alessandria Area: a machine learning approach. - Marta Betti; Marinella Bertolotti; Tatiana Bolgeo; Alessio Bottrighi; Antonella Cassinari; Antonio Maconi; Costanza Massarino; Marzio Pennisi; Emanuele Rava; Annalisa Roveta (COINS, 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)

Model verification tools: a computational framework for verification assessment of mechanistic agent-based models. - Giulia Russo; Giuseppe Alessandro Parasiliti Palumbo; Marzio Pennisi; Francesco Pappalardo 001 (BMC Bioinform., 2021)

UISS-GPU: Accelerated In-Silico Tuberculosis Vaccine Trials Using FLAME GPU. - Paul Richmond; Matthew Leach; Peter Heywood; Francesco Pappalardo 001; Giulia Russo; Marzio Pennisi (BIBM, 2022)

A machine learning approach for predicting high risk hospitalized patients with COVID-19 SARS-Cov-2. - Alessio Bottrighi; Marzio Pennisi; Annalisa Roveta; Costanza Massarino; Antonella Cassinari; Marta Betti; Tatiana Bolgeo; Marinella Bertolotti; Emanuele Rava; Antonio Maconi (BMC Medical Informatics Decis. Mak., 2022)

Modeling and Simulation of anakinra effects on severe COVID19 Patients. - William Cavallaro; Marzio Pennisi; Evdoxia Kyriazopoulou; Giulia Russo; Maria Cristina Jori; Evangelos J. Giamarellos-Bourboulis; Francesco Pappalardo 001 (BIBM, 2023)

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)

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)

Exploiting Structural Dependency Relations for Efficient Agent Based Model Simulation. - Marzio Pennisi; Elvio G. Amparore; Giuliana Franceschinis (EPEW, 2023)

Exploring the State of Machine Learning and Deep Learning in Medicine: A Survey of the Italian Research Community. - Alessio Bottrighi; Marzio Pennisi (Inf., 2023)

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)

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

AutoML-Med: A Framework for Automated Machine Learning in Medical Tabular Data. - Riccardo Francia; Maurizio Leone; Giorgio Leonardi; Stefania Montani; Marzio Pennisi; Manuel Striani; Sandra D'Alfonso (CoRR, 2025)