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2020 – today
- 2024
[j29]Elvio Gilberto Amparore
, Marco Beccuti, Paolo Castagno, Simone Pernice, Giuliana Franceschinis, Marzio Pennisi:
From Compositional Petri Net Modeling to Macro and Micro Simulation by Means of Stochastic Simulation and Agent-Based Models. ACM Trans. Model. Perform. Evaluation Comput. Syst. 9(1): 1:1-1:30 (2024)- 2023
- [j28]Alessio Bottrighi, Marzio Pennisi:
Exploring the State of Machine Learning and Deep Learning in Medicine: A Survey of the Italian Research Community. Inf. 14(9): 513 (2023) - [c44]William Cavallaro, Marzio Pennisi, Evdoxia Kyriazopoulou, Giulia Russo, Maria Cristina Jori, Evangelos J. Giamarellos-Bourboulis, Francesco Pappalardo:
Modeling and Simulation of anakinra effects on severe COVID19 Patients. BIBM 2023: 3684-3691 - [c43]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, Francesca Cordero:
OmniReprodubileCellAnalysis: a comprehensive toolbox for the analysis of cellular biology data. BIBM 2023: 3748-3755 - [c42]Marzio Pennisi, Elvio G. Amparore, Giuliana Franceschinis:
Exploiting Structural Dependency Relations for Efficient Agent Based Model Simulation. EPEW 2023: 353-368 - 2022
- [j27]Alessio Bottrighi, Marzio Pennisi, Annalisa Roveta, Costanza Massarino, Antonella Cassinari, Marta Betti, Tatiana Bolgeo, Marinella Bertolotti, Emanuele Rava, Antonio Maconi:
A machine learning approach for predicting high risk hospitalized patients with COVID-19 SARS-Cov-2. BMC Medical Informatics Decis. Mak. 22(1): 340 (2022) - [c41]Paul Richmond, Matthew Leach, Peter Heywood, Francesco Pappalardo, Giulia Russo, Marzio Pennisi:
UISS-GPU: Accelerated In-Silico Tuberculosis Vaccine Trials Using FLAME GPU. BIBM 2022: 3562-3568 - 2021
- [j26]Giulia Russo, Giuseppe Alessandro Parasiliti Palumbo, Marzio Pennisi, Francesco Pappalardo:
Model verification tools: a computational framework for verification assessment of mechanistic agent-based models. BMC Bioinform. 22-S(14): 626 (2021) - [c40]Elvio Gilberto Amparore, Marco Beccuti, Paolo Castagno, Giuliana Franceschinis, Marzio Pennisi, Simone Pernice:
Multiformalism modeling and simulation of immune system mechanisms. BIBM 2021: 3259-3266 - [c39]Marzio Pennisi:
Multi-scale Agent-based Models in Immunology. A Short Review. CIKM Workshops 2021 - [c38]Marta Betti, Marinella Bertolotti, Tatiana Bolgeo, Alessio Bottrighi, Antonella Cassinari, Antonio Maconi, Costanza Massarino, Marzio Pennisi, Emanuele Rava, Annalisa Roveta:
A Preliminary Analysis of Hospitalized Covid-19 Patients in Alessandria Area: a machine learning approach. COINS 2021: 1-6 - [c37]Marco Beccuti, Paolo Castagno, Giuliana Franceschinis, Marzio Pennisi, Simone Pernice:
A Petri Net Formalism to Study Systems at Different Scales Exploiting Agent-Based and Stochastic Simulations. EPEW 2021: 22-43 - 2020
- [j25]Miguel A. Juárez, Marzio Pennisi, Giulia Russo, Dimitrios Kiagias, Cristina Curreli, Marco Viceconti, Francesco Pappalardo:
Generation of digital patients for the simulation of tuberculosis with UISS-TB. BMC Bioinform. 21-S(17): 449 (2020) - [j24]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:
Moving forward through the in silico modeling of tuberculosis: a further step with UISS-TB. BMC Bioinform. 21-S(17): 458 (2020) - [j23]Giulia Russo, Marzio Pennisi, Epifanio Fichera, Santo Motta, Giuseppina Raciti, Marco Viceconti, Francesco Pappalardo:
In silico trial to test COVID-19 candidate vaccines: a case study with UISS platform. BMC Bioinform. 21-S(17): 527 (2020) - [j22]Simone Pernice, Laura Follia, Alessandro Maglione, Marzio Pennisi, Francesco Pappalardo, Francesco Novelli, Marinella Clerico, Marco Beccuti, Francesca Cordero, Simona Rolla:
Computational modeling of the immune response in multiple sclerosis using epimod framework. BMC Bioinform. 21-S(17): 550 (2020) - [j21]Marco Viceconti, Miguel A. Juárez, Cristina Curreli, Marzio Pennisi, Giulia Russo, Francesco Pappalardo:
Credibility of In Silico Trial Technologies - A Theoretical Framing. IEEE J. Biomed. Health Informatics 24(1): 4-13 (2020) - [c36]Giuseppe Alessandro Parasiliti Palumbo, Giulia Russo, Giuseppe Sgroi, Marco Viceconti, Marzio Pennisi, Cristina Curreli, Francesco Pappalardo:
Verify: a toolbox for deterministic verification of computational models. BIBM 2020: 1262-1267 - [c35]Giuseppe Sgroi, Marzio Pennisi, Giulia Russo, Francesco Pappalardo, Giuseppe Alessandro Parasiliti Palumbo:
Evaluation of the predictive capability of PETAL tool: a retrospective study on potential tyrosine kinases drug resistance targets. BIBM 2020: 1275-1280 - [i5]Giulia Russo, Marzio Pennisi, Marco Viceconti, Francesco Pappalardo:
In Silico Trial to test COVID-19 candidate vaccines: a case study with UISS platform. CoRR abs/2005.02289 (2020) - [i4]Simone Pernice, Marco Beccuti, Greta Romano, Marzio Pennisi, Alessandro Maglione, Santina Cutrupi, Francesco Pappalardo, Lorenzo Capra, Giuliana Franceschinis, Massimiliano De Pierro, Gianfranco Balbo, Francesca Cordero, Raffaele A. Calogero:
Multiple Sclerosis disease: a computational approach for investigating its drug interactions. CoRR abs/2006.00813 (2020)
2010 – 2019
- 2019
- [j20]Fiorenza Gianì, Giulia Russo, Marzio Pennisi, Laura Sciacca, Francesco Frasca, Francesco Pappalardo:
Computational modeling reveals MAP3K8 as mediator of resistance to vemurafenib in thyroid cancer stem cells. Bioinform. 35(13): 2267-2275 (2019) - [j19]Saverio Candido, Giuseppe Alessandro Parasiliti Palumbo, Marzio Pennisi, Giulia Russo, Giuseppe Sgroi, Valentina Di Salvatore, Massimo Libra, Francesco Pappalardo:
EpiMethEx: a tool for large-scale integrated analysis in methylation hotspots linked to genetic regulation. BMC Bioinform. 19-S(13): 43-53 (2019) - [j18]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:
Predicting the artificial immunity induced by RUTI® vaccine against tuberculosis using universal immune system simulator (UISS). BMC Bioinform. 20-S(6): 504 (2019) - [j17]Mozhgan Kabiri Chimeh, Peter Heywood, Marzio Pennisi, Francesco Pappalardo, Paul Richmond:
Parallelisation strategies for agent based simulation of immune systems. BMC Bioinform. 20-S(6): 579 (2019) - [j16]Francesco Pappalardo, Marzio Pennisi, Pedro A. Reche, Giulia Russo:
Toward computational modelling on immune system function. BMC Bioinform. 20-S(6): 622 (2019) - [j15]Simone Pernice, Marzio Pennisi, Greta Romano, Alessandro Maglione, Santina Cutrupi, Francesco Pappalardo, Gianfranco Balbo, Marco Beccuti, Francesca Cordero, Raffaele A. Calogero:
A computational approach based on the colored Petri net formalism for studying multiple sclerosis. BMC Bioinform. 20-S(6): 623 (2019) - [c34]Giuseppe Alessandro Parasiliti Palumbo, Pietro Biondi, Giuseppe Sgroi, Marzio Pennisi, Giulia Russo, Francesco Pappalardo:
A MapReduce tool for in-depth analysis of KEGG pathways: identification and visualization of therapeutic target candidates. BIBM 2019: 2157-2162 - [c33]Marzio Pennisi, Miguel A. Juárez, Giulia Russo, Marco Viceconti, Francesco Pappalardo:
Generation of digital patients for the simulation of tuberculosis with UISS-TB. BIBM 2019: 2163-2167 - [c32]Simone Pernice, Greta Romano, Giulia Russo, Marco Beccuti, Marzio Pennisi, Francesco Pappalardo:
Exploiting Stochastic Petri Net formalism to capture the Relapsing Remitting Multiple Sclerosis variability under Daclizumab administration. BIBM 2019: 2168-2175 - [c31]Giulia Russo, Francesco Pappalardo, Miguel A. Juárez, Marzio Pennisi, Pere-Joan Cardona, Rhea Coler, Epifanio Fichera, Marco Viceconti:
Evaluation of the efficacy of RUTI and ID93/GLA-SE vaccines in tuberculosis treatment: in silico trial through UISS-TB simulator. BIBM 2019: 2197-2201 - [c30]Valentina Di Salvatore, Fiorenza Gianì, Giulia Russo, Marzio Pennisi, Pasqualino Malandrino, Francesco Frasca, Francesco Pappalardo:
Gene expression and pathway bioinformatics analysis detect a potential predictive value of MAP3K8 in thyroid cancer progression. BIBM 2019: 2202-2206 - [c29]Marzio Pennisi, Giulia Russo, Giuseppe Sgroi, Giuseppe Alessandro Parasiliti Palumbo, Francesco Pappalardo:
In Silico Evaluation of Daclizumab and Vitamin D Effects in Multiple Sclerosis Using Agent Based Models. CIBB 2019: 285-298 - [c28]Simone Pernice, Marco Beccuti, Greta Romano, Marzio Pennisi, Alessandro Maglione, Santina Cutrupi, Francesco Pappalardo, Lorenzo Capra, Giuliana Franceschinis, Massimiliano De Pierro, Gianfranco Balbo, Francesca Cordero, Raffaele A. Calogero:
Multiple Sclerosis Disease: A Computational Approach for Investigating Its Drug Interactions. CIBB 2019: 299-308 - [c27]Giuseppe Parasiliti, Marzio Pennisi, Pietro Biondi, Giuseppe Sgroi, Giulia Russo, Christian Napoli, Francesco Pappalardo:
A MapReduce Based Tool for the Analysis and Discovery of Novel Therapeutic Targets. PDP 2019: 323-328 - [r1]Marta Gomez-Perosanz, Giulia Russo, Jose Luis Sanchez-Trincado Lopez, Marzio Pennisi, Pedro A. Reche, Adrian J. Shepherd, Francesco Pappalardo:
Computational Immunogenetics. Encyclopedia of Bioinformatics and Computational Biology (2) 2019: 906-930 - [i3]Marco Viceconti, Miguel A. Juárez, Cristina Curreli, Marzio Pennisi, Giulia Russo, Francesco Pappalardo:
POSITION PAPER: Credibility of In Silico Trial Technologies: A Theoretical Framing. CoRR abs/1909.04660 (2019) - [i2]Valentina Di Salvatore, Fiorenza Gianì, Giulia Russo, Marzio Pennisi, Pasqualino Malandrino, Francesco Frasca, Francesco Pappalardo:
Gene expression and pathway bioinformatics analysis detect a potential predictive value of MAP3K8 in thyroid cancer progression. CoRR abs/1910.12055 (2019) - [i1]Marzio Pennisi, Miguel A. Juárez, Giulia Russo, Marco Viceconti, Francesco Pappalardo:
Generation of digital patients for the simulation of tuberculosis with UISS-TB. CoRR abs/1910.12293 (2019) - 2018
- [j14]Giulia Russo, Marzio Pennisi, Roberta Boscarino, Francesco Pappalardo:
Continuous Petri Nets and microRNA Analysis in Melanoma. IEEE ACM Trans. Comput. Biol. Bioinform. 15(5): 1492-1499 (2018) - [c26]Mozhgan K. Chimeh, Peter Heywood, Marzio Pennisi, Francesco Pappalardo, Paul Richmond:
Parallel Pair-Wise Interaction for Multi-Agent Immune Systems Modelling. BIBM 2018: 1367-1373 - [c25]Francesco Pappalardo, Giulia Russo, Marzio Pennisi, Giuseppe Sgroi, Giuseppe Alessandro Parasiliti Palumbo, Santo Motta, Davide Maimone, Ferdinando Chiacchio:
Agent based modeling of relapsing multiple sclerosis: a possible approach to predict treatment outcome. BIBM 2018: 1380-1385 - [c24]Francesco Pappalardo, Giulia Russo, Marzio Pennisi, Giuseppe Sgroi, Giuseppe Alessandro Parasiliti Palumbo, Santo Motta, Epifanio Fichera:
An agent based modeling approach for the analysis of tuberculosis - immune system dynamics. BIBM 2018: 1386-1392 - [c23]Simone Pernice, Marco Beccuti, Pietro Do', Marzio Pennisi, Francesco Pappalardo:
Estimating Daclizumab effects in Multiple Sclerosis using Stochastic Symmetric Nets. BIBM 2018: 1393-1400 - [c22]Niccoló Totis, Andrea Tangherloni, Marco Beccuti, Paolo Cazzaniga, Marco S. Nobile, Daniela Besozzi, Marzio Pennisi, Francesco Pappalardo:
Efficient and Settings-Free Calibration of Detailed Kinetic Metabolic Models with Enzyme Isoforms Characterization. CIBB 2018: 187-202 - [c21]Marco Beccuti, Paolo Cazzaniga, Marzio Pennisi, Daniela Besozzi, Marco S. Nobile, Simone Pernice, Giulia Russo, Andrea Tangherloni, Francesco Pappalardo:
GPU Accelerated Analysis of Treg-Teff Cross Regulation in Relapsing-Remitting Multiple Sclerosis. Euro-Par Workshops 2018: 626-637 - [c20]Marzio Pennisi, Gabriele Forzano, Giulia Russo, Barbara Tomasello, Marco Favetta, Marcella Renis, Francesco Pappalardo:
BIOESOnet: A Tool for the Generation of Personalized Human Metabolic Pathways from 23andMe Exome Data. ICIC (2) 2018: 345-352 - [c19]Marzio Pennisi, Giulia Russo, Francesco Pappalardo:
Combining Parallel Genetic Algorithms and Machine Learning to Improve the Research of Optimal Vaccination Protocols. PDP 2018: 399-405 - 2017
- [j13]Marzio Pennisi, Giulia Russo, Silvia Ravalli, Francesco Pappalardo:
Combining agent based-models and virtual screening techniques to predict the best citrus-derived vaccine adjuvants against human papilloma virus. BMC Bioinform. 18(16): 87-97 (2017) - [c18]Giorgia Chivassa, Chiara Fornari, Roberta Sirovich, Marzio Pennisi, Marco Beccuti, Francesca Cordero:
A mathematical model to study breast cancer growth. BIBM 2017: 1438-1445 - [c17]Marzio Pennisi, Juan A. Sanchez-Lantaron, Pedro A. Reche, Giulia Russo, Francesco Pappalardo:
Optimization and analisys of vaccination schedules using simulated annealing and agent based models. BIBM 2017: 1455-1460 - [c16]Juan A. Sanchez-Lantaron, Pedro A. Reche, Marzio Pennisi, Giulia Russo, Francesco Pappalardo:
Introducing scale factor adjustments on agent-based simulations of the immune system. BIBM 2017: 1461-1468 - [c15]Marzio Pennisi, Giulia Russo, Giuseppe Sgroi, Giuseppe Parasiliti, Francesco Pappalardo:
2DIs: A SBML Compliant Web Platform for the Design and Modeling of Immune System Interactions. ICIC (2) 2017: 145-154 - [c14]Giulia Russo, Marzio Pennisi, Roberta Boscarino, Francesco Pappalardo:
Modeling PI3K/PDK1/Akt and MAPK Signaling Pathways Using Continuous Petri Nets. ICIC (2) 2017: 169-175 - 2016
- [j12]Francesco Pappalardo, Epifanio Fichera, Nicoletta Paparone, Alessandro Lombardo, Marzio Pennisi, Giulia Russo, Marco Leotta, Alessandro Pedretti, Francesco De Fiore, Santo Motta:
A computational model to predict the immune system activation by citrus-derived vaccine adjuvants. Bioinform. 32(17): 2672-2680 (2016) - [j11]Marzio Pennisi, Salvatore Cavalieri, Santo Motta, Francesco Pappalardo:
A methodological approach for using high-level Petri Nets to model the immune system response. BMC Bioinform. 17(S-19): 91-105 (2016) - [j10]Ferdinando Chiacchio, Diego D'Urso, Lucio Compagno, Marzio Pennisi, Francesco Pappalardo, Gabriele Manno:
SHyFTA, a Stochastic Hybrid Fault Tree Automaton for the modelling and simulation of dynamic reliability problems. Expert Syst. Appl. 47: 42-57 (2016) - 2015
- [j9]Francesca Gullo, Mark van der Garde, Giulia Russo, Marzio Pennisi, Santo Motta, Francesco Pappalardo, Suzanne Watt:
Computational modeling of the expansion of human cord blood CD133+ hematopoietic stem/progenitor cells with different cytokine combinations. Bioinform. 31(15): 2514-2522 (2015) - 2014
- [j8]Francesco Pappalardo, Marzio Pennisi, Alessia Ricupito, Francesco Topputo, Matteo Bellone:
Induction of T-cell memory by a dendritic cell vaccine: a computational model. Bioinform. 30(13): 1884-1891 (2014) - [c13]Francesco Pappalardo, Marzio Pennisi, Abdul Mateen Rajput, Ferdinando Chiacchio, Santo Motta:
Relapsing-remitting multiple scleroris and the role of vitamin D: an agent based model. BCB 2014: 744-748 - [c12]Abdul Mateen Rajput, Marzio Pennisi, Santo Motta, Francesco Pappalardo:
OntoFast: Construct Ontology Rapidly. KESW 2014: 237-241 - 2013
- [j7]Marzio Pennisi, Abdul Mateen Rajput, Luca Toldo, Francesco Pappalardo:
Agent based modeling of Treg-Teff cross regulation in relapsing-remitting multiple sclerosis. BMC Bioinform. 14(S-16): S9 (2013) - [c11]Francesco Pappalardo, Marzio Pennisi, Ferdinando Chiacchio, Salvatore Musumeci, Santo Motta:
iAtheroSim: atherosclerosis process simulator on smart devices. BCB 2013: 815 - 2012
- [j6]Carlo Bianca, Ferdinando Chiacchio, Francesco Pappalardo, Marzio Pennisi:
Mathematical modeling of the immune system recognition to mammary carcinoma antigen. BMC Bioinform. 13(S-17): S21 (2012) - [j5]Marzio Pennisi:
A Mathematical Model of Immune-System-Melanoma Competition. Comput. Math. Methods Medicine 2012: 850754:1-850754:13 (2012) - 2011
- [c10]Marzio Pennisi, Dario Motta, Alessandro Cincotti, Francesco Pappalardo:
Predicting Long-Term Vaccine Efficacy against Metastases Using Agents. ICIC (3) 2011: 97-106 - 2010
- [j4]Marzio Pennisi, Francesco Pappalardo, Arianna Palladini, Giordano Nicoletti, Patrizia Nanni, Pierluigi Lollini, Santo Motta:
Modeling the competition between lung metastases and the immune system using agents. BMC Bioinform. 11(S-7): S13 (2010) - [c9]Francesco Pappalardo, Marzio Pennisi, Santo Motta:
Universal immune system simulator framework (UISS). BCB 2010: 649-650 - [c8]Francesco Pappalardo, Marzio Pennisi, Alessandro Cincotti, Ferdinando Chiacchio, Santo Motta, Pierluigi Lollini:
Cancer Immunoprevention: What Can We Learn from in Silico Models? ICIC (3) 2010: 111-118 - [c7]Francesco Pappalardo, Marzio Pennisi, Ferdinando Chiacchio, Alessandro Cincotti, Santo Motta:
GRIDUISS - A Grid Based Universal Immune System Simulator Framework. ICIC (1) 2010: 285-290
2000 – 2009
- 2009
- [j3]Francesco Pappalardo, Mark D. Halling-Brown, Nicolas Rapin, Ping Zhang, Davide Alemani, Andrew P. J. Emerson, Paola Paci, Patrice Duroux, Marzio Pennisi, Arianna Palladini, Olivo Miotto, Daniel Churchill, Elda Rossi, Adrian J. Shepherd, David S. Moss, Filippo Castiglione, Massimo Bernaschi, Marie-Paule Lefranc, Søren Brunak, Santo Motta, Pierluigi Lollini, Kaye E. Basford, Vladimir Brusic:
ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization. Briefings Bioinform. 10(3): 330-340 (2009) - [j2]Marzio Pennisi, Roberto Catanuto, Francesco Pappalardo, Santo Motta, Emilio Mastriani, Alessandro Cincotti:
Simulated Annealing and Optimal Protocols. J. Circuits Syst. Comput. 18(8): 1565-1579 (2009) - [c6]Francesco Pappalardo, Mark D. Halling-Brown, Marzio Pennisi, Ferdinando Chiacchio, Clare Sansom, Adrian J. Shepherd, David S. Moss, Santo Motta, Vladimir Brusic:
The ImmunoGrid Simulator: How to Use It. CIBB 2009: 1-19 - [c5]Francesco Pappalardo, Cristiano Calonaci, Marzio Pennisi, Emilio Mastriani, Santo Motta:
HAMFAST: Fast Hamming Distance Computation. CSIE (1) 2009: 569-572 - [c4]Marzio Pennisi, Francesco Pappalardo, Santo Motta:
Agent Based Modeling of Lung Metastasis-Immune System Competition. ICARIS 2009: 1-3 - [c3]Francesco Pappalardo, Alessandro Cincotti, Alfredo Motta, Marzio Pennisi:
Agent Based Modeling of Atherosclerosis: A Concrete Help in Personalized Treatments. ICIC (2) 2009: 386-396 - 2008
- [j1]Marzio Pennisi, Roberto Catanuto, Francesco Pappalardo, Santo Motta:
Optimal vaccination schedules using simulated annealing. Bioinform. 24(15): 1740-1742 (2008) - 2007
- [c2]Marzio Pennisi, Francesco Pappalardo, Alfredo Motta, Alessandro Cincotti:
A Genetic Algorithm for Shortest Path Motion Problem in Three Dimensions. ICIC (2) 2007: 534-542 - [c1]Francesco Pappalardo, Santo Motta, Pierluigi Lollini, Emilio Mastriani, Marzio Pennisi:
Towards a Personalized Schedule with Triplex Vaccine. WILF 2007: 620-626
Coauthor Index
Giuseppe Alessandro Parasiliti Palumbo
aka: Giuseppe Parasiliti
aka: Giuseppe Parasiliti
[c44] [c41] [j26] [j25] [j24] [j23] [j22] [j21] [c36] [c35] [i5] [i4] [j20] [j19] [j18] [j17] [j16] [j15] [c34] [c33] [c32] [c31] [c30] [c29] [c28] [c27] [r1] [i3] [i2] [i1] [j14] [c26] [c25] [c24] [c23] [c22] [c21] [c20] [c19] [j13] [c17] [c16] [c15] [c14] [j12] [j11] [j10] [j9] [j8] [c13] [c12] [j7] [c11] [j6] [c10] [j4] [c9] [c8] [c7] [j3] [j2] [c6] [c5] [c4] [c3] [j1] [c2] [c1]
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