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2020 – today
- 2024
[j29]Simone Alessandri, Maria L. Ratto
, Sergio Rabellino, Gabriele Piacenti, Sandro Gepiro Contaldo, Simone Pernice, Marco Beccuti, Raffaele A. Calogero, Luca Alessandrì:
CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications. BMC Bioinform. 25(1): 110 (2024)- [j28]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
- [j27]Simone Pernice, Roberta Sirovich, Elena Grassi, Marco Viviani, Martina Ferri, Francesco Sassi, Luca Alessandrì, Dora Tortarolo, Raffaele A. Calogero, Livio Trusolino, Andrea Bertotti, Marco Beccuti, Martina Olivero, Francesca Cordero:
CONNECTOR, fitting and clustering of longitudinal data to reveal a new risk stratification system. Bioinform. 39(5) (2023) - [j26]Simone Pernice, Alessandro Maglione, Dora Tortarolo, Roberta Sirovich, Marinella Clerico, Simona Rolla, Marco Beccuti, Francesca Cordero:
A new computational workflow to guide personalized drug therapy. J. Biomed. Informatics 148: 104546 (2023) - [c48]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 - [c47]Simone Avesani, Vincenzo Bonnici, Simone Pernice, Marco Beccuti, Rosalba Giugno:
MODIMO: Workshop on Multi-Omics Data Integration for Modelling Biological Systems. CIKM 2023: 5259-5262 - [c46]Marco Beccuti, Antonio d'Acierno, Simone Donetti, Sandro Gepiro Contaldo, Paolo Romano, Giovanna Cristina Varese:
ICT Infrastructure Supporting the Italian Research Infrastructure on Microbial Resources MIRRI-IT. CoRDI 2023 - [c45]Carlo Alberto Barbano, Marco Beccuti, Francesca Cordero, Desislav Nikolaev Ivanov, Nicola Licheri, Simone Pernice, Alberto Presta, Riccardo Renzulli, Marco Grangetto:
Artificial intelligence methods for biomedical imaging and omics data. Ital-IA 2023: 154-159 - 2022
- [j25]Daniele Baccega, Simone Pernice, Pietro Terna, Paolo Castagno, Giovenale Moirano, Lorenzo Richiardi, Matteo Sereno, Sergio Rabellino, Milena Maria Maule, Marco Beccuti:
An Agent-Based Model to Support Infection Control Strategies at School. J. Artif. Soc. Soc. Simul. 25(3) (2022) - 2021
- [j24]Nicola Licheri, Vincenzo Bonnici, Marco Beccuti, Rosalba Giugno:
GRAPES-DD: exploiting decision diagrams for index-driven search in biological graph databases. BMC Bioinform. 22(1): 209 (2021) - [c44]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 - [c43]Marco Beccuti, Vincenzo Bonnici, Rosalba Giugno:
MODIMO: Workshop on Multi-Omics Data Integration for Modelling Biological Systems. CIKM 2021: 4870-4871 - [c42]Nicola Licheri, Elvio Amparone, Vincenzo Bonnici, Rosalba Giugno, Marco Beccuti:
An Entropy Heuristic to Optimize Decision Diagrams for Index-driven Search in Biological Graph Databases. CIKM Workshops 2021 - [c41]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
- [j23]Paolo Castagno, Simone Pernice, Gianni Ghetti, Massimiliano Povero, Lorenzo Pradelli, Daniela Paolotti, Gianfranco Balbo, Matteo Sereno, Marco Beccuti:
A computational framework for modeling and studying pertussis epidemiology and vaccination. BMC Bioinform. 21-S(8): 344 (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]Simone Pernice, Laura Follia, Gianfranco Balbo, Luciano Milanesi, Giulia Sartini, Niccoló Totis, Pietro Lió, Ivan Merelli, Francesca Cordero, Marco Beccuti:
Integrating Petri Nets and Flux Balance Methods in Computational Biology Models: a Methodological and Computational Practice. Fundam. Informaticae 171(1-4): 367-392 (2020) - [i5]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]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) - [c40]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 - [c39]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 - [c38]Marco Beccuti, Lorenzo Capra, Massimiliano De Pierro, Giuliana Franceschinis, Laura Follia, Simone Pernice:
A Tool for the Automatic Derivation of Symbolic ODE from Symmetric Net Models. MASCOTS 2019: 36-48 - [e1]Gabriele Mencagli, Dora B. Heras, Valeria Cardellini, Emiliano Casalicchio, Emmanuel Jeannot, Felix Wolf, Antonio Salis, Claudio Schifanella, Ravi Reddy Manumachu, Laura Ricci, Marco Beccuti, Laura Antonelli, José Daniel García Sánchez, Stephen L. Scott:
Euro-Par 2018: Parallel Processing Workshops - Euro-Par 2018 International Workshops, Turin, Italy, August 27-28, 2018, Revised Selected Papers. Lecture Notes in Computer Science 11339, Springer 2019, ISBN 978-3-030-10548-8 [contents] - 2018
- [j19]Marco Beccuti, Francesca Cordero, Maddalena Arigoni, Riccardo Panero, Elvio Gilberto Amparore, Susanna Donatelli, Raffaele A. Calogero:
SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer. Bioinform. 34(5): 871-872 (2018) - [j18]Neha Kulkarni, Luca Alessandrì, Riccardo Panero, Maddalena Arigoni, Martina Olivero, Giulio Ferrero, Francesca Cordero, Marco Beccuti, Raffaele A. Calogero:
Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines. BMC Bioinform. 19-S(10): 211-219 (2018) - [j17]Elvio Gilberto Amparore, Susanna Donatelli, Marco Beccuti, Giulio Garbi, Andrew S. Miner:
Decision Diagrams for Petri Nets: A Comparison of Variable Ordering Algorithms. Trans. Petri Nets Other Model. Concurr. 13: 73-92 (2018) - [j16]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, Torsten Liebke, Jeroen Meijer, Jirí Srba, Yann Thierry-Mieg, Jaco van de Pol, Karsten Wolf:
MCC'2017 - The Seventh Model Checking Contest. Trans. Petri Nets Other Model. Concurr. 13: 181-209 (2018) - [c37]Simone Pernice, Marco Beccuti, Pietro Do', Marzio Pennisi, Francesco Pappalardo:
Estimating Daclizumab effects in Multiple Sclerosis using Stochastic Symmetric Nets. BIBM 2018: 1393-1400 - [c36]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 - [c35]Marco Beccuti, Lorenzo Capra, Massimiliano De Pierro, Giuliana Franceschinis, Simone Pernice:
Deriving Symbolic Ordinary Differential Equations from Stochastic Symmetric Nets Without Unfolding. EPEW 2018: 30-45 - [c34]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 - [c33]Elvio Gilberto Amparore, Marco Beccuti, Marco Botta, Susanna Donatelli, Fabio Tango:
Adaptive Artificial Co-pilot as Enabler for Autonomous Vehicles and Intelligent Transportation Systems. ATT@IJCAI 2018: 70-77 - 2017
- [j15]Marco Beccuti, Elisa Genuardi, Greta Romano, Luigia Monitillo, Daniela Barbero, Mario Boccadoro, Marco Ladetto, Raffaele A. Calogero, Simone Ferrero, Francesca Cordero:
HashClone: a new tool to quantify the minimal residual disease in B-cell lymphoma from deep sequencing data. BMC Bioinform. 18(1): 516 (2017) - [j14]Niccoló Totis, Laura Follia, Chiara Riganti, Francesco Novelli, Francesca Cordero, Marco Beccuti:
Overcoming the lack of kinetic information in biochemical reactions networks. SIGMETRICS Perform. Evaluation Rev. 44(4): 91-102 (2017) - [c32]Elvio Gilberto Amparore, Susanna Donatelli, Marco Beccuti, Giulio Garbi, Andrew S. Miner:
Decision Diagrams for Petri Nets: Which Variable Ordering? PNSE @ Petri Nets 2017: 31-50 - [c31]Elvio Gilberto Amparore, Marco Beccuti, Susanna Donatelli:
Gradient-Based Variable Ordering of Decision Diagrams for Systems with Structural Units. ATVA 2017: 184-200 - [c30]Giorgia Chivassa, Chiara Fornari, Roberta Sirovich, Marzio Pennisi, Marco Beccuti, Francesca Cordero:
A mathematical model to study breast cancer growth. BIBM 2017: 1438-1445 - [c29]Paolo Ballarini, Marco Beccuti, Enrico Bibbona, András Horváth, Roberta Sirovich, Jeremy Sproston:
Analysis of Timed Properties Using the Jump-Diffusion Approximation. EPEW 2017: 69-84 - 2016
- [c28]Niccoló Totis, Marco Beccuti, Francesca Cordero, Laura Follia, Chiara Riganti, Francesco Novelli:
Dealing with indetermination in biochemical networks. VALUETOOLS 2016 - 2015
- [j13]Matteo Carrara, Josephine Lum, Francesca Cordero, Marco Beccuti, Michael Poidinger, Susanna Donatelli, Raffaele A. Calogero, Francesca Zolezzi:
Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis. BMC Bioinform. 16(S-9): S2 (2015) - [j12]Chiara Fornari, Gianfranco Balbo, Sami M. Halawani, Omar M. Ba-Rukab, Ab Rahman Ahmad, Raffaele A. Calogero, Francesca Cordero, Marco Beccuti:
A versatile mathematical work-flow to explore how Cancer Stem Cell fate influences tumor progression. BMC Syst. Biol. 9(S-3): S1 (2015) - [j11]Marco Beccuti, Chiara Fornari, Giuliana Franceschinis, Sami M. Halawani, Omar M. Ba-Rukab, Ab Rahman Ahmad, Gianfranco Balbo:
From Symmetric Nets to Differential Equations exploiting Model Symmetries. Comput. J. 58(1): 23-39 (2015) - [j10]Alessio Angius, Gianfranco Balbo, Marco Beccuti, Enrico Bibbona, András Horváth, Roberta Sirovich:
Approximate analysis of biological systems by hybrid switching jump diffusion. Theor. Comput. Sci. 587: 49-72 (2015) - [c27]Marco Beccuti, Elvio Gilberto Amparore, Susanna Donatelli, Dimitri Scheftelowitsch, Peter Buchholz, Giuliana Franceschinis:
Markov Decision Petri Nets with Uncertainty. EPEW 2015: 177-192 - [c26]Denise Duma, Francesca Cordero, Marco Beccuti, Gianfranco Ciardo, Timothy J. Close, Stefano Lonardi:
Scrible: Ultra-Accurate Error-Correction of Pooled Sequenced Reads. WABI 2015: 162-174 - 2014
- [j9]Marco Beccuti, Matteo Carrara, Francesca Cordero, Fulvio Lazzarato, Susanna Donatelli, Francesca Nadalin, Alberto Policriti, Raffaele A. Calogero:
Chimera: a Bioconductor package for secondary analysis of fusion products. Bioinform. 30(24): 3556-3557 (2014) - [j8]Marco Beccuti, Giuliana Franceschinis, Daniele Codetta Raiteri, Serge Haddad:
Computing Optimal Repair Strategies by Means of NdRFT Modeling and Analysis. Comput. J. 57(12): 1870-1892 (2014) - [c25]Marco Beccuti:
Mathematical models on cancer progression. BioPPN@Petri Nets 2014: 1-2 - [c24]Marco Beccuti, Enrico Bibbona, András Horváth, Roberta Sirovich, Alessio Angius, Gianfranco Balbo:
Analysis of Petri Net Models through Stochastic Differential Equations. Petri Nets 2014: 273-293 - [c23]Elvio Gilberto Amparore, Marco Beccuti, Susanna Donatelli:
(Stochastic) Model Checking in GreatSPN. Petri Nets 2014: 354-363 - [c22]Elvio Gilberto Amparore, Marco Beccuti, Simona Collina, Flavia De Simone, Susanna Donatelli, Fabio Tango:
Cognitive Systems in Intelligent Vehicles - A New Frontier for Autonomous Driving. ICINCO (2) 2014: 817-822 - [i4]Marco Beccuti, Enrico Bibbona, András Horváth, Roberta Sirovich, Alessio Angius, Gianfranco Balbo:
Analysis of Petri Net Models through Stochastic Differential Equations. CoRR abs/1404.0975 (2014) - [i3]Alessio Angius, Gianfranco Balbo, Marco Beccuti, Enrico Bibbona, András Horváth, Roberta Sirovich:
Approximate analysis of biological systems by hybrid switching jump diffusion. CoRR abs/1406.1352 (2014) - 2013
- [j7]Francesca Cordero, Marco Beccuti, Chiara Fornari, Stefania Lanzardo, Laura Conti, Federica Cavallo, Gianfranco Balbo, Raffaele A. Calogero:
Multi-level model for the investigation of oncoantigen-driven vaccination effect. BMC Bioinform. 14(S-6): S11 (2013) - [j6]Matteo Carrara, Marco Beccuti, Federica Cavallo, Susanna Donatelli, Fulvio Lazzarato, Francesca Cordero, Raffaele A. Calogero:
State of art fusion-finder algorithms are suitable to detect transcription-induced chimeras in normal tissues? BMC Bioinform. 14(S-7): S2 (2013) - [j5]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, Serdar Bozdag, Ming-Cheng Luo, Timothy J. Close:
Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space. PLoS Comput. Biol. 9(4) (2013) - [c21]Elvio Gilberto Amparore, Paolo Ballarini, Marco Beccuti, Susanna Donatelli, Giuliana Franceschinis:
Expressing and Computing Passage Time Measures of GSPN Models with HASL. Petri Nets 2013: 110-129 - [c20]Elvio Gilberto Amparore, Benoît Barbot, Marco Beccuti, Susanna Donatelli, Giuliana Franceschinis:
Simulation-based verification of hybrid automata stochastic logic formulas for stochastic symmetric nets. SIGSIM-PADS 2013: 253-264 - [i2]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, César Rodríguez, Christian Rohr, Yann Thierry-Mieg, Harro Wimmel, Karsten Wolf:
Model Checking Contest @ Petri Nets, Report on the 2013 edition. CoRR abs/1309.2485 (2013) - 2012
- [j4]Marco Beccuti, Silvano Chiaradonna, Felicita Di Giandomenico, Susanna Donatelli, Giovanna Dondossola, Giuliana Franceschinis:
Quantification of dependencies between electrical and information infrastructures. Int. J. Crit. Infrastructure Prot. 5(1): 14-27 (2012) - [c19]Marco Beccuti, Andrea Bobbio, Giuliana Franceschinis, Roberta Terruggia:
A new symbolic approach for network reliability analysis. DSN 2012: 1-12 - [c18]Marco Beccuti, Giuliana Franceschinis:
Efficient simulation of stochastic well-formed nets through symmetry exploitation. WSC 2012: 296:1-296:13 - 2011
- [j3]Gianfranco Balbo, Marco Beccuti, Massimiliano De Pierro, Giuliana Franceschinis:
First Passage Time Computation in Tagged GSPNs with Queue Places. Comput. J. 54(5): 653-673 (2011) - [j2]Souheib Baarir, Marco Beccuti, Claude Dutheillet, Giuliana Franceschinis, Serge Haddad:
Lumping partially symmetrical stochastic models. Perform. Evaluation 68(1): 21-44 (2011) - [c17]Elvio Gilberto Amparore, Marco Beccuti, Susanna Donatelli, Giuliana Franceschinis:
Probe Automata for Passage Time Specification. QEST 2011: 101-110 - [c16]Marco Beccuti, Massimiliano De Pierro, András Horváth, Ádám Horváth, Károly Farkas:
A Mean Field Based Methodology for Modeling Mobility in Ad Hoc Networks. VTC Spring 2011: 1-5 - [c15]Gianfranco Balbo, Marco Beccuti, Massimiliano De Pierro, Giuliana Franceschinis:
Computing first passage time distributions in stochastic well-formed nets. ICPE 2011: 7-18 - [i1]Stefano Lonardi, Denisa Duma, Matthew Alpert, Francesca Cordero, Marco Beccuti, Prasanna Bhat, Yonghui Wu, Gianfranco Ciardo, Burair Alsaihati, Yaqin Ma, Steve Wanamaker, Josh Resnik, Timothy J. Close:
Barcoding-free BAC Pooling Enables Combinatorial Selective Sequencing of the Barley Gene Space. CoRR abs/1112.4438 (2011) - 2010
- [c14]Junaid Babar, Marco Beccuti, Susanna Donatelli, Andrew S. Miner:
GreatSPN Enhanced with Decision Diagram Data Structures. Petri Nets 2010: 308-317 - [c13]Gianfranco Balbo, Marco Beccuti, Massimiliano De Pierro, Giuliana Franceschinis:
Stochastic Petri Nets Sensitivity to Token Scheduling Policies. OR 2010: 181-186 - [c12]Marco Beccuti, V. Fragnelli, Giuliana Franceschinis, S. Villa:
Dynamic Simulations of Kidney Exchanges. OR 2010: 539-544
2000 – 2009
- 2009
- [j1]Souheib Baarir, Marco Beccuti, Davide Cerotti, Massimiliano De Pierro, Susanna Donatelli, Giuliana Franceschinis:
The GreatSPN tool: recent enhancements. SIGMETRICS Perform. Evaluation Rev. 36(4): 4-9 (2009) - [c11]Marco Beccuti, Alessio Bottrighi, Giuliana Franceschinis, Stefania Montani, Paolo Terenziani:
Modeling Clinical Guidelines through Petri Nets. AIME 2009: 61-70 - [c10]Marco Beccuti, Giuliana Franceschinis, Daniele Codetta Raiteri, Serge Haddad:
Parametric NdRFT for the derivation of optimal repair strategies. DSN 2009: 399-408 - [c9]Souheib Baarir, Marco Beccuti, Claude Dutheillet, Giuliana Franceschinis:
From partially to fully lumped Markov chains in stochastic well formed Petri nets. VALUETOOLS 2009: 43 - [c8]Marco Beccuti, Daniele Codetta Raiteri, Giuliana Franceschinis:
Multiple abstraction levels in performance analysis of WSN monitoring systems. VALUETOOLS 2009: 73 - 2008
- [c7]Marco Beccuti, Giuliana Franceschinis, Mohamed Kaâniche, Karama Kanoun:
Multi-level Dependability Modeling of Interdependencies between the Electricity and Information Infrastructures. CRITIS 2008: 48-59 - [c6]Souheib Baarir, Marco Beccuti, Giuliana Franceschinis:
New Solvers for Asymmetric Systems in GreatSPN. QEST 2008: 235-236 - [c5]Marco Beccuti, Daniele Codetta Raiteri, Giuliana Franceschinis, Serge Haddad:
Non deterministic repairable fault trees for computing optimal repair strategy. VALUETOOLS 2008: 56 - 2007
- [c4]Marco Beccuti, Giuliana Franceschinis, Serge Haddad:
Markov Decision Petri Net and Markov Decision Well-Formed Net Formalisms. ICATPN 2007: 43-62 - [c3]Marco Beccuti, Daniele Codetta Raiteri, Giuliana Franceschinis, Serge Haddad:
A framework to design and solve Markov Decision Well-formed Net models. QEST 2007: 165-166 - 2006
- [c2]Marco Beccuti, Giuliana Franceschinis, Souheib Baarir, Jean-Michel Ilié:
Efficient lumpability check in partially symmetric systems. QEST 2006: 211-220 - 2004
- [c1]Jean-Michel Ilié, Souheib Baarir, Marco Beccuti, Clément Delamare, Susanna Donatelli, Claude Dutheillet, Giuliana Franceschinis, Rossano Gaeta, Patrice Moreaux:
Extended SWN Solvers in GreatSPN. QEST 2004: 324-325
Coauthor Index
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