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2020 – today
- 2023
[j28]Gianluca Ascolani, Fabrizio Angaroni, Davide Maspero, Francesco Craighero, Narra Lakshmi Sai Bhavesh, Rocco Piazza, Chiara Damiani, Daniele Ramazzotti
, Marco Antoniotti, Alex Graudenzi:
LACE 2.0: an interactive R tool for the inference and visualization of longitudinal cancer evolution. BMC Bioinform. 24(1): 99 (2023)- [j27]Valentina Crippa, Federica Malighetti, Matteo Villa, Alex Graudenzi, Rocco Piazza, Luca Mologni, Daniele Ramazzotti:
Characterization of cancer subtypes associated with clinical outcomes by multi-omics integrative clustering. Comput. Biol. Medicine 162: 107064 (2023) - [j26]Francesco Craighero, Fabrizio Angaroni, Fabio Stella, Chiara Damiani, Marco Antoniotti, Alex Graudenzi:
Unity is strength: Improving the detection of adversarial examples with ensemble approaches. Neurocomputing 554: 126576 (2023) - [j25]Lucrezia Patruno, Salvatore Milite, Riccardo Bergamin, Nicola Calonaci, Alberto d'Onofrio, Fabio Anselmi, Marco Antoniotti, Alex Graudenzi, Giulio Caravagna:
A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing. PLoS Comput. Biol. 19(11) (2023) - 2022
- [j24]Fabrizio Angaroni, Kevin Chen, Chiara Damiani, Giulio Caravagna, Alex Graudenzi, Daniele Ramazzotti:
PMCE: efficient inference of expressive models of cancer evolution with high prognostic power. Bioinform. 38(3): 754-762 (2022) - [j23]Fabrizio Angaroni, Alessandro Guidi, Gianluca Ascolani, Alberto d'Onofrio, Marco Antoniotti, Alex Graudenzi:
J-SPACE: a Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments. BMC Bioinform. 23(1): 269 (2022) - [j22]Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Gianluca Ascolani, Isabella Castiglioni, Rocco Piazza, Marco Antoniotti, Alex Graudenzi:
LACE: Inference of cancer evolution models from longitudinal single-cell sequencing data. J. Comput. Sci. 58: 101523 (2022) - [c22]Davide Maspero, Fabrizio Angaroni, Lucrezia Patruno, Daniele Ramazzotti, David Posada, Alex Graudenzi:
Exploring the Solution Space of Cancer Evolution Inference Frameworks for Single-Cell Sequencing Data. WIVACE 2022: 70-81 - 2021
- [j21]Lucrezia Patruno, Francesco Craighero, Davide Maspero, Alex Graudenzi, Chiara Damiani:
Combining multi-target regression deep neural networks and kinetic modeling to predict relative fluxes in reaction systems. Inf. Comput. 281: 104798 (2021) - [j20]Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Carlo Gambacorti Passerini, Marco Antoniotti, Alex Graudenzi, Rocco Piazza:
VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples. Patterns 2(3): 100212 (2021) - [c21]Gianluca D'Addese, Alex Graudenzi, Luca La Rocca, Marco Villani:
Two-Level Detection of Dynamic Organization in Cancer Evolution Models. WIVACE 2021: 207-224 - [i7]Francesco Craighero, Fabrizio Angaroni, Fabio Stella, Chiara Damiani, Marco Antoniotti, Alex Graudenzi:
EAD: an ensemble approach to detect adversarial examples from the hidden features of deep neural networks. CoRR abs/2111.12631 (2021) - 2020
- [j19]Davide Maspero, Chiara Damiani, Marco Antoniotti, Alex Graudenzi, Marzia Di Filippo, Marco Vanoni, Giulio Caravagna, Riccardo Colombo, Daniele Ramazzotti, Dario Pescini:
The Influence of Nutrients Diffusion on a Metabolism-driven Model of a Multi-cellular System. Fundam. Informaticae 171(1-4): 279-295 (2020) - [j18]Alex Graudenzi, Davide Maspero, Chiara Damiani:
FBCA, A Multiscale Modeling Framework Combining Cellular Automata and Flux Balance Analysis. J. Cell. Autom. 15(1-2): 75-95 (2020) - [c20]Francesco Craighero, Alex Graudenzi, Fabrizio Angaroni, Fabio Stella, Marco Antoniotti:
Understanding Deep Learning with Activation Pattern Diagrams. XAI.it@AI*IA 2020: 119-126 - [c19]Fabrizio Angaroni, Mattia Pennati, Lucrezia Patruno, Davide Maspero, Marco Antoniotti, Alex Graudenzi:
A closed-loop optimization framework for personalized cancer therapy design. CIBCB 2020: 1-9 - [c18]Francesco Craighero, Fabrizio Angaroni, Alex Graudenzi, Fabio Stella, Marco Antoniotti:
Investigating the Compositional Structure of Deep Neural Networks. LOD (1) 2020: 322-334 - [i6]Francesco Craighero, Fabrizio Angaroni, Alex Graudenzi, Fabio Stella, Marco Antoniotti:
Investigating the Compositional Structure Of Deep Neural Networks. CoRR abs/2002.06967 (2020)
2010 – 2019
- 2019
- [j17]Daniele Ramazzotti, Alex Graudenzi, Luca De Sano, Marco Antoniotti, Giulio Caravagna:
Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data. BMC Bioinform. 20(1): 210:1-210:13 (2019) - [j16]Daniele Ramazzotti, Marco S. Nobile, Marco Antoniotti, Alex Graudenzi:
Efficient computational strategies to learn the structure of probabilistic graphical models of cumulative phenomena. J. Comput. Sci. 30: 1-10 (2019) - [j15]Chiara Damiani, Davide Maspero, Marzia Di Filippo, Riccardo Colombo, Dario Pescini, Alex Graudenzi, Hans V. Westerhoff, Lilia Alberghina, Marco Vanoni, Giancarlo Mauri:
Integration of single-cell RNA-seq data into population models to characterize cancer metabolism. PLoS Comput. Biol. 15(2) (2019) - [c17]Lucrezia Patruno, Edoardo Galimberti, Daniele Ramazzotti, Giulio Caravagna, Luca De Sano, Marco Antoniotti, Alex Graudenzi:
cyTRON and cyTRON/JS: Two Cytoscape-Based Applications for the Inference of Cancer Evolution Models. CIBB 2019: 13-18 - [c16]Davide Maspero, Marzia Di Filippo, Fabrizio Angaroni, Dario Pescini, Giancarlo Mauri, Marco Vanoni, Alex Graudenzi, Chiara Damiani:
Integration of Single-Cell RNA-Sequencing Data into Flux Balance Cellular Automata. CIBB 2019: 207-215 - [c15]Laura Sani, Gianluca D'Addese, Alex Graudenzi, Marco Villani:
The Detection of Dynamical Organization in Cancer Evolution Models. WIVACE 2019: 49-61 - 2018
- [j14]Alex Graudenzi, Davide Maspero, Marzia Di Filippo, Marco Gnugnoli, Claudio Isella, Giancarlo Mauri, Enzo Medico, Marco Antoniotti, Chiara Damiani:
Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power. J. Biomed. Informatics 87: 37-49 (2018) - [c14]Alex Graudenzi, Davide Maspero, Chiara Damiani:
Modeling Spatio-Temporal Dynamics of Metabolic Networks with Cellular Automata and Constraint-Based Methods. ACRI 2018: 16-29 - [c13]Daniele Ramazzotti, Marco S. Nobile, Marco Antoniotti, Alex Graudenzi:
Structural Learning of Probabilistic Graphical Models of Cumulative Phenomena. ICCS (1) 2018: 678-693 - [c12]Davide Maspero, Alex Graudenzi, Satwinder Singh, Dario Pescini, Giancarlo Mauri, Marco Antoniotti, Chiara Damiani:
Synchronization Effects in a Metabolism-Driven Model of Multi-cellular System. WIVACE 2018: 115-126 - 2017
- [i5]Daniele Ramazzotti, Marco S. Nobile, Marco Antoniotti, Alex Graudenzi:
Learning the Probabilistic Structure of Cumulative Phenomena with Suppes-Bayes Causal Networks. CoRR abs/1703.03074 (2017) - [i4]Lucrezia Patruno, Edoardo Galimberti, Daniele Ramazzotti, Giulio Caravagna, Luca De Sano, Marco Antoniotti, Alex Graudenzi:
cyTRON and cyTRON/JS: two Cytoscape-based applications for the inference of cancer evolution models. CoRR abs/1705.03067 (2017) - [i3]Daniele Ramazzotti, Alex Graudenzi, Luca De Sano, Marco Antoniotti, Giulio Caravagna:
Learning mutational graphs of individual tumor evolution from multi-sample sequencing data. CoRR abs/1709.01076 (2017) - 2016
- [j13]Luca De Sano, Giulio Caravagna, Daniele Ramazzotti, Alex Graudenzi, Giancarlo Mauri, Bud Mishra, Marco Antoniotti:
TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data. Bioinform. 32(12): 1911-1913 (2016) - [j12]Andrea Paroni, Alex Graudenzi, Giulio Caravagna, Chiara Damiani, Giancarlo Mauri, Marco Antoniotti:
CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks. BMC Bioinform. 17: 64 (2016) - [j11]Alex Graudenzi, Giulio Caravagna, Iuliana M. Bocicor, Claudia Cava, Marco Antoniotti, Giancarlo Mauri:
Ordering cancer mutational profiles of cross-sectional copy number alterations. Int. J. Data Min. Bioinform. 15(1): 59-83 (2016) - [j10]Marco Antoniotti, Giulio Caravagna, Luca De Sano, Alex Graudenzi, Giancarlo Mauri, Bud Mishra, Daniele Ramazzotti:
Design of the TRONCO BioConductor Package for TRanslational ONCOlogy. R J. 8(2): 39 (2016) - [i2]Daniele Ramazzotti, Alex Graudenzi, Marco Antoniotti:
Modeling cumulative biological phenomena with Suppes-Bayes causal networks. CoRR abs/1602.07857 (2016) - 2015
- [j9]Daniele Ramazzotti, Giulio Caravagna, Loes Olde Loohuis, Alex Graudenzi, Ilya Korsunsky, Giancarlo Mauri, Marco Antoniotti, Bud Mishra:
CAPRI: efficient inference of cancer progression models from cross-sectional data. Bioinform. 31(18): 3016-3026 (2015) - 2014
- [j8]Alex Graudenzi, Giulio Caravagna, Giancarlo Mauri:
Preface. Nat. Comput. 13(3): 285-286 (2014) - [j7]Roberto Serra, Alessandro Filisetti, Marco Villani, Alex Graudenzi, Chiara Damiani, Tommaso Panini:
A stochastic model of catalytic reaction networks in protocells. Nat. Comput. 13(3): 367-377 (2014) - [c11]Alessandro Filisetti, Marco Villani, Chiara Damiani, Alex Graudenzi, Andrea Roli, Wim Hordijk, Roberto Serra:
On RAF Sets and Autocatalytic Cycles in Random Reaction Networks. WIVACE 2014: 113-126 - [c10]Alex Graudenzi, Chiara Damiani, Andrea Paroni, Alessandro Filisetti, Marco Villani, Roberto Serra, Marco Antoniotti:
Investigating the Role of Network Topology and Dynamical Regimes on the Dynamics of a Cell Differentiation Model. WIVACE 2014: 151-168 - [i1]Roberto Serra, Alessandro Filisetti, Marco Villani, Alex Graudenzi, Chiara Damiani, Tommaso Panini:
A stochastic model of catalytic reaction networks in protocells. CoRR abs/1407.8508 (2014) - 2013
- [j6]Marco Antoniotti, Gary D. Bader, Giulio Caravagna, Silvia Crippa, Alex Graudenzi, Giancarlo Mauri:
GeStoDifferent: a Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process. Bioinform. 29(4): 513-514 (2013) - [j5]Chiara Damiani, Alessandro Filisetti, Alex Graudenzi, Paola Lecca:
Parameter sensitivity analysis of stochastic models: Application to catalytic reaction networks. Comput. Biol. Chem. 42: 5-17 (2013) - [c9]Alessandro Filisetti, Alex Graudenzi, Chiara Damiani, Marco Villani, Roberto Serra:
The role of backward reactions in a stochastic model of catalytic reaction networks. ECAL 2013: 793-801 - [c8]Chiara Damiani, Alessandro Filisetti, Alex Graudenzi, Marco Villani, Roberto Serra:
Recent developments in research on catalytic reaction networks. WIVACE 2013: 3-13 - [c7]Roberto Serra, Alessandro Filisetti, Alex Graudenzi, Chiara Damiani, Marco Villani:
A model of protocell based on the introduction of a semi-permeable membrane in a stochastic model of catalytic reaction networks. WIVACE 2013: 70-73 - [c6]Giulio Caravagna, Alex Graudenzi, Marco Antoniotti, Giovanni De Matteis:
Analysis of the spatial and dynamical properties of a multiscale model of intestinal crypts. WIVACE 2013: 79-82 - [e1]Alex Graudenzi, Giulio Caravagna, Giancarlo Mauri, Marco Antoniotti:
Proceedings Wivace 2013 - Italian Workshop on Artificial Life and Evolutionary Computation, Milan, Italy, July 1-2, 2013. EPTCS 130, 2013 [contents] - 2012
- [j4]Alessandro Filisetti, Alex Graudenzi, Roberto Serra, Marco Villani, Rudolf M. Füchslin, Norman H. Packard, Stuart A. Kauffman, Irene Poli:
A stochastic model of autocatalytic reaction networks. Theory Biosci. 131(2): 85-93 (2012) - [c5]Giulio Caravagna, Alex Graudenzi, Marco Antoniotti, Giancarlo Mauri, Alberto d'Onofrio:
Effects of delayed immune-response in tumor immune-system interplay. HSB 2012: 106-121 - 2011
- [j3]Alex Graudenzi, Roberto Serra, Marco Villani, Annamaria Colacci, Stuart A. Kauffman:
Robustness Analysis of a Boolean Model of Gene Regulatory Network with Memory. J. Comput. Biol. 18(4): 559-577 (2011) - [j2]Alex Graudenzi, Roberto Serra, Marco Villani, Chiara Damiani, Annamaria Colacci, Stuart A. Kauffman:
Dynamical Properties of a Boolean Model of Gene Regulatory Network with Memory. J. Comput. Biol. 18(10): 1291-1303 (2011) - [c4]Alessandro Filisetti, Alex Graudenzi, Roberto Serra, Marco Villani, Davide De Lucrezia, Irene Poli:
The role of energy in a stochastic model of the emergence of autocatalytic sets. ECAL 2011: 226-233 - 2010
- [c3]Alessandro Filisetti, Roberto Serra, Marco Villani, Alex Graudenzi, Rudolf M. Füchslin, Irene Poli:
The influence of the residence time on the dynamics of catalytic reaction networks. WIRN 2010: 243-251
2000 – 2009
- 2008
- [j1]Roberto Serra, Marco Villani, Alex Graudenzi, Annamaria Colacci, Stuart A. Kauffman:
The simulation of gene knock-out in scale-free random Boolean models of genetic networks. Networks Heterog. Media 3(2): 333-343 (2008) - [c2]Roberto Serra, Marco Villani, Chiara Damiani, Alex Graudenzi, Annamaria Colacci:
The Diffusion of Perturbations in a Model of Coupled Random Boolean Networks. ACRI 2008: 315-322 - [c1]Roberto Serra, Alex Graudenzi, Marco Villani:
Genetic Regulatory Networks and Neural Networks. WIRN 2008: 109-117
Coauthor Index
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