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ORCIDMarco Antoniotti
- > Home > Persons > Marco Antoniotti
Publications
- 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]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) - [j26]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
- [j25]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) - [j24]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) - 2021
- [j23]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) - [i9]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
- [j22]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) - [c28]Francesco Craighero, Alex Graudenzi, Fabrizio Angaroni, Fabio Stella, Marco Antoniotti:
Understanding Deep Learning with Activation Pattern Diagrams. XAI.it@AI*IA 2020: 119-126 - [c27]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 - [c24]Francesco Craighero, Fabrizio Angaroni, Alex Graudenzi, Fabio Stella, Marco Antoniotti:
Investigating the Compositional Structure of Deep Neural Networks. LOD (1) 2020: 322-334 - [i8]Francesco Craighero, Fabrizio Angaroni, Alex Graudenzi, Fabio Stella, Marco Antoniotti:
Investigating the Compositional Structure Of Deep Neural Networks. CoRR abs/2002.06967 (2020) - 2019
- [j21]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) - [j20]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) - [c23]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 - 2018
- [j19]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) - [c22]Daniele Ramazzotti, Marco S. Nobile, Marco Antoniotti, Alex Graudenzi:
Structural Learning of Probabilistic Graphical Models of Cumulative Phenomena. ICCS (1) 2018: 678-693 - [c21]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
- [j18]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) - [j17]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) - [j16]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) - [j15]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
- [j14]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
- [c19]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 - 2013
- [j10]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) - [c16]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 - [e2]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
- [c13]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
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