Alex Graudenzi

Publication Activity (10 Years)

Years Active: 2008-2023
Publications (10 Years): 36

Top Topics

Structural Learning

Efficient Inference

Top Venues

Publications

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)
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 (2023)
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 (2023)
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) (2023)
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) (2022)
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)
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 (2022)
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) (2022)
Gianluca D'Addese, Alex Graudenzi, Luca La Rocca, Marco Villani
Two-Level Detection of Dynamic Organization in Cancer Evolution Models. WIVACE (2021)
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 (2021)
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) (2021)
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 (2021)
Francesco Craighero, Fabrizio Angaroni, Alex Graudenzi, Fabio Stella, Marco Antoniotti
Investigating the Compositional Structure Of Deep Neural Networks. CoRR (2020)
Francesco Craighero, Alex Graudenzi, Fabrizio Angaroni, Fabio Stella, Marco Antoniotti
Understanding Deep Learning with Activation Pattern Diagrams. XAI.it@AI*IA (2020)
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) (2020)
Alex Graudenzi, Davide Maspero, Chiara Damiani
FBCA, A Multiscale Modeling Framework Combining Cellular Automata and Flux Balance Analysis. J. Cell. Autom. 15 (1-2) (2020)
Francesco Craighero, Fabrizio Angaroni, Alex Graudenzi, Fabio Stella, Marco Antoniotti
Investigating the Compositional Structure of Deep Neural Networks. LOD (1) (2020)
Fabrizio Angaroni, Mattia Pennati, Lucrezia Patruno, Davide Maspero, Marco Antoniotti, Alex Graudenzi
A closed-loop optimization framework for personalized cancer therapy design. CIBCB (2020)
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 (2019)
Laura Sani, Gianluca D'Addese, Alex Graudenzi, Marco Villani
The Detection of Dynamical Organization in Cancer Evolution Models. WIVACE (2019)
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)
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) (2019)
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)
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)
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)
Alex Graudenzi, Davide Maspero, Chiara Damiani
Modeling Spatio-Temporal Dynamics of Metabolic Networks with Cellular Automata and Constraint-Based Methods. ACRI (2018)
Daniele Ramazzotti, Marco S. Nobile, Marco Antoniotti, Alex Graudenzi
Structural Learning of Probabilistic Graphical Models of Cumulative Phenomena. ICCS (1) (2018)
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 (2018)
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 (2017)
Daniele Ramazzotti, Marco S. Nobile, Marco Antoniotti, Alex Graudenzi
Learning the Probabilistic Structure of Cumulative Phenomena with Suppes-Bayes Causal Networks. CoRR (2017)
Daniele Ramazzotti, Alex Graudenzi, Luca De Sano, Marco Antoniotti, Giulio Caravagna
Learning mutational graphs of individual tumor evolution from multi-sample sequencing data. CoRR (2017)
Daniele Ramazzotti, Alex Graudenzi, Marco Antoniotti
Modeling cumulative biological phenomena with Suppes-Bayes causal networks. CoRR (2016)
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) (2016)
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) (2016)
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) (2016)
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 (2016)
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) (2015)
Roberto Serra, Alessandro Filisetti, Marco Villani, Alex Graudenzi, Chiara Damiani, Tommaso Panini
A stochastic model of catalytic reaction networks in protocells. CoRR (2014)
Alex Graudenzi, Giulio Caravagna, Giancarlo Mauri
Preface. Nat. Comput. 13 (3) (2014)
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)
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)
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) (2014)
Chiara Damiani, Alessandro Filisetti, Alex Graudenzi, Marco Villani, Roberto Serra
Recent developments in research on catalytic reaction networks. WIVACE (2013)
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)
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)
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)
Chiara Damiani, Alessandro Filisetti, Alex Graudenzi, Paola Lecca
Parameter sensitivity analysis of stochastic models: Application to catalytic reaction networks. Comput. Biol. Chem. 42 (2013)
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) (2013)
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) (2012)
Giulio Caravagna, Alex Graudenzi, Marco Antoniotti, Giancarlo Mauri, Alberto d'Onofrio
Effects of delayed immune-response in tumor immune-system interplay HSB (2012)
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)
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) (2011)
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) (2011)
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)
Roberto Serra, Alex Graudenzi, Marco Villani
Genetic Regulatory Networks and Neural Networks. WIRN (2008)
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) (2008)
Roberto Serra, Marco Villani, Chiara Damiani, Alex Graudenzi, Annamaria Colacci
The Diffusion of Perturbations in a Model of Coupled Random Boolean Networks. ACRI (2008)