Alex Graudenzi

59 papers C 1Journal 36Unranked 21

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Phylogenetic analysis of TET2 gene variants in Pakistani acute myeloid Leukemia patients. Briefings Bioinform. Mawada Elmagboul Abdalla Abakar, Mehad Almagboul Abdalla Abaker, Marco Antoniotti, Alex Graudenzi
2023	J	`jnl`	A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing. PLoS Comput. Biol. Lucrezia Patruno, Salvatore Milite, Riccardo Bergamin, Nicola Calonaci, Alberto d'Onofrio, Fabio Anselmi, Marco Antoniotti, Alex Graudenzi, Giulio Caravagna
2023	J	`jnl`	Characterization of cancer subtypes associated with clinical outcomes by multi-omics integrative clustering. Comput. Biol. Medicine Valentina Crippa, Federica Malighetti, Matteo Villa, Alex Graudenzi, Rocco Piazza, Luca Mologni, Daniele Ramazzotti
2023	J	`jnl`	LACE 2.0: an interactive R tool for the inference and visualization of longitudinal cancer evolution. BMC Bioinform. Gianluca Ascolani, Fabrizio Angaroni, Davide Maspero, Francesco Craighero, Narra Lakshmi Sai Bhavesh, Rocco Piazza, Chiara Damiani, Daniele Ramazzotti, Marco Antoniotti, Alex Graudenzi
2023	J	`jnl`	Unity is strength: Improving the detection of adversarial examples with ensemble approaches. Neurocomputing Francesco Craighero, Fabrizio Angaroni, Fabio Stella, Chiara Damiani, Marco Antoniotti, Alex Graudenzi
2022	—	`conf`	Exploring the Solution Space of Cancer Evolution Inference Frameworks for Single-Cell Sequencing Data. WIVACE Davide Maspero, Fabrizio Angaroni, Lucrezia Patruno, Daniele Ramazzotti, David Posada, Alex Graudenzi
2022	J	`jnl`	J-SPACE: a Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments. BMC Bioinform. Fabrizio Angaroni, Alessandro Guidi, Gianluca Ascolani, Alberto d'Onofrio, Marco Antoniotti, Alex Graudenzi
2022	J	`jnl`	LACE: Inference of cancer evolution models from longitudinal single-cell sequencing data. J. Comput. Sci. Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Gianluca Ascolani, Isabella Castiglioni, Rocco Piazza, Marco Antoniotti, Alex Graudenzi
2022	J	`jnl`	PMCE: efficient inference of expressive models of cancer evolution with high prognostic power. Bioinform. Fabrizio Angaroni, Kevin Chen, Chiara Damiani, Giulio Caravagna, Alex Graudenzi, Daniele Ramazzotti
2021	J	`jnl`	Combining multi-target regression deep neural networks and kinetic modeling to predict relative fluxes in reaction systems. Inf. Comput. Lucrezia Patruno, Francesco Craighero, Davide Maspero, Alex Graudenzi, Chiara Damiani
2021	J	`jnl`	EAD: an ensemble approach to detect adversarial examples from the hidden features of deep neural networks. CoRR Francesco Craighero, Fabrizio Angaroni, Fabio Stella, Chiara Damiani, Marco Antoniotti, Alex Graudenzi
2021	—	`conf`	Two-Level Detection of Dynamic Organization in Cancer Evolution Models. WIVACE Gianluca D'Addese, Alex Graudenzi, Luca La Rocca, Marco Villani
2021	J	`jnl`	VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples. Patterns Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Carlo Gambacorti Passerini, Marco Antoniotti, Alex Graudenzi, Rocco Piazza
2020	C	`conf`	A closed-loop optimization framework for personalized cancer therapy design. CIBCB Fabrizio Angaroni, Mattia Pennati, Lucrezia Patruno, Davide Maspero, Marco Antoniotti, Alex Graudenzi
2020	J	`jnl`	FBCA, A Multiscale Modeling Framework Combining Cellular Automata and Flux Balance Analysis. J. Cell. Autom. Alex Graudenzi, Davide Maspero, Chiara Damiani
2020	J	`jnl`	Investigating the Compositional Structure Of Deep Neural Networks. CoRR Francesco Craighero, Fabrizio Angaroni, Alex Graudenzi, Fabio Stella, Marco Antoniotti
2020	—	`conf`	Investigating the Compositional Structure of Deep Neural Networks. LOD (1) Francesco Craighero, Fabrizio Angaroni, Alex Graudenzi, Fabio Stella, Marco Antoniotti
2020	J	`jnl`	The Influence of Nutrients Diffusion on a Metabolism-driven Model of a Multi-cellular System. Fundam. Informaticae Davide Maspero, Chiara Damiani, Marco Antoniotti, Alex Graudenzi, Marzia Di Filippo, Marco Vanoni, Giulio Caravagna, Riccardo Colombo, Daniele Ramazzotti, Dario Pescini
2020	—	`conf`	Understanding Deep Learning with Activation Pattern Diagrams. XAI.it@AI*IA Francesco Craighero, Alex Graudenzi, Fabrizio Angaroni, Fabio Stella, Marco Antoniotti
2019	J	`jnl`	Efficient computational strategies to learn the structure of probabilistic graphical models of cumulative phenomena. J. Comput. Sci. Daniele Ramazzotti, Marco S. Nobile, Marco Antoniotti, Alex Graudenzi
2019	—	`conf`	Integration of Single-Cell RNA-Sequencing Data into Flux Balance Cellular Automata. CIBB Davide Maspero, Marzia Di Filippo, Fabrizio Angaroni, Dario Pescini, Giancarlo Mauri, Marco Vanoni, Alex Graudenzi, Chiara Damiani
2019	J	`jnl`	Integration of single-cell RNA-seq data into population models to characterize cancer metabolism. PLoS Comput. Biol. Chiara Damiani, Davide Maspero, Marzia Di Filippo, Riccardo Colombo, Dario Pescini, Alex Graudenzi, Hans V. Westerhoff, Lilia Alberghina, Marco Vanoni, Giancarlo Mauri
2019	J	`jnl`	Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data. BMC Bioinform. Daniele Ramazzotti, Alex Graudenzi, Luca De Sano, Marco Antoniotti, Giulio Caravagna
2019	—	`conf`	The Detection of Dynamical Organization in Cancer Evolution Models. WIVACE Laura Sani, Gianluca D'Addese, Alex Graudenzi, Marco Villani
2019	—	`conf`	cyTRON and cyTRON/JS: Two Cytoscape-Based Applications for the Inference of Cancer Evolution Models. CIBB Lucrezia Patruno, Edoardo Galimberti, Daniele Ramazzotti, Giulio Caravagna, Luca De Sano, Marco Antoniotti, Alex Graudenzi
2018	J	`jnl`	Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power. J. Biomed. Informatics Alex Graudenzi, Davide Maspero, Marzia Di Filippo, Marco Gnugnoli, Claudio Isella, Giancarlo Mauri, Enzo Medico, Marco Antoniotti, Chiara Damiani
2018	—	`conf`	Modeling Spatio-Temporal Dynamics of Metabolic Networks with Cellular Automata and Constraint-Based Methods. ACRI Alex Graudenzi, Davide Maspero, Chiara Damiani
2018	—	`conf`	Structural Learning of Probabilistic Graphical Models of Cumulative Phenomena. ICCS (1) Daniele Ramazzotti, Marco S. Nobile, Marco Antoniotti, Alex Graudenzi
2018	—	`conf`	Synchronization Effects in a Metabolism-Driven Model of Multi-cellular System. WIVACE Davide Maspero, Alex Graudenzi, Satwinder Singh, Dario Pescini, Giancarlo Mauri, Marco Antoniotti, Chiara Damiani
2017	J	`jnl`	Learning mutational graphs of individual tumor evolution from multi-sample sequencing data. CoRR Daniele Ramazzotti, Alex Graudenzi, Luca De Sano, Marco Antoniotti, Giulio Caravagna
2017	J	`jnl`	Learning the Probabilistic Structure of Cumulative Phenomena with Suppes-Bayes Causal Networks. CoRR Daniele Ramazzotti, Marco S. Nobile, Marco Antoniotti, Alex Graudenzi
2017	J	`jnl`	cyTRON and cyTRON/JS: two Cytoscape-based applications for the inference of cancer evolution models. CoRR Lucrezia Patruno, Edoardo Galimberti, Daniele Ramazzotti, Giulio Caravagna, Luca De Sano, Marco Antoniotti, Alex Graudenzi
2016	J	`jnl`	CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks. BMC Bioinform. Andrea Paroni, Alex Graudenzi, Giulio Caravagna, Chiara Damiani, Giancarlo Mauri, Marco Antoniotti
2016	J	`jnl`	Design of the TRONCO BioConductor Package for TRanslational ONCOlogy. R J. Marco Antoniotti, Giulio Caravagna, Luca De Sano, Alex Graudenzi, Giancarlo Mauri, Bud Mishra, Daniele Ramazzotti
2016	J	`jnl`	Modeling cumulative biological phenomena with Suppes-Bayes causal networks. CoRR Daniele Ramazzotti, Alex Graudenzi, Marco Antoniotti
2016	J	`jnl`	Ordering cancer mutational profiles of cross-sectional copy number alterations. Int. J. Data Min. Bioinform. Alex Graudenzi, Giulio Caravagna, Iuliana M. Bocicor, Claudia Cava, Marco Antoniotti, Giancarlo Mauri
2016	J	`jnl`	TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data. Bioinform. Luca De Sano, Giulio Caravagna, Daniele Ramazzotti, Alex Graudenzi, Giancarlo Mauri, Bud Mishra, Marco Antoniotti
2015	J	`jnl`	CAPRI: efficient inference of cancer progression models from cross-sectional data. Bioinform. Daniele Ramazzotti, Giulio Caravagna, Loes Olde Loohuis, Alex Graudenzi, Ilya Korsunsky, Giancarlo Mauri, Marco Antoniotti, Bud Mishra
2014	J	`jnl`	A stochastic model of catalytic reaction networks in protocells. CoRR Roberto Serra, Alessandro Filisetti, Marco Villani, Alex Graudenzi, Chiara Damiani, Tommaso Panini
2014	J	`jnl`	A stochastic model of catalytic reaction networks in protocells. Nat. Comput. Roberto Serra, Alessandro Filisetti, Marco Villani, Alex Graudenzi, Chiara Damiani, Tommaso Panini
2014	—	`conf`	Investigating the Role of Network Topology and Dynamical Regimes on the Dynamics of a Cell Differentiation Model. WIVACE Alex Graudenzi, Chiara Damiani, Andrea Paroni, Alessandro Filisetti, Marco Villani, Roberto Serra, Marco Antoniotti
2014	—	`conf`	On RAF Sets and Autocatalytic Cycles in Random Reaction Networks. WIVACE Alessandro Filisetti, Marco Villani, Chiara Damiani, Alex Graudenzi, Andrea Roli, Wim Hordijk, Roberto Serra
2014	J	`jnl`	Preface. Nat. Comput. Alex Graudenzi, Giulio Caravagna, Giancarlo Mauri
2013	—	`conf`	A model of protocell based on the introduction of a semi-permeable membrane in a stochastic model of catalytic reaction networks. WIVACE Roberto Serra, Alessandro Filisetti, Alex Graudenzi, Chiara Damiani, Marco Villani
2013	—	`conf`	Analysis of the spatial and dynamical properties of a multiscale model of intestinal crypts. WIVACE Giulio Caravagna, Alex Graudenzi, Marco Antoniotti, Giovanni De Matteis
2013	J	`jnl`	GeStoDifferent: a Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process. Bioinform. Marco Antoniotti, Gary D. Bader, Giulio Caravagna, Silvia Crippa, Alex Graudenzi, Giancarlo Mauri
2013	J	`jnl`	Parameter sensitivity analysis of stochastic models: Application to catalytic reaction networks. Comput. Biol. Chem. Chiara Damiani, Alessandro Filisetti, Alex Graudenzi, Paola Lecca
2013	—	`ed.`	Proceedings Wivace 2013 - Italian Workshop on Artificial Life and Evolutionary Computation, Milan, Italy, July 1-2, 2013. WIVACE Alex Graudenzi, Giulio Caravagna, Giancarlo Mauri, Marco Antoniotti
2013	—	`conf`	Recent developments in research on catalytic reaction networks. WIVACE Chiara Damiani, Alessandro Filisetti, Alex Graudenzi, Marco Villani, Roberto Serra
2013	—	`conf`	The role of backward reactions in a stochastic model of catalytic reaction networks. ECAL Alessandro Filisetti, Alex Graudenzi, Chiara Damiani, Marco Villani, Roberto Serra
2012	J	`jnl`	A stochastic model of autocatalytic reaction networks. Theory Biosci. Alessandro Filisetti, Alex Graudenzi, Roberto Serra, Marco Villani, Rudolf M. Füchslin, Norman H. Packard, Stuart A. Kauffman, Irene Poli
2012	—	`conf`	Effects of delayed immune-response in tumor immune-system interplay HSB Giulio Caravagna, Alex Graudenzi, Marco Antoniotti, Giancarlo Mauri, Alberto d'Onofrio
2011	J	`jnl`	Dynamical Properties of a Boolean Model of Gene Regulatory Network with Memory. J. Comput. Biol. Alex Graudenzi, Roberto Serra, Marco Villani, Chiara Damiani, Annamaria Colacci, Stuart A. Kauffman
2011	J	`jnl`	Robustness Analysis of a Boolean Model of Gene Regulatory Network with Memory. J. Comput. Biol. Alex Graudenzi, Roberto Serra, Marco Villani, Annamaria Colacci, Stuart A. Kauffman
2011	—	`conf`	The role of energy in a stochastic model of the emergence of autocatalytic sets. ECAL Alessandro Filisetti, Alex Graudenzi, Roberto Serra, Marco Villani, Davide De Lucrezia, Irene Poli
2010	—	`conf`	The influence of the residence time on the dynamics of catalytic reaction networks. WIRN Alessandro Filisetti, Roberto Serra, Marco Villani, Alex Graudenzi, Rudolf M. Füchslin, Irene Poli
2008	—	`conf`	Genetic Regulatory Networks and Neural Networks. WIRN Roberto Serra, Alex Graudenzi, Marco Villani
2008	—	`conf`	The Diffusion of Perturbations in a Model of Coupled Random Boolean Networks. ACRI Roberto Serra, Marco Villani, Chiara Damiani, Alex Graudenzi, Annamaria Colacci
2008	J	`jnl`	The simulation of gene knock-out in scale-free random Boolean models of genetic networks. Networks Heterog. Media Roberto Serra, Marco Villani, Alex Graudenzi, Annamaria Colacci, Stuart A. Kauffman