popFBA: tackling intratumour heterogeneity with Flux Balance Analysis. - Chiara Damiani; Marzia Di Filippo; Dario Pescini; Davide Maspero; Riccardo Colombo; Giancarlo Mauri (Bioinform., 2017)

Modeling Spatio-Temporal Dynamics of Metabolic Networks with Cellular Automata and Constraint-Based Methods. - Alex Graudenzi; Davide Maspero; Chiara Damiani (ACRI, 2018)

Synchronization Effects in a Metabolism-Driven Model of Multi-cellular System. - Davide Maspero; Alex Graudenzi; Satwinder Singh; Dario Pescini; Giancarlo Mauri; Marco Antoniotti; Chiara Damiani (WIVACE, 2018)

Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power. - Alex Graudenzi; Davide Maspero; Marzia Di Filippo; Marco Gnugnoli; Claudio Isella; Giancarlo Mauri; Enzo Medico; Marco Antoniotti; Chiara Damiani (J. Biomed. Informatics, 2018)

Integration of Single-Cell RNA-Sequencing Data into Flux Balance Cellular Automata. - Davide Maspero; Marzia Di Filippo; Fabrizio Angaroni; Dario Pescini; Giancarlo Mauri; Marco Vanoni; Alex Graudenzi; Chiara Damiani (CIBB, 2019)

Integration of single-cell RNA-seq data into population models to characterize cancer metabolism. - Chiara Damiani; Davide Maspero; Marzia Di Filippo; Riccardo Colombo; Dario Pescini; Alex Graudenzi; Hans V. Westerhoff; Lilia Alberghina; Marco Vanoni; Giancarlo Mauri (PLoS Comput. Biol., 2019)

A closed-loop optimization framework for personalized cancer therapy design. - Fabrizio Angaroni; Mattia Pennati; Lucrezia Patruno; Davide Maspero; Marco Antoniotti; Alex Graudenzi (CIBCB, 2020)

The Influence of Nutrients Diffusion on a Metabolism-driven Model of a Multi-cellular System. - Davide Maspero; Chiara Damiani; Marco Antoniotti; Alex Graudenzi; Marzia Di Filippo; Marco Vanoni; Giulio Caravagna; Riccardo Colombo; Daniele Ramazzotti; Dario Pescini (Fundam. Informaticae, 2020)

FBCA, A Multiscale Modeling Framework Combining Cellular Automata and Flux Balance Analysis. - Alex Graudenzi; Davide Maspero; Chiara Damiani (J. Cell. Autom., 2020)

Combining multi-target regression deep neural networks and kinetic modeling to predict relative fluxes in reaction systems. - Lucrezia Patruno; Francesco Craighero; Davide Maspero; Alex Graudenzi; Chiara Damiani (Inf. Comput., 2021)

VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples. - Daniele Ramazzotti; Fabrizio Angaroni; Davide Maspero; Carlo Gambacorti Passerini; Marco Antoniotti; Alex Graudenzi; Rocco Piazza (Patterns, 2021)

Exploring the Solution Space of Cancer Evolution Inference Frameworks for Single-Cell Sequencing Data. - Davide Maspero; Fabrizio Angaroni; Lucrezia Patruno; Daniele Ramazzotti; David Posada; Alex Graudenzi (WIVACE, 2022)

LACE: Inference of cancer evolution models from longitudinal single-cell sequencing data. - Daniele Ramazzotti; Fabrizio Angaroni; Davide Maspero; Gianluca Ascolani; Isabella Castiglioni; Rocco Piazza; Marco Antoniotti; Alex Graudenzi (J. Comput. Sci., 2022)

LACE 2.0: an interactive R tool for the inference and visualization of longitudinal cancer evolution. - Gianluca Ascolani; Fabrizio Angaroni; Davide Maspero; Francesco Craighero; Narra Lakshmi Sai Bhavesh; Rocco Piazza; Chiara Damiani; Daniele Ramazzotti; Marco Antoniotti; Alex Graudenzi (BMC Bioinform., 2023)