cyTRON and cyTRON/JS: Two Cytoscape-Based Applications for the Inference of Cancer Evolution Models. - Lucrezia Patruno; Edoardo Galimberti; Daniele Ramazzotti; Giulio Caravagna; Luca De Sano; Marco Antoniotti; Alex Graudenzi (CIBB, 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)

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)

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)

A Bayesian method to cluster single-cell RNA sequencing data using copy number alterations. - Salvatore Milite; Riccardo Bergamin; Lucrezia Patruno; Nicola Calonaci; Giulio Caravagna (Bioinform., 2022)

A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing. - Lucrezia Patruno; Salvatore Milite; Riccardo Bergamin; Nicola Calonaci; Alberto d'Onofrio; Fabio Anselmi; Marco Antoniotti; Alex Graudenzi; Giulio Caravagna (PLoS Comput. Biol., 2023)