A Bioinformatics Procedure to Identify and Annotate Somatic Mutations in Whole-Exome Sequencing Data. - Roberta Spinelli; Rocco Piazza; Alessandra Pirola; Simona Valletta; Roberta Rostagno; Angela Mogavero; Manuela Marega; Hima Raman; Carlo Gambacorti Passerini (CIBB, 2011)

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)

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)

Characterization of cancer subtypes associated with clinical outcomes by multi-omics integrative clustering. - Valentina Crippa; Federica Malighetti; Matteo Villa; Alex Graudenzi; Rocco Piazza; Luca Mologni; Daniele Ramazzotti (Comput. Biol. Medicine, 2023)

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)

Control-FREEC viewer: a tool for the visualization and exploration of copy number variation data. - Valentina Crippa; Emanuela Fina; Daniele Ramazzotti; Rocco Piazza (BMC Bioinform., 2024)