Mapping RNA-seq Data to a Transcript Graph via Approximate Pattern Matching to a Hypertext. - Stefano Beretta 001; Paola Bonizzoni; Luca Denti; Marco Previtali; Raffaella Rizzi (AlCoB, 2017)

ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events. - Luca Denti; Raffaella Rizzi; Stefano Beretta 001; Gianluca Della Vedova; Marco Previtali; Paola Bonizzoni (BMC Bioinform., 2018)

Graph Theory and Definitions. - Stefano Beretta 001; Luca Denti; Marco Previtali (Encyclopedia of Bioinformatics and Computational Biology (1), 2019)

Network Properties. - Stefano Beretta 001; Luca Denti; Marco Previtali (Encyclopedia of Bioinformatics and Computational Biology (1), 2019)

Algorithms for analyzing genetic variability from Next-Generation Sequencing data. - Luca Denti (2020)

Triplet-based similarity score for fully multilabeled trees with poly-occurring labels. - Simone Ciccolella; Giulia Bernardini 001; Luca Denti; Paola Bonizzoni; Marco Previtali; Gianluca Della Vedova (Bioinform., 2021)

Shark: fishing relevant reads in an RNA-Seq sample. - Luca Denti; Yuri Pirola; Marco Previtali; Tamara Ceccato; Gianluca Della Vedova; Raffaella Rizzi; Paola Bonizzoni (Bioinform., 2021)

MALVIRUS: an integrated application for viral variant analysis. - Simone Ciccolella; Luca Denti; Paola Bonizzoni; Gianluca Della Vedova; Yuri Pirola; Marco Previtali (BMC Bioinform., 2021)

ESGq: Alternative Splicing Events Quantification across Conditions based on Event Splicing Graphs. - Davide Cozzi; Paola Bonizzoni; Luca Denti (ITAT, 2023)

Differential quantification of alternative splicing events on spliced pangenome graphs. - Simone Ciccolella; Davide Cozzi; Gianluca Della Vedova; Stephen Njuguna Kuria; Paola Bonizzoni; Luca Denti (PLoS Comput. Biol., 2024)

PangeBlocks: customized construction of pangenome graphs via maximal blocks. - Jorge Avila Cartes; Paola Bonizzoni; Simone Ciccolella; Gianluca Della Vedova; Luca Denti (BMC Bioinform., 2024)

Pangenome Graph Indexing via the Multidollar-BWT. - Davide Cozzi; Brian Riccardi; Luca Denti; Simone Ciccolella; Kunihiko Sadakane; Paola Bonizzoni (SEA, 2025)

Differential analysis of alternative splicing events in gene regions using residual neural networks. - Simone Ciccolella; Luca Denti; Jorge Avila Cartes; Gianluca Della Vedova; Yuri Pirola; Raffaella Rizzi; Paola Bonizzoni (Neural Comput. Appl., 2025)