Beyond Perfect Phylogeny: Multisample Phylogeny Reconstruction via ILP. - Paola Bonizzoni; Simone Ciccolella; Gianluca Della Vedova; Mauricio Soto Gomez (BCB, 2017)

Does Relaxing the Infinite Sites Assumption Give Better Tumor Phylogenies? An ILP-Based Comparative Approach. - Paola Bonizzoni; Simone Ciccolella; Gianluca Della Vedova; Mauricio Soto Gomez (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data. - Simone Ciccolella; Mauricio Soto Gomez; Murray D. Patterson; Gianluca Della Vedova; Iman Hajirasouliha; Paola Bonizzoni (BMC Bioinform., 2020)

Clustering SARS-CoV-2 Variants from Raw High-Throughput Sequencing Reads Data. - Prakash Chourasia; Sarwan Ali; Simone Ciccolella; Gianluca Della Vedova; Murray Patterson (ICCABS, 2021)

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)

Inferring cancer progression from Single-Cell Sequencing while allowing mutation losses. - Simone Ciccolella; Camir Ricketts; Mauricio Soto Gomez; Murray Patterson; Dana Silverbush; Paola Bonizzoni; Iman Hajirasouliha; Gianluca Della Vedova (Bioinform., 2021)

Simpler and Faster Development of Tumor Phylogeny Pipelines. - Sarwan Ali; Simone Ciccolella; Lorenzo Lucarella; Gianluca Della Vedova; Murray Patterson (J. Comput. Biol., 2021)

Effective Clustering for Single Cell Sequencing Cancer Data. - Simone Ciccolella; Murray Patterson; Paola Bonizzoni; Gianluca Della Vedova (IEEE J. Biomed. Health Informatics, 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)

Plastic: An Easy to Use and Modular Tool for Benchmarking Tumor Phylogeny Reconstruction Pipelines. - Akshay Juyal; Zahra Tayebi; Alexander Zelikovsky; Mauricio Soto Gomez; Simone Ciccolella; Gianluca Della Vedova; Murray Patterson (ICCABS, 2023)

Reads2Vec: Efficient Embedding of Raw High-Throughput Sequencing Reads Data. - Prakash Chourasia; Sarwan Ali; Simone Ciccolella; Gianluca Della Vedova; Murray Patterson (J. Comput. Biol., 2023)

Three Metaheuristic Approaches for Tumor Phylogeny Inference: An Experimental Comparison. - Simone Ciccolella; Gianluca Della Vedova; Vladimir Filipovic; Mauricio Soto Gomez (Algorithms, 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)