Simone Ciccolella

According to our database, Simone Ciccolella authored at least 17 papers between 2017 and 2025.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2025

Cancer progression inference using a finite-state model to allow recurrences and losses of mutations.

Simone Ciccolella, Murray Patterson, Iman Hajirasouliha, Gianluca Della Vedova

Neural Comput. Appl., September, 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., March, 2025

Pangenome Graph Indexing via the Multidollar-BWT.

Davide Cozzi, Brian Riccardi, Luca Denti, Simone Ciccolella, Kunihiko Sadakane, Paola Bonizzoni

Proceedings of the 23rd International Symposium on Experimental Algorithms, 2025

2024

PangeBlocks: customized construction of pangenome graphs via maximal blocks.

Jorge Avila Cartes, Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Luca Denti

BMC Bioinform., December, 2024

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

2023

Three Metaheuristic Approaches for Tumor Phylogeny Inference: An Experimental Comparison.

Simone Ciccolella, Gianluca Della Vedova, Vladimir Filipovic, Mauricio Soto Gomez

Algorithms, July, 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., April, 2023

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

Proceedings of the Computational Advances in Bio and Medical Sciences, 2023

2021

MALVIRUS: an integrated application for viral variant analysis.

Simone Ciccolella, Luca Denti, Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali

BMC Bioinform., November, 2021

Simpler and Faster Development of Tumor Phylogeny Pipelines.

Sarwan Ali, Simone Ciccolella, Lorenzo Lucarella, Gianluca Della Vedova, Murray Patterson

J. Comput. Biol., 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

Triplet-based similarity score for fully multilabeled trees with poly-occurring labels.

Simone Ciccolella, Giulia Bernardini, Luca Denti, Paola Bonizzoni, Marco Previtali, Gianluca Della Vedova

Bioinform., 2021

Clustering SARS-CoV-2 Variants from Raw High-Throughput Sequencing Reads Data.

Prakash Chourasia, Sarwan Ali, Simone Ciccolella, Gianluca Della Vedova, Murray Patterson

Proceedings of the Computational Advances in Bio and Medical Sciences: 11th International Conference, 2021

2019

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

Effective Clustering for Single Cell Sequencing Cancer Data.

Simone Ciccolella, Murray D. Patterson, Paola Bonizzoni, Gianluca Della Vedova

Proceedings of the 10th ACM International Conference on Bioinformatics, 2019

2018

gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data.

Simone Ciccolella, Mauricio Soto Gomez, Murray Patterson, Gianluca Della Vedova, Iman Hajirasouliha, Paola Bonizzoni

Proceedings of the 8th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2018

2017

Beyond Perfect Phylogeny: Multisample Phylogeny Reconstruction via ILP.

Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Mauricio Soto Gomez

Proceedings of the 8th ACM International Conference on Bioinformatics, 2017