| PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data S Malikic, FR Mehrabadi, S Ciccolella, MK Rahman, C Ricketts, ... Genome research 29 (11), 1860-1877, 2019 | 92 | 2019 |
| Inferring cancer progression from single-cell sequencing while allowing mutation losses S Ciccolella, C Ricketts, M Soto Gomez, M Patterson, D Silverbush, ... Bioinformatics 37 (3), 326-333, 2021 | 54* | 2021 |
| Beyond perfect phylogeny: Multisample phylogeny reconstruction via ilp P Bonizzoni, S Ciccolella, G Della Vedova, M Soto Proceedings of the 8th ACM International Conference on Bioinformatics …, 2017 | 26 | 2017 |
| Triplet-based similarity score for fully multilabeled trees with poly-occurring labels S Ciccolella, G Bernardini, L Denti, P Bonizzoni, M Previtali, ... Bioinformatics 37 (2), 178-184, 2021 | 25 | 2021 |
| Does relaxing the infinite sites assumption give better tumor phylogenies? An ILP-based comparative approach P Bonizzoni, S Ciccolella, G Della Vedova, M Soto IEEE/ACM transactions on computational biology and bioinformatics 16 (5 …, 2018 | 22 | 2018 |
| Simpler and faster development of tumor phylogeny pipelines S Ali, S Ciccolella, L Lucarella, GD Vedova, M Patterson Journal of Computational Biology 28 (11), 1142-1155, 2021 | 20 | 2021 |
| gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data S Ciccolella, M Soto Gomez, MD Patterson, G Della Vedova, ... BMC bioinformatics 21, 1-16, 2020 | 18 | 2020 |
| Effective clustering for single cell sequencing cancer data S Ciccolella, MD Patterson, P Bonizzoni, G Della Vedova Proceedings of the 10th ACM International Conference on Bioinformatics …, 2019 | 15* | 2019 |
| Reads2vec: Efficient embedding of raw high-throughput sequencing reads data P Chourasia, S Ali, S Ciccolella, GD Vedova, M Patterson Journal of Computational Biology 30 (4), 469-491, 2023 | 12 | 2023 |
| Clustering sars-cov-2 variants from raw high-throughput sequencing reads data P Chourasia, S Ali, S Ciccolella, G Della Vedova, M Patterson International Conference on Computational Advances in Bio and Medical …, 2021 | 12 | 2021 |
| MALVIRUS: an integrated application for viral variant analysis S Ciccolella, L Denti, P Bonizzoni, G Della Vedova, Y Pirola, M Previtali BMC bioinformatics 22 (Suppl 15), 625, 2021 | 10* | 2021 |
| Accurate and fast clade assignment via deep learning and frequency chaos game representation J Avila Cartes, S Anand, S Ciccolella, P Bonizzoni, G Della Vedova GigaScience 12, giac119, 2023 | 7 | 2023 |
| RecGraph: adding recombinations to sequence-to-graph alignments J Avila, P Bonizzoni, S Ciccolella, G Della Vedova, L Denti, D Monti, ... bioRxiv, 2022.10. 27.513962, 2022 | 3 | 2022 |
| Differential quantification of alternative splicing events on spliced pangenome graphs S Ciccolella, D Cozzi, G Della Vedova, SN Kuria, P Bonizzoni, L Denti PLOS Computational Biology 20 (12), e1012665, 2024 | 1 | 2024 |
| RecGraph: recombination-aware alignment of sequences to variation graphs J Avila Cartes, P Bonizzoni, S Ciccolella, G Della Vedova, L Denti, ... Bioinformatics 40 (5), btae292, 2024 | 1 | 2024 |
| Three Metaheuristic Approaches for Tumor Phylogeny Inference: An Experimental Comparison S Ciccolella, G Della Vedova, V Filipović, M Soto Gomez Algorithms 16 (7), 333, 2023 | 1 | 2023 |
| Differential analysis of alternative splicing events in gene regions using residual neural networks S Ciccolella, L Denti, J Avila Cartes, G Della Vedova, Y Pirola, R Rizzi, ... Neural Computing and Applications, 1-11, 2025 | | 2025 |
| PangeBlocks: customized construction of pangenome graphs via maximal blocks J Avila Cartes, P Bonizzoni, S Ciccolella, G Della Vedova, L Denti BMC bioinformatics 25 (1), 344, 2024 | | 2024 |
| PangeBlocks: customized construction of pangenome graphs via maximal blocks P Bonizzoni, JE Avila Cartes, S Ciccolella, G Della Vedova, L Denti bioRxiv, 2024.09. 17.613426, 2024 | | 2024 |
| Practical algorithms for Computational Phylogenetics S Ciccolella Università degli Studi di Milano-Bicocca, 2022 | | 2022 |
