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Simone Ciccolella
Simone Ciccolella
University of Study Milano-Bicocca
Verified email at unimib.it
Title
Cited by
Cited by
Year
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
802019
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
49*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
242017
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
212018
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
182020
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
162021
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
162021
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
13*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
102023
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
102021
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
8*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
12023
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
12022
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
2023
Differential quantification of alternative splicing events on spliced pangenome graphs
S Ciccolella, D Cozzi, G Della Vedova, S Kuria, P Bonizzoni, L Denti
bioRxiv, 2023.11. 06.565751, 2023
2023
Practical algorithms for Computational Phylogenetics
S Ciccolella
Università degli Studi di Milano-Bicocca, 2022
2022
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