Our Publications

Our lab focuses on the design and development of computational methods to analyse tumour sequencing data and to study the cancer evolutionary process.

1. Zaccaria, S., Raphael, B.J. Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL. Nature Biotechnology (2020). https://doi.org/10.1038/s41587-020-0661-6
2. Zaccaria, S., Raphael, B.J. Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data. Nature Communications 11, 4301 (2020). https://doi.org/10.1038/s41467-020-17967-y
3. Myers, M.A., Zaccaria, S.†, Raphael, B.J. Identifying tumor clones in sparse single-cell mutation data, Bioinformatics 36: i186–i193 (2020). Accepted and presented at ISMB 2020. https://doi.org/10.1093/bioinformatics/btaa449
4. Satas, G., Zaccaria, S., Mon, G., & Raphael, B. J. SCARLET: Single-Cell Tumor Phylogeny Inference with Copy-Number Constrained Mutation Losses. Cell Systems, 10(4): 323-332 (2020). Accepted and presented at RECOMB 2020. https://doi.org/10.1016/j.cels.2020.04.001
5. Zaccaria, S., El-Kebir, M., Klau, G. W., & Raphael, B. J. Phylogenetic copy-number factorization of multiple tumor samples. Journal of Computational Biology, 25(7): 689-708 (2018). Accepted and presented at RECOMB 2017. https://doi.org/10.1089/cmb.2017.0253
6. Beretta, S., Patterson, M. D., Zaccaria, S., Della Vedova, G., & Bonizzoni, P. HapCHAT: Adaptive haplotype assembly for efficiently leveraging high coverage in long reads. BMC bioinformatics, 19(1), 252 (2018). https://doi.org/10.1186/s12859-018-2253-8
7. El-Kebir, M., Raphael, B. J., Shamir, R., Sharan, R., Zaccaria, S., Zehavi, M., & Zeira, R. Complexity and algorithms for copy-number evolution problems. Algorithms for Molecular Biology, 12(1), 13 (2017). https://doi.org/10.1186/s13015-017-0103-2
8. Zaccaria, S., El-Kebir, M., Klau, G. W., & Raphael, B. J. The copy-number tree mixture deconvolution problem and applications to multi-sample bulk sequencing tumor data. In International Conference on Research in Computational Molecular Biology (pp. 318-335). Springer, Cham (2017). https://doi.org/10.1007/978-3-319-56970-3_20
9. Pirola, Y., Zaccaria, S.†, Dondi, R., Klau, G. W., Pisanti, N., & Bonizzoni, P. HapCol: accurate and memory-efficient haplotype assembly from long reads. Bioinformatics, 32(11), 1610-1617 (2016). Accepted and presented at ISMB-HITSeq 2015. https://doi.org/10.1093/bioinformatics/btv495
10. Bonizzoni, P., Dondi, R., Klau, G. W., Pirola, Y., Pisanti, N., & Zaccaria, S. On the minimum error correction problem for haplotype assembly in diploid and polyploid genomes. Journal of Computational Biology, 23(9), 718-736 (2016). https://doi.org/10.1089/cmb.2015.0220
11. El-Kebir, M., Raphael, B. J., Shamir, R., Sharan, R., Zaccaria, S., Zehavi, M., & Zeira, R. Copy-number evolution problems: complexity and algorithms. In International Workshop on Algorithms in Bioinformatics (pp. 137-149). Springer, Cham (2016). https://doi.org/10.1007/978-3-319-43681-4_11
12. Bonizzoni, P., Dondi, R., Klau, G. W., Pirola, Y., Pisanti, N., & Zaccaria, S. On the fixed parameter tractability and approximability of the minimum error correction problem. In Annual Symposium on Combinatorial Pattern Matching (pp. 100-113). Springer, Cham (2015). https://doi.org/10.1007/978-3-319-19929-0_9
13. Willing, E., Zaccaria, S., Braga, M. D., & Stoye, J. On the inversion-indel distance. BMC bioinformatics 14, S3-15 (2013). https://doi.org/10.1186/1471-2105-14-S15-S3