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