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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.听Nature Biotechnology听(2020).听
- Zaccaria, S., Raphael, B.J. Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data.听Nature Communications听11,听4301 (2020).听
- Myers, M.A.,听Zaccaria, S.鈥�, Raphael, B.J.听Identifying tumor clones in sparse single-cell mutation data,听叠颈辞颈苍蹿辞谤尘补迟颈肠蝉听36:听i186鈥搃193 (2020). Accepted and presented at ISMB 2020.听
- Satas, G.,听Zaccaria, S., Mon, G., & Raphael, B. J.听SCARLET: Single-Cell Tumor Phylogeny Inference with Copy-Number Constrained Mutation Losses.听Cell Systems,听10(4):听323-332 (2020). Accepted and presented at RECOMB 2020.听
- Zaccaria, S., El-Kebir, M., Klau, G. W., & Raphael, B. J. Phylogenetic copy-number factorization of multiple tumor samples.听Journal of Computational Biology,听25(7):听689-708 (2018). Accepted and presented at RECOMB 2017.听
- 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).听
- El-Kebir, M., Raphael, B. J., Shamir, R., Sharan, R., Zaccaria, S., Zehavi, M., & Zeira, R. Complexity and algorithms for copy-number evolution problems.听Algorithms for Molecular Biology,听12(1), 13 (2017).听
- Zaccaria, S., El-Kebir, M., Klau, G. W., & Raphael, B. J.听The copy-number tree mixture deconvolution problem and applications to multi-sample bulk sequencing tumor data. In听International Conference on Research in Computational Molecular Biology听(pp. 318-335). Springer, Cham (2017).听
- Pirola, Y.,听Zaccaria, S.鈥�, Dondi, R., Klau, G. W., Pisanti, N., & Bonizzoni, P. HapCol: accurate and memory-efficient haplotype assembly from long reads.听Bioinformatics,听32(11), 1610-1617 (2016). Accepted and presented at ISMB-HITSeq 2015.听
- 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.听Journal of Computational Biology,听23(9), 718-736 (2016).听
- El-Kebir, M., Raphael, B. J., Shamir, R., Sharan, R., Zaccaria, S., Zehavi, M., & Zeira, R. Copy-number evolution problems: complexity and algorithms. In听International Workshop on Algorithms in Bioinformatics听(pp. 137-149). Springer, Cham (2016).听
- 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听Annual Symposium on Combinatorial Pattern Matching听(pp. 100-113). Springer, Cham (2015).听
- Willing, E., Zaccaria, S., Braga, M. D., & Stoye, J. On the inversion-indel distance. BMC bioinformatics听14,听S3-15 (2013).听
