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.ÌýNature BiotechnologyÌý(2020).Ìý
- Zaccaria, S., Raphael, B.J. Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data.ÌýNature CommunicationsÌý11,Ìý4301 (2020).Ìý
- Myers, M.A.,ÌýZaccaria, S.†, Raphael, B.J.ÌýIdentifying tumor clones in sparse single-cell mutation data,Ìýµþ¾±´Ç¾±²Ô´Ú´Ç°ù³¾²¹³Ù¾±³¦²õÌý36:Ìýi186–i193 (2020). Accepted and presented at ISMB 2020.Ìý
- Satas, G.,ÌýZaccaria, S., Mon, G., & Raphael, B. J.ÌýSCARLET: Single-Cell Tumor Phylogeny Inference with Copy-Number Constrained Mutation Losses.ÌýCell Systems,Ìý10(4):Ìý323-332 (2020). Accepted and presented at RECOMB 2020.Ìý
- Zaccaria, S., El-Kebir, M., Klau, G. W., & Raphael, B. J. Phylogenetic copy-number factorization of multiple tumor samples.ÌýJournal of Computational Biology,Ìý25(7):Ìý689-708 (2018). Accepted and presented at RECOMB 2017.Ìý
- 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).Ìý
- El-Kebir, M., Raphael, B. J., Shamir, R., Sharan, R., Zaccaria, S., Zehavi, M., & Zeira, R. Complexity and algorithms for copy-number evolution problems.ÌýAlgorithms for Molecular Biology,Ìý12(1), 13 (2017).Ìý
- Zaccaria, S., El-Kebir, M., Klau, G. W., & Raphael, B. J.ÌýThe copy-number tree mixture deconvolution problem and applications to multi-sample bulk sequencing tumor data. InÌýInternational Conference on Research in Computational Molecular BiologyÌý(pp. 318-335). Springer, Cham (2017).Ìý
- Pirola, Y.,ÌýZaccaria, S.†, Dondi, R., Klau, G. W., Pisanti, N., & Bonizzoni, P. HapCol: accurate and memory-efficient haplotype assembly from long reads.ÌýBioinformatics,Ìý32(11), 1610-1617 (2016). Accepted and presented at ISMB-HITSeq 2015.Ìý
- 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.ÌýJournal of Computational Biology,Ìý23(9), 718-736 (2016).Ìý
- El-Kebir, M., Raphael, B. J., Shamir, R., Sharan, R., Zaccaria, S., Zehavi, M., & Zeira, R. Copy-number evolution problems: complexity and algorithms. InÌýInternational Workshop on Algorithms in BioinformaticsÌý(pp. 137-149). Springer, Cham (2016).Ìý
- 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. InÌýAnnual Symposium on Combinatorial Pattern MatchingÌý(pp. 100-113). Springer, Cham (2015).Ìý
- Willing, E., Zaccaria, S., Braga, M. D., & Stoye, J. On the inversion-indel distance. BMC bioinformaticsÌý14,ÌýS3-15 (2013).Ìý