On the inversion-indel distance
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E. Willing, S. Zaccaria et al. On the inversion-indel distance. BMC bioinformatics. Vol. 14. No. 15. BioMed Central, 2013 https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-S15-S3
Y. Pirola*, S. Zaccaria*, et al. HAPCOL: accurate and memory-efficient haplotype assembly from long reads. Bioinformatics 32.11 (2015): 1610-1617. https://academic.oup.com/bioinformatics/article/32/11/1610/1742594
P. Bonizzoni, R. Dondi, GW. Klau, Y. Pirola, N. Pisanti, and S. Zaccaria. On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid Genomes. Journal of Computational Biology 23, no. 9 (2016): 718-736. https://www.liebertpub.com/doi/full/10.1089/cmb.2015.0220
M. El-Kebir, B.J. Raphael, R. Shamir, R. Sharan, S. Zaccaria, M. Zehavi, and R. Zeira. Complexity and algorithms for copy-number evolution problems. Algorithms for Molecular Biology, 12(1), 13. 2017 https://almob.biomedcentral.com/articles/10.1186/s13015-017-0103-2
S. Zaccaria et al. Phylogenetic copy-number factorization of multiple tumor samples. Journal of Computational Biology 25.7 (2018): 689-708. https://www.liebertpub.com/doi/full/10.1089/cmb.2017.0253
S. Beretta, M.D. Patterson, S. Zaccaria, G. Della Vedova, and P. Bonizzoni. HapCHAT: Adaptive haplotype assembly for efficiently leveraging high coverage in long reads. BMC Bioinformatics 19, no. 1 (2018): 252. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2253-8
S. Zaccaria and B.J. Raphael. Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data. bioRxiv, 2018 (https://doi.org/10.1101/496174) https://www.biorxiv.org/content/10.1101/496174v1
P. Bonizzoni, R. Dondi, G.W. Klau, Y. Pirola, N. Pisanti, and S. Zaccaria. On the fixed parameter tractability and approximability of the minimum error correction problem. In Annual Symposium on Combinatorial Pattern Matching (CPM 2015), pp. 100-113. Springer, 2015. https://link.springer.com/chapter/10.1007/978-3-319-19929-0_9
M. El-Kebir, B.J. Raphael, R. Shamir, R. Sharan, S. Zaccaria, M. Zehavi, and R. Zeira. Copy-number evolution problems: complexity and algorithms. In International Workshop on Algorithms in Bioinformatics (WABI 2016), pp. 137-149. Springer, 2016. https://link.springer.com/chapter/10.1007/978-3-319-43681-4_11
S. Zaccaria et al. The copy-number tree mixture deconvolution problem and applications to multi-sample bulk sequencing tumor data. International Conference on Research in Computational Molecular Biology (RECOMB 2017). Springer, 2017. https://link.springer.com/chapter/10.1007/978-3-319-56970-3_20