Publications

Please find the most updated versions of the list of publications on Scholar, ORCID, or Scopus.

Preprints

Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data

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

Peer-reviewed journal

HapCHAT: Adaptive haplotype assembly for efficiently leveraging high coverage in long reads

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

Phylogenetic copy-number factorization of multiple tumor samples

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

Complexity and algorithms for copy-number evolution problems

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

On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid Genomes

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

HAPCOL: accurate and memory-efficient haplotype assembly from long reads

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

On the inversion-indel distance

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

Peer-reviewed conference

The copy-number tree mixture deconvolution problem and applications to multi-sample bulk sequencing tumor data

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

Copy-number evolution problems: complexity and algorithms

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

On the fixed parameter tractability and approximability of the minimum error correction problem

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