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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
Pages
Posts
journals
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
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 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
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
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
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
posters
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
proceedings
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
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
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