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Simone Zaccaria
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Year
Characterizing allele-and haplotype-specific copy numbers in single cells with CHISEL
S Zaccaria, BJ Raphael
Nature biotechnology 39 (2), 207-214, 2021
502021
HapCol: accurate and memory-efficient haplotype assembly from long reads
Y Pirola, S Zaccaria, R Dondi, GW Klau, N Pisanti, P Bonizzoni
Bioinformatics 32 (11), 1610-1617, 2016
492016
Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data
S Zaccaria, BJ Raphael
Nature communications 11 (1), 1-13, 2020
452020
SCARLET: single-cell tumor phylogeny inference with copy-number constrained mutation losses
G Satas, S Zaccaria, G Mon, BJ Raphael
Cell Systems 10 (4), 323-332. e8, 2020
382020
Complexity and algorithms for copy-number evolution problems
M El-Kebir, BJ Raphael, R Shamir, R Sharan, S Zaccaria, M Zehavi, ...
Algorithms for Molecular Biology 12 (1), 1-11, 2017
292017
On the minimum error correction problem for haplotype assembly in diploid and polyploid genomes
P Bonizzoni, R Dondi, GW Klau, Y Pirola, N Pisanti, S Zaccaria
Journal of Computational Biology 23 (9), 718-736, 2016
292016
Copy-number evolution problems: complexity and algorithms
M El-Kebir, BJ Raphael, R Shamir, R Sharan, S Zaccaria, M Zehavi, ...
International Workshop on Algorithms in Bioinformatics, 137-149, 2016
252016
Phylogenetic copy-number factorization of multiple tumor samples
S Zaccaria, M El-Kebir, GW Klau, BJ Raphael
Journal of Computational Biology 25 (7), 689-708, 2018
232018
The copy-number tree mixture deconvolution problem and applications to multi-sample bulk sequencing tumor data
S Zaccaria, M El-Kebir, GW Klau, BJ Raphael
International Conference on Research in Computational Molecular Biology, 318-335, 2017
202017
On the inversion-indel distance
E Willing, S Zaccaria, MDV Braga, J Stoye
BMC bioinformatics 14 (15), 1-10, 2013
162013
Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidates for targeted treatment
H Sun, S Cao, RJ Mashl, CK Mo, S Zaccaria, MC Wendl, SR Davies, ...
Nature communications 12 (1), 1-20, 2021
142021
On the fixed parameter tractability and approximability of the minimum error correction problem
P Bonizzoni, R Dondi, GW Klau, Y Pirola, N Pisanti, S Zaccaria
Annual Symposium on Combinatorial Pattern Matching, 100-113, 2015
132015
HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads
S Beretta, MD Patterson, S Zaccaria, G Della Vedova, P Bonizzoni
BMC bioinformatics 19 (1), 1-19, 2018
122018
Identifying tumor clones in sparse single-cell mutation data
MA Myers, S Zaccaria, BJ Raphael
Bioinformatics 36 (Supplement_1), i186-i193, 2020
72020
Characterizing the allele-and haplotype-specific copy number landscape of cancer genomes at single-cell resolution with CHISEL
S Zaccaria, BJ Raphael
bioRxiv, 837195, 2019
52019
DeCiFering the elusive cancer cell fraction in tumor heterogeneity and evolution
G Satas, S Zaccaria, M El-Kebir, BJ Raphael
Cell Systems 12 (10), 1004-1018. e10, 2021
32021
Single-cell tumor phylogeny inference with copy-number constrained mutation losses
G Satas, S Zaccaria, G Mon, BJ Raphael
bioRxiv, 840355, 2019
22019
Parsimonious clone tree reconciliation in cancer
P Sashittal, S Zaccaria, M El-Kebir
Leibniz International Proceedings in Informatics, LIPIcs 201, 9, 2021
12021
HAPCOL: Accurate and Memory-efficient Haplotype Assembly from Long Reads
P Bonizzoni, R Dondi, GW Klau, Y Pirola, N Pisanti, S Zaccaria
High Throughput Sequencing SIG of ISMB/ECCB (HitSeq), 1-1, 2015
12015
Parsimonious Clone Tree Integration in cancer
P Sashittal, S Zaccaria, M El-Kebir
Algorithms for Molecular Biology 17 (1), 1-14, 2022
2022
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Articles 1–20