Simone Zaccaria
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Characterizing allele-and haplotype-specific copy numbers in single cells with CHISEL
S Zaccaria, BJ Raphael
Nature biotechnology 39 (2), 207-214, 2021
The evolution of lung cancer and impact of subclonal selection in TRACERx
AM Frankell, M Dietzen, M Al Bakir, EL Lim, T Karasaki, S Ward, ...
Nature 616 (7957), 525-533, 2023
Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data
S Zaccaria, BJ Raphael
Nature communications 11 (1), 4301, 2020
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), 5086, 2021
The evolution of non-small cell lung cancer metastases in TRACERx
M Al Bakir, A Huebner, C Martínez-Ruiz, K Grigoriadis, TBK Watkins, ...
Nature 616 (7957), 534-542, 2023
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
The translational challenges of precision oncology
O Pich, C Bailey, TBK Watkins, S Zaccaria, M Jamal-Hanjani, C Swanton
Cancer Cell 40 (5), 458-478, 2022
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
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, 1-11, 2017
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
Evolutionary characterization of lung adenocarcinoma morphology in TRACERx
T Karasaki, DA Moore, S Veeriah, C Naceur-Lombardelli, A Toncheva, ...
Nature medicine 29 (4), 833-845, 2023
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
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
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
Research in Computational Molecular Biology: 21st Annual International …, 2017
On the inversion-indel distance
E Willing, S Zaccaria, MDV Braga, J Stoye
BMC bioinformatics 14, 1-10, 2013
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
Identifying tumor clones in sparse single-cell mutation data
MA Myers, S Zaccaria, BJ Raphael
Bioinformatics 36 (Supplement_1), i186-i193, 2020
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
Combinatorial Pattern Matching: 26th Annual Symposium, CPM 2015, Ischia …, 2015
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, 1-19, 2018
CONIPHER: a computational framework for scalable phylogenetic reconstruction with error correction
K Grigoriadis, A Huebner, A Bunkum, E Colliver, AM Frankell, MS Hill, ...
Nature Protocols 19 (1), 159-183, 2024
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