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Nature Communications|September 4, 2020
Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing dataSimone Zaccaria, Benjamin J RaphaelNature Biotechnology|September 4, 2020
Characterizing allele- and haplotype-specific copy numbers in single cells with CHISELSimone Zaccaria, Benjamin J RaphaelBioinformatics (Oxford, England)|July 14, 2020
Identifying tumor clones in sparse single-cell mutation dataMatthew A Myers, Simone Zaccaria, Benjamin J RaphaelCell Systems|September 1, 2020
SCARLET: Single-cell tumor phylogeny inference with copy-number constrained mutation lossesGryte Satas, Simone Zaccaria, Geoffrey Mon, et al.Cell Systems|August 20, 2021
DeCiFering the elusive cancer cell fraction in tumor heterogeneity and evolutionGryte Satas, Simone Zaccaria, Mohammed El-Kebir, et al.Journal of Computational Biology : a Journal of Computational Molecular Cell Biology|April 17, 2018
Phylogenetic Copy-Number Factorization of Multiple Tumor SamplesSimone Zaccaria, Mohammed El-Kebir, Gunnar W Klau, et al.Algorithms for Molecular Biology : AMB|May 19, 2017
Complexity and algorithms for copy-number evolution problemsMohammed El-Kebir, Benjamin J Raphael, Ron Shamir, et al.Biorxiv : the Preprint Server for Biology|July 28, 2023
HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing dataMatthew A Myers, Brian J Arnold, Vineet Bansal, et al.Cancer Research Communications|April 17, 2023
Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary TimeSanjana Rajan, Simone Zaccaria, Matthew V Cannon, et al.Genome Biology|May 21, 2024
HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing dataMatthew A Myers, Brian J Arnold, Vineet Bansal, et al.Pageof 19