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

Zaccaria, Simone ; Raphael, Benjamin J

Nature communications, 2020-09, Vol.11 (1), p.4301-13, Article 4301 [Periódico revisado por pares]

England: Nature Publishing Group

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2
THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data
THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data
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THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data

Oesper, Layla ; Mahmoody, Ahmad ; Raphael, Benjamin J

Genome Biology (Online Edition), 2013-01, Vol.14 (7), p.R80-R80 [Periódico revisado por pares]

England: Springer-Verlag

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3
ConDoR: tumor phylogeny inference with a copy-number constrained mutation loss model
ConDoR: tumor phylogeny inference with a copy-number constrained mutation loss model
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ConDoR: tumor phylogeny inference with a copy-number constrained mutation loss model

Sashittal, Palash ; Zhang, Haochen ; Iacobuzio-Donahue, Christine A ; Raphael, Benjamin J

Genome Biology, 2023-11, Vol.24 (1), p.272-23, Article 272 [Periódico revisado por pares]

England: BioMed Central

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4
HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data
HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data
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HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data

Myers, Matthew A ; Arnold, Brian J ; Bansal, Vineet ; Balaban, Metin ; Mullen, Katelyn M ; Zaccaria, Simone ; Raphael, Benjamin J

Genome Biology, 2024-05, Vol.25 (1), p.130-28, Article 130 [Periódico revisado por pares]

England: BioMed Central

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5
Detecting non-allelic homologous recombination from high-throughput sequencing data
Detecting non-allelic homologous recombination from high-throughput sequencing data
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Detecting non-allelic homologous recombination from high-throughput sequencing data

Parks, Matthew M ; Lawrence, Charles E ; Raphael, Benjamin J

Genome Biology, 2015-04, Vol.16 (1), p.72-72, Article 72 [Periódico revisado por pares]

England: BioMed Central Ltd

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6
Using controls to limit false discovery in the era of big data
Using controls to limit false discovery in the era of big data
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Using controls to limit false discovery in the era of big data

Parks, Matthew M ; Raphael, Benjamin J ; Lawrence, Charles E

BMC bioinformatics, 2018-09, Vol.19 (1), p.323-323, Article 323 [Periódico revisado por pares]

England: BioMed Central Ltd

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7
Reconstructing cancer genomes from paired-end sequencing data
Reconstructing cancer genomes from paired-end sequencing data
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Reconstructing cancer genomes from paired-end sequencing data

Oesper, Layla ; Ritz, Anna ; Aerni, Sarah J ; Drebin, Ryan ; Raphael, Benjamin J

BMC bioinformatics, 2012-04, Vol.13 Suppl 6 (Suppl 6), p.S10-S10, Article S10 [Periódico revisado por pares]

England: BioMed Central

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8
Identification of polymorphic inversions from genotypes
Identification of polymorphic inversions from genotypes
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Identification of polymorphic inversions from genotypes

Cáceres, Alejandro ; Sindi, Suzanne S ; Raphael, Benjamin J ; Cáceres, Mario ; González, Juan R

BMC bioinformatics, 2012-02, Vol.13 (1), p.28-28, Article 28 [Periódico revisado por pares]

England: BioMed Central Ltd

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9
Complexity and algorithms for copy-number evolution problems
Complexity and algorithms for copy-number evolution problems
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Complexity and algorithms for copy-number evolution problems

El-Kebir, Mohammed ; Raphael, Benjamin J ; Shamir, Ron ; Sharan, Roded ; Zaccaria, Simone ; Zehavi, Meirav ; Zeira, Ron

Algorithms for molecular biology, 2017-05, Vol.12 (1), p.13-13, Article 13 [Periódico revisado por pares]

England: BioMed Central

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10
Convergent evolution and multi-wave clonal invasion in H3 K27-altered diffuse midline gliomas treated with a PDGFR inhibitor
Convergent evolution and multi-wave clonal invasion in H3 K27-altered diffuse midline gliomas treated with a PDGFR inhibitor
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Convergent evolution and multi-wave clonal invasion in H3 K27-altered diffuse midline gliomas treated with a PDGFR inhibitor

Arunachalam, Sasi ; Szlachta, Karol ; Brady, Samuel W ; Ma, Xiaotu ; Ju, Bensheng ; Shaner, Bridget ; Mulder, Heather L ; Easton, John ; Raphael, Benjamin J ; Myers, Matthew ; Tinkle, Christopher ; Allen, Sariah J ; Orr, Brent A ; Wetmore, Cynthia J ; Baker, Suzanne J ; Zhang, Jinghui

Acta neuropathologica communications, 2022-05, Vol.10 (1), p.80-80, Article 80 [Periódico revisado por pares]

England: BioMed Central Ltd

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