Searching journal content for articles similar to Zafar et al. 29 (11): 1847.

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  1. Method: Integrating SNVs and CNAs on a phylogenetic tree from single-cell DNA sequencing data
    • Liting Zhang,
    • Hank W. Bass,
    • Jerome Irianto,
    • and Xian Mallory
    Genome Res. November 2023 33: 2002-2017; Published in Advance November 22, 2023, doi:10.1101/gr.277249.122
    ...are shown for SCsnvcna, SCARLET, COMPASS, SiFit, SCG, RobustClone, and SiCloneFit on varying FP rate (A), varying FN rate (B), and varying missing rate (C).View larger version: In this window In a new window Figure 3. Group 2: evaluation of scalability. Genotype error, pairwise SNV error, and pairwise SNV...
  2. Method: A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data
    • Fei Qin,
    • Guoshuai Cai,
    • Christopher I. Amos,
    • and Feifei Xiao
    Genome Res. January 2024 34: 85-93; Published in Advance January 30, 2024, doi:10.1101/gr.278098.123
    ....823941 ↵Zaccaria S, Raphael BJ. 2021. Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL. Nat Biotechnol 39: 207–214. doi:10.1038/s41587-020-0661-6 ↵Zafar H, Navin N, Chen K, Nakhleh L. 2019. SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny...
  3. Method: PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data
    • Salem Malikic,
    • Farid Rashidi Mehrabadi,
    • Simone Ciccolella,
    • Md. Khaledur Rahman,
    • Camir Ricketts,
    • Ehsan Haghshenas,
    • Daniel Seidman,
    • Faraz Hach,
    • Iman Hajirasouliha,
    • and S. Cenk Sahinalp
    Genome Res. November 2019 29: 1860-1877; Published in Advance October 18, 2019, doi:10.1101/gr.234435.118
    .... There already exist computational tools for identifying and decoupling doublets, in particular Single Cell Genotyper (Roth et al. 2016), which we employ in this study as a preprocessing step for the purpose of reducing their impact in our analysis. Furthermore, a recently developed tool, SiCloneFit (Zafar et al...
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