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Article

Inference of single-cell phylogenies from lineage tracing data using Cassiopeia.

Genome biology - 14 Apr 2020

Jones Matthew G, Khodaverdian Alex, Quinn Jeffrey J, Chan Michelle M, Hussmann Jeffrey A, Wang Robert, Xu Chenling, Weissman Jonathan S, Yosef Nir

Abstract excerpt

The pairing of CRISPR/Cas9-based gene editing with massively parallel single-cell readouts now enables large-scale lineage tracing. However, the rapid growth in complexity of data from these assays has outpaced our ability to accurately infer phylogenetic relationships. First, we introduce Cassiopeia-a suite of scalable maximum parsimony approaches for tree reconstruction. Second, we provide a simulation...

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Identifiers

PMID: 32290857
DOI: 10.1186/s13059-020-02000-8
PMCID: PMC7155257

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