Maximum Likelihood Inference of Time-scaled Cell Lineage Trees with Mixed-type Missing Data.

ABSTRACT: Recent dynamic lineage tracing technologies combine CRISPR-based genome editing with single-cell sequencing to track cell divisions during development. A key computational problem in dynamic lineage tracing is to infer a cell lineage tree from the measured CRISPR-induced mutations. Three features of dynamic lineage tracing data distinguish this problem from standard phylogenetic tree inference. First, the CRISPR-editing process modifies a genomic location exactly once. This non-modifiable property is not well described by the time-reversible models commonly used in phylogenetics. Second, as a consequence of non-modifiability, the number of mutations per time unit decreases over time. Third, CRISPR-based genome-editing and single-cell sequencing results in high rates of both heritabl

SUBMITTER: Mai U 

PROVIDER: S-EPMC10942411 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature