SCOUT: Ornstein-Uhlenbeck modelling of gene expression evolution on single-cell lineage trees

Building on advances in single-cell lineage tracing and transcriptomics, we present SCOUT (Single-Cell Ornstein-Uhlenbeck Trees), a computational framework that models gene expression dynamics along single-cell lineage trees using Ornstein-Uhlenbeck processes to distinguish neutral drift from selective pressure.

We validated our approach through simulations, developmental studies in C. elegans, and analysis of lung cancer xenografts. Our findings identified biological processes under evolutionary selection in different developmental stages and revealed key regulators of metastatic progression and tumor microenvironmental adaptation.

SCOUT integrates lineage tracing data with transcriptomics to provide insights into the forces that shape cell fate.