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Updated: Jan 10, 2026
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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
Published on: May 28, 2021
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SCOUT: Ornstein-Uhlenbeck modelling of gene expression evolution on single-cell lineage trees.
Hannah Stuart1,2, Aaron McKenna1,3
1Molecular and Systems Biology, Dartmouth College, Hanover, NH.
Biorxiv : the Preprint Server for Biology
|November 26, 2025
Summary
SCOUT models gene expression dynamics along cell lineage trees to distinguish neutral drift from selection. This framework aids in understanding evolution in development and disease, like cancer progression.
Area of Science:
- Evolutionary biology
- Genomics
- Computational biology
Background:
- Understanding clonal population evolution is key for development, disease, and therapy.
- Single-cell lineage tracing and transcriptomics offer new analytical approaches.
Purpose of the Study:
- To present SCOUT (single-cell Ornstein-Uhlenbeck trees), a novel framework for modeling gene expression dynamics in single-cell lineage trees.
- To differentiate neutral evolutionary drift from selective pressures.
Main Methods:
- Developed SCOUT, a computational framework utilizing Ornstein-Uhlenbeck processes.
- Applied SCOUT to simulated data, Caenorhabditis elegans development, and a lung adenocarcinoma xenograft model.
Main Results:
- SCOUT accurately classifies genes based on evolutionary models in simulations.
- Identified biological processes under selection during C. elegans development.
- Revealed key regulators of metastatic progression and tumor adaptation in lung cancer.
Conclusions:
- SCOUT provides a powerful evolutionary perspective for analyzing cell fate.
- Integrates lineage and transcriptomic data to dissect evolutionary forces.
- Applicable across diverse biological systems from development to cancer.
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