PMCID
PMC12746066

Fundamental errors in RNA velocity arising from the omission of cell growth.

bioRxiv : the preprint server for biology
Authors
Abstract

The ultimate promise of single cell "RNA velocity" methods is compelling: in principle, one can project forward the transcriptional state of each cell and map long-term expression trajectories. While there has been robust and ongoing articulation of limitations of existing methods, consensus frameworks continue to overlook a fundamental aspect of cellular dynamics: growth. In a growing population, biomass (including RNA and other macromolecules) is constantly accumulating. This implies a homeostatic velocity (defined in the terms of production and degradation) that is positive, which is at odds with the conventional estimation, interpretation, and uses of velocity. Here, we investigate the consequences of omitting cell growth from the RNA velocity framework. We demonstrate systematic errors that arise from ignoring cell growth and show evidence for these artifacts in existing data. Finally, we point the way forward and highlight that explicitly accounting for cell growth can lead to new biological insights.

Year of Publication
2025
Journal
bioRxiv : the preprint server for biology
Date Published
12/2025
ISSN
2692-8205
DOI
10.64898/2025.12.18.695252
PubMed ID
41473271
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