ArticlePLoS computational biology2025
Optimal transport reveals dynamic gene regulatory networks via gene velocity estimation.
Article in PLoS computational biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Cell type-specific gene regulatory network inference from single cell transcriptomics with ctOTVelo.bioRxiv : the preprint server for biology · 2026Article
- Temporal network analysis in systems biology: concepts, inference, and validation.Frontiers in bioinformatics · 2026Review
- Deciphering cell-fate trajectories using spatiotemporal single-cell transcriptomic data.NPJ systems biology and applications · 2025Review
- Inferring the regulation dynamics of oscillatory networks from scRNA-seq data.bioRxiv : the preprint server for biology · 2025Article
- Double optimal transport for differential gene regulatory network inference with unpaired samples.Bioinformatics (Oxford, England) · 2025Article
- Integrating Dynamical Systems Modeling with Spatiotemporal scRNA-Seq Data Analysis.Entropy (Basel, Switzerland) · 2025Review
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4 authors.
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Abstract
Inferring gene regulatory networks from gene expression data is an important and challenging problem in the biology community. We propose OTVelo, a methodology that takes time-stamped single-cell gene expression data as input and predicts gene regulation across two time points. It is known that the rate of change of gene expression, which we will refer to as gene velocity, provides crucial information that enhances such inference; however, this information is not always available due to the limitations in sequencing depth. Our algorithm overcomes this limitation by estimating gene velocities using optimal transport. We then infer gene regulation using time-lagged correlation and Granger causality via regularized linear regression. Instead of providing an aggregated network across all time points, our method uncovers the underlying dynamical mechanism across time points. We validate our algorithm on 13 simulated datasets with both synthetic and curated networks and demonstrate its efficacy on 9 experimental data sets.
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