ArticlePLoS computational biology2022
RNA velocity unraveled.
Article in PLoS computational biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 102 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
102 citing papers in PubMed.
- Article
- Genome-wide chromatin recording resolves dynamic cell state changes.Cell systems · 2026Article
- mmVelo: a deep generative model for estimating cell state-dependent dynamics across multiple modalities.Bioinformatics (Oxford, England) · 2026Article
- Article
- Uncovering smooth structures in single-cell data with neighbor embeddings guided by predictability-computability-stability.Patterns (New York, N.Y.) · 2026Article
- Deciphering global transcriptional dynamics coordinated by gene-gene regulatory interactions using single-cell data.Molecular systems biology · 2026Article
- Comprehensive benchmarking of RNA velocity methods across single-cell datasets.Genome biology · 2026Article
- Genome-wide chromatin recording resolves dynamic cell state changes.bioRxiv : the preprint server for biology · 2026Article
- PseudoVelo: Inferring Gene Expression Derivatives Along Pseudotime as Pseudo-Velocity.International journal of molecular sciences · 2026Article
- Single-cell analysis of microglia and monocyte dynamics uncovers distinct TNF-driven neuroimmune signatures in humans after intracerebral hemorrhage.Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism · 2026Article
- Deep dynamical models of single-cell multiomic velocities predict loss-of-function and rescue perturbations in B cells.bioRxiv : the preprint server for biology · 2026Article
- ArchVelo: archetypal velocity modeling for single-cell multi-omic trajectories.Nature communications · 2026Article
- Challenges and progress in RNA velocity: Comparative analysis across multiple biological contexts.PLoS computational biology · 2026Article
- Comparison between a conventional tool and deep learning models for RNA velocity analysis of scRNA-Seq data.Molecular genetics and genomics : MGG · 2026Article
- Loss of Chromosome Y Associates With Altered Immune Cell Trajectories and X-Inactivation Features.Aging cell · 2026Article
- STEER: decoupling kinetics with Spatial-Temporal Explainable Expert model for RNA velocity inference.National science review · 2026Article
- Benchmarking RNA velocity methods across 17 independent studies.Cell reports methods · 2026Article
- Quantifying stability via count splitting to guide model selection in RNA velocity analyses.bioRxiv : the preprint server for biology · 2026Article
- Interpretable learning of temporal cellular dynamics from single-cell data.Cell reports methods · 2026Article
- Elucidating the coordination of RNA processing using short-read and long-read RNA-sequencing methods.Nature reviews. Molecular cell biology · 2026Review
42 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
We perform a thorough analysis of RNA velocity methods, with a view towards understanding the suitability of the various assumptions underlying popular implementations. In addition to providing a self-contained exposition of the underlying mathematics, we undertake simulations and perform controlled experiments on biological datasets to assess workflow sensitivity to parameter choices and underlying biology. Finally, we argue for a more rigorous approach to RNA velocity, and present a framework for Markovian analysis that points to directions for improvement and mitigation of current problems.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.