ArticleNature biotechnology2024
A relay velocity model infers cell-dependent RNA velocity.
Article in Nature biotechnology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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Who cites it
68 citing papers in PubMed, 102 citations in OpenAlex.
- Article
- mmVelo: a deep generative model for estimating cell state-dependent dynamics across multiple modalities.Bioinformatics (Oxford, England) · 2026Article
- Prenatal PMNature communications · 2026Article
- CellRank: consistent and data view agnostic fate mapping for single-cell genomics.Nature protocols · 2026Review
- Comprehensive benchmarking of RNA velocity methods across single-cell datasets.Genome biology · 2026Article
- PseudoVelo: Inferring Gene Expression Derivatives Along Pseudotime as Pseudo-Velocity.International journal of molecular sciences · 2026Article
- Dissecting and steering cell dynamics using spatially-informed RNA velocity with veloAgent.Molecular systems biology · 2026Article
- Decoding and steering spatially resolved cellular dynamics.Molecular systems biology · 2026Article
- STEER: decoupling kinetics with Spatial-Temporal Explainable Expert model for RNA velocity inference.National science review · 2026Article
- Serial Spatial Transcriptomes Reveal Regulatory Transitions in Maize Leaf Development.Plant biotechnology journal · 2026Article
- Benchmarking RNA velocity methods across 17 independent studies.Cell reports methods · 2026Article
- Disease insights from brain somatic mosaicism.Experimental & molecular medicine · 2026Review
- 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
- Bayesian inference of RNA velocity incorporating timepoints, lineage bifurcations, and count data.PLoS computational biology · 2026Article
- stVCR: spatiotemporal dynamics of single cells.Nature methods · 2026Article
- Defining the cellular and molecular identities of histologic subtypes in lung adenocarcinoma.Experimental hematology & oncology · 2026Article
- Article
- RNAPaceDB: a dedicated database to dissect RNA velocity across diverse cell types.Nucleic acids research · 2026Article
- Multi-omic relay velocity modeling uncovers dynamic chromatin-transcription regulation across cell states.Nature communications · 2025Article
8 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors at 2 institutions in 1 country.
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Abstract
RNA velocity provides an approach for inferring cellular state transitions from single-cell RNA sequencing (scRNA-seq) data. Conventional RNA velocity models infer universal kinetics from all cells in an scRNA-seq experiment, resulting in unpredictable performance in experiments with multi-stage and/or multi-lineage transition of cell states where the assumption of the same kinetic rates for all cells no longer holds. Here we present cellDancer, a scalable deep neural network that locally infers velocity for each cell from its neighbors and then relays a series of local velocities to provide single-cell resolution inference of velocity kinetics. In the simulation benchmark, cellDancer shows robust performance in multiple kinetic regimes, high dropout ratio datasets and sparse datasets. We show that cellDancer overcomes the limitations of existing RNA velocity models in modeling erythroid maturation and hippocampus development. Moreover, cellDancer provides cell-specific predictions of transcription, splicing and degradation rates, which we identify as potential indicators of cell fate in the mouse pancreas.
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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.