ArticleNature methods2025
Cell2fate infers RNA velocity modules to improve cell fate prediction.
Article in Nature methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- 3D multi-omics tumour atlases: from technology to biology and clinical translation.Nature reviews. Cancer · 2026Review
- Prefibrotic bone marrow microenvironment is a hallmark of clonal hematopoiesis.Nature immunology · 2026Article
- 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
- ArchVelo: archetypal velocity modeling for single-cell multi-omic trajectories.Nature communications · 2026Article
- Interpretation, extrapolation and perturbation of single cells.Nature reviews. Genetics · 2026Review
- Benchmarking RNA velocity methods across 17 independent studies.Cell reports methods · 2026Article
- Uncovering Immune Niches in Health and Disease Using Spatial Transcriptomics.European journal of immunology · 2026Review
- Single-Cell Mitochondrial Lineage Tracing Decodes Fate Decision and Spatial Clonal Architecture in Human Hematopoietic Organoids.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Prior-guided factorization for reliable imputation of scRNA-seq data.PLoS computational biology · 2026Article
- Article
- RNAPaceDB: a dedicated database to dissect RNA velocity across diverse cell types.Nucleic acids research · 2026Article
- Leveraging Single-Cell Technologies to Advance Understanding of Myocardial Disease.Circulation research · 2026Review
- Fundamental errors in RNA velocity arising from the omission of cell growth.bioRxiv : the preprint server for biology · 2025Article
- A conserved differentiation programme facilitates inhibitory neuron production in the developing mouse and human cerebellum.Development (Cambridge, England) · 2025Article
- Spatiotemporal Atlas of Heart Development Reveals Blood-Flow-Dependent Cellular, Structural, Metabolic, and Spatial Remodeling.bioRxiv : the preprint server for biology · 2025Article
- Insights, opportunities, and challenges provided by large cell atlases.Genome biology · 2025Review
- InterVelo: a mutually enhancing model for estimating pseudotime and RNA velocity in multi-omic single-cell data.Bioinformatics (Oxford, England) · 2025Article
- Trajectory inference from single-cell genomics data with a process time model.PLoS computational biology · 2025Article
- KSRV: a Kernel PCA-Based framework for inferring spatial RNA velocity at single-cell resolution.Frontiers in genetics · 2025Article
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Authors and funding
7 authors.
Funding
Abstract
RNA velocity exploits the temporal information contained in spliced and unspliced RNA counts to infer transcriptional dynamics. Existing velocity models often rely on coarse biophysical simplifications or numerical approximations to solve the underlying ordinary differential equations (ODEs), which can compromise accuracy in challenging settings, such as complex or weak transcription rate changes across cellular trajectories. Here we present cell2fate, a formulation of RNA velocity based on a linearization of the velocity ODE, which allows solving a biophysically more accurate model in a fully Bayesian fashion. As a result, cell2fate decomposes the RNA velocity solutions into modules, providing a biophysical connection between RNA velocity and statistical dimensionality reduction. We comprehensively benchmark cell2fate in real-world settings, demonstrating enhanced interpretability and power to reconstruct complex dynamics and weak dynamical signals in rare and mature cell types. Finally, we apply cell2fate to the developing human brain, where we spatially map RNA velocity modules onto the tissue architecture, connecting the spatial organization of tissues with temporal dynamics of transcription.
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