ArticleNature methods2024
Spatial transition tensor of single cells.
Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Article
- Comprehensive benchmarking of RNA velocity methods across single-cell datasets.Genome biology · 2026Article
- A dependency-aware deep generative model for inferring RNA velocity from spatial transcriptomics.Bioinformatics (Oxford, England) · 2026Article
- Robust identification of cell-cell communication heterogeneity in single cells.bioRxiv : the preprint server for biology · 2026Article
- STEER: decoupling kinetics with Spatial-Temporal Explainable Expert model for RNA velocity inference.National science review · 2026Article
- stVCR: spatiotemporal dynamics of single cells.Nature methods · 2026Article
- Article
- Deciphering cell-fate trajectories using spatiotemporal single-cell transcriptomic data.NPJ systems biology and applications · 2025Review
- Learning stochastic processes with intrinsic noise from cross-sectional biological data.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Quantifying Landscape and Flux from Single-Cell Omics: Unraveling the Physical Mechanisms of Cell Function.JACS Au · 2025Review
- spVelo: RNA velocity inference for multi-batch spatial transcriptomics data.Genome biology · 2025Article
- Unravelling tumour spatiotemporal heterogeneity using spatial multimodal data.Clinical and translational medicine · 2025Review
- Integrating Dynamical Systems Modeling with Spatiotemporal scRNA-Seq Data Analysis.Entropy (Basel, Switzerland) · 2025Review
- Quantifying and interpreting biologically meaningful spatial signatures within tumor microenvironments.NPJ precision oncology · 2025Review
- KSRV: a Kernel PCA-Based framework for inferring spatial RNA velocity at single-cell resolution.Frontiers in genetics · 2025Article
- Unraveling the spatial and signaling dynamics and splicing kinetics of immune infiltration in osteoarthritis synovium.Frontiers in immunology · 2025Article
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Authors and funding
4 authors.
Funding
Abstract
Spatial transcriptomics and messenger RNA splicing encode extensive spatiotemporal information for cell states and transitions. The current lineage-inference methods either lack spatial dynamics for state transition or cannot capture different dynamics associated with multiple cell states and transition paths. Here we present spatial transition tensor (STT), a method that uses messenger RNA splicing and spatial transcriptomes through a multiscale dynamical model to characterize multistability in space. By learning a four-dimensional transition tensor and spatial-constrained random walk, STT reconstructs cell-state-specific dynamics and spatial state transitions via both short-time local tensor streamlines between cells and long-time transition paths among attractors. Benchmarking and applications of STT on several transcriptome datasets via multiple technologies on epithelial-mesenchymal transitions, blood development, spatially resolved mouse brain and chicken heart development, indicate STT's capability in recovering cell-state-specific dynamics and their associated genes not seen using existing methods. Overall, STT provides a consistent multiscale description of single-cell transcriptome data across multiple spatiotemporal scales.
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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 Socratic graph.