Deciphering cell-fate trajectories using spatiotemporal single-cell transcriptomic data

Cellular processes evolve dynamically across time and space. Single-cell and spatial omics technologies have provided high-resolution snapshots of gene expression, greatly expanding the capability to characterize cellular states. More recently, temporally resolved single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics data have made it possible to investigate population-level changes across multiple time points and tissue contexts, creating new opportunities to reconstruct cellular dynamics. In this review, we summarize recent progresses in modeling strategies for time-series scRNA-seq and spatiotemporal data. We introduce the mathematical foundations of dynamical systems and generative modeling and highlight algorithmic advances that bring these approaches into practice. We further provide practical guidelines for selecting and applying appropriate methods in various research scenarios. By connecting mathematical frameworks with biological applications, this review illustrates how computational tools can deepen our understanding of the dynamic nature of single cells. Supplementary Material File (deciphering_cell_fate_review.pdf) - Download - 5.38 MB Information & Authors Information Version history Peer review timeline Published npj Systems Biology and Applications Version of Record4 Dec 2025Published Copyright This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License

Authors Metrics & Citations Metrics Article Usage 650views 357downloads Citations Download citation Zhenyi Zhang, Zihan Wang, Yuhao Sun, et al. Deciphering cell-fate trajectories using spatiotemporal single-cell transcriptomic data. Authorea. 08 September 2025. DOI: https://doi.org/10.22541/au.175735334.45794622/v1 DOI: https://doi.org/10.22541/au.175735334.45794622/v1 If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download. For more information or tips please see 'Downloading to a citation manager' in the Help menu.