Sc4D: spatio-temporal single-cell transcriptomics analysis through embedded optimal transport identifies joint glial response to Alzheimer's disease pathology.

ABSTRACT: A precise understanding of disease-associated spatio-temporal transcriptional dynamics is critical for nominating therapeutic interventions that drive desired perturbation responses. In disease contexts, pathological processes unfold across diverse cellular states, spatial environments, and timescales; however, current computational approaches have a limited ability to jointly model these complex dynamics or infer cellular trajectories from in silico perturbation experiments. Here, we present sc4D, a biologically interpretable spatio-temporal (4D) analysis framework for single-cell transcriptomics in disease studies, integrating autoencoder embeddings with optimal transport. Applying sc4D to longitudinal spatial transcriptomics samples from Alzheimer's disease mouse models, we repor

SUBMITTER: Rao I 

PROVIDER: S-EPMC12667907 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature