ArticleNature communications2025
Stereopy: modeling comparative and spatiotemporal cellular heterogeneity via multi-sample spatial transcriptomics.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Spatial transcriptomics reveal developmental dynamics of the human cerebral cortex and striatum.Science China. Life sciences · 2026Article
- A High-Resolution Stereo-Seq Spatial Transcriptomic Resource for Adult Holstein Cattle Liver.International journal of molecular sciences · 2026Article
- Spatial isoform sequencing at single-cell resolution reveals cell-type-specific spatial isoform variability in multiple brain cell types.Nature methods · 2026Article
- Human and mouse adrenal glands are characterized by species-specific steroidogenic states and tissue turnover.Nature genetics · 2026Article
- The DLX/Notch axis is necessary for spatiotemporal regulation of neural cell fate.Nature communications · 2026Article
- Spatially organized regulated cell death-immune coupling in solid tumors: integrating spatial omics with actionable regulated cell death biology.Molecular cancer · 2026Review
- Clearance of intracranial debris by ultrasound reduces inflammation and improves outcomes in hemorrhagic stroke models.Nature biotechnology · 2026Article
- GenOT: generative optimal transport enables spatiotemporal interpolation and generation in cross-platform spatial transcriptomics.Genome biology · 2026Article
- Application of spatial transcriptomics across organoids for a high-resolution, spatial whole-transcriptome benchmarking dataset.iScience · 2026Article
- Accurate, scalable and cross-platform cell identification for high-resolution spatial transcriptomics.Nature genetics · 2026Article
- Organ-Specific and Conserved Regulatory Logic Orchestrates Gene Expression in the Embryonic Mesothelium.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- RegFormer: a single-cell foundation model powered by gene regulatory hierarchies.Nature communications · 2026Article
- Article
- Single-Cell and Spatial Omics: Methods and Applications.MedComm · 2026Review
- Mutational Signatures and Clonal Hematopoiesis in Intestinal Metaplasia across Countries with Varying Stomach Cancer Incidence.Cancer discovery · 2026Article
- Leucine-Dependent SLC7A5-PGAM5 Interaction Promotes Advanced Atherosclerosis Through Hindering Mitochondrial Function of Macrophages.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Unveiling the early defense response dynamics in grapevines against Plasmopara viticola by single-cell transcriptomics.Genome biology · 2026Article
- Spatial FBA reveals heterogeneous Warburg niches in renal tumors and lactate consumption in colorectal cancer.NPJ systems biology and applications · 2026Article
- 4D single-cell spatial transcriptomics reveals dynamic morphogenetic gradients and regenerative domains in planarians.GigaScience · 2026Article
- Robust characterization and interpretation of rare pathogenic cell populations from spatial omics using GARDEN.Nature communications · 2026Article
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Authors and funding
37 authors.
Funding
Abstract
Understanding complex biological systems requires tracing cellular dynamic changes across conditions, time, and space. However, integrating multi-sample data in a unified way to explore cellular heterogeneity remains challenging. Here, we present Stereopy, a flexible framework for modeling and dissecting comparative and spatiotemporal patterns in multi-sample spatial transcriptomics with interactive data visualization. To optimize this framework, we devise a universal container, a scope controller, and an integrative transformer tailored for multi-sample multimodal data storage, management, and processing. Stereopy showcases three representative applications: investigating specific cell communities and genes responsible for pathological changes, detecting spatiotemporal gene patterns by considering spatial and temporal features, and inferring three-dimensional niche-based cell-gene interaction network that bridges intercellular communications and intracellular regulations. Stereopy serves as both a comprehensive bioinformatics toolbox and an extensible framework that empowers researchers with enhanced data interpretation abilities and new perspectives for mining multi-sample spatial transcriptomics data.
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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.