ArticleNature biotechnology2021
Spatial transcriptomics at subspot resolution with BayesSpace.
Article in Nature biotechnology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 620 papers.
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Who cites it
620 citing papers in PubMed.
- Spatial transcriptomics profiling across tissue boundaries in the developing mouse brain.iScience · 2026Article
- Accurate and well-powered case-control analysis of spatial molecular data.Nature methods · 2026Article
- Decoding epithelial-mesenchymal transitions with multi-omics.Nature reviews. Genetics · 2026Review
- Asynchronous Evolution of Epithelium and Stroma Differentiates Precursor Lesions from Pancreatic Cancer.Cancer discovery · 2026Article
- 3D multi-omics tumour atlases: from technology to biology and clinical translation.Nature reviews. Cancer · 2026Review
- Single-cell RNA Sequencing Analysis Reveals That Targeting PLG-PLGRKT Signaling-mediated Pro-fibrotic Scar-associated Macrophages Ameliorates Liver Fibrosis in Biliary Atresia.Journal of clinical and translational hepatology · 2026Article
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- A multiperspective evaluation framework of spatial transcriptomics clustering methods.NAR genomics and bioinformatics · 2026Article
- Ten quick tips for spatial transcriptomics analysis.PLoS computational biology · 2026Review
- Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering.Nature methods · 2026Article
- SANNO: A Graph-Transformer Enhanced Optimal Transport Tool for Spatial Transcriptomic Annotation.Interdisciplinary sciences, computational life sciences · 2026Article
- spMosaic: multi-sample integration for scalable spatial domain discovery based on spatial transcriptomics.Briefings in bioinformatics · 2026Article
- Unified representation learning for spatial multi-omics.Bioinformatics (Oxford, England) · 2026Article
- STADiffuser: high-fidelity simulation and full-view 3D modeling of spatial transcriptomics.Nature communications · 2026Article
- STWave: Fine-Scale Spatial Structure Discovery in Microscopic-Resolution Spatial Transcriptomics via Patchwise Wavelet Graphs.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Spatial omics illuminates tumor heterogeneity.Cell reports methods · 2026Review
- Article
- hoodscanR: profiling single-cell neighborhoods in spatial transcriptomics data.Bioinformatics (Oxford, England) · 2026Article
- Single-cell and spatial transcriptomics analysis of osteoarthritis: pathway regulation, cell interaction networks, and therapeutic translation.Journal of translational medicine · 2026Review
- DESpace2: detection of differential spatial patterns in spatial omics data.Bioinformatics (Oxford, England) · 2026Article
560 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors.
Funding
Abstract
Recent spatial gene expression technologies enable comprehensive measurement of transcriptomic profiles while retaining spatial context. However, existing analysis methods do not address the limited resolution of the technology or use the spatial information efficiently. Here, we introduce BayesSpace, a fully Bayesian statistical method that uses the information from spatial neighborhoods for resolution enhancement of spatial transcriptomic data and for clustering analysis. We benchmark BayesSpace against current methods for spatial and non-spatial clustering and show that it improves identification of distinct intra-tissue transcriptional profiles from samples of the brain, melanoma, invasive ductal carcinoma and ovarian adenocarcinoma. Using immunohistochemistry and an in silico dataset constructed from scRNA-seq data, we show that BayesSpace resolves tissue structure that is not detectable at the original resolution and identifies transcriptional heterogeneity inaccessible to histological analysis. Our results illustrate BayesSpace's utility in facilitating the discovery of biological insights from spatial transcriptomic datasets.
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Registered trials
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