ArticleGenome biology2022
BASS: multi-scale and multi-sample analysis enables accurate cell type clustering and spatial domain detection in spatial transcriptomic studies.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 116 papers.
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Who cites it
116 citing papers in PubMed, 164 citations in OpenAlex.
- Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering.Nature methods · 2026Article
- spMosaic: multi-sample integration for scalable spatial domain discovery based on spatial transcriptomics.Briefings in bioinformatics · 2026Article
- STWave: Fine-Scale Spatial Structure Discovery in Microscopic-Resolution Spatial Transcriptomics via Patchwise Wavelet Graphs.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Immune niche composed of C1QNature communications · 2026Article
- DESpace2: detection of differential spatial patterns in spatial omics data.Bioinformatics (Oxford, England) · 2026Article
- Spatial multi-omics identifies early synaptic pruning and context-specific dopaminergic vulnerability in synucleinopathies.Nature communications · 2026Article
- ViMST: vision transformer-based dual modality multi-task graph contrastive network for spatial transcriptomics microenvironments investigation.BMC biology · 2026Article
- Computational analysis in spatial transcriptomics: methods and perspectives.Briefings in bioinformatics · 2026Review
- Diffusion-based representation integration for foundation models improves spatial transcriptomics analysis.Bioinformatics (Oxford, England) · 2026Article
- SPEAK: Spatial Prompting with Expert Aligned Knowledge for Tissue Domain Identification in Spatial Transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- GenOT: generative optimal transport enables spatiotemporal interpolation and generation in cross-platform spatial transcriptomics.Genome biology · 2026Article
- Histology-informed spatial domain identification through multi-view graph convolutional networks.PLoS computational biology · 2026Article
- spAttClu: a spatial domain clustering model leveraging spatially weighted graph attention and contrastive learning.Bioinformatics (Oxford, England) · 2026Article
- SECTOR: structural entropy-based learning of spatiotemporal organisation in spatial transcriptomics.Bioinformatics (Oxford, England) · 2026Article
- Review
- Multiscale domain identification for spatial transcriptomics via persistent homology.Cell reports methods · 2026Article
- ModelistsGCN: a multimodal graph convolutional network framework for single-cell spatial transcriptomic cell typing.Briefings in bioinformatics · 2026Article
- Evaluating the Utilities of Foundation Models in Single-Cell Data Analysis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- SpatialESD: Spatial Ensemble Domain Detection in Spatial Transcriptomics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Interpretable, flexible and spatially aware integration of multiple spatial transcriptomics datasets from diverse sources.Nature genetics · 2026Article
56 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Spatial transcriptomic studies are reaching single-cell spatial resolution, with data often collected from multiple tissue sections. Here, we present a computational method, BASS, that enables multi-scale and multi-sample analysis for single-cell resolution spatial transcriptomics. BASS performs cell type clustering at the single-cell scale and spatial domain detection at the tissue regional scale, with the two tasks carried out simultaneously within a Bayesian hierarchical modeling framework. We illustrate the benefits of BASS through comprehensive simulations and applications to three datasets. The substantial power gain brought by BASS allows us to reveal accurate transcriptomic and cellular landscape in both cortex and hypothalamus.
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Registered trials
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.