ArticleNature biotechnology2022
Integrative spatial analysis of cell morphologies and transcriptional states with MUSE.
Article in Nature biotechnology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 85 papers.
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Who cites it
85 citing papers in PubMed, 118 citations in OpenAlex.
- Accurate and well-powered case-control analysis of spatial molecular data.Nature methods · 2026Article
- 3D multi-omics tumour atlases: from technology to biology and clinical translation.Nature reviews. Cancer · 2026Review
- HIT-MAP: A scalable approach to multimodal mapping of subcellular organization.Cell reports methods · 2026Article
- HESTIA: scalable multimodal integration of histology and high-resolution spatial Transcriptomics for robust spatial domain identification.Briefings in bioinformatics · 2026Article
- SpaMOAL is a deep learning method that enables accurate spatial domain identification from multi-omics data.PLoS biology · 2026Article
- Unified representation learning for spatial multi-omics.Bioinformatics (Oxford, England) · 2026Article
- KSTITCH links cellular morphology and gene expression in spatial transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- Multimodal spatial omics: From data acquisition to computational integration.Patterns (New York, N.Y.) · 2026Review
- Representation learning for multi-modal spatially resolved transcriptomics data.Bioinformatics (Oxford, England) · 2026Article
- SPOmiAlign: a modality-agnostic computational framework for multimodal spatial omics alignment enabled by a feature matching foundation model.Briefings in bioinformatics · 2026Article
- Review of Progress of AI in Biomimetics: From Biological Patterns to Closed-Loop Discovery.Biomimetics (Basel, Switzerland) · 2026Review
- Systematically decoding pathological morphologies and molecular profiles with unified multimodal embedding.Nature methods · 2026Article
- Spatial relationships between vinculin tension and actin at cell adhesions define cell colony positioning and identity.Biophysical journal · 2026Article
- stDyer-image improves clustering analysis of spatially resolved transcriptomics and proteomics with morphological images.Bioinformatics (Oxford, England) · 2026Article
- The interpretable multimodal dimension reduction framework SpaHDmap enhances resolution in spatial transcriptomics.Nature cell biology · 2026Article
- Spatial architecture of development and disease.Nature reviews. Genetics · 2026Review
- Stability of non-canonical nucleic acid structure as a potential modulator of cell fate.Nucleic acids research · 2026Review
- Network models for bridging denoising and identifying spatial domains of spatially resolved transcriptomics.PLoS computational biology · 2026Article
- Spatially resolving cancer: from cell states to therapy.Trends in cancer · 2026Review
- Multi-view deep learning of highly multiplexed imaging data improves association of cell states with clinical outcomes.Bioinformatics advances · 2026Article
25 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
8 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Spatial transcriptomics enables the simultaneous measurement of morphological features and transcriptional profiles of the same cells or regions in tissues. Here we present multi-modal structured embedding (MUSE), an approach to characterize cells and tissue regions by integrating morphological and spatially resolved transcriptional data. We demonstrate that MUSE can discover tissue subpopulations missed by either modality as well as compensate for modality-specific noise. We apply MUSE to diverse datasets containing spatial transcriptomics (seqFISH+, STARmap or Visium) and imaging (hematoxylin and eosin or fluorescence microscopy) modalities. MUSE identified biologically meaningful tissue subpopulations and stereotyped spatial patterning in healthy brain cortex and intestinal tissues. In diseased tissues, MUSE revealed gene biomarkers for proximity to tumor region and heterogeneity of amyloid precursor protein processing across Alzheimer brain regions. MUSE enables the integration of multi-modal data to provide insights into the states, functions and organization of cells in complex biological tissues.
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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.