ArticleNature methods2021
SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment.
Article in Nature methods, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers, 1 of them a synthesis that pooled it.
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Who cites it
73 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Metabolomics and metabolites in cancer diagnosis and treatment.Molecular biomedicine · 2025Pooled it
- RamanOmics decodes the spatial vibrational-molecular architecture of senescence in aging and repair.Nature aging · 2026Article
- Review
- All-optical multimodal mapping of single-cell-type-specific metabolic activities via REDCAT.Nature methods · 2026Article
- Multi-omics-driven precision medicine.iMeta · 2026Review
- Integrated Spatial and Bulk Untargeted Metabolomics Characterize Location- and Histology-Associated Metabolic Heterogeneity in Colorectal Cancer.Journal of proteome research · 2026Article
- SOFisher: reinforcement learning-guided experiment designs for spatial omics.Nature communications · 2026Article
- DECODE: deep learning-based common deconvolution framework for various omics data.Nature methods · 2026Article
- Hallmarks of nuclear metabolism: implications for genome integrity, nuclear signaling, and therapeutic targeting.npj metabolic health and disease · 2026Review
- Bridging the dimensional gap from planar spatial transcriptomics to 3D cell atlases.Nature methods · 2026Article
- From the brain cell atlas to precision neurology: a review of the application of AI-driven multi-omics in brain science.GigaScience · 2026Review
- Spider: a flexible and unified framework for simulating spatial transcriptomics data.Bioinformatics (Oxford, England) · 2026Article
- MMSpa is a deep learning-based tool that enhances the identification of spatial domains in spatial transcriptomics studies.PLoS biology · 2026Article
- Spatial omics of neuroinflammation: insights across brain diseases.Frontiers in immunology · 2026Review
- Hepatic Zonation in MASLD: Old Question, New Challenge in the Era of Spatial Omics.International journal of molecular sciences · 2025Review
- Decoding cell fate: integrated experimental and computational analysis at the single-cell level.Bioinformatics (Oxford, England) · 2025Review
- Spatial Immunometabolism: Integrating Technologies to Decode Cellular Metabolism in Tissues.European journal of immunology · 2025Review
- Review
- Spatial isotope deep tracing deciphers inter-tissue metabolic crosstalk.Nature communications · 2025Article
- Advances and applications in single-cell and spatial genomics.Science China. Life sciences · 2025Review
13 more citing papers are in PubMed but not listed here.
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Authors and funding
15 authors.
Funding
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Abstract
Spatial metabolomics can reveal intercellular heterogeneity and tissue organization. Here we report on the spatial single nuclear metabolomics (SEAM) method, a flexible platform combining high-spatial-resolution imaging mass spectrometry and a set of computational algorithms that can display multiscale and multicolor tissue tomography together with identification and clustering of single nuclei by their in situ metabolic fingerprints. We first applied SEAM to a range of wild-type mouse tissues, then delineated a consistent pattern of metabolic zonation in mouse liver. We further studied the spatial metabolic profile in the human fibrotic liver. We discovered subpopulations of hepatocytes with special metabolic features associated with their proximity to the fibrotic niche, and validated this finding by spatial transcriptomics with Geo-seq. These demonstrations highlighted SEAM's ability to explore the spatial metabolic profile and tissue histology at the single-cell level, leading to a deeper understanding of tissue metabolic organization.
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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.