ArticleNature genetics2024
CellCharter reveals spatial cell niches associated with tissue remodeling and cell plasticity.
Article in Nature genetics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 139 papers.
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Who cites it
139 citing papers in PubMed, 149 citations in OpenAlex.
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- Accurate and well-powered case-control analysis of spatial molecular data.Nature methods · 2026Article
- Unlocking the full potential of spatial omics in plants: practical challenges, solutions, and a path forward.The Plant cell · 2026Review
- The dual roles of uterine monocytes in regulation of tissue homeostasis throughout reproductive cycles in health and disease.Nature immunology · 2026Article
- STAT3D as a new image-tailored Xenium-based spatial transcriptomics tool for accurately dissecting the tumor microenvironment.Nucleic acids research · 2026Article
- Review
- Microenvironment-aware transcriptome reconstruction in spatial transcriptomics.Nature communications · 2026Article
- Epigenetic modulation of stromal cell states underpins pathological tissue niches in Crohn's disease.Nature immunology · 2026Article
- Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering.Nature methods · 2026Article
- Analysis of multicellular anatomical structures from spatial omics data using sosta.PLoS computational biology · 2026Article
- Article
- Multi-omics-driven precision medicine.iMeta · 2026Review
- TTNCell reports · 2026Article
- Myasthenia thymus reprograms class-switched B cells into BAFF-dependent survivors.Science advances · 2026Article
- Spatially defined microenvironmental niches are associated with clinical outcome and tumor ecosystem diversity in head and neck cancer.Med (New York, N.Y.) · 2026Article
- NicheDeSig: niche-aware deconvolution and adaptive signature analysis for spatial transcriptomics.Bioinformatics (Oxford, England) · 2026Article
- Spatialproteomics: an interoperable toolbox for analyzing highly multiplexed fluorescence image data.Nature methods · 2026Article
- Single-cell spatial transcriptomics of formalin-fixed, paraffin-embedded biopsies reveals colitis-associated cell networks.The Journal of clinical investigation · 2026Article
- Macrophage signaling associates with fibrogenic program activation in periductal fibroblasts in pediatric primary sclerosing cholangitis.JCI insight · 2026Article
79 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Tissues are organized in cellular niches, the composition and interactions of which can be investigated using spatial omics technologies. However, systematic analyses of tissue composition are challenged by the scale and diversity of the data. Here we present CellCharter, an algorithmic framework to identify, characterize, and compare cellular niches in spatially resolved datasets. CellCharter outperformed existing approaches and effectively identified cellular niches across datasets generated using different technologies, and comprising hundreds of samples and millions of cells. In multiple human lung cancer cohorts, CellCharter uncovered a cellular niche composed of tumor-associated neutrophil and cancer cells expressing markers of hypoxia and cell migration. This cancer cell state was spatially segregated from more proliferative tumor cell clusters and was associated with tumor-associated neutrophil infiltration and poor prognosis in independent patient cohorts. Overall, CellCharter enables systematic analyses across data types and technologies to decode the link between spatial tissue architectures and cell plasticity.
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