ArticleNature communications2025
Identification and characterization of cell niches in tissue from spatial omics data at single-cell resolution.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
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Who cites it
22 citing papers in PubMed.
- Nitric Oxide in the Intestinal Stem Cell Niche: A Spatial Model of Nitrosative Stress and Clonal Evolution in Colitis-Associated Colorectal Cancer.Digestive diseases and sciences · 2026Review
- A human single-cell atlas identifies OLR1Nature genetics · 2026Article
- Review
- NicheDeSig: niche-aware deconvolution and adaptive signature analysis for spatial transcriptomics.Bioinformatics (Oxford, England) · 2026Article
- SHIELD: A weakly supervised graph attention neural network for decoding disease-relevant cell-cell interactions.Patterns (New York, N.Y.) · 2026Article
- Interpretable and scalable spatial gene set activity analysis with GESSO uncovers functional tissue architecture.bioRxiv : the preprint server for biology · 2026Article
- Decoding the breast cancer microenvironment by spatial multi-omics: from architecture to clinical translation.Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico · 2026Review
- MultiSP deciphers tissue structure and multicellular communication from spatial multi-omics data.Cell genomics · 2026Article
- Estimating tumour immune infiltration: methodological convergence across histology and spatial technologies.Briefings in bioinformatics · 2026Review
- Single-Cell and Spatial Omics: Methods and Applications.MedComm · 2026Review
- Macrophage-rich niches regulate T cell dynamics at the liver invasive margin during gallbladder cancer progression.The Journal of clinical investigation · 2026Article
- Spatial omics at the forefront: emerging technologies, analytical innovations, and clinical applications.Cancer cell · 2026Review
- Review
- Spatial multiomics to inform immunocytokine engineering: knowledge base, gaps, and QC solutions.Frontiers in immunology · 2026Review
- Editorial: Artificial intelligence in multi-omics: advancing tumor metastasis prediction and mechanism analysis.Frontiers in cell and developmental biology · 2026Article
- Editorial: Formation and remodeling of immunological niches in tumors: organ-specific mechanisms and inflammatory parallels, volume II.Frontiers in oncology · 2026Article
- Hypergraph-driven spatial multimodal fusion for precise domain delineation and tumor microenvironment decoding.Communications biology · 2025Article
- Decrypting cancer's spatial code: from single cells to tissue niches.Molecular oncology · 2025Review
- Special Issue "Advanced Research on Immune Cells and Cytokines (2nd Edition)".International journal of molecular sciences · 2025Article
- S3R: Modeling spatially varying associations with Spatially Smooth Sparse Regression.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Deciphering the features, structure, and functions of the cell niche in tissues remains a major challenge. Here, we present scNiche, a computational framework to identify and characterize cell niches from spatial omics data at single-cell resolution. We benchmark scNiche with both simulated and biological datasets, and demonstrate that scNiche can effectively and robustly identify cell niches while outperforming other existing methods. In spatial proteomics data from human triple-negative breast cancer, scNiche reveals the influence of the microenvironment on cellular phenotypes, and further dissects patient-specific niches with distinct cellular compositions or phenotypic characteristics. By analyzing mouse liver spatial transcriptomics data across normal and early-onset liver failure donors, scNiche uncovers disease-specific liver injury niches, and further delineates the niche remodeling from normal liver to liver failure. Overall, scNiche enables decoding the cellular microenvironment in tissues from single-cell spatial omics data.
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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.