ArticleNature communications2024
NiCo identifies extrinsic drivers of cell state modulation by niche covariation analysis.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Spatially resolved multiomics of human meningeal development reveal lineage and disease dynamics.Nature cell biology · 2026Article
- Spatial ecotype in tumor immune exclusion: from spatial architecture to therapeutic strategies.Molecular cancer · 2026Review
- Leveraging Single-Cell and Spatial Transcriptomics in Gut Nutrition and Mucosal Immunology.The Journal of nutrition · 2026Article
- Ubiquitin-like proteins NEDD8 and SUMO2 control epithelial homeostasis, regeneration, and inflammation.Science (New York, N.Y.) · 2026Article
- Decoding cellular population dynamics through mechanistic modelling and statistical data analysis.NPJ systems biology and applications · 2026Review
- Deciphering microenvironmental heterogeneity by scalable Niche Guided Module Discovery.Communications biology · 2026Article
- An immunobiliary single-cell atlas resolves crosstalk between type 2 conventional dendritic cells and γδ T cells in cholangitis.Nature communications · 2026Article
- Cell-cell crosstalk in kidney health and disease.Nature reviews. Nephrology · 2026Review
- Decrypting cancer's spatial code: from single cells to tissue niches.Molecular oncology · 2025Review
- Assessing the relative contributions of mosaic and regulatory developmental modes from single-cell trajectories.PLoS computational biology · 2025Article
- Article
- Spatiotemporal dynamics of the cardioimmune niche during lesion repair.Nature cardiovascular research · 2025Article
- OrgaCCC: Orthogonal graph autoencoders for constructing cell-cell communication networks on spatial transcriptomics data.PLoS computational biology · 2025Article
- NiCo identifies extrinsic drivers of cell state modulation by niche covariation analysis.Nature communications · 2024Article
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4 authors.
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Abstract
Cell states are modulated by intrinsic driving forces such as gene expression noise and extrinsic signals from the tissue microenvironment. The distinction between intrinsic and extrinsic cell state determinants is essential for understanding the regulation of cell fate in tissues during development, homeostasis and disease. The rapidly growing availability of single-cell resolution spatial transcriptomics makes it possible to meet this challenge. However, available computational methods to infer topological tissue domains, spatially variable genes, or ligand-receptor interactions are limited in their capacity to capture cell state changes driven by crosstalk between individual cell types within the same niche. We present NiCo, a computational framework for integrating single-cell resolution spatial transcriptomics with matched single-cell RNA-sequencing reference data to infer the influence of the spatial niche on the cell state. By applying NiCo to mouse embryogenesis, adult small intestine and liver data, we demonstrate the ability to predict novel niche interactions that govern cell state variation underlying tissue development and homeostasis. In particular, NiCo predicts a feedback mechanism between Kupffer cells and neighboring stellate cells dampening stellate cell activation in the normal liver. NiCo provides a powerful tool to elucidate tissue architecture and to identify drivers of cellular states in local niches.
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