ArticleGenome biology2024
Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Spatially resolved multiomics of human meningeal development reveal lineage and disease dynamics.Nature cell biology · 2026Article
- Microenvironment-aware transcriptome reconstruction in spatial transcriptomics.Nature communications · 2026Article
- Decoding cell-cell communication in spatial transcriptomics: mechanistic insights, modeling constraints, and analytical caveats.Briefings in bioinformatics · 2026Review
- Spatial ecotype in tumor immune exclusion: from spatial architecture to therapeutic strategies.Molecular cancer · 2026Review
- Article
- Differential expression analysis in single-cell and spatial RNA-seq without model assumptions.Cell reports methods · 2026Article
- Logistic regression for estimating functional effects with spatial transcriptomics.Nucleic acids research · 2026Article
- Artificial Intelligence for Spatial Immunometabolic Analysis of the Tumor Microenvironment: Current Evidence and Future Directions.Current issues in molecular biology · 2026Review
- SpatialQuery: scalable discovery and molecular characterization of multicellular motifs from spatial omics data.bioRxiv : the preprint server for biology · 2026Article
- Benchmarking tools for deciphering cellular crosstalk in spatially-resolved transcriptomics.Genome biology · 2026Article
- CELLama: Foundation Model for Single Cell and Spatial Transcriptomics by Cell Embedding Leveraging Language Model Abilities.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Impact and correction of segmentation errors in spatial transcriptomics.Nature genetics · 2026Article
- Tumor-infiltrating bacteria disrupt cancer epithelial cell interactions and induce cell-cycle arrest.Cancer cell · 2026Article
- Differential expression analysis for spatially correlated data using smiDE.Genome biology · 2026Article
- SpatialRNA: a Python package for easy application of Graph Neural Network models on single-molecule spatial transcriptomics dataset.Bioinformatics (Oxford, England) · 2026Article
- Multi-Omics Integration IdentifiesInternational journal of molecular sciences · 2025Article
- Differential expression analysis in single cell and spatial RNASeq without model assumptions.bioRxiv : the preprint server for biology · 2025Article
- Why "Where" Matters as Much as "How Much": Single-Cell and Spatial Transcriptomics in Plants.International journal of molecular sciences · 2025Review
- Decrypting cancer's spatial code: from single cells to tissue niches.Molecular oncology · 2025Review
- A unified framework for identification of cell-type-specific spatially variable genes in spatial transcriptomic studies.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
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10 authors.
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Abstract
Existing methods for analysis of spatial transcriptomic data focus on delineating the global gene expression variations of cell types across the tissue, rather than local gene expression changes driven by cell-cell interactions. We propose a new statistical procedure called niche-differential expression (niche-DE) analysis that identifies cell-type-specific niche-associated genes, which are differentially expressed within a specific cell type in the context of specific spatial niches. We further develop niche-LR, a method to reveal ligand-receptor signaling mechanisms that underlie niche-differential gene expression patterns. Niche-DE and niche-LR are applicable to low-resolution spot-based spatial transcriptomics data and data that is single-cell or subcellular in resolution.
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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.