ArticleGenome biology2024
scHolography: a computational method for single-cell spatial neighborhood reconstruction and analysis.
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 7 papers.
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Who cites it
7 citing papers in PubMed.
- Stepwise multi-scale reconstruction of cell spatial organization from single-cell RNA sequencing data with Cell2space.Briefings in bioinformatics · 2026Article
- SHIELD: A weakly supervised graph attention neural network for decoding disease-relevant cell-cell interactions.Patterns (New York, N.Y.) · 2026Article
- Single-cell and spatial profiling in cancer biology and clinical oncology.Nature cancer · 2026Review
- DeepPNCC: reconstructing pseudo-spatial cell-cell interaction landscapes from single-cell data to decipher breast cancer pathogenesis.Journal of translational medicine · 2025Article
- Timing of immune checkpoint blockade shapes anti-tumor immunity via a clock-dependent chemokine axis.bioRxiv : the preprint server for biology · 2025Article
- Decoding immune low-response states in sepsis: single-cell and 3D spatial transcriptomic insights into immunoparalysis.Frontiers in immunology · 2025Review
- scHolography: a computational method for single-cell spatial neighborhood reconstruction and analysis.Genome biology · 2024Article
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Authors and funding
5 authors.
Funding
Abstract
Spatial transcriptomics has transformed our ability to study tissue complexity. However, it remains challenging to accurately dissect tissue organization at single-cell resolution. Here we introduce scHolography, a machine learning-based method designed to reconstruct single-cell spatial neighborhoods and facilitate 3D tissue visualization using spatial and single-cell RNA sequencing data. scHolography employs a high-dimensional transcriptome-to-space projection that infers spatial relationships among cells, defining spatial neighborhoods and enhancing analyses of cell-cell communication. When applied to both human and mouse datasets, scHolography enables quantitative assessments of spatial cell neighborhoods, cell-cell interactions, and tumor-immune microenvironment. Together, scHolography offers a robust computational framework for elucidating 3D tissue organization and analyzing spatial dynamics at the cellular level.
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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.