ArticleNature biotechnology2022
Spatial charting of single-cell transcriptomes in tissues.
Article in Nature biotechnology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 158 papers.
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Who cites it
158 citing papers in PubMed, 275 citations in OpenAlex.
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- Data-driven identification of cell subtypes for single-cell transcriptomic data with Subtypist.Briefings in bioinformatics · 2026Article
- The Single-Cell and Spatial Transcriptomics Atlas of Epithelial-Fibroblast Interactions in Colorectal Cancer.Digestive diseases and sciences · 2026Article
- Advances in single-cell and spatial multi-omics for plant development and stress responses.Plant diversity · 2026Review
- Multi-omics characterization of a GPRC5AJournal of translational medicine · 2026Article
- Multi-omic analysis of androgen-deprived human testes reveals Sertoli cell regulation and niche reprogramming.Nature communications · 2026Article
- Single-cell and spatial transcriptomic profiling reveals distinct immune landscapes in murine lungs infected with H1N1 versus H5N1 influenza viruses.Journal of virology · 2026Article
- Multi-modality Graph Representation Learning for Malignant Cell Identification from scRNA-seq using DeepMalignant.bioRxiv : the preprint server for biology · 2026Article
- Single cell and spatial atlas of macrophage and astrocyte interactions in glioblastoma.Discover oncology · 2026Article
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- SOFisher: reinforcement learning-guided experiment designs for spatial omics.Nature communications · 2026Article
- Spatial single-cell landscape of tumor-associated macrophages and their crosstalk with the tumor microenvironment.Cell discovery · 2026Article
- Decoding spatial transcriptomics across multicellular and subcellular resolutions.Nature communications · 2026Article
- Navigating cell maps by deep learning integration of single-cell and spatially resolved transcriptomics.Briefings in bioinformatics · 2026Article
- Multiomics and multi-region spatial transcriptome analysis reveal cellular networks and pathways associated with HCC recurrence.JHEP reports : innovation in hepatology · 2026Article
- Integrating single-cell and spatial transcriptomics to decipher the neuro-immune microenvironment of breast cancer brain metastasis: a key regulatory axis, prognostic model, and drug discovery.Translational cancer research · 2026Article
- UNLOCKING MULTI-SAMPLE DIFFERENTIAL EXPRESSION FOR SPATIAL TRANSCRIPTOMICS DATA WITH TESSERA.bioRxiv : the preprint server for biology · 2026Article
- Spatial Mapping of Single Cells via Correlation and Importance Between Cells and Spots.Interdisciplinary sciences, computational life sciences · 2026Article
98 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
Abstract
Single-cell RNA sequencing methods can profile the transcriptomes of single cells but cannot preserve spatial information. Conversely, spatial transcriptomics assays can profile spatial regions in tissue sections, but do not have single-cell resolution. Here, we developed a computational method called CellTrek that combines these two datasets to achieve single-cell spatial mapping through coembedding and metric learning approaches. We benchmarked CellTrek using simulation and in situ hybridization datasets, which demonstrated its accuracy and robustness. We then applied CellTrek to existing mouse brain and kidney datasets and showed that CellTrek can detect topological patterns of different cell types and cell states. We performed single-cell RNA sequencing and spatial transcriptomics experiments on two ductal carcinoma in situ tissues and applied CellTrek to identify tumor subclones that were restricted to different ducts, and specific T cell states adjacent to the tumor areas. Our data show that CellTrek can accurately map single cells in diverse tissue types to resolve their spatial organization.
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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.