ArticleNature biotechnology2023
High-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE.
Article in Nature biotechnology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 125 papers.
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Who cites it
125 citing papers in PubMed.
- Results of the Phase I/II Study and Preliminary B-cell Gene Signature of Combined Inhibition of Glutamine Metabolism and EGFR in Colorectal Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2025Trial
- Characterization of SPP1 + macrophages and their correlation with resistance to neoadjuvant chemotherapy in colorectal cancer liver metastasis.Molecular biomedicine · 2026Article
- Effects of SSRIs on the spatial transcriptome of dorsal raphe serotonin neurons.Molecular psychiatry · 2026Article
- PhenoMapR: scalable mapping of sample phenotypes to single-cell, spatial, and bulk transcriptomics data.bioRxiv : the preprint server for biology · 2026Article
- Single-cell and single-nucleus transcriptomics of the dorsal root ganglion in neuropathic pain: cell-state remodeling and translational prospects.Journal of translational medicine · 2026Review
- Spatially guided in vivo single-cell functional genomics of postnatal heart.Nature cardiovascular research · 2026Article
- Stepwise multi-scale reconstruction of cell spatial organization from single-cell RNA sequencing data with Cell2space.Briefings in bioinformatics · 2026Article
- Airway cell-cell communication in smoking through integration of spatial and single-cell transcriptomics.Respiratory research · 2026Article
- NicheDeSig: niche-aware deconvolution and adaptive signature analysis for spatial transcriptomics.Bioinformatics (Oxford, England) · 2026Article
- Single-Cell Annotation and Localization via Integrating Spatial Transcriptomics Maps the Mouse Ocular Atlas and RAO Dynamics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- STAID: A Self-Refining Deep Learning Framework for Spatial Cell-Type Deconvolution with Biologically Informed Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Mapping mesenchymal diversity in the human small intestine and organoids.Nature cell biology · 2026Article
- Toward simultaneous pseudo-space reconstruction and cell-type deconvolution of single-cell spatial transcriptome using SpaDicer.Cell reports methods · 2026Article
- Dissecting and steering cell dynamics using spatially-informed RNA velocity with veloAgent.Molecular systems biology · 2026Article
- Spatial Orchestration of Skin Fibrosis by a CD8+ T cell- Myofibroblast Axis.bioRxiv : the preprint server for biology · 2026Article
- ST-LDAW: A Topic-Model and Damped Weighted Least-Squares Method for Integrative Deconvolution of Single-Cell and Spatial Transcriptomics.Interdisciplinary sciences, computational life sciences · 2026Article
- Article
- Spatiotemporal Profiling Defines the Epithelial and Mesenchymal Transition Window in Embryonic Lung Morphogenesis.Journal of developmental biology · 2026Article
- Review
- Targeting VEGF signaling and stromal remodeling enhances chemoimmunotherapy efficacy in esophageal cancer.Journal for immunotherapy of cancer · 2026Article
65 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
Abstract
Recent studies have emphasized the importance of single-cell spatial biology, yet available assays for spatial transcriptomics have limited gene recovery or low spatial resolution. Here we introduce CytoSPACE, an optimization method for mapping individual cells from a single-cell RNA sequencing atlas to spatial expression profiles. Across diverse platforms and tissue types, we show that CytoSPACE outperforms previous methods with respect to noise tolerance and accuracy, enabling tissue cartography at single-cell resolution.
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