ArticleNature methods2025
Spotiphy enables single-cell spatial whole transcriptomics across an entire section.
Article in Nature methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Spatial omics illuminates tumor heterogeneity.Cell reports methods · 2026Review
- Single-cell insights into plant growth, adaptation, and evolution.Journal of integrative plant biology · 2026Review
- SlotDeconv: spatial transcriptomics deconvolution via diversity-constrained prototype learning and spatial refinement.Bioinformatics (Oxford, England) · 2026Article
- Interpretable and scalable spatial gene set activity analysis with GESSO uncovers functional tissue architecture.bioRxiv : the preprint server for biology · 2026Article
- Deciphering microenvironmental heterogeneity by scalable Niche Guided Module Discovery.Communications biology · 2026Article
- Spatial atlas of human diabetic kidney uncovered podocyte-driven metabolic-inflammatory crosstalk via glycerolipid reprogramming and DUSP4/MMP3 axis.Fundamental research · 2026Article
- PD-1 blockade plus tyrosine kinase inhibitor remodels the tumor microenvironment in advanced renal cell carcinoma.Nature communications · 2026Article
- Ultra-precision deconvolution of spatial transcriptomics decodes immune heterogeneity and fate-defining programs in tissues.Nature communications · 2026Article
- Advances in predicting omics profiles from imaging data.Briefings in bioinformatics · 2026Review
- Cell type-resolved proteomics reveals intra- and intercellular signaling in Alzheimer's disease.bioRxiv : the preprint server for biology · 2026Article
- Spatial omics at the forefront: emerging technologies, analytical innovations, and clinical applications.Cancer cell · 2026Review
- An unsupervised method for spatial transcriptomics analysis based on adversarial autoencoder.Briefings in bioinformatics · 2026Article
- AI-driven multi-omics integration in breast cancer: clinical applications, immunotherapy prediction, and translational challenges.Frontiers in molecular biosciences · 2026Review
- Mapping safety in space: the emerging role of spatial transcriptomics in safe drug development.Frontiers in toxicology · 2026Review
- Spatially resolving cancer: from cell states to therapy.Trends in cancer · 2026Review
- Review
- Multidimensional decoding of colorectal cancer heterogeneity: Artificial intelligence-enabled precision exploration of single-cell and spatial transcriptomics.World journal of gastrointestinal oncology · 2025Review
- Review
- Artificial Intelligence for Multiscale Spatial Analysis in Oncology: Current Applications and Future Implications.International journal of molecular sciences · 2025Review
- Thor: a platform for cell-level investigation of spatial transcriptomics and histology.Nature communications · 2025Article
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
Spatial transcriptomics (ST) has advanced our understanding of tissue regionalization by enabling the visualization of gene expression within whole-tissue sections, but current approaches remain plagued by the challenge of achieving single-cell resolution without sacrificing whole-genome coverage. Here we present Spotiphy (spot imager with pseudo-single-cell-resolution histology), a computational toolkit that transforms sequencing-based ST data into single-cell-resolved whole-transcriptome images. Spotiphy delivers the most precise cellular proportions in extensive benchmarking evaluations. Spotiphy-derived inferred single-cell profiles reveal astrocyte and disease-associated microglia regional specifications in Alzheimer's disease and healthy mouse brains. Spotiphy identifies multiple spatial domains and alterations in tumor-tumor microenvironment interactions in human breast ST data. Spotiphy bridges the information gap and enables visualization of cell localization and transcriptomic profiles throughout entire sections, offering highly informative outputs and an innovative spatial analysis pipeline for exploring complex biological systems.
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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.