ArticleNature biotechnology2025
Starfysh integrates spatial transcriptomic and histologic data to reveal heterogeneous tumor-immune hubs.
Article in Nature biotechnology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed, 49 citations in OpenAlex.
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- ParTIpy: a scalable framework for archetypal analysis and Pareto task inference.Molecular systems biology · 2026Article
- IrMn-Cluster-Based Artificial Metalloenzymes with Radiosensitized Systemic Antitumor Responses to Prevent Malignant Tumor Metastasis and Recurrence.Nano-micro letters · 2026Article
- RETROFIT: Reference-free deconvolution of cell-type mixtures in spatial transcriptomics.Nature communications · 2026Article
- LYNX: a deep generative model for linking spatial dynamics and cell interactions in multimodal spatial data.bioRxiv : the preprint server for biology · 2026Article
- Dissecting human organ development using spatial technologies.Developmental cell · 2026Review
- Scalable multi-group nonnegative spatial factorization for spatial genomics data with cell-type heterogeneity.bioRxiv : the preprint server for biology · 2026Article
- Cancer Heterogeneity and Cancer Cell Plasticity: Molecular Mechanisms and Precision Therapy.MedComm · 2026Review
- Generalist biological artificial intelligence in modeling the language of life.Nature biotechnology · 2026Review
- Deciphering microenvironmental heterogeneity by scalable Niche Guided Module Discovery.Communications biology · 2026Article
- Single-cell and spatial profiling in cancer biology and clinical oncology.Nature cancer · 2026Review
- The Evolution of Spatial Omics Technologies Introduces A Novel Avenue for Lung Cancer Research.Genomics, proteomics & bioinformatics · 2026Review
- StrucGAP: a modular, streamlined and traceable data mining platform for structural and site-specific glycoproteomics.Nature communications · 2026Article
- FineST: contrastive learning integrates histology and spatial transcriptomics for nuclei-resolved ligand-receptor analysis.Nature communications · 2026Article
- stGrads: decoding spatial gene expression gradients through proximity-driven analysis in complex tissues.Briefings in bioinformatics · 2026Article
- Spatial architecture of development and disease.Nature reviews. Genetics · 2026Review
- An expanded role for single-cell chemical genomics profiling in drug discovery.The Biochemical journal · 2026Review
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Authors and funding
23 authors at 8 institutions in 1 country.
Funding
Abstract
Spatially resolved gene expression profiling provides insight into tissue organization and cell-cell crosstalk; however, sequencing-based spatial transcriptomics (ST) lacks single-cell resolution. Current ST analysis methods require single-cell RNA sequencing data as a reference for rigorous interpretation of cell states, mostly do not use associated histology images and are not capable of inferring shared neighborhoods across multiple tissues. Here we present Starfysh, a computational toolbox using a deep generative model that incorporates archetypal analysis and any known cell type markers to characterize known or new tissue-specific cell states without a single-cell reference. Starfysh improves the characterization of spatial dynamics in complex tissues using histology images and enables the comparison of niches as spatial hubs across tissues. Integrative analysis of primary estrogen receptor (ER)-positive breast cancer, triple-negative breast cancer (TNBC) and metaplastic breast cancer (MBC) tissues led to the identification of spatial hubs with patient- and disease-specific cell type compositions and revealed metabolic reprogramming shaping immunosuppressive hubs in aggressive MBC.
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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.