ArticleNature methods2025
Novae: a graph-based foundation model for spatial transcriptomics data.
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 30 papers.
What it found
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Who cites it
30 citing papers in PubMed.
- Unveiling the role of spatial transcriptomics in the analysis of the tumor immune microenvironment (Review).International journal of molecular medicine · 2026Review
- spaGFM is a scalable graph foundation model for spatial transcriptomics analyses.Research square · 2026Article
- SemanticST: A Scalable Multi-Contextual Graph Learning Framework for Uncovering Spatial Niches and Robust Multi-Sample Integration in Spatial Transcriptomics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Multi-omics-driven precision medicine.iMeta · 2026Review
- Single-Cell and Spatial Transcriptomics Across Populations With Perianal Fistulizing Crohn's Disease Shows Proinflammatory CD4Cellular and molecular gastroenterology and hepatology · 2026Article
- Leveraging multi-modal foundation models for analysing spatial multi-omic and histopathology data.Nature biomedical engineering · 2026Article
- [Applications and Challenges of Deep Learning in Human Genome Research].Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition · 2026Review
- LYNX: a deep generative model for linking spatial dynamics and cell interactions in multimodal spatial data.bioRxiv : the preprint server for biology · 2026Article
- Advancing bioinformatics with language models: components, applications, and perspectives.Briefings in bioinformatics · 2026Review
- Histopathology-centered computational evolution of spatial omics: integration, mapping, and foundation models.Briefings in bioinformatics · 2026Review
- Computational analysis in spatial transcriptomics: methods and perspectives.Briefings in bioinformatics · 2026Review
- Tumor microenvironment-specific nanomedicine: from biology-driven to multi-omics-guided precision engineering.Journal of hematology & oncology · 2026Review
- SECTOR: structural entropy-based learning of spatiotemporal organisation in spatial transcriptomics.Bioinformatics (Oxford, England) · 2026Article
- Review
- STORM: spatial transcriptomics optimization by resolution via matrix factorization.Briefings in bioinformatics · 2026Article
- Evaluating the Utilities of Foundation Models in Single-Cell Data Analysis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- SpatialQuery: scalable discovery and molecular characterization of multicellular motifs from spatial omics data.bioRxiv : the preprint server for biology · 2026Article
- A single-cell and spatial atlas of early human olfactory development.Nature communications · 2026Article
- spRefine denoises and imputes spatial transcriptomic data with a reference-free framework powered by genomic language model.Genome research · 2026Article
- Single-cell and spatial profiling in cancer biology and clinical oncology.Nature cancer · 2026Review
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Spatial transcriptomics is advancing molecular biology by providing high-resolution insights into gene expression within the spatial context of tissues. This context is essential for identifying spatial domains, enabling the understanding of microenvironment organizations and their implications for tissue function and disease progression. To improve current model limitations on multiple slides, we have designed Novae ( https://github.com/MICS-Lab/novae ), a graph-based foundation model that extracts representations of cells within their spatial contexts. Our model was trained on a large dataset of nearly 30 million cells across 18 tissues, allowing Novae to perform zero-shot domain inference across multiple gene panels, tissues and technologies. Unlike other models, it also natively corrects batch effects and constructs a nested hierarchy of spatial domains. Furthermore, Novae supports various downstream tasks, including spatially variable gene or pathway analysis and spatial domain trajectory analysis. Overall, Novae provides a robust and versatile tool for advancing spatial transcriptomics and its applications in biomedical research.
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41372623What OpenQuestion holds
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.