ArticleNature communications2024
Tissue characterization at an enhanced resolution across spatial omics platforms with deep generative model.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis that pooled it.
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Who cites it
18 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Deep learning in single-cell and spatial transcriptomics data analysis: advances and challenges from a data science perspective.Briefings in bioinformatics · 2025Pooled it
- From descriptive to generative: foundation-model approaches for spatial transcriptomics.Briefings in bioinformatics · 2026Review
- AI-Enabled Shrinkage Analysis and Morphology Control in Food Processing: Mechanisms, Multimodal Perception, Modeling, and Intelligent Regulation.Comprehensive reviews in food science and food safety · 2026Review
- Image-guided spatial omics enhancement reveals hidden spatial microstructures.Bioinformatics (Oxford, England) · 2026Article
- Mapping mesenchymal diversity in the human small intestine and organoids.Nature cell biology · 2026Article
- Integrating Spatial Proteogenomics in Cancer Research.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Spatial proteomics in precision medicine: technologies, bioinformatics, and translational applications.Precision clinical medicine · 2026Review
- Optimization of potential targets for antidepressant Chinese medicines: AI and multi-omics methods.Chinese medicine · 2026Review
- The interpretable multimodal dimension reduction framework SpaHDmap enhances resolution in spatial transcriptomics.Nature cell biology · 2026Article
- Multisensory Neuromorphic Devices: From Physics to Integration.Nano-micro letters · 2026Review
- Generative Model Enhanced X-ray Computed Tomography Imaging for Pharmaceutical Powder Microstructure Reconstruction and Evaluation.AAPS PharmSciTech · 2025Article
- Comprehensive linkage between molecular biology and imaging radiomics for thyroid nodules.World journal of radiology · 2025Article
- soFusion: facilitating tissue structure identification via spatial multi-omics data fusion.Briefings in bioinformatics · 2025Article
- A novel deep learning framework with dynamic tokenization for identifying chromatin interactions along with motif importance investigation.Briefings in bioinformatics · 2025Article
- Systematic inference of super-resolution cell spatial profiles from histology images.Nature communications · 2025Article
- Bridging ancient wisdom and modern technology: an AI and multi-omics framework for three causes tailored treatment in personalized medicine.Frontiers in molecular biosciences · 2025Review
- Article
- Tissue characterization at an enhanced resolution across spatial omics platforms with deep generative model.Nature communications · 2024Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent advances in spatial omics have expanded the spectrum of profiled molecular categories beyond transcriptomics. However, many of these technologies are constrained by limited spatial resolution, hindering our ability to deeply characterize intricate tissue architectures. Existing computational methods primarily focus on the resolution enhancement of transcriptomics data, lacking the adaptability to address the emerging spatial omics technologies that profile various omics types. Here, we introduce soScope, a unified generative framework designed to enhance data quality and spatial resolution for molecular profiles obtained from diverse spatial technologies. soScope aggregates multimodal tissue information from omics, spatial relations and images, and jointly infers omics profiles at enhanced resolutions with omics-specific modeling through distribution priors. With comprehensive evaluations on diverse spatial omics platforms, including Visium, Xenium, spatial-CUT&Tag, and slide-DNA/RNA-seq, soScope improves performances in identifying biologically meaningful intestine and kidney architectures, revealing embryonic heart structure that cannot be resolved at the original resolution and correcting sample and technical biases arising from sequencing and sample processing. Furthermore, soScope extends to spatial multiomics technology spatial-CITE-seq and spatial ATAC-RNA-seq, leveraging cross-omics reference for simultaneous multiomics enhancement. soScope provides a versatile tool to improve the utilization of continually expanding spatial omics technologies and resources.
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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.