ArticleNucleic acids research2024
STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers, 1 of them a synthesis that pooled it.
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Who cites it
100 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
- Unlocking the full potential of spatial omics in plants: practical challenges, solutions, and a path forward.The Plant cell · 2026Review
- Article
- Ten quick tips for spatial transcriptomics analysis.PLoS computational biology · 2026Review
- HO-1 Nuclear Interactome Implications in Neuroendocrine Transdifferentiation in Prostate Cancer.International journal of molecular sciences · 2026Article
- Pasta, a Versatile Transcriptomic Clock, Maps the Chemical and Genetic Determinants of Aging and Rejuvenation.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Trimodal, uncertainty-guided whole-slide framework for genome-scale spatial expression and image-only virtual perturbation in cancer cohorts.Genome medicine · 2026Article
- Dissecting human organ development using spatial technologies.Developmental cell · 2026Review
- Computational analysis in spatial transcriptomics: methods and perspectives.Briefings in bioinformatics · 2026Review
- Representation learning for multi-modal spatially resolved transcriptomics data.Bioinformatics (Oxford, England) · 2026Article
- Inflammation-driven mitochondrial dysfunction and ROS accumulation orchestrate pulmonary fibrotic remodeling in sepsis.Redox biology · 2026Article
- Integrated Single-Cell and Spatial Analysis Reveals a Metabolic-Immune Axis Driving Aortic Dissection.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Tumor microenvironment-specific nanomedicine: from biology-driven to multi-omics-guided precision engineering.Journal of hematology & oncology · 2026Review
- Comprehensive multi-omics pan-cancer analysis revealed that ANTXR1 is a potential biomarker for diagnosis and immunotherapy.Biology direct · 2026Article
- Review
- ErbB4 in the Dorsolateral Prefrontal Cortex is Required for Sensory Gating and Working Memory in Monkey.Neuroscience bulletin · 2026Article
- Benchmarking sketching methods on spatial transcriptomics data.Nucleic acids research · 2026Article
- Cross-modality representation and multi-sample integration of spatially resolved omics data.Briefings in bioinformatics · 2026Article
- Article
- Benchmarking tools for deciphering cellular crosstalk in spatially-resolved transcriptomics.Genome biology · 2026Article
40 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
30 authors.
Funding
Abstract
Recent technological developments in spatial transcriptomics allow researchers to measure gene expression of cells and their spatial locations at the single-cell level, generating detailed biological insight into biological processes. A comprehensive database could facilitate the sharing of spatial transcriptomic data and streamline the data acquisition process for researchers. Here, we present the Spatial TranscriptOmics DataBase (STOmicsDB), a database that serves as a one-stop hub for spatial transcriptomics. STOmicsDB integrates 218 manually curated datasets representing 17 species. We annotated cell types, identified spatial regions and genes, and performed cell-cell interaction analysis for these datasets. STOmicsDB features a user-friendly interface for the rapid visualization of millions of cells. To further facilitate the reusability and interoperability of spatial transcriptomic data, we developed standards for spatial transcriptomic data archiving and constructed a spatial transcriptomic data archiving system. Additionally, we offer a distinctive capability of customizing dedicated sub-databases in STOmicsDB for researchers, assisting them in visualizing their spatial transcriptomic analyses. We believe that STOmicsDB could contribute to research insights in the spatial transcriptomics field, including data archiving, sharing, visualization and analysis. STOmicsDB is freely accessible at https://db.cngb.org/stomics/.
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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.