ArticleGenome biology2024
Multi-slice spatial transcriptome domain analysis with SpaDo.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Combining Spatial Multi-Omics Data to Decipher Spatial Domains and Elucidate Cell Heterogeneity Based on Self-Supervised Graph Learning.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Accurate, scalable and cross-platform cell identification for high-resolution spatial transcriptomics.Nature genetics · 2026Article
- SpaPheno: linking spatial transcriptomics to clinical phenotypes with interpretable machine learning.Genome medicine · 2026Article
- A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell types.Cell reports · 2026Article
- Counting cells can accurately predict small-molecule bioactivity benchmarks.Nature communications · 2026Article
- Network models for bridging denoising and identifying spatial domains of spatially resolved transcriptomics.PLoS computational biology · 2026Article
- MMSpa is a deep learning-based tool that enhances the identification of spatial domains in spatial transcriptomics studies.PLoS biology · 2026Article
- MaskGraphene: an advanced framework for interpretable joint representation for multi-slice, multi-condition spatial transcriptomics.Genome biology · 2025Article
- A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell types.Research square · 2025Article
- Benchmarking multi-slice integration and downstream applications in spatial transcriptomics data analysis.Genome biology · 2025Article
- BISON: bi-clustering of spatial omics data with feature selection.Bioinformatics (Oxford, England) · 2025Article
- Heterogeneous graph contrastive learning for integration and alignment of spatial transcriptomics data.Briefings in bioinformatics · 2025Article
- SpaLinker identifies phenotype-associated spatial tumor microenvironment features by integrating bulk and spatial sequencing data.Cell genomics · 2025Article
- Cancer therapy resistance from a spatial-omics perspective.Clinical and translational medicine · 2025Review
- stDyer enables spatial domain clustering with dynamic graph embedding.Genome biology · 2025Article
- Identification and characterization of cell niches in tissue from spatial omics data at single-cell resolution.Nature communications · 2025Article
- Single-cell genomics and spatial transcriptomics in islet transplantation for diabetes treatment: advancing towards personalized therapies.Frontiers in immunology · 2025Review
- Decoding immune low-response states in sepsis: single-cell and 3D spatial transcriptomic insights into immunoparalysis.Frontiers in immunology · 2025Review
- Deciphering progressive lesion areas in breast cancer spatial transcriptomics via TGR-NMF.Briefings in bioinformatics · 2024Article
- BayeSMART: Bayesian clustering of multi-sample spatially resolved transcriptomics data.Briefings in bioinformatics · 2024Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
With the rapid advancements in spatial transcriptome sequencing, multiple tissue slices are now available, enabling the integration and interpretation of spatial cellular landscapes. Herein, we introduce SpaDo, a tool for multi-slice spatial domain analysis, including modules for multi-slice spatial domain detection, reference-based annotation, and multiple slice clustering at both single-cell and spot resolutions. We demonstrate SpaDo's effectiveness with over 40 multi-slice spatial transcriptome datasets from 7 sequencing platforms. Our findings highlight SpaDo's potential to reveal novel biological insights in multi-slice spatial transcriptomes.
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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.