ArticleGenome biology2023
SPIRAL: integrating and aligning spatially resolved transcriptomics data across different experiments, conditions, and technologies.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- spMosaic: multi-sample integration for scalable spatial domain discovery based on spatial transcriptomics.Briefings in bioinformatics · 2026Article
- Spatial multi-omics imputation and embedding with SpaMIE.Cell reports methods · 2026Article
- Stress-induced motivational impairment is marked by diminished frontocortical cellular communication and neuropeptide signaling.bioRxiv : the preprint server for biology · 2026Article
- A comprehensive survey of computer vision methods for spatial transcriptomics.Briefings in bioinformatics · 2026Review
- Cross-modality representation and multi-sample integration of spatially resolved omics data.Briefings in bioinformatics · 2026Article
- The Evolution of Spatial Omics Technologies Introduces A Novel Avenue for Lung Cancer Research.Genomics, proteomics & bioinformatics · 2026Review
- GALA: a unified landmark-free framework for coarse-to-fine spatial alignment across resolutions and modalities in spatial transcriptomics.Briefings in bioinformatics · 2026Article
- JADE: Joint Alignment and Deep Embedding for Multi-Slice Spatial Transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- stGCL: a versatile cross-modality fusion method based on multi-modal graph contrastive learning for spatial transcriptomics.Genome biology · 2026Article
- haCCA: multi-module Integration of spot-based spatial transcriptomes and metabolomes.Communications biology · 2026Article
- Integration of habitat radiomics and traditional radiomic features for predicting pathological complete response in esophageal squamous cell carcinoma following neoadjuvant immunotherapy and chemotherapy: a multicenter comparative study.Journal of translational medicine · 2026Article
- Unified integration of spatial transcriptomics across platforms with LLOKI.Genome research · 2025Article
- Spatial omics: applications and utility in profiling the tumor microenvironment.Cancer metastasis reviews · 2025Review
- JADE: Joint Alignment and Deep Embedding for Multi-Slice Spatial Transcriptomics.Advances in neural information processing systems · 2025Article
- A deep learning-based multiscale integration of spatial omics with tumor morphology.Nature communications · 2025Article
- Bridging single cells to organs: Mesoscale modules as fundamental units of tissue function.Cell · 2025Review
- MaskGraphene: an advanced framework for interpretable joint representation for multi-slice, multi-condition spatial transcriptomics.Genome biology · 2025Article
- Timing of immune checkpoint blockade shapes anti-tumor immunity via a clock-dependent chemokine axis.bioRxiv : the preprint server for biology · 2025Article
- Multitask benchmarking of single-cell multimodal omics integration methods.Nature methods · 2025Article
- SpaBatch: Deep Learning-Based Cross-Slice Integration and 3D Spatial Domain Identification in Spatial Transcriptomics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
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7 authors.
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Abstract
Properly integrating spatially resolved transcriptomics (SRT) generated from different batches into a unified gene-spatial coordinate system could enable the construction of a comprehensive spatial transcriptome atlas. Here, we propose SPIRAL, consisting of two consecutive modules: SPIRAL-integration, with graph domain adaptation-based data integration, and SPIRAL-alignment, with cluster-aware optimal transport-based coordination alignment. We verify SPIRAL with both synthetic and real SRT datasets. By encoding spatial correlations to gene expressions, SPIRAL-integration surpasses state-of-the-art methods in both batch effect removal and joint spatial domain identification. By aligning spots cluster-wise, SPIRAL-alignment achieves more accurate coordinate alignments than existing methods.
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