ArticleNature communications2025
INSTINCT: Multi-sample integration of spatial chromatin accessibility sequencing data via stochastic domain translation.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- MultiSP deciphers tissue structure and multicellular communication from spatial multi-omics data.Cell genomics · 2026Article
- Cross-modality representation and multi-sample integration of spatially resolved omics data.Briefings in bioinformatics · 2026Article
- INSTINCT: Multi-sample integration of spatial chromatin accessibility sequencing data via stochastic domain translation.Nature communications · 2025Article
- Deciphering spatially confined immune evasion niches in osteosarcoma with 3-D spatial transcriptomics: a literature review.Frontiers in oncology · 2025Review
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6 authors.
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Abstract
Recent advances in spatial epigenomic techniques have given rise to spatial assay for transposase-accessible chromatin using sequencing (spATAC-seq) data, enabling the characterization of epigenomic heterogeneity and spatial information simultaneously. Integrative analysis of multiple spATAC-seq samples, for which no method has been developed, allows for effective identification and elimination of unwanted non-biological factors within the data, enabling comprehensive exploration of tissue structures and providing a holistic epigenomic landscape, thereby facilitating the discovery of biological implications and the study of regulatory processes. In this article, we present INSTINCT, a method for multi-sample INtegration of Spatial chromaTIN accessibility sequencing data via stochastiC domain Translation. INSTINCT can efficiently handle the high dimensionality of spATAC-seq data and eliminate the complex noise and batch effects of samples through a stochastic domain translation procedure. We demonstrate the superiority and robustness of INSTINCT in integrating spATAC-seq data across multiple simulated scenarios and real datasets. Additionally, we highlight the advantages of INSTINCT in spatial domain identification, visualization, spot-type annotation, and various downstream analyses, including motif enrichment analysis, expression enrichment analysis, and partitioned heritability analysis.
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Registered trials
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