ArticleNature communications2024
Intracellular spatial transcriptomic analysis toolkit (InSTAnT).
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 14 papers.
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The trial behind it
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Who cites it
14 citing papers in PubMed.
- STAID: A Self-Refining Deep Learning Framework for Spatial Cell-Type Deconvolution with Biologically Informed Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- D3aist: data-driven detection of atypical interactions in spatial transcriptomics.BMC genomics · 2026Article
- RESCUE: recovery of unattributed expression patterns in spatial transcriptomics.Nature communications · 2026Article
- Simultaneous spatial transcriptomics and morphology profiling as tools to explore how microglia change with age.Nature aging · 2026Article
- MANTIS: Analytics toolkit for spatial metabolomics with matching spatial transcriptomics data.bioRxiv : the preprint server for biology · 2026Article
- Spatial transcriptomics in Alzheimer's disease: technologies, challenges and discoveries.Molecular neurodegeneration advances · 2026Review
- High-throughput Screening of Sequence Elements Associated with RNA Localization.Computational and structural biotechnology journal · 2026Article
- SPICEiST: subcellular RNA pattern enhances cell clustering of imaging-based spatial transcriptomics.Genomics & informatics · 2025Article
- CellSP enables module discovery and visualization for subcellular spatial transcriptomics data.Communications biology · 2025Article
- Spatial omics enters the microscopic realm: opportunities and challenges.Trends in genetics : TIG · 2025Review
- Spatial Transcriptomics in Human Cardiac Tissue.International journal of molecular sciences · 2025Review
- Perspective on recent developments and challenges in regulatory and systems genomics.Bioinformatics advances · 2025Review
- Intracellular spatial transcriptomic analysis toolkit (InSTAnT).Nature communications · 2024Article
- Spot-Based Global Registration for Subpixel Stitching of Single-Molecule Resolution Images for Tissue-Scale Spatial Transcriptomics.Analytical chemistry · 2024Article
Corrections and comments
- Erratum issued
- Update of
Authors and funding
10 authors.
Funding
Abstract
Imaging-based spatial transcriptomics technologies such as Multiplexed error-robust fluorescence in situ hybridization (MERFISH) can capture cellular processes in unparalleled detail. However, rigorous and robust analytical tools are needed to unlock their full potential for discovering subcellular biological patterns. We present Intracellular Spatial Transcriptomic Analysis Toolkit (InSTAnT), a computational toolkit for extracting molecular relationships from spatial transcriptomics data at single molecule resolution. InSTAnT employs specialized statistical tests and algorithms to detect gene pairs and modules exhibiting intriguing patterns of co-localization, both within individual cells and across the cellular landscape. We showcase the toolkit on five different datasets representing two different cell lines, two brain structures, two species, and three different technologies. We perform rigorous statistical assessment of discovered co-localization patterns, find supporting evidence from databases and RNA interactions, and identify associated subcellular domains. We uncover several cell type and region-specific gene co-localizations within the brain. Intra-cellular spatial patterns discovered by InSTAnT mirror diverse molecular relationships, including RNA interactions and shared sub-cellular localization or function, providing a rich compendium of testable hypotheses regarding molecular functions.
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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.