ArticleNature communications2025
Deconvolution of cell types and states in spatial multiomics utilizing TACIT.
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 14 papers.
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Who cites it
14 citing papers in PubMed.
- Single-cell landscape of peripheral and tumor-infiltrating immune cells in HPV-negative HNSCC.Oncoimmunology · 2026Article
- Binary-SPA: a reference-free method for cell annotation in high-resolution spatial transcriptomics.Nucleic acids research · 2026Article
- Autoreactive B cells in systemic lupus erythematosus: insights from integrative multi-omics analyses.Inflammation and regeneration · 2026Review
- CellFuse Enables Multimodal Integration of Single-Cell and Spatial Proteomics Data for Systems-Level Analysis in Cancer.Cancer research · 2026Article
- CD38⁺ endothelial remodeling marks spatially patterned vasculopathy in rapidly advancing periodontitis and peri-implantitis.Nature communications · 2026Article
- Immune cell annotation in the single-cell studies: technologies, challenges, and integrative solutions.Immunologic research · 2026Review
- An integrated single-cell and spatial proteotranscriptomics atlas of fibroblast-driven immunoregulation within the human adult oral cavity.Cell press blue · 2026Article
- Binary-SPA: A Reference-Free Method for Cell Annotation in High-Resolution Spatial Transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- Exploring endothelial cell environments across organs in spatially resolved omics data.bioRxiv : the preprint server for biology · 2025Article
- CD38bioRxiv : the preprint server for biology · 2025Article
- Integrating Intermediate Traits in Phylogenetic Genotype-to-Phenotype Studies.Integrative and comparative biology · 2025Review
- Deconvolution of cell types and states in spatial multiomics utilizing TACIT.Nature communications · 2025Article
- Salivary gland transcriptomic analysis and immunophenotyping in the IL-14α transgenic mouse model of Sjögren's disease.Frontiers in dental medicine · 2025Article
- Integrating spatial omics with routine haematoxylin and eosin in formalin-fixed paraffin-embedded: a step-by-step clinical workflow.F1000Research · 2025Review
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Abstract
Identifying cell types and states remains a time-consuming, error-prone challenge for spatial biology. While deep learning increasingly plays a role, it is difficult to generalize due to variability at the level of cells, neighborhoods, and niches in health and disease. To address this, we develop TACIT, an unsupervised algorithm for cell annotation using predefined signatures that operates without training data. TACIT uses unbiased thresholding to distinguish positive cells from background, focusing on relevant markers to identify ambiguous cells in multiomic assays. Using five datasets (5,000,000 cells; 51 cell types) from three niches (brain, intestine, gland), TACIT outperforms existing unsupervised methods in accuracy and scalability. Integrating TACIT-identified cell types reveals new phenotypes in two inflammatory gland diseases. Finally, using combined spatial transcriptomics and proteomics, we discover under- and overrepresented immune cell types and states in regions of interest, suggesting multimodality is essential for translating spatial biology to clinical applications.
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