ArticleNature communications2024
scConfluence: single-cell diagonal integration with regularized Inverse Optimal Transport on weakly connected features.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Explainable data generation from observed small samples by matrix tri-factorization.Nature communications · 2026Article
- Network methods for diagonal integration of unpaired single-cell multiomics data: a review.Bioinformatics (Oxford, England) · 2026Review
- Robust integration of single-cell datasets with imbalanced modality composition.Nature communications · 2026Article
- Single-cell data integration across weakly linked modalities.PLoS computational biology · 2026Article
- Mapping multipathology via spatial omic integration.Current opinion in biotechnology · 2026Review
- High-parameter spatial multi-omics through histology-anchored integration.Nature methods · 2026Article
- An interpretable Graph-Regularized Optimal Transport Framework for Diagonal Single-Cell Integrative Analysis.GigaScience · 2026Article
- AUTOENCODIX: a generalized and versatile framework to train and evaluate autoencoders for biological representation learning and beyond.Nature computational science · 2026Article
- scCotag: Diagonal integration of single-cell multi-omics data via prior-informed co-optimal transport and regularized barycentric mapping.bioRxiv : the preprint server for biology · 2025Article
- CelLink: integrating single-cell multi-omics data with weak feature linkage and imbalanced cell populations.Nucleic acids research · 2025Article
- Single-Cell Multi-Omics in Type 2 Diabetes Mellitus: Revealing Cellular Heterogeneity and Mechanistic Insights.International journal of molecular sciences · 2025Review
- Multi-omics: a bridge connecting genotype and phenotype for epilepsy?Biomarker research · 2025Review
- Leveraging Multi-omics to Disentangle the Complexity of Ovarian Cancer.Molecular diagnosis & therapy · 2025Review
- Single-cell genomics and spatial transcriptomics in islet transplantation for diabetes treatment: advancing towards personalized therapies.Frontiers in immunology · 2025Review
- scConfluence: single-cell diagonal integration with regularized Inverse Optimal Transport on weakly connected features.Nature communications · 2024Article
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3 authors.
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Abstract
The abundance of unpaired multimodal single-cell data has motivated a growing body of research into the development of diagonal integration methods. However, the state-of-the-art suffers from the loss of biological information due to feature conversion and struggles with modality-specific populations. To overcome these crucial limitations, we here introduce scConfluence, a method for single-cell diagonal integration. scConfluence combines uncoupled autoencoders on the complete set of features with regularized Inverse Optimal Transport on weakly connected features. We extensively benchmark scConfluence in several single-cell integration scenarios proving that it outperforms the state-of-the-art. We then demonstrate the biological relevance of scConfluence in three applications. We predict spatial patterns for Scgn, Synpr and Olah in scRNA-smFISH integration. We improve the classification of B cells and Monocytes in highly heterogeneous scRNA-scATAC-CyTOF integration. Finally, we reveal the joint contribution of Fezf2 and apical dendrite morphology in Intra Telencephalic neurons, based on morphological images and scRNA.
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