ArticleNature communications2022
UINMF performs mosaic integration of single-cell multi-omic datasets using nonnegative matrix factorization.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed.
- Single-cell and spatial RNA sequencing in prostate cancer.Nature reviews. Urology · 2026Review
- LIGER2: Scalable Single-Cell Integration with On-Disk Datasets.bioRxiv : the preprint server for biology · 2026Article
- Representation Retrieval Learning for Heterogeneous Data Integration.Journal of the American Statistical Association · 2026Article
- Scalable joint non-negative matrix factorization for paired single cell gene expression and chromatin accessibility data.NAR genomics and bioinformatics · 2026Article
- Interpretable spatial multi-omics data integration and dimensionality reduction with SpaMV.Nature communications · 2026Article
- Robust integration of single-cell datasets with imbalanced modality composition.Nature communications · 2026Article
- A comprehensive benchmarking study on computational tools for cross-omics label transfer from single-cell RNA to ATAC data.G3 (Bethesda, Md.) · 2026Article
- Mapping multipathology via spatial omic integration.Current opinion in biotechnology · 2026Review
- Unveiling patterns: an exploration of machine learning techniques for unsupervised feature selection in single-cell data.Briefings in bioinformatics · 2026Review
- AI-integrated single-cell multi-omics decodes the hepatocellular carcinoma metabolism-immune axis: a new strategy for precision therapeutic targeting.Frontiers in oncology · 2026Review
- Single-cell transcriptomics of granulocytes in asthma and atopic diseases.Frontiers in molecular biosciences · 2026Review
- Single-Cell Multi-Omics in Type 2 Diabetes Mellitus: Revealing Cellular Heterogeneity and Mechanistic Insights.International journal of molecular sciences · 2025Review
- Benchmarking single-cell multi-modal data integrations.Nature methods · 2025Article
- The cell as a token: high-dimensional geometry in language models and cell embeddings.Bioinformatics (Oxford, England) · 2025Review
- Multitask benchmarking of single-cell multimodal omics integration methods.Nature methods · 2025Article
- Disrupted developmental signaling induces novel transcriptional states.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- ACE: A Versatile Contrastive Learning Framework for Single-cell Mosaic Integration.Genomics, proteomics & bioinformatics · 2025Article
- A technical review of multi-omics data integration methods: from classical statistical to deep generative approaches.Briefings in bioinformatics · 2025Review
- Empowering integrative and collaborative exploration of single-cell and spatial multimodal data with SGS genome browser.Cell genomics · 2025Article
- Examining the dynamics of three-dimensional genome organization with multitask matrix factorization.Genome research · 2025Article
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Abstract
Single-cell genomic technologies provide an unprecedented opportunity to define molecular cell types in a data-driven fashion, but present unique data integration challenges. Many analyses require "mosaic integration", including both features shared across datasets and features exclusive to a single experiment. Previous computational integration approaches require that the input matrices share the same number of either genes or cells, and thus can use only shared features. To address this limitation, we derive a nonnegative matrix factorization algorithm for integrating single-cell datasets containing both shared and unshared features. The key advance is incorporating an additional metagene matrix that allows unshared features to inform the factorization. We demonstrate that incorporating unshared features significantly improves integration of single-cell RNA-seq, spatial transcriptomic, SNARE-seq, and cross-species datasets. We have incorporated the UINMF algorithm into the open-source LIGER R package ( https://github.com/welch-lab/liger ).
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