ArticleNature biotechnology2022
Multi-omics single-cell data integration and regulatory inference with graph-linked embedding.
Article in Nature biotechnology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 341 papers, 3 of them syntheses that pooled it.
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Who cites it
341 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Graph neural networks for single-cell omics data: a review of approaches and applications.Briefings in bioinformatics · 2025Pooled it
- Deep learning in single-cell and spatial transcriptomics data analysis: advances and challenges from a data science perspective.Briefings in bioinformatics · 2025Pooled it
- Visible neural networks for multi-omics integration: a critical review.Frontiers in artificial intelligence · 2025Pooled it
- Regulatory-prior-guided attention preserves biological structure during unpaired single-cell RNA-ATAC integration.Bioinformatics (Oxford, England) · 2026Article
- Unifying multimodal single-cell data with a mixture-of-experts β-variational autoencoder framework.Genome research · 2026Article
- Single-Nucleus Multi-Omic Atlas Maps Regulatory Architecture and Non-Coding Variant Effects across Adult Human Tissues.bioRxiv : the preprint server for biology · 2026Article
- A cross-species single-cell kidney epigenome atlas reveals epithelial-dominant aging-like states in disease.Nature aging · 2026Article
- Personalized single-cell transcriptomics reveals molecular diversity in Alzheimer's disease.Nature communications · 2026Article
- Flow Orchestrated Regulatory Genomics Engine (FORGE): A Configurable Nextflow Pipeline for End-to-End snMultiome Analysis.bioRxiv : the preprint server for biology · 2026Article
- Explainable data generation from observed small samples by matrix tri-factorization.Nature communications · 2026Article
- Multi-omics technologies: Novel tools and methods for assessing nerve injury and regeneration.Neural regeneration research · 2026Article
- Continual integration of single-cell multimodal data with MIRACLE.Nature computational science · 2026Article
- Topology-guided dual-masked contrastive learning for weakly supervised cell-type annotation in single-cell multi-omics.Briefings in bioinformatics · 2026Article
- Unified representation learning for spatial multi-omics.Bioinformatics (Oxford, England) · 2026Article
- scProtoTransformer: Scalable reference mapping across molecules, cells, and donors.Science advances · 2026Article
- Multi-omics-driven precision medicine.iMeta · 2026Review
- scKanFormer: A Transformer-KAN framework with biologically informed attention for cell type annotation in large-scale scRNA-seq data.PLoS computational biology · 2026Article
- ARCADIA reveals spatially dependent transcriptional programs through integration of scRNA-seq and spatial proteomics.Bioinformatics (Oxford, England) · 2026Article
- An Integrated Multi-omics Single Cell Atlas of the Human RPE and Choroid.bioRxiv : the preprint server for biology · 2026Article
- Single-cell multimodal profiling of pan-cancer cell lines uncovers gene regulatory principles underlying intrinsic cell states and environmental features.Nature communications · 2026Article
281 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Despite the emergence of experimental methods for simultaneous measurement of multiple omics modalities in single cells, most single-cell datasets include only one modality. A major obstacle in integrating omics data from multiple modalities is that different omics layers typically have distinct feature spaces. Here, we propose a computational framework called GLUE (graph-linked unified embedding), which bridges the gap by modeling regulatory interactions across omics layers explicitly. Systematic benchmarking demonstrated that GLUE is more accurate, robust and scalable than state-of-the-art tools for heterogeneous single-cell multi-omics data. We applied GLUE to various challenging tasks, including triple-omics integration, integrative regulatory inference and multi-omics human cell atlas construction over millions of cells, where GLUE was able to correct previous annotations. GLUE features a modular design that can be flexibly extended and enhanced for new analysis tasks. The full package is available online at https://github.com/gao-lab/GLUE .
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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.