ArticleNature genetics2023
Precise identification of cell states altered in disease using healthy single-cell references.
Article in Nature genetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
47 citing papers in PubMed.
- Article
- Hybrid CNN and multi-head attention model for analyzing epigenetic mechanisms and gene expression across fungal phylogenetic distances.iScience · 2026Article
- Condensates and cell states: A new paradigm for understanding tumor biology.Biophysical journal · 2026Review
- scDiagnostics: systematic assessment of cell type annotation in single-cell transcriptomics data.Briefings in bioinformatics · 2026Article
- Φ-Space ST: A platform-agnostic method to identify cell states in spatial transcriptomics studies.Cell reports methods · 2026Article
- Binary-SPA: a reference-free method for cell annotation in high-resolution spatial transcriptomics.Nucleic acids research · 2026Article
- Tissueformer: extending single-cell foundation models to predict population-level phenotypes.BMC bioinformatics · 2026Article
- The pleuroparenchymal fibroelastosis atlas reveals aberrant cell states and their zonation as an alternate roadmap to lung fibrosis.Science advances · 2026Article
- scHILL: deciphering individual-level immune cell heterogeneity with single-cell RNA sequencing data.Briefings in bioinformatics · 2026Article
- Interpretable neural network for risk stratification and drug target discovery based on PBMC transcriptomes.iScience · 2026Article
- Hidden immune memory niches in inflammatory skin diseases.bioRxiv : the preprint server for biology · 2026Article
- Binary-SPA: A Reference-Free Method for Cell Annotation in High-Resolution Spatial Transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- Decoding Alzheimer's Disease One Cell Class at a Time.Cellular and molecular neurobiology · 2026Review
- Spatial architecture of development and disease.Nature reviews. Genetics · 2026Review
- Interpretable inflammation landscape of circulating immune cells.Nature medicine · 2026Article
- An expanded role for single-cell chemical genomics profiling in drug discovery.The Biochemical journal · 2026Review
- From the brain cell atlas to precision neurology: a review of the application of AI-driven multi-omics in brain science.GigaScience · 2026Review
- Exploring phenotype-related single-cells through attention-enhanced representation learning.Genome medicine · 2026Article
- The normal human lymph node cell classification and landscape defined by high-dimensional spatial proteomics.PloS one · 2026Article
- Single Cell RNA Sequencing in Colorectal Cancer Immunology: Recent Updates, Application, and Emerging Challenges.Current molecular medicine · 2026Review
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Joint analysis of single-cell genomics data from diseased tissues and a healthy reference can reveal altered cell states. We investigate whether integrated collections of data from healthy individuals (cell atlases) are suitable references for disease-state identification and whether matched control samples are needed to minimize false discoveries. We demonstrate that using a reference atlas for latent space learning followed by differential analysis against matched controls leads to improved identification of disease-associated cells, especially with multiple perturbed cell types. Additionally, when an atlas is available, reducing control sample numbers does not increase false discovery rates. Jointly analyzing data from a COVID-19 cohort and a blood cell atlas, we improve detection of infection-related cell states linked to distinct clinical severities. Similarly, we studied disease states in pulmonary fibrosis using a healthy lung atlas, characterizing two distinct aberrant basal states. Our analysis provides guidelines for designing disease cohort studies and optimizing cell atlas use.
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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.