ArticleNature2025
A cell atlas foundation model for scalable search of similar human cells.
Article in Nature, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 papers.
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Who cites it
81 citing papers in PubMed.
- Identification of candidate markers for the isolation of neuron-specific extracellular vesicles.Nature neuroscience · 2026Article
- Reconstructing signaling histories of single cells via perturbation screens and transfer learning.Nature methods · 2026Article
- 3D multi-omics tumour atlases: from technology to biology and clinical translation.Nature reviews. Cancer · 2026Review
- celltypeEnrich: a consensus-based scRNA-seq cluster annotation tool.bioRxiv : the preprint server for biology · 2026Article
- Article
- scTransMIL bridges patient-level disease states and single-cell transcriptomics for cancer screening and heterogeneity inference.Nature communications · 2026Article
- scDiagnostics: systematic assessment of cell type annotation in single-cell transcriptomics data.Briefings in bioinformatics · 2026Article
- Multi-Technique Integration Identifies O-GlcNAc Transferase in Fibroblast-Like Synoviocytes as a Therapeutic Target for Rheumatoid Arthritis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- scProtoTransformer: Scalable reference mapping across molecules, cells, and donors.Science advances · 2026Article
- Article
- scDIVA: semi-supervised integration and fine-grained annotation of tumor-immune single-cell atlases.bioRxiv : the preprint server for biology · 2026Article
- Are different populations fairly represented in single-cell omic atlases?Cell genomics · 2026Review
- GPNMB-directed CAR T cell therapy against MiT/TFE-family fusion-driven solid tumors.Nature cancer · 2026Article
- Ancestry Matters in Decoding Immunity.Immunology and cell biology · 2026Article
- Transcriptional landscape of direct reprogramming toward the hematopoietic lineage.bioRxiv : the preprint server for biology · 2026Article
- Organism-scale annotation with Pan-human Azimuth.bioRxiv : the preprint server for biology · 2026Article
- Deep learning representations of human Immune Health for precision immunology.bioRxiv : the preprint server for biology · 2026Article
- The Single-Cell Pediatric Cancer Atlas: Data portal and open-source tools for single-cell transcriptomics of pediatric tumors.Cell genomics · 2026Article
- scDifformer: diffusion-based post-training for virtual cell modeling across large-scale single-cell data.Nucleic acids research · 2026Article
- Evaluating the role of pretraining dataset size and diversity on single-cell foundation model performance.Nature methods · 2026Article
21 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single-cell RNA sequencing has profiled hundreds of millions of human cells across organs, diseases, development and perturbations to date. Mining these growing atlases could reveal cell-disease associations, identify cell states in unexpected tissue contexts and relate in vivo biology to in vitro models. These require a common measure of cell similarity across the body and an efficient way to search. Here we develop SCimilarity, a metric-learning framework to learn a unified and interpretable representation that enables rapid queries of tens of millions of cell profiles from diverse studies for cells that are transcriptionally similar to an input cell profile or state. We use SCimilarity to query a 23.4-million-cell atlas of 412 single-cell RNA-sequencing studies for macrophage and fibroblast profiles from interstitial lung disease
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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.