ArticleNature methods2024
Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis.
Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 155 papers, 1 of them a synthesis that pooled it.
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Who cites it
155 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Human researchers are superior to large language models in writing a medical systematic review in a comparative multitask assessment.Scientific reports · 2025Pooled it
- scPlantAnnotate: an accurate and robust transformer-based model for plant cell type annotation.Journal of advanced research · 2026Article
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- Single-Cell RNA Sequencing Reveals Immune Dysregulation and Candidate Drug Targets in Endometriosis.Cells · 2026Article
- Ten quick tips for spatial transcriptomics analysis.PLoS computational biology · 2026Review
- scDiagnostics: systematic assessment of cell type annotation in single-cell transcriptomics data.Briefings in bioinformatics · 2026Article
- Mapping ovarian cellular and molecular landscape across the lifespan of women: a scoping review.Human reproduction update · 2026Article
- Benchmarking biomedical foundation models.Nature methods · 2026Review
- Halo: a pretrained model for whole-cell segmentation from nuclei images in spatial transcriptomics.Briefings in bioinformatics · 2026Article
- Benchmarking cell type annotation in spatial transcriptomics: resolving cellular hierarchies, biological fidelity, and dynamic cell states.Research square · 2026Article
- Integrative evidence-knowledge marker selection enhances LLM-based cell type annotation in single-cell RNA-seq analysis.BioData mining · 2026Article
- APOEScience advances · 2026Article
- Tracing the rise of biomedical foundation models.Nature biotechnology · 2026Article
- CellTypeAI: cell annotation for scRNA-seq using local generative-AI.Bioinformatics (Oxford, England) · 2026Article
- Mathematical and Computational Models of Biochemical Reactions and Cell Signaling-From Ordinary Differential Equations to Machine Learning.International journal of molecular sciences · 2026Review
- Tutorial: guidance on the use of large language models for medical research.Nature protocols · 2026Review
- Application of human induced pluripotent stem cells for tissue modeling and therapy: are we on track?Stem cells (Dayton, Ohio) · 2026Review
- ATACompass enables cross-species cell identity mapping for scATAC-seq without gene annotations.Cell reports methods · 2026Article
95 more citing papers are in PubMed but not listed here.
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Abstract
Here we demonstrate that the large language model GPT-4 can accurately annotate cell types using marker gene information in single-cell RNA sequencing analysis. When evaluated across hundreds of tissue and cell types, GPT-4 generates cell type annotations exhibiting strong concordance with manual annotations. This capability can considerably reduce the effort and expertise required for cell type annotation. Additionally, we have developed an R software package GPTCelltype for GPT-4's automated cell type annotation.
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