ArticleNature methods2024
Large-scale foundation model on single-cell transcriptomics.
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 340 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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
340 citing papers in PubMed.
- scYeast: a biological-knowledge-guided foundation model on yeast single-cell transcriptomics.Synthetic and systems biotechnology · 2027Article
- AI-based multimodal integration of genomics and electronic health records.Nature reviews. Genetics · 2026Review
- scPlantAnnotate: an accurate and robust transformer-based model for plant cell type annotation.Journal of advanced research · 2026Article
- 3D multi-omics tumour atlases: from technology to biology and clinical translation.Nature reviews. Cancer · 2026Review
- Computational approaches for multimodal lineage tracing.Nature reviews. Genetics · 2026Review
- Review
- Mapping Gene Expression to an Interpretable Semantic Space.bioRxiv : the preprint server for biology · 2026Article
- spaGFM is a scalable graph foundation model for spatial transcriptomics analyses.Research square · 2026Article
- Foundation model reveals the shared organization of transcription and topologically associating domains.Cell systems · 2026Article
- Cell-level random splits leak group-owned answers in single-cell benchmarks.bioRxiv : the preprint server for biology · 2026Article
- scTransMIL bridges patient-level disease states and single-cell transcriptomics for cancer screening and heterogeneity inference.Nature communications · 2026Article
- GEM-GPT Enables Personalized Cell Type-Resolved Therapeutic Design for Systems Pharmacology.bioRxiv : the preprint server for biology · 2026Article
- A systematic comparison of single-cell perturbation response prediction models.Science advances · 2026Article
- PHAROS: turning single-cell perturbation models into target-directed drug-combination screens.bioRxiv : the preprint server for biology · 2026Article
- Article
- PlantCAD2: A DNA foundation model for interpreting genomes across flowering plants.Cell genomics · 2026Article
- A transcription factor regulatory atlas for activity inference and perturbation prediction.Nucleic acids research · 2026Article
- Review
- Large Language Models in Preclinical Spine Research: A Scoping Review and Expert Perspective on Evidence-Aware Experimental Workflows.JOR spine · 2026Article
- AI proteomics: from protein identification to virtual cells.Nature methods · 2026Review
280 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
Abstract
Large pretrained models have become foundation models leading to breakthroughs in natural language processing and related fields. Developing foundation models for deciphering the 'languages' of cells and facilitating biomedical research is promising yet challenging. Here we developed a large pretrained model scFoundation, also named 'xTrimoscFoundation
Indexed as
Identifiers
38844628What OpenQuestion holds
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.