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Top AI Repos tracks AI repositories on GitHub and answers two different questions about each one: is it moving right now, and would you bet a product on it.
Top AI Repos tracks AI repositories on GitHub and answers two different questions about each one: is it moving right now, and would you bet a product on it.
| Date | Stars |
|---|---|
| 2026-07-31 | 514 |
| 2026-08-06 | 522 |
Today
+8 stars today
This week
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This month
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Momentum
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growth rate 0.00%/day
<h1 align="center">Awesome Foundation Models for Single-Cell</h1>
<p align="center">
<a href="https://awesome.re"><img src="https://awesome.re/badge.svg" alt="Awesome"></a>
<a href="http://makeapullrequest.com"><img src="https://img.shields.io/badge/PRs-welcome-brightgreen.svg" alt="PRs Welcome"></a>
<a href="https://github.com/OmicsML/awesome-foundation-model-single-cell-papers/stargazers"><img src="https://img.shields.io/github/stars/OmicsML/awesome-foundation-model-single-cell-papers?style=social" alt="GitHub stars"></a>
<a href="https://github.com/OmicsML/awesome-foundation-model-single-cell-papers/commits/main"><img src="https://img.shields.io/github/last-commit/OmicsML/awesome-foundation-model-single-cell-papers" alt="Last Commit"></a>
</p>
<p align="center">
A curated, continuously updated reading list of <b>foundation-model</b> research for <b>single-cell genomics</b>. The structure follows our review <b><i>"The landscape of single-cell foundation models: design principles, applications, and open challenges"</i></b>: single-cell foundation models are organized into <b>unimodal</b>, <b>multimodal</b>, and <b>LLM-based</b> scFMs, and the surrounding literature is grouped into perturbation modeling, virtual cells, pretraining datasets, benchmarks, infrastructure & agents, and surveys.
</p>
<p align="center">
Contributions are very welcome! Found a paper we missed, or a broken link? Open an issue or a pull request.
</p>
<p align="center">
Evolutionary tree credit: <a href="https://github.com/Mooler0410/LLMsPracticalGuide/tree/main">Mooler0410/LLMsPracticalGuide</a>
</p>
<p align="center">
<a href="figs/evo_tree.pdf"><img src="figs/evo_tree.png" alt="Evolutionary tree of single-cell foundation models" width="80%"></a>
</p>
## Catalog
- [Catalog](#catalog)
- [Single-Cell Foundation Models](#single-cell-foundation-models)
- [Unimodal scFMs](#unimodal-scfms)
- [scRNA-seq](#scrna-seq)
- [scATAC-seq](#scatac-seq)
- [Multimodal scFMs](#multimodal-scfms)
- [Transcriptomics and Perturbation](#transcriptomics-and-perturbation)
- [Spatial, Proteomics and Histology](#spatial-proteomics-and-histology)
- [Multi-omics: RNA, ATAC and Protein](#multi-omics-rna-atac-and-protein)
- [LLM-based scFMs](#llm-based-scfms)
- [Genetic Perturbation: Models, Atlases and Benchmarks](#genetic-perturbation-models-atlases-and-benchmarks)
- [Models and prediction frameworks](#models-and-prediction-frameworks)
- [Perturbation atlases and datasets](#perturbation-atlases-and-datasets)
- [Perturbation benchmarks](#perturbation-benchmarks)
- [Virtual Cell, World Models and Digital Human](#virtual-cell-world-models-and-digital-human)
- [Reviews, comments, and perspectives](#reviews-comments-and-perspectives)
- [Models and frameworks](#models-and-frameworks)
- [Pretraining Datasets and Resources](#pretraining-datasets-and-resources)
- [Single-cell transcriptomic atlases and repositories](#single-cell-transcriptomic-atlases-and-repositories)
- [Multimodal and spatial pretraining corpora](#multimodal-and-spatial-pretraining-corpora)
- [Data formats and frameworks](#data-formats-and-frameworks)
- [Benchmarks and Evaluation](#benchmarks-and-evaluation)
- [Benchmarks and critical evaluations](#benchmarks-and-critical-evaluations)
- [Data privacy and accessibility](#data-privacy-and-accessibility)
- [Infrastructure, Platforms and AI Agents](#infrastructure-platforms-and-ai-agents)
- [Infrastructure and platforms](#infrastructure-and-platforms)
- [AI agents for single-cell discovery](#ai-agents-for-single-cell-discovery)
- [Lab-in-the-loop and active discovery](#lab-in-the-loop-and-active-discovery)
- [Surveys and Perspectives](#surveys-and-perspectives)
- [Foundation Models for Pathology (related work)](#foundation-models-for-pathology-related-work)
- [Foundation Models for Bulk Transcriptomes (related work)](#foundation-models-for-bulk-transcriptome)
## Single-Cell Foundation Models
Single-cell fouExcerpt of 61,912 characters
Read on GitHub
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Caffery Yang · Texas A&M University
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Jérémie Kalfon · BroadInstitute - PiPle - PasteurInstitute
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Would you bet a product on this? Bounded 0–100 and slow moving.
matched fp:68e77ace9b70c78a, topic:large-language-models