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Sep 9, 2026
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Update GPN-Star citation to Nature #115

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18 changes: 9 additions & 9 deletions README.md
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![GPN-Star architecture, evolutionary scales, and genomic prediction tasks](docs/_static/gpn_star_overview.png)

Code and resources for genomic language models [GPN](https://doi.org/10.1073/pnas.2311219120), [GPN-MSA](https://www.nature.com/articles/s41587-024-02511-w), [PhyloGPN](https://link.springer.com/chapter/10.1007/978-3-031-90252-9_7) and [GPN-Star](https://doi.org/10.1101/2025.09.21.677619).
Code and resources for genomic language models [GPN](https://doi.org/10.1073/pnas.2311219120), [GPN-MSA](https://www.nature.com/articles/s41587-024-02511-w), [PhyloGPN](https://link.springer.com/chapter/10.1007/978-3-031-90252-9_7) and [GPN-Star](https://www.nature.com/articles/s41586-026-11005-5).

## Quick start

Expand All @@ -38,7 +38,7 @@ Explore the [GPN-Star models, alignments, scores, and benchmark datasets](https:
| [GPN](https://gpn.readthedocs.io/en/latest/models/gpn/) | [Benegas et al. 2023](https://doi.org/10.1073/pnas.2311219120) | Requires unaligned genomes |
| [GPN-MSA](https://gpn.readthedocs.io/en/latest/models/gpn-msa/) | [Benegas et al. 2025](https://www.nature.com/articles/s41587-024-02511-w) | Requires aligned genomes for training and inference; deprecated in favor of GPN-Star |
| [PhyloGPN](https://gpn.readthedocs.io/en/latest/models/phylogpn/) | [Albors et al. 2025](https://link.springer.com/chapter/10.1007/978-3-031-90252-9_7) | Uses an alignment during training, but does not require it for inference or fine-tuning |
| [GPN-Star](https://gpn.readthedocs.io/en/latest/models/gpn-star/) | [Ye et al. 2025](https://doi.org/10.1101/2025.09.21.677619) | Requires aligned genomes for training and inference |
| [GPN-Star](https://gpn.readthedocs.io/en/latest/models/gpn-star/) | [Ye et al. 2026](https://www.nature.com/articles/s41586-026-11005-5) | Requires aligned genomes for training and inference |

## Command line

Expand Down Expand Up @@ -116,16 +116,16 @@ GPN is developed in the [Song Lab at UC Berkeley](https://people.eecs.berkeley.e
}
```

[GPN-Star](https://doi.org/10.1101/2025.09.21.677619):
[GPN-Star](https://www.nature.com/articles/s41586-026-11005-5):

```bibtex
@article{ye2025predicting,
title={Predicting functional constraints across evolutionary timescales with phylogeny-informed genomic language models},
@article{ye2026predicting,
title={Predicting genome-wide functional constraints with GPN-Star},
author={Ye, Chengzhong and Benegas, Gonzalo and Albors, Carlos and Li, Jianan Canal and Prillo, Sebastian and Fields, Peter D and Clarke, Brian and Song, Yun S},
journal={bioRxiv},
pages={2025--09},
year={2025},
publisher={Cold Spring Harbor Laboratory}
journal={Nature},
pages={1--10},
year={2026},
publisher={Nature Publishing Group}
}
```

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2 changes: 1 addition & 1 deletion docs/index.md
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# GPN

Code and resources for genomic language models [GPN](https://doi.org/10.1073/pnas.2311219120), [GPN-MSA](https://www.nature.com/articles/s41587-024-02511-w), [PhyloGPN](https://link.springer.com/chapter/10.1007/978-3-031-90252-9_7) and [GPN-Star](https://doi.org/10.1101/2025.09.21.677619).
Code and resources for genomic language models [GPN](https://doi.org/10.1073/pnas.2311219120), [GPN-MSA](https://www.nature.com/articles/s41587-024-02511-w), [PhyloGPN](https://link.springer.com/chapter/10.1007/978-3-031-90252-9_7) and [GPN-Star](https://www.nature.com/articles/s41586-026-11005-5).

</div>

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2 changes: 1 addition & 1 deletion docs/models/gpn-star.md
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## Published assets

The [GPN-Star collection](https://huggingface.co/collections/songlab/gpn-star-68c0c055acc2ee51d5c4f129)
accompanies the [bioRxiv paper](https://doi.org/10.1101/2025.09.21.677619).
accompanies the [Nature paper](https://www.nature.com/articles/s41586-026-11005-5).

### Alignments and scores

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2 changes: 1 addition & 1 deletion docs/models/index.md
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| {doc}`GPN <gpn>` | [Benegas et al. 2023](https://doi.org/10.1073/pnas.2311219120) | Requires unaligned genomes |
| {doc}`GPN-MSA <gpn-msa>` | [Benegas et al. 2025](https://www.nature.com/articles/s41587-024-02511-w) | Requires aligned genomes for training and inference; deprecated in favor of GPN-Star |
| {doc}`PhyloGPN <phylogpn>` | [Albors et al. 2025](https://link.springer.com/chapter/10.1007/978-3-031-90252-9_7) | Uses an alignment during training, but does not require it for inference or fine-tuning |
| {doc}`GPN-Star <gpn-star>` | [Ye et al. 2025](https://doi.org/10.1101/2025.09.21.677619) | Requires aligned genomes for training and inference |
| {doc}`GPN-Star <gpn-star>` | [Ye et al. 2026](https://www.nature.com/articles/s41586-026-11005-5) | Requires aligned genomes for training and inference |

## Maintained support

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14 changes: 7 additions & 7 deletions docs/reference/citations.md
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}
```

## [GPN-Star](https://doi.org/10.1101/2025.09.21.677619)
## [GPN-Star](https://www.nature.com/articles/s41586-026-11005-5)

```bibtex
@article{ye2025predicting,
title={Predicting functional constraints across evolutionary timescales with phylogeny-informed genomic language models},
@article{ye2026predicting,
title={Predicting genome-wide functional constraints with GPN-Star},
author={Ye, Chengzhong and Benegas, Gonzalo and Albors, Carlos and Li, Jianan Canal and Prillo, Sebastian and Fields, Peter D and Clarke, Brian and Song, Yun S},
journal={bioRxiv},
pages={2025--09},
year={2025},
publisher={Cold Spring Harbor Laboratory}
journal={Nature},
pages={1--10},
year={2026},
publisher={Nature Publishing Group}
}
```

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