# Citations

Please cite the paper for each model or fine-tuned application you use.

## [GPN](https://doi.org/10.1073/pnas.2311219120)

```bibtex
@article{benegas2023dna,
  title={DNA language models are powerful predictors of genome-wide variant effects},
  author={Benegas, Gonzalo and Batra, Sanjit Singh and Song, Yun S},
  journal={Proceedings of the National Academy of Sciences},
  volume={120},
  number={44},
  pages={e2311219120},
  year={2023},
  publisher={National Acad Sciences}
}
```

## [GPN-MSA](https://www.nature.com/articles/s41587-024-02511-w)

```bibtex
@article{benegas2025dna,
  title={A DNA language model based on multispecies alignment predicts the effects of genome-wide variants},
  author={Benegas, Gonzalo and Albors, Carlos and Aw, Alan J and Ye, Chengzhong and Song, Yun S},
  journal={Nature Biotechnology},
  pages={1--6},
  year={2025},
  publisher={Nature Publishing Group US New York}
}
```

## [PhyloGPN](https://link.springer.com/chapter/10.1007/978-3-031-90252-9_7)

```bibtex
@inproceedings{albors2025phylogenetic,
  title={A Phylogenetic Approach to Genomic Language Modeling},
  author={Albors, Carlos and Li, Jianan Canal and Benegas, Gonzalo and Ye, Chengzhong and Song, Yun S},
  booktitle={International Conference on Research in Computational Molecular Biology},
  pages={99--117},
  year={2025},
  organization={Springer}
}
```

## [GPN-Star](https://doi.org/10.1101/2025.09.21.677619)

```bibtex
@article{ye2025predicting,
  title={Predicting functional constraints across evolutionary timescales with phylogeny-informed genomic language models},
  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}
}
```

## [Sorghum gene-expression prediction with fine-tuned GPN](https://www.nature.com/articles/s41587-026-03046-y)

```bibtex
@article{groover2026mapping,
  title={Mapping cis-regulatory mutations at scale in sorghum enables modulation of gene expression},
  author={Groover, Evan D and Ding, David and Wang, Flora Z and Benegas, Gonzalo and Rivera, Joseph and Schwartz, Shahar and Chen, Stephen and Moubarak, Michael F and Georgieva, Viktoriya and Lemaux, Peggy G and others},
  journal={Nature Biotechnology},
  pages={1--11},
  year={2026},
  publisher={Nature Publishing Group US New York}
}
```