Citation

If you use Shorkie, please cite the preprint:

Chao, K.-H., Magzoub, M. M., Stoops, E. H., Hackett, S. R., Linder, J., & Kelley, D. R. (2025). Predicting dynamic expression patterns in budding yeast with a fungal DNA language model. bioRxiv. https://doi.org/10.1101/2025.09.19.677475

BibTeX

@article{chao2025shorkie,
  title   = {Predicting dynamic expression patterns in budding yeast with a fungal DNA language model},
  author  = {Chao, Kuan-Hao and Magzoub, Majed M. and Stoops, Emily H. and Hackett, Sean R. and Linder, Johannes and Kelley, David R.},
  journal = {bioRxiv},
  year    = {2025},
  doi     = {10.1101/2025.09.19.677475},
  url     = {https://www.biorxiv.org/content/10.1101/2025.09.19.677475v1}
}

The repository also ships a CITATION.cff, so GitHub’s “Cite this repository” button produces the same reference.

Datasets

If you use the benchmark or training data, please also cite the original sources:

  • Hackett, S. R. et al. Learning causal networks using inducible transcription factors and transcriptome-wide time series. Mol Syst Biol (2020). — IDEA

  • Caudal, É. et al. Pan-transcriptome reveals a large accessory genome contribution to gene expression variation in yeast. Nat Genet 56, 1278–1287 (2024).

  • Peter, J. et al. Genome evolution across 1,011 Saccharomyces cerevisiae isolates. Nature 556, 339–344 (2018).

  • Rossi, M. J. et al. A high-resolution protein architecture of the budding yeast genome. Nature (2021). — ChIP-exo / ChIP-MNase

  • Kita, R. et al. High-resolution mapping of cis-regulatory variation in budding yeast. PNAS 114 (2017).

  • Renganaath, K. et al. Systematic identification of cis-regulatory variants that cause gene expression differences in a yeast cross. eLife 9, e62669 (2020).

  • Rafi, A. M. et al. A community effort to optimize sequence-based deep learning models of gene regulation. Nat Biotechnol (2024). — DREAM Challenge MPRA