Publications and Citation
=========================

**Publications:**
We have two publications linked to our de novo gene annotation format and the 
**denofo** `toolkit <https://github.com/EDohmen/denofo>`_:

- `DeNoFo: a file format and toolkit for standardised, comparable de novo gene annotation (2025) E. Dohmen, M. Aubel, L. A. Eicholt, P. Roginski, V. Luria, A. Karger, A. Grandchamp; bioRxiv <https://doi.org/10.1101/2025.03.31.644673>`_ An Application Note introducing the **denofo** toolkit.
- `De Novo Gene Emergence: Summary, Classification, and Challenges of Current Methods (2025) A. Grandchamp, M. Aubel, L. A. Eicholt, P. Roginski, V. Luria, A. Karger, E. Dohmen; EcoEvoRxiv <https://doi.org/10.32942/X2DP88>`_ A review introducing the concepts and decisions for the standardized de novo annotation format.

**Citation:**
If you used **denofo** for your work, please cite the `Application Note <https://doi.org/10.1101/2025.03.31.644673>`_ linked above.