Publications and Citation

Publications: We have two publications linked to our de novo gene annotation format and the denofo toolkit:

• 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 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 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 linked above.