RepliCNN: High-resolution inference of the DNA replication program from strand-specific 3′ DNA end sequencing

Code to reproduce figures of the RepliCNN paper (https://doi.org/10.64898/2026.03.12.710907).

Funding

This works was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) via project ID 393547839 – SFB 1361, to K.Z., H.D.U., V.R. and M.C.C., via project ID 533767322 – EXC 3113/1, Cluster for Nucleic Acid Sciences and Technologies – NUCLEATE, to K.Z., and via project ID 529989072 – CA 198/20-1, to M.C.C. We gratefully acknowledge the IMB Genomics Core Facility and its NextSeq 2000 sequencer (funded by the DFG – INST 247/870-1 FUGG).

Acknowledgements

We would like to express our gratitude to the Genomics and Bioinformatics Core Facilities of the IMB gGmbH (Mainz, Germany) for their assistance in sequencing and data processing. We thank Nicolas Delhomme, Maximilian Reuter, Mario Keller, and all members of the Zarnack group for helpful discussions.

Citing

If you use RepliCNN in your research, please cite this project like this:

RepliCNN: High-resolution inference of the DNA replication program from strand-specific 3′ DNA end sequencing
Dominik Stroh, Nicola Zilio, Maruthi K. Pabba, Vassilis Roukos, M. Cristina Cardoso, Helle D. Ulrich, Kathi Zarnack
bioRxiv 2026.03.12.710907; doi: https://doi.org/10.64898/2026.03.12.710907

BibTex:

@article {Stroh2026.03.12.710907,
	author = {Stroh, Dominik and Zilio, Nicola and Pabba, Maruthi K. and Roukos, Vassilis and Cardoso, M. Cristina and Ulrich, Helle D. and Zarnack, Kathi},
	title = {RepliCNN: High-resolution inference of the DNA replication program from strand-specific 3' DNA end sequencing},
	elocation-id = {2026.03.12.710907},
	year = {2026},
	doi = {10.64898/2026.03.12.710907},
	publisher = {Cold Spring Harbor Laboratory},
	URL = {https://www.biorxiv.org/content/early/2026/03/14/2026.03.12.710907},
	journal = {bioRxiv}
}