References

References#

[KDWB+25]

Niklas Kempynck, Seppe De Winter, Casper H. Blaauw, Vasileios Konstantakos, Sam Dieltiens, Eren Can Ekşi, Valérie Bercier, Ibrahim I. Taskiran, Gert Hulselmans, Katina Spanier, Valerie Christiaens, Ludo Van Den Bosch, Lukas Mahieu, and Stein Aerts. Crested: modeling genomic and synthetic cell type-specific enhancers across tissues and species. bioRxiv, 2025. URL: https://www.biorxiv.org/content/early/2025/04/03/2025.04.02.646812, arXiv:https://www.biorxiv.org/content/early/2025/04/03/2025.04.02.646812.full.pdf, doi:10.1101/2025.04.02.646812.

[Sch25a]

Jacob Schreiber. Tomtom-lite: accelerating tomtom enables large-scale and real-time motif similarity scoring. bioRxiv, 2025. URL: https://www.biorxiv.org/content/early/2025/05/31/2025.05.27.656386, arXiv:https://www.biorxiv.org/content/early/2025/05/31/2025.05.27.656386.full.pdf, doi:10.1101/2025.05.27.656386.

[Sch25b]

Jacob Schreiber. Tangermeme: a toolkit for understanding cis-regulatory logic using deep learning models. bioRxiv, 2025. URL: https://www.biorxiv.org/content/early/2025/08/23/2025.08.08.669296, arXiv:https://www.biorxiv.org/content/early/2025/08/23/2025.08.08.669296.full.pdf, doi:10.1101/2025.08.08.669296.

[VBH+23]

Isaac Virshup, Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso, Ilia Kats, Mikaela Koutrouli, Philipp Angerer, Volker Bergen, Pierre Boyeau, Maren Büttner, Gokcen Eraslan, David Fischer, Max Frank, Justin Hong, Michal Klein, Marius Lange, Romain Lopez, Mohammad Lotfollahi, Malte D. Luecken, Fidel Ramirez, Jeffrey Regier, Sergei Rybakov, Anna C. Schaar, Valeh Valiollah Pour Amiri, Philipp Weiler, Galen Xing, Bonnie Berger, Dana Pe'er, Aviv Regev, Sarah A. Teichmann, Francesca Finotello, F. Alexander Wolf, Nir Yosef, Oliver Stegle, and Fabian J. Theis and. The scverse project provides a computational ecosystem for single-cell omics data analysis. Nature Biotechnology, apr 2023. URL: https://doi.org/10.1038%2Fs41587-023-01733-8, doi:10.1038/s41587-023-01733-8.