Acknowledgments

LoopSage was developed in the group of Dariusz Plewczynski (Warsaw University of Technology, Centre of New Technologies of the University of Warsaw, and the SFGlab group). I thank him for his support and supervision throughout this work.

I thank Michał Denkiewicz, who introduced me to this field and whose ideas inspired the extension of LoopSage with the topology (links and knots) analysis, and Mateusz Chiliński, who helped with the motif finder and the analysis of CTCF orientation.

Use of AI assistance

LoopSage is not a product of AI generation. It is an idea that has evolved over all the years of my PhD, and the model, its design and its scientific choices are mine. The implementation, however, is mostly the work of one person, and the project grew large. I therefore used an AI assistant (an agent) to help write the documentation and to help with parts of the code, working under my direction and review.

Software

LoopSage builds on open-source software: OpenMM for molecular dynamics, numba and NumPy for the Monte Carlo sampler, hic-straw for reading Hi-C files, and MkDocs Material for this documentation. Thanks to their authors and maintainers.

How to cite

If you use LoopSage, please cite the paper listed in the introduction.