Publications
Reverse chronological list of publications
- Open-closed mod-minimizer preprint (PDF)
- Groot Koerkamp, Ragnar, Daniel Liu, and Giulio Ermanno Pibiri. 2024. “The Open-Closed Mod-Minimizer Algorithm.” Biorxiv. https://doi.org/10.1101/2024.11.02.621600.
- Forward sampling scheme density lower bound (PDF)
- Kille, Bryce, Ragnar Groot Koerkamp, Drake McAdams, Alan Liu, and Todd Treangen. 2024. “A near-Tight Lower Bound on the Density of Forward Sampling Schemes.” Biorxiv. https://doi.org/10.1101/2024.09.06.611668.
- Mod-minimizer (PDF)
- Groot Koerkamp, Ragnar, and Giulio Ermanno Pibiri. 2024a. “The mod-minimizer: A Simple and Efficient Sampling Algorithm for Long k-mers.” In 24th International Workshop on Algorithms in Bioinformatics (Wabi 2024), edited by Solon P. Pissis and Wing-Kin Sung, 312:11:1–11:23. Leibniz International Proceedings in Informatics (Lipics). Dagstuhl, Germany: Schloss Dagstuhl – Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.WABI.2024.11.
- Mod-minimizer preprint
- Groot Koerkamp, Ragnar, and Giulio Ermanno Pibiri. 2024b. “The Mod-Minimizer: A Simple and Efficient Sampling Algorithm for Long k-mers,” May. https://doi.org/10.1101/2024.05.25.595898.
- A*PA2 (PDF)
- Groot Koerkamp, Ragnar. 2024a. “A*PA2: Up to 19 Faster Exact Global Alignment.” In 24th International Workshop on Algorithms in Bioinformatics (Wabi 2024), edited by Solon P. Pissis and Wing-Kin Sung, 312:17:1–17:25. Leibniz International Proceedings in Informatics (Lipics). Dagstuhl, Germany: Schloss Dagstuhl – Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.WABI.2024.17.
- A*PA2 preprint
- Groot Koerkamp, Ragnar. 2024b. “A*PA2: Up to 20 Times Faster Exact Global Alignment,” March. https://doi.org/10.1101/2024.03.24.586481.
- A*PA (PDF)
- Groot Koerkamp, Ragnar, and Pesho Ivanov. 2024. “Exact Global Alignment Using A* with Chaining Seed Heuristic and Match Pruning.” Edited by Tobias Marschall. Bioinformatics 40 (3). https://doi.org/10.1093/bioinformatics/btae032.
- A*PA preprint
- Groot Koerkamp, Ragnar, and Pesho Ivanov. 2022. “Exact Global Alignment Using A* with Chaining Seed Heuristic and Match Pruning,” September. https://doi.org/10.1101/2022.09.19.508631.
- MSc thesis paper: Rainbow-free colourings
- Groot Koerkamp, Ragnar, and Stanislav Živný. 2021. “On Rainbow-Free Colourings of Uniform Hypergraphs.” Theoretical Computer Science 885 (September): 69–76. https://doi.org/10.1016/j.tcs.2021.06.022.
- BSc thesis paper: Stably gonality
- Groot Koerkamp, Ragnar, and Marieke van der Wegen. 2019. “Stable Gonality Is Computable.” Discrete Mathematics & Theoretical Computer Science vol. 21 no. 1, ICGT 2018 (June). https://doi.org/10.23638/DMTCS-21-1-10.
Talks
Conference talks
- WABI 2024: Mod-minimizer, slides
- WABI 2024: A*PA2
- MemPanG 2024: A*PA2
- RECOMB-SEQ 2024: A*PA & A*PA2,
- IGGSY 2024: A*PA2
- IGGSY 2022: A*PA, slides
Slides
- A*PA & A*PA2 slide deck
- Minimizers
Recorded seminar talks
Blackboard talks on A*PA:
- CWI Amsterdam: December 2023
- 60 min recording, but unfortunately it does not show the blackboard well.
- UU Utrecht, Applied math seminar: November 2023
Talks on minimizers:
- Johns Hopkins, October 2024:
- 90 min recording on the fast minimizers blog post, ending with a brief overview of progress on low density minimizers.
Guest lectures
I gave numerous guest lectures on A*PA in competitive programming courses. These are mostly blackboard talks with a few supporting videos by running A*PA on some sample data.
- FAU Erlangen: 2023, 2024
- RUG Groningen: September 2022, October 2023
- TU/e Eindhoven: November 2022