Publications

Reverse chronological list of publications

PACE24 one-sided crossing minimization solver OCMu64 (PDF)
Groot Koerkamp, Ragnar, and Mees de Vries. 2024. “Pace Solver Description: Ocmu64, a Solver for One-Sided Crossing Minimization.” Schloss Dagstuhl – Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.IPEC.2024.35.
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

Recorded seminar talks

Blackboard talks on A*PA:

  • CWI Amsterdam: December 2023
  • UU Utrecht, Applied math seminar: November 2023

Talks on 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