Publications

Chronological list of publications

Mod-minimizer preprint
Groot Koerkamp, Ragnar, and Giulio Ermanno Pibiri. 2024. “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 preprint
Groot Koerkamp, Ragnar. 2024. “A*PA2: Up to 20 Times Faster Exact Global Alignment,” March. https://doi.org/10.1101/2024.03.24.586481.
A*PA
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
  • 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

Seminar talks

Blackboard talks on A*PA:

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

Guest lectures

I gave numerous guest lectures on A*PA in competitive programming courses. These are mostly blackboard talks with a view 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