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
- A*PA & A*PA2 slide deck
- Minimizers
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