Publications

PtrHash preprint (PDF): Groot Koerkamp, Ragnar. 2025. “Ptrhash: Minimal Perfect Hashing at RAM Throughput.” arXiv. https://doi.org/10.48550/arXiv.2502.15539.
U-index preprint (PDF): Ayad, Lorraine A. K., Gabriele Fici, Ragnar Groot Koerkamp, Grigorios Loukides, Rob Patro, Giulio Ermanno Pibiri, and Solon P. Pissis. 2025. “U-Index: A Universal Indexing Framework for Matching Long Patterns.” arXiv. https://doi.org/10.48550/arXiv.2502.14488.
Simd-minimizers preprint (PDF): Groot Koerkamp, Ragnar, and Igor Martayan. 2025. “SimdMinimizers: Computing Random Minimizers, Fast,” January. https://doi.org/10.1101/2025.01.27.634998.
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 (PDF, bioRxiv, preprint PDF+supplements): Groot Koerkamp, Ragnar, Daniel Liu, and Giulio Ermanno Pibiri. 2025. “The Open-Closed Mod-Minimizer Algorithm.” Algorithms for Molecular Biology 20 (4). https://doi.org/10.1186/s13015-025-00270-0.
Forward sampling scheme density lower bound (PDF, bioRxiv, preprint PDF+supplements): Kille, Bryce, Ragnar Groot Koerkamp, Drake McAdams, Alan Liu, and Todd J Treangen. 2024. “A near-tight Lower Bound on the Density of Forward Sampling Schemes.” Edited by Yann Ponty. Bioinformatics, December. https://doi.org/10.1093/bioinformatics/btae736.
Mod-minimizer (PDF, bioRxiv): Groot Koerkamp, Ragnar, and Giulio Ermanno Pibiri. 2024. “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.
A*PA2 (PDF, bioRxiv): Groot Koerkamp, Ragnar. 2024. “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*PA (PDF, bioRxiv, full PDF+supplements): 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.
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.