Publications

See also talks & slides below.

Preprints Link to heading

Mim (PDF)
Patro, Rob, Siddhant Bharti, Prajwal Singhania, Rakrish Dhakal, Thomas J. Dahlstrom, and Ragnar Groot Koerkamp. 2025. “Mim: A Lightweight Auxiliary Index to Enable Fast, Parallel, Gzipped Fastq Parsing,” November. https://doi.org/10.1101/2025.11.24.690271.
Barbell (PDF)
Beeloo, Rick, Ragnar Groot Koerkamp, Xiu Jia, Marian J. Broekhuizen-Stins, Lieke van IJken, Els M. Broens, Aldert Zomer, and Bas E. Dutilh. 2025. “Barbell Resolves Demultiplexing and Trimming Issues in Nanopore Data,” October. https://doi.org/10.1101/2025.10.22.683865.
Deacon (pending next version)
Constantinides, Bede, John Lees, and Derrick W Crook. 2025. “Deacon: Fast Sequence Filtering and Contaminant Depletion,” June. https://doi.org/10.1101/2025.06.09.658732.
Sassy (PDF)
Beeloo, Rick, and Ragnar Groot Koerkamp. 2025. “Sassy: Searching Short DNA Strings in the 2020s,” July. https://doi.org/10.1101/2025.07.22.666207.
STPD (PDF)
Becker, Ruben, Davide Cenzato, Travis Gagie, Ragnar Groot Koerkamp, Sung-Hwan Kim, Giovanni Manzini, and Nicola Prezza. 2025. “Compressing Suffix Trees by Path Decompositions.” arXiv; arXiv. https://doi.org/10.48550/ARXIV.2506.14734.

Published Link to heading

PhD thesis (PDF)
Groot Koerkamp, Ragnar. 2025a. “Optimal Throughput Bioinformatics.” ETH Zurich. https://doi.org/10.3929/ETHZ-C-000783091.
PtrHash (SEA 25 best paper, PDF)
Groot Koerkamp, Ragnar. 2025b. “PtrHash: Minimal Perfect Hashing at RAM Throughput.” In SEA 2025, 338:21:1–21:21. Lipics. https://doi.org/10.4230/LIPIcs.SEA.2025.21.
U-index (SEA 25, 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.” In SEA 2025, 338:4:1–4:18. Lipics. https://doi.org/10.4230/LIPIcs.SEA.2025.4.
SimdMinimizers (SEA 25, PDF)
Groot Koerkamp, Ragnar, and Igor Martayan. 2025. “SimdMinimizers: Computing Random Minimizers, fast.” In SEA 2025, 338:20:1–20:19. Lipics. https://doi.org/10.4230/LIPIcs.SEA.2025.20.
PACE24 one-sided crossing minimization solver OCMu64 (IPEC 24, PDF)
Groot Koerkamp, Ragnar, and Mees de Vries. 2024. “PACE Solver Description: OCMu64, a Solver for One-Sided Crossing Minimization.” In Ipec. https://doi.org/10.4230/LIPICS.IPEC.2024.35.
Open-closed mod-minimizer (AMB 25, 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 (Bioinformatics 24, 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 (WABI 24, PDF, bioRxiv)
Groot Koerkamp, Ragnar, and Giulio Ermanno Pibiri. 2024. “The Mod-Minimizer: A Simple and Efficient Sampling Algorithm for Long $k$-Mers.” In Wabi 2024, 312:11:1–11:23. Lipics. https://doi.org/10.4230/LIPIcs.WABI.2024.11.
A*PA2 (WABI 24, PDF, bioRxiv)
Groot Koerkamp, Ragnar. 2024. “A*PA2: Up to 19 Faster Exact Global Alignment.” In Wabi 2024, 312:17:1–17:25. Lipics. https://doi.org/10.4230/LIPIcs.WABI.2024.17.
A*PA (Bioinformatics 24, 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.

Talks Link to heading

Conference talks Link to heading

  • P99 2025: 40x faster binary search, slides, recording (reveal-js)
  • SEA 2025: PtrHash (best paper), slides (reveal-js)
  • DSB 2025: Near-optimal sampling schemes, slides (reveal-js)
  • WABI 2024: Mod-minimizer, slides (pdf)
  • WABI 2024: A*PA2
  • MemPanG 2024: A*PA2
  • RECOMB-SEQ 2024: A*PA & A*PA2,
  • IGGSY 2024: A*PA2
  • IGGSY 2022: A*PA, slides (google slides)

Recorded seminar talks Link to heading

Blackboard talks on A*PA:

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

Talks on minimizers:

Guest lectures Link to heading

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