Publications

See also talks & slides below.

Blogposts Link to heading

These might become papers eventually:

  • Pairwise alignment history (thesis chapter, blog)
  • Introduction to minimizers (thesis chapter, blog)
  • Near-optimal small-\(k\) sampling schemes (blog, slides)
  • Simd-Sketch (blog, code)

Preprints Link to heading

SimdQuickHeap: fastest priority queue by 2x (PDF, arXiv, code)
Breitling, Johannes, Ragnar Groot Koerkamp, and Marvin Williams. 2026. “SimdQuickHeap: The QuickHeap Reconsidered.” Arxiv. https://doi.org/10.48550/ARXIV.2604.25681.
Sassy2: batch searching short DNA patterns (PDF, bioRxiv, code)
Beeloo, Rick, and Ragnar Groot Koerkamp. 2026. “Sassy2: Batch Searching of Short DNA Patterns,” March. https://doi.org/10.64898/2026.03.10.710811.
Mim: multi-threaded gzip decompression (PDF, bioRxiv, code)
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.
Deacon: fast record filtering (pending next version, bioRxiv, code)
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.

Accepted Link to heading

Barbell: fast & accurate demultiplexing (Bioinformatics 26, PDF, bioRxiv, code)
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.
Sassy: 10x faster approximate string matching (Bioinformatics 26, PDF, bioRxiv, code)
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.
QuadRank: single-cache-miss rank queries (SEA 26, PDF, arXiv, slides, code)
Groot Koerkamp, Ragnar. 2026. “Quadrank: Engineering a High Throughput Rank.” arXiv. https://doi.org/10.48550/ARXIV.2602.04103.
STPD: a new text index (ICALP 26, PDF, code)
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: Optimal throughput bioinformatics (PDF, posts, slides)
Groot Koerkamp, Ragnar. 2025a. “Optimal Throughput Bioinformatics.” ETH Zurich. https://doi.org/10.3929/ETHZ-C-000783091.
PtrHash: single-cache-miss PHF (SEA 25 best paper, PDF, arXiv, blog, slides, code)
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: text-index for long patterns (SEA 25, PDF, arXiv)
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: 10x faster random minimizers (SEA 25, PDF, bioRxiv, blog, code, talk)
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 (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: for \(k\approx w\) (AMB 25, PDF, bioRxiv, preprint PDF)
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.
Minimizer density lower bound (Bioinformatics 24, PDF, bioRxiv, preprint PDF, blog, slides, code, analysis)
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: scheme for \(k\gg w\) (WABI 24, PDF, bioRxiv, Giulio’s slides, blog, Rust code, C++ code)
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: faster A*PA (WABI 24, PDF, bioRxiv, slides, code)
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: near-linear global alignment (Bioinformatics 24, PDF, bioRxiv, full PDF, slides, code)
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: Stable 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 & posters Link to heading

Further slides Link to heading

  • PhD Defense (slides)
  • Group meeting: minimizer density lower bound (slides)

Seminar talks Link to heading

  • INRIA Rennes (June 2025): SimdSketch
  • A*PA & A*PA2 blackboard talks:
    • CWI Amsterdam (December 2023, 60 min recording)
    • Utrecht University, Applied math seminar (November 2023)
  • Johns Hopkins (October 2024): minimizers (90 min recording)

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

Reviewing Link to heading

Committees:

  • WABI 2026 PC member
  • ISMB 2026 PC member
  • WABI 2025 PC member

Conferences:

  • SEA 2026
  • ESA 2026
  • SPIRE 2025
  • CPM 2025
  • ESA 2025
  • ISMB 2024
  • RECOMB 2023

Journals:

  • Bioinformatics: 2025, 2026
  • Bioinformatics Advances: 2025
  • Algorithms for Molecular Biology: 2026
  • Computing Surveys: 2025
  • Natural Computing

I was/am jury member for various programming contests:

  • BAPC: 2017-2024, head of jury: 2018-2021
  • NWERC: 2019-present, head of jury: 2022-2025

Travel Link to heading

TODO

Education & Professions Link to heading

15/12/2025 - ?
Postdoc at the Algorithm Engineering group at Karlsruhe Institute of Technology.
01/10/2021 - 01/05/2025
PhD at the Biomedical Informatics Lab at ETH Zurich.
Thesis: Optimal Throughput Bioinformatics
Defense: 10/04/2025
01/01/2021 - 01/08/2021
Internship at the Biomedical Informatics Lab at ETH Zurich.
01/10/2017 - 01/05/2020
Software Engineer III at Google Zurich
01/10/2016 - 01/10/2017
MSc. Mathematics and the Foundations of Computer Science at University of Oxford (distinction)
Thesis: On rainbow free colourings of uniform hypergraphs
Grade: 90/100
01/09/2013 - 01/08/2016
BSc. Mathematics at Utrecht University (cum laude)
BSc. Physics at Utrecht University (cum laude)
Minor Computer Science at Utrecht University
Thesis: Calculating the stable gonality of finite graphs (grade 9.5/10)
GPA: 4.0 (Grade 9/10)

Prizes & Awards Link to heading

  • SEA 2025 best paper for PtrHash
  • PACE 2024 challenge 2nd place in parameterized track
  • ICPC 2016 world finals 51st place
  • IMO 2013 bronze medal
  • IMO 2011 honourable mention

Supervision & Mentoring Link to heading

  • František Kmječ, Semester Project, spring 2025:
    Binary search variants and the effects of batching
  • Marcel Pokorski, Bachelor Thesis, fall 2024:
    Accelerating Genomic Alignment: Integrating Mod-Minimizers into Minimap2
  • Bjarni Dagur Thor Kárason, Semester Project, fall 2024:
    Extending A*PA to Affine Costs
  • Yurii Ketkov: Intern summer 2022 to summer 2023
  • Mykola Akulov: Intern summer 2022

Teaching Link to heading

  • Summer 2026: Lecturer for Advanced Data Structures

  • Fall 2024: TA for Big Data

  • Spring 2024: TA for Big Data for Engineers

  • Fall 2022: TA for Algorithms and Data Structures for Population Scale Genomics

  • Summer 2022: TA for Algorithms and Data Structures for Population Scale Genomics

  • 2013-2016: undergrad TA for various courses (what is mathematics, graph theory, discrete mathematics).

Software Link to heading

See software.

Patents Link to heading

  • Accuracy Evaluation Of Automated Speech Transcription Via User Feedback
    Omar Abdelaziz, Justice Ogbonna, Ágoston Weisz, Ragnar Groot Koerkamp, Xinran Lu, Saisuresh Krishnakumaran, Tâmara Baía, Vladimir Vuskovic, Tony Yu
    2020
  • Error Correction in Automatic Speech Recognition
    Ágoston Weisz, Ragnar Groot Koerkamp
    2020