CV

Name: Groot Koerkamp, Ragnar

Education & Professions Link to heading

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 - 01/09/2021
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)

Publications Link to heading

Includes papers, preprints, and blog posts.

PhD thesis (PDF)
Groot Koerkamp, Ragnar. 2025a. “Optimal Throughput Bioinformatics.” ETH Zurich. https://doi.org/10.3929/ETHZ-C-000783091.
Sassy (preprint, 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 (preprint, 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.
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.
40x faster binary search (blog)
Groot Koerkamp, Ragnar. 2024c. “Static Search Trees: $40\times$ Faster than Binary Search.” https://curiouscoding.nl/posts/static-search-tree/.
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. 2024a. “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.
1BRC (blog)
Groot Koerkamp, Ragnar. 2024b. “1 Billion Row Challenge.” https://curiouscoding.nl/posts/1brc/.
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.

Software Link to heading

Talks Link to heading

Conference talks:

  • SEA 2025: PtrHash
  • DSB 2025: near-optimal sampling schemes
  • WABI 2024: A*PA2
  • MemPanG 2024: A*PA2
  • RECOMB-SEQ 2024: A*PA & A*PA2
  • IGGSY 2024: A*PA2
  • IGGSY 2022: A*PA

Seminar talks:

  • INRIA Rennes (June 2024): SimdSketch
  • Johns hopkins (Oct 2024): Minimizers
  • CWI Amsterdam (Dec 2023): A*PA & A*PA2
  • Utrecht University, Applied math seminar (Nov 2023): A*PA & A*PA2

Guest lectures on pairwise alignment:

  • FAU Erlanen: 2022, 2023
  • RUG Groningen: 2022, 2023
  • TU/e Eindhoven: 2022

Committees Link to heading

  • WABI 2025 PC

Further conferences & journals I have reviewed for:

  • SPIRE 2025
  • CPM 2025
  • ESA 2025
  • ISMB 2024
  • Recomb 2023
  • Bioinformatics Advances
  • Bioinformatics
  • Computing Surveys
  • 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

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

  • 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

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