1 Abstract
2 Introduction
Summary.
2.1 Objectives
2.2 Challenges
2.3 List of papers
Pairwise alignment.
A*PA, Bioinformatics 24.
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*PA2, WABI24.
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.
Minimizers.
Mod-minimizer, WABI24.
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.
Open-closed mod-minimizer, AMB 25.
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.
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.
High throughput bioinformatics.
TODO SimdMinimizers, submitted to SEA25.
Groot Koerkamp, Ragnar, and Igor Martayan. 2025. “SimdMinimizers: Computing Random Minimizers, Fast,” January. https://doi.org/10.1101/2025.01.27.634998.
TODO PtrHash, submitted to SEA25.
Groot Koerkamp, Ragnar. 2025. “Ptrhash: Minimal Perfect Hashing at RAM Throughput.” arXiv. https://doi.org/10.48550/arXiv.2502.15539.
Additional papers, not covered in this thesis.
U-index, submitted to SEA25.
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.
Sketching, Genome Research 23.
Joudaki, Amir, Alexandru Meterez, Harun Mustafa, Ragnar Groot Koerkamp, André Kahles, and Gunnar Rätsch. 2023. “Aligning Distant Sequences to Graphs Using Long Seed Sketches.” Genome Research, April. https://doi.org/10.1101/gr.277659.123.
2.4 Thesis structure and contributions
Pairwise alignment.
- A*PA
Minimizers.
High throughput bioinformatics.
2.5 Personal note
3 Discussion and conclusion
Summary.