Ragnar {Groot Koerkamp}

High Throughput Bioinformatics @ KIT Karlsruhe

I write about bioinformatics: pairwise alignment , minimizers , HPC , and data structures .

See my publications and talks, software, project overviews, and all posts.

Popular

December 2024 Static search trees: 40x faster than binary search
results walkthrough hpc binary-search popular data-structure
January 2024 One Billion Row Challenge
lablog hpc popular

Recent

January 2026 Recent results on hash tables
survey data-structure
January 2026 CI for Rust testing and releasing
devops rust highlight
January 2026 Trying to understand DDR memory
lablog hpc linux highlight
January 2026 Quotes from "The Evolution of Mathematical Software"
paper-review quote hpc data-movement

Highlights

January 2026 CI for Rust testing and releasing
devops rust highlight
January 2026 Trying to understand DDR memory
lablog hpc linux highlight
December 2025 Asymptotic elevators
misc physics highlight
December 2025 Overview of static data structures
survey data-structure mphf highlight
August 2025 Three log scientist
proposition highlight
March 2025 Beyond Global Alignment
thesis pairwise-alignment highlight
March 2025 SimdSketch: a fast bucket sketch
results survey sketching hpc software highlight
February 2025 Thesis: Optimal Throughput Bioinformatics
thesis highlight
February 2025 A History of Pairwise Alignment
thesis survey pairwise-alignment highlight
February 2025 Low Density Minimizers
thesis survey minimizers highlight
February 2025 High Throughput Bioinformatics
thesis hpc highlight
February 2025 PtrHash: Minimal Perfect Hashing at RAM Throughput
paper highlight mphf data-structure software
July 2024 SimdMinimizers: Computing random minimizers, fast
results walkthrough highlight hpc minimizers nthash software
June 2024 CPU performance
highlight hpc wip
March 2024 A*PA2: Up to 19x faster exact global alignment
paper highlight pairwise-alignment astar hpc software
November 2022 String algorithm visualizations
ideas highlight suffix-array visualization data-structure
May 2021 28000x speedup with Numba.CUDA
results walkthrough highlight hpc