About

Hi there ;) I’m doing a PhD in bioinformatics at the BMI lab at ETH Zurich. I’m working on near-linear algorithms for exact pairwise alignment, low-density minimizer schemes, and generally on high throughput bioinformatics software.

This blog is where I dump my thoughts on my PhD research. It includes numerous short notes/remarks/ideas for research, and a few longer posts, some of which may turn into papers.

Feel free to use this blog as inspiration and build on the ideas you see here, as long as you cite appropriately.

If you spot mistakes or have suggestions for improvement, comment at the bottom of each page or make an issue on the GitHub source for this blog.

Trivia (i.e. i18n)

My first name is Ragnar. My last name is Groot Koerkamp. Yes, that has a space. No, you cannot get away with Groot, and no, you cannot say Koerkamp.

Don’t even try to say Ragnar G. Koerkamp. In fact, my middle name starts with a G, so you’d have to write R. G. Groot Koerkamp, or Groot Koerkamp, R. G.. To not complicate things more than they already are, use one of the following for purposes of publishing and citing:

  • R. Groot Koerkamp,
  • Ragnar Groot Koerkamp,
  • Groot Koerkamp, Ragnar,
  • Groot Koerkamp, R.,
  • Groot Koerkamp, Ragnar or Ragnar {Groot Koerkamp} (but not Ragnar Groot Koerkamp) in BibTeX files.

Note that not all BibTex exports get this right. In particular, Arxiv does not support my name, and downloading BibTex entries (derived) from it may give wrong results.

CV highlights

  • IMO 2011: Honourable mention

  • IMO 2013: Bronze medal

  • ICPC world finals 2016: 51st place

  • At some point I solved all ~700 Project Euler problems at the time.

  • Won the parameterized track of the 2024 PACE challenge.

  • 2013-2016: double bachelors Mathematics and Physics @ Utrecht University

  • 2016-2017: masters Mathematics and the Foundations of Computer Science @ University of Oxford

  • 2017-2020: Software engineer @ Google Zurich

  • 2021-2024: PhD bioinformatics @ ETH Zurich

Services

Committees

I am jury member for various programming contests:

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

Reviewing

I have reviewed for:

  • Bioinformatics
  • Bioinformatics Advances

Teaching

  • 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