klmr.me

About me

Hi. 👋 My name is Konrad.

I’m a senior research engineer and software developer at PetaGene.

In my previous life I was a postdoctoral researcher in Eric Miska’s group at the University of Cambridge (Gurdon Institute). My PhD was supervised by John Marioni at the European Bioinformatics Institute (EMBL-EBI).

Here are some of the things I do:

Research

I do most of my research on genomics and the regulation of translation in mammals through changes in tRNA abundance and codon usage. The title of my PhD thesis was “Investigating the link between tRNA and mRNA abundance in mammals”.

Before that, I’ve worked in algorithms and software development, in particular implementing high-throughput sequencing read mapping tools, and creating frameworks for the automatic parallelisation of high-performance code on multicore architecture. I have also done work in cell regulatory networks.

Open Source projects

Some of my most widely used projects are

To see more of my contributions to Open Source projects, visit my GitHub profile.

Teaching

I have, at various times, taught on the following subjects:

  • High-throughput sequence analysis
  • CS 101 & CS 102
  • Algorithms in bioinformatics
  • Database systems & SQL
  • C++ · VB · Unix/Bash · LaTeX · R · Git
  • Basics of data compression

I’m also occasionally active on Stack Overflow, where I’m one of the 0.01% most active contributors of all time, although in recent years I have massively reduced my activity (for a brief moment in 2009 I was #1, but that turns out to have been a miscalculation due to a bug in the Stack Overflow software).

Selected publications

For more, see my Google Scholar profile. * indicates joint first authors

CV

You can find my more or less up-to-date CV as a Developer Story on Stack Overflow.