klmr.me

About me

Hi. My name is Konrad.

I’m a postdoctoral researcher in Eric Miska’s group at the Gurdon Institute (University of Cambridge). Before that, I worked with John Marioni at the European Bioinformatics Institute (EMBL-EBI). I analyse genomic data to answer biological questions.

Here are some of the things I’ve been up to:

Research

My current work is on the regulation of translation in mammals through changes in tRNA abundance and codon usage. I am also looking at the extended polymerase III transcriptome, in particular SINEs. My PhD thesis was titled “Investigating the link between tRNA and mRNA abundance in mammals”.

Before this, 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.

Hacking

I’m the developer of ‹modules›, an alternative R code modularisation system. It replaces conventional R packages and fixes some of its flaws. The mechanism is borrowed from Python packages and JavaScript modules.

I developed the first version of the LaTeX package ‹minted›, which provides code pretty-printing by wrapping Pygments.

I strive to make development with C++ less painful by showcasing the use of clean, high-level code over low-level constructs. C++11 has made this immensely easier.

Teaching

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

  • High-throughput sequencing with focus on RNA-seq & ChIP-seq (University of Cambridge)
  • Computer science 101/102 (Freie Universität Berlin)
  • Algorithms in bioinformatics (Freie Universität Berlin)
  • Database systems (Freie Universität Berlin)
  • C++ (Freie Universität Berlin)
  • VB (ActiveVB workshop)
  • Unix/Bash (EMBL workshop)
  • LaTeX (EMBL workshop)
  • R (EMBL workshop)
  • Git (EMBL workshop)

Selected publications

* indicates joint first authors

For more, see my Google Scholar profile.

CV

You can download my CV, or view the source code.

Online

You can follow my activity online: