I'm Jakob, a biologist-turned-programmer, happy in my role as a research software engineer.
I work as an assistant professor at CPR, Copenhagen University researching metagenomics with particular interest in virus- and plasmid metagenomics. Biologically, my interests are in phylogenetics, molecular evolution and sub-genomic replicons. On the computer science side, I'm a Julia, Rust and Python enthusiast, contributing to BioJulia and Julia. I particularly enjoy writing optimized and generic software packages for bioinformatics.
Selected repositories
- Vamb - variational autoencoders for metagenomic binning
- Course material for introductory Python course
- Alen - simple terminal alignment viewer.
- BinBencherBackend.jl - metagenomic binning benchmarking and analysis software
- LibDeflate.jl - bindings to the fast de/compression library libdeflate
- StackCollections.jl - optimized, fixed-bit collections in Julia
- MinHash.jl - efficient, generic minhashing.
Repositories I maintain