Welcome to my GitHub page
I'm Jakob, a biologist-turned-programmer, happy in my role as a research software engineer.
I've done my PhD in metagenomic binning, and now do a post doc at Statens Serum Institut (Danish CDC) researching the zoonotic and pandemic potential of influenza virus. Biologically, my interests are in phylogenetics (wished I knew more about it!), molecular evolution and microbial genomics. On the computer science side, I'm a Julia and Python enthusiast, contributing to BioJulia and Julia. I particularly enjoy writing optimized and generic software packages for bioinformatics.
- What scientists must know about hardware to write fast code
- On the performance and design of BioSequences compared to the Seq language
- An introduction to writing machine-generated parsers with Automa.jl
- Vamb - variational autoencoders for metagenomic binning
- StackCollections.jl - optimized, fixed-bit collections in Julia
- MinHash.jl - efficient, generic minhashing.
- LibDeflate.jl - bindings to the fast de/compression library libdeflate
- CodecBGZF - read and write BGZF files
- [In progress - Probably.jl - generic, probabilistic data structures]
- [In progress - Kash.jl - efficient k-mer minhashing in Julia]