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@BioJulia @ssi-dk

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.

Highlighted work:



  • 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]


  1. Variational autoencoder for metagenomic binning

    Python 43 12

  2. What scientific programmers must know about CPUs and RAM to write fast code.

    Jupyter Notebook 201 19

  3. Fixed-bit collections in Julia

    Julia 9 1

  4. Fast and generic implementation of the minhash algorithm

    Julia 2

  5. Probabilistic data structures in Julia

    Julia 6 1

  6. BGZF codecs for TranscodingStreams.jl


420 contributions in the last year

Dec Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Mon Wed Fri

Contribution activity

November 2020

Created 1 repository

Created a pull request in BioJulia/FASTX.jl that received 1 comment

Fix FASTQ line counting bug

MWE: using FASTX s = join(collect("@A+J@A/J"), '\n') println(collect(FASTQ.Reader(IOBuffer(s)))) Output: ERROR: LoadError: ArgumentError: malformed…

+1 −1 1 comment
Opened 6 other pull requests in 3 repositories
2 open 2 merged
1 open
1 merged

Created an issue in BioJulia/Automa.jl that received 2 comments

Pushdown automata

So @BenJWard recently mentioned it might be a good idea to implement pushdown automata (PDA) in order to broaden in the types of formats that Autom…

Opened 2 other issues in 2 repositories

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