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@BioJulia @ssi-dk
jakobnissen/README.md

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:

Blogposts

Packages

  • 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]

Pinned

  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

    Julia

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
BioJulia/Automa.jl
2 open 2 merged
BioJulia/FASTX.jl
1 open
superwhiskers/question
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…

2 comments
Opened 2 other issues in 2 repositories

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