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BioNumPy is a fast Python library for the analysis of biological sequence data, be sure to check it out: biorxiv.org/content/10.110…

Every day this week, we'll share a small example of how BioNumPy can be used. First out: FASTQ filtering (try out the code yourself here: colab.research.google.com/github/bionump…) .. and remember to follow us for daily updates ☺️

Day 2/5 of small BioNumPy examples: Motif matching. We download a motif from Jaspar, compute max motif score per read in a FASTQ file and plot a histogram of the scores. Run the code here: colab.research.google.com/github/bionump…

Day 4 of small #BioNumPy examples: Sequence matching (searching for a sequence in a set of reads). Try out the code here: colab.research.google.com/github/bionump…

Day 5/5 of short BioNumPy examples: Finding the most common kmers in a FASTQ-file. Try out the code here: colab.research.google.com/github/bionump… Check out our documentation for more cool examples: bionumpy.github.io/bionumpy🤠

A 4-year PhD fellowship in Informatics/Bioinformatics is available at Centre for Bioinformatics, University of Oslo as part of @UiO_LifeSci. The projects will focus on synthetic data generation, applied machine learning and benchmarking within molecular life sciences: jobbnorge.no/en/available-j…. Please RT.

BioNumPy has been updated with changes that make it a lot easier to work with genomic intervals and data on a reference genome 😀 Here are a few cool examples to illustrate the new stuff:

TCR people: you may be interested to know that my tool stitchr (for making full length coding sequences from V/J/CDR3 info) is now on PyPI, so you can install it and not have to faff with files and folders so much github.com/JamieHeather/s…

Happy to announce an open PhD position in a collaboration between Bjoern Peter's group and mine (simula.no/about/job/6-ph…). And I can for sure not present this opportunity as well as Lonneke, who has experienced this great PhD program herself:)

1/8 New preprint: generative modeling of AIRR repertoires, the last piece of my PhD, >2 years of work, a project that is very dear to me biorxiv.org/content/10.110…

(1/8)🎉A fresh preprint in which we present LIgO — a powerful tool to simulate adaptive immune receptor (AIR) and repertoire (AIRR) data for the development and benchmarking of AIRR-based ML 🧵⬇️ biorxiv.org/content/10.110…

Postdoc position available in my group! You will be working with breast cancer data (bulk and single-cell) to model regulatory rewiring in breast cancer metastasis. This is a 3y position funded through the Norwegian Cancer Society. More info: jobbnorge.no/en/available-j…

KAGE2 is out! Enables very fast and accurate genotyping of structural variants using pangenomes: biorxiv.org/content/10.110…. I’ve spent the last 6+ months going deep into the SV rabbit hole, and had some surprises I thought it’s worth to also share (1/6)

Are you developing new machine learning methods for immune receptor/repertoire data? You can save yourself a lot of time by developing your method inside immuneML. Read all about it in our updated documentation: docs.immuneml.uio.no/latest/develop… (1/3)

Our paper on the linguistics-based formalization of antibody language is out in Nature Computational Science. Work led by Mai Ha Rahmad Akbar and Philippe A. Robert . Summary thread: x.com/PRobertImmodel….

BioNumPy: array programming for biology Nature Methods • BioNumPy revolutionizes biological data analysis by integrating the power of NumPy-like arrays, making Python even more accessible to bioinformaticians. • It enables direct handling of biological formats (like FASTQ,

Finally biologists can also use numpy (array programming). Handling e.g. DNA and protein sequences with convenience and speed, like physicists and machine learners for decades have worked with numerical data: nature.com/articles/s4159… (1/3)