Our perspective on adapting LMs for protein sequences with the help of linguistic knowledge is now out in Nature Machine Intelligence. Led by Mai Ha, 🧍‍♂️ and Philippe A. Robert. Great collboration with Bartlomiej Swiatczak, Geir Kjetil Sandve and Dag Haug. nature.com/articles/s4225…

This project can also be a fun way to learn snakemake, plotting, Python, github actions, etc for anyone interested, e.g. fresh phd students Check out the github repo for more info, and free free to send me an email or DM if there are questions 😊 github.com/bioinf-benchma…

RSG-Norway in collaboration with Centre for Bioinformatics, University of Oslo is inviting you to a panel discussion: "Is DNA agile? Software engineering challenges in bioinformatics", which will happen on May 11th 17:30 CET at Ole-Johan Dahls hus, Smalltalk auditorium. Register at forms.gle/cr9WMLu6qmJTgD…

The next AIRR-C Seminar is on May 25, 16:00 CET, with Geir Kjetil Sandve (topic: deciphering the rules of immune receptor-antigen binding) and Thomas Konstantinovsky (topic: merging compression theory and immunology). Talk and registration info are here: antibodysociety.org/the-airr-commu…

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…

Do you want to model gene regulatory or co-expression networks based on large-scale heterogeneous data, such as data derived from different tissues or cancer types? Have a look at our new normalization method SNAIL 🐌, now out in Bioinformatics 👇: academic.oup.com/bioinformatics…

(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…

It's not often a new method ends up being both faster and more accurate than existing methods, so I believe KAGE2 by @IvarGrtytten and @knutrand (powered by BioNumPy) will be a great addition to the toolboxes of structural variant discovery researchers  biorxiv.org/content/10.110…

It took us some time to chew on this, and a bunch of (intriguing) nuances came up as we dug deeper, but I think it landed as a quite accessible and useful overview of concerns and opportunities connected to causality and study design for biomarkers! (with AIRR as case)

Tissue proteomics with clinical value in #celiac disease: - bitly.ws/3fGa2 Great work Anette Johansen and thank you collaborators in particular Geir Kjetil Sandve for expert ML knowledge! Celiac Disease Foundation UiO - Det medisinske fakultet Coeliac_UK Gastroenterology NorskCøliakiforening

One more baby is out! A perspective led by Mai Ha bring a salt of linguistic in the soup of biological sequence ML models! She describes how antibody sequences of different specificities may form a language, which has implications on the design of future LLM models.

Very happy to announce that our perspective is finally out in Nature Comp. Sci! Many thanks to Mat Akbar, Philippe A. Robert, Bartlomiej Swiatczak, Geir Kjetil Sandve, Dag Haug, and GreiffLab 💻🔬💊 for the fantastic work.

Our biophysical cartography of native and human-engineered antibody landscapes is out: nature.com/articles/s4200…. Study led by Habib Bashour Eva Smorodina Jahn Zhong e/🧬 Matteo Pariset. Great collab with Adaptyv Bio naturalantibody Geir Kjetil Sandve JTA Andersen.

NEWS: @unioslo's Titan magazine published an in-depth article about DHIS2's Wellcome-funded Climate & Health work (in Norwegian), featuring colleagues Geir Kjetil Sandve, Zeferino Saugene & Patrick Omiel Okecho. Read more: buff.ly/3yHo4Cb @Saudigitus @HISP_Uganda

This morning, Minister of State Yvan Butera launched the Kigali Hub for Spatial & Spatio-Temporal Modelling in Africa — a new go-to center for climate-health modelling, smarter policy, and regional teamwork. The launch wrapped up the 2nd Conference on Spatial Modelling in Africa.