Lonneke Scheffer, PhD🧬💻
@LonnekeScheffer
Postdoctoral researcher @ La Jolla Institute for Immunology ~ Computational Immunology ~ Developer of @immuneml
In preparation for #AAI #immunology2025 I’ve designed these super cute labels for #mAcademia nuts - thanks Peters lab for helping out with the labelling! Visit booths #535 & #537 to get your hands on them & learn more about @iedb_ @CEDAR_epitopes @hipcProject @AIRR_Knowledge
the immuneML documentation has gotten an update :) better documentation for new developers, and a cleaner look!
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)
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)
UPDATED: We have identified 492 funding opportunities for early-career researchers/faculty. Download for free the database here: research.jhu.edu/rdt/funding-op… For each entry, we provide description, deadline, $ amount, eligibility, link to funder.
Predictability of antigen binding based on short motifs in the antibody CDRH3 @BriefingBioinfo • This study demonstrates that short motifs in the antibody CDRH3 region can be predictive of antigen binding, addressing a key question in adaptive immunology. • Researchers…
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)
Our perspective on the generalization of machine learning-identified biomarkers is now published in @NatMachIntell 🎉 nature.com/articles/s4225…
(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…
A 2-year postdoc position is available at @unioslo_bioinfo to contribute to the European project @EOSC4Cancer, specifically for advancing cancer data analysis platforms. Job announcement: jobbnorge.no/en/available-j… Please RT and circulate to relevant candidates.