Author

Jonas Birkelund Nilsson

Technical University of DenmarkORCID 0000-0002-1322-2644Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 3

Signature Assays, Organisms & Methods

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Research Focus:gene regulatory network inference· 2 Organism:human· 2 Approach:statistical model· 2 Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1 Research Focus:cell-cell communication· 1 Research Focus:differential expression· 1 Approach:machine learning (classical)· 1

Frequent Co-Authors

Morten NielseniD· 3 shared Bjoern PetersiD· 2 shared Amalie Kai BentzeniD· 1 shared Aurélien PélissieriD· 1 shared Binbin CheniD· 1 shared Brian G. PierceiD· 1 shared Carolina BarraiD· 1 shared Chengkai Xiao· 1 shared

Activity by Year

2023-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 31 mutual co-author links

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3 shared papersBioinformatics

Morten NielsenORCID

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3 papers

Recent·Most cited

BioinformaticsbioRxivPreprintApr 1, 2026

IMMREP25: Unseen Peptides

Eve Richardson, Yannick Jurriaan Maria Aarts, John A. Altin…·Bjoern Peters

IMMREP25 evaluates TCR:pMHC binding prediction for unseen peptides, showing improved performance with structural modeling but still below random guessing.

12 citations

statistical modelbenchmarking

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BioinformaticsbioRxivPreprintDec 23, 2025

ITRAP2, a flexible and robust strategy to assign antigen recognition of T-cells in a coupled single-cell TCR-pMHC assay

Grigorii Nos, Amalie Kai Bentzen, Marie Christine Viuff…·Sine Reker Hadrup

ITRAP2 improves TCR-pMHC pairing accuracy by reducing noise and cross-contamination in single-cell data, outperforming existing methods on both in-house and public datasets.

4 citations

humanscRNA-seq

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BioinformaticsCommunications BiologyPeer-reviewedApr 21, 2023

Machine learning reveals limited contribution of trans-only encoded variants to the HLA-DQ immunopeptidome by accurate and comprehensive HLA-DQ antigen presentation prediction

Jonas Birkelund Nilsson, Saghar Kaabinejadian, Hooman Yari…·Morten Nielsen

The paper improves HLA-DQ antigen presentation prediction using machine learning and shows trans-only variants have limited impact on the immunopeptidome.

55 citationstop 3%

humanproteomics

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