ArticleCommunications biology2023
Machine learning reveals limited contribution of trans-only encoded variants to the HLA-DQ immunopeptidome.
Article in Communications biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 45 citations in OpenAlex.
- Current landscape and future directions of neoantigen vaccines: A new era of personalized cancer immunotherapy.Innovation (Cambridge (Mass.)) · 2026Review
- Molecular Mimicry by the Tick-Borne Encephalitis Virus E Protein: A Hidden Link to Autoimmunity.International journal of molecular sciences · 2026Article
- NetMHCIIphosPan: A Machine Learning Tool for Predicting HLA Class II Antigen Presentation of Phosphorylated Peptides.Journal of proteome research · 2026Article
- AI-driven computational methods and benchmarking for T-cell antigen identification.Briefings in bioinformatics · 2026Review
- T cell receptor clonotypes predict human leukocyte antigen allele carriage and antigen exposure history.Communications biology · 2026Article
- NetMHCIIphosPan: a machine learning tool for predicting HLA class II antigen presentation of phosphorylated peptides.bioRxiv : the preprint server for biology · 2026Article
- Classical HLA class II associations with ALS in Kuwait reveal a DR7-DQ2.2 risk haplotype.Frontiers in immunology · 2026Article
- From immunoinformatics insights to assay development: establishment of a peptide-based indirect elisa for cynomolgus tuberculosis detection.Frontiers in cellular and infection microbiology · 2026Article
- Review: application and opportunities for machine learning and artificial intelligence in preclinical immunogenicity risk assessment.Frontiers in immunology · 2026Review
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- SARS-CoV-2 Spike Protein and Molecular Mimicry: An Immunoinformatic Screen for Cross-Reactive Autoantigen Candidates.International journal of molecular sciences · 2025Article
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- HLAIIPred: cross-attention mechanism for modeling the interaction of HLA class II molecules with peptides.Communications biology · 2025Article
- Computation strategies and clinical applications in neoantigen discovery towards precision cancer immunotherapy.Biomarker research · 2025Review
- Identifying T cell antigen at the atomic level with graph convolutional network.Nature communications · 2025Article
- Transcript-targeted antigen mapping reveals the potential of POSTN splicing junction epitopes in glioblastoma immunotherapy.Genes and immunity · 2025Article
- Pan-Variant SARS-CoV-2 Vaccines Induce Protective Immunity by Targeting Conserved Epitopes.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- The Impact of HLA-DQαβ Heterodimer Mismatch on Living Donor Kidney Allograft Outcomes.Transplantation · 2025Article
- Donor HLA-DQ genetic and functional divergence affect the control of BK polyoma virus infection after kidney transplantation.Science advances · 2025Article
- A multi-epitope vaccine incorporating adhesin-derived antigens protects againstFrontiers in immunology · 2025Article
Corrections and comments
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Authors and funding
8 authors at 5 institutions in 2 countries.
Funding
Abstract
Human leukocyte antigen (HLA) class II antigen presentation is key for controlling and triggering T cell immune responses. HLA-DQ molecules, which are believed to play a major role in autoimmune diseases, are heterodimers that can be formed as both cis and trans variants depending on whether the α- and β-chains are encoded on the same (cis) or opposite (trans) chromosomes. So far, limited progress has been made for predicting HLA-DQ antigen presentation. In addition, the contribution of trans-only variants (i.e. variants not observed in the population as cis) in shaping the HLA-DQ immunopeptidome remains largely unresolved. Here, we seek to address these issues by integrating state-of-the-art immunoinformatics data mining models with large volumes of high-quality HLA-DQ specific mass spectrometry immunopeptidomics data. The analysis demonstrates highly improved predictive power and molecular coverage for models trained including these novel HLA-DQ data. More importantly, investigating the role of trans-only HLA-DQ variants reveals a limited to no contribution to the overall HLA-DQ immunopeptidome. In conclusion, this study furthers our understanding of HLA-DQ specificities and casts light on the relative role of cis versus trans-only HLA-DQ variants in the HLA class II antigen presentation space. The developed method, NetMHCIIpan-4.2, is available at https://services.healthtech.dtu.dk/services/NetMHCIIpan-4.2 .
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.