ArticleiScience2022
The role of antigen expression in shaping the repertoire of HLA presented ligands.
Article in iScience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
13 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A meta-analysis of experimentally validated neo-epitopes: patterns, biases, and opportunities.Cancer immunology, immunotherapy : CII · 2025Pooled it
- Cancer epitope prediction tools and analysis pipelines in CEDAR.Nucleic acids research · 2026Article
- Advances in predicting T cell epitope recognition for cancer immunotherapy.Nature cancer · 2026Review
- Integrating biocomputational techniques for vaccine development for glioblastoma multiforme: a possible way of enhancing precision.Frontiers in immunology · 2026Review
- Leveraging mRNA technology for antigen based immuno-oncology therapies.Journal for immunotherapy of cancer · 2025Review
- Towards designing improved cancer immunotherapy targets with a peptide-MHC-I presentation model, HLApollo.Nature communications · 2024Article
- Epstein-Barr virus and immune status imprint the immunogenomics of non-Hodgkin lymphomas occurring in immune-suppressed environments.Haematologica · 2024Article
- A large-scale study of peptide features defining immunogenicity of cancer neo-epitopes.NAR cancer · 2024Article
- VACCIMEL, an allogeneic melanoma vaccine, efficiently triggers T cell immune responses against neoantigens and alloantigens, as well as against tumor-associated antigens.Frontiers in immunology · 2024Article
- IMPROVE: a feature model to predict neoepitope immunogenicity through broad-scale validation of T-cell recognition.Frontiers in immunology · 2024Article
- FASTMAP-a flexible and scalable immunopeptidomics pipeline for HLA- and antigen-specific T-cell epitope mapping based on artificial antigen-presenting cells.Frontiers in immunology · 2024Article
- In Silico Tools for Predicting Novel Epitopes.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Estimating tissue-specific peptide abundance from public RNA-Seq data.Frontiers in genetics · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Human leukocyte antigen (HLA) presentation of peptides is a prerequisite of T cell immune activation. The understanding of the rules defining this event has large implications for our knowledge of basic immunology and for the rational design of immuno-therapeutics and vaccines. Historically, most of the available prediction methods have been solely focused on the information related to antigen processing and presentation. Recent work has, however, demonstrated that method performance can be boosted by integrating information related to antigen abundance. Here we expand on these later findings and develop an extended version of NetMHCpan, called NetMHCpanExp, integrating information on antigen abundance from RNA-Seq experiments. In line with earlier works, the model demonstrates improved performance for both HLA ligand and cancer neoantigen epitope prediction. Optimal results are obtained by use of sample-specific abundance information but also reference datasets can be applied with a limited performance drop. The developed tool is available at https://services.healthtech.dtu.dk/service.php?NetMHCpanExp-1.0.
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Registered trials
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.