ArticleCell systems2020
Computationally Optimized SARS-CoV-2 MHC Class I and II Vaccine Formulations Predicted to Target Human Haplotype Distributions.
Article in Cell systems, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
36 citing papers in PubMed, 76 citations in OpenAlex.
- A targetable dependency on nonsense-mediated decay for cellular homeostasis and immune control in small cell lung cancer.Molecular cancer · 2026Article
- A computational method to design broad-spectrum T cell-inducing vaccines applied to Betacoronaviruses.Cell reports methods · 2026Article
- Benchmarking sequence-based and AlphaFold-based methods for pMHC-II binding core prediction: distinct strengths and consensus approaches.BMC medical genomics · 2026Article
- Artificial intelligence for coordinating vaccine design, antiviral discovery, and real-world monitoring in the era of emerging and endemic viral threats.Frontiers in pharmacology · 2026Review
- Mapping the landscape of AI and ML in vaccine innovation: A bibliometric study.Human vaccines & immunotherapeutics · 2025Article
- Immunopeptidomics can inform the design of mRNA vaccines for the delivery ofScience translational medicine · 2025Article
- Article
- Developing T Cell Epitope-Based Vaccines Against Infection: Challenging but Worthwhile.Vaccines · 2025Review
- Molecular modeling to design a multiepitope vaccine against emerging tick-borne Yezo virus and its validation through biophysics techniques.In silico pharmacology · 2025Article
- Review
- Graph-pMHC: graph neural network approach to MHC class II peptide presentation and antibody immunogenicity.Briefings in bioinformatics · 2024Article
- Immune Epitopes of SARS-CoV-2 Spike Protein and Considerations for Universal Vaccine Development.ImmunoHorizons · 2024Review
- Immune Epitopes of SARS-CoV-2 Spike Protein and Considerations for Universal Vaccine Development.bioRxiv : the preprint server for biology · 2023Article
- Strategies and Trends in COVID-19 Vaccination Delivery: What We Learn and What We May Use for the Future.Vaccines · 2023Article
- A pan-variant mRNA-LNP T cell vaccine protects HLA transgenic mice from mortality after infection with SARS-CoV-2 Beta.Frontiers in immunology · 2023Article
- Design and preclinical evaluation of a universal SARS-CoV-2 mRNA vaccine.Frontiers in immunology · 2023Article
- On the peptide binding affinity changes in population-specific HLA repertoires to the SARS-CoV-2 variants Delta and Omicron.Journal of autoimmunity · 2022Article
- A high-throughput yeast display approach to profile pathogen proteomes for MHC-II binding.eLife · 2022Article
- Computationally validated SARS-CoV-2 CTL and HTL Multi-Patch vaccines, designed by reverse epitomics approach, show potential to cover large ethnically distributed human population worldwide.Journal of biomolecular structure & dynamics · 2022Article
- Single Nucleotide Polymorphisms in the Human Leukocyte Antigen Region Are Associated With Hemagglutination Inhibition Antibody Response to Influenza Vaccine.Frontiers in genetics · 2022Article
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Authors and funding
7 authors at 4 institutions in 1 country.
Funding
Abstract
We present a combinatorial machine learning method to evaluate and optimize peptide vaccine formulations for SARS-CoV-2. Our approach optimizes the presentation likelihood of a diverse set of vaccine peptides conditioned on a target human-population HLA haplotype distribution and expected epitope drift. Our proposed SARS-CoV-2 MHC class I vaccine formulations provide 93.21% predicted population coverage with at least five vaccine peptide-HLA average hits per person (≥ 1 peptide: 99.91%) with all vaccine peptides perfectly conserved across 4,690 geographically sampled SARS-CoV-2 genomes. Our proposed MHC class II vaccine formulations provide 97.21% predicted coverage with at least five vaccine peptide-HLA average hits per person with all peptides having an observed mutation probability of ≤ 0.001. We provide an open-source implementation of our design methods (OptiVax), vaccine evaluation tool (EvalVax), as well as the data used in our design efforts here: https://github.com/gifford-lab/optivax.
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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.