OptiVax

This repository contains code and part of the data for the following papers:

Computationally Optimized SARS-CoV-2 MHC Class I and II Vaccine Formulations Predicted to Target Human Haplotype Distributions
Cell Systems, 2020
Code location: vaccine_paper/
Authors: Ge Liu, Brandon Carter, Trenton Bricken, Siddhartha Jain, Mathias Viard, Mary Carrington, David K. Gifford

Predicted Cellular Immunity Population Coverage Gaps for SARS-CoV-2 Subunit Vaccines and their Augmentation by Compact Peptide Sets
Cell Systems, 2021
Code location: augmentation_paper/
Authors: Ge Liu, Brandon Carter, David K. Gifford

Data

HLA haplotype frequencies are available in Mendeley Data: https://doi.org/10.17632/cfxkfy9zp4.1

Additional data (model predictions and processed haplotype frequencies) are available in Mendeley Data: https://doi.org/10.17632/gs8c2jpvdn.1

Citation

Please cite:

@article{optivax2020,
  title={Computationally Optimized {SARS-CoV-2} {MHC} Class {I} and {II} Vaccine Formulations Predicted to Target Human Haplotype Distributions},
  author={Liu, Ge and Carter, Brandon and Bricken, Trenton and Jain, Siddhartha and Viard, Mathias and Carrington, Mary and Gifford, David K},
  journal={Cell Systems},
  volume={11},
  number={2},
  pages={131--144},
  year={2020},
  publisher={Elsevier}
}

@article{optivax2021augmentation,
  title={Predicted cellular immunity population coverage gaps for {SARS-CoV-2} subunit vaccines and their augmentation by compact peptide sets},
  author={Liu, Ge and Carter, Brandon and Gifford, David K},
  journal={Cell systems},
  volume={12},
  number={1},
  pages={102--107},
  year={2021},
  publisher={Elsevier}
}