@article{fdi:010087414,
  title = {{SILVI}, an open-source pipeline for {T}-cell epitope selection},
  author = {{P}issarra, {J}. and {D}orkeld, {F}. and {L}oire, {E}. and {B}onhomme, {V}. and {S}ereno, {D}enis and {L}emesre, {J}ean-{L}oup and {H}olzmuller, {P}.},
  editor = {},
  language = {{ENG}},
  abstract = {{H}igh-throughput screening of available genomic data and identification of potential antigenic candidates have promoted the development of epitope-based vaccines and therapeutics. {S}everal immunoinformatic tools are available to predict potential epitopes and other immunogenicity-related features, yet it is still challenging and time-consuming to compare and integrate results from different algorithms. {W}e developed the {R} script {SILVI} (short for: from in silico to in vivo), to assist in the selection of the potentially most immunogenic {T}-cell epitopes from {H}uman {L}eukocyte {A}ntigen ({HLA})-binding prediction data. {SILVI} merges and compares data from available {HLA}-binding prediction servers, and integrates additional relevant information of predicted epitopes, namely {BLAST}p alignments with host proteins and physical-chemical properties. {T}he two default criteria applied by {SILVI} and additional filtering allow the fast selection of the most conserved, promiscuous, strong binding {T}-cell epitopes. {U}sers may adapt the script at their discretion as it is written in open-source {R} language. {T}o demonstrate the workflow and present selection options, {SILVI} was used to integrate {HLA}-binding prediction results of three example proteins, from viral, bacterial and parasitic microorganisms, containing validated epitopes included in the {I}mmune {E}pitope {D}atabase ({IEDB}), plus the {H}uman {P}apillomavirus ({HPV}) proteome. {A}pplying different filters on predicted {IC}50, hydrophobicity and mismatches with host proteins allows to significantly reduce the epitope lists with favourable sensitivity and specificity to select immunogenic epitopes. {W}e contemplate {SILVI} will assist {T}-cell epitope selections and can be continuously refined in a community-driven manner, helping the improvement and design of peptide-based vaccines or immunotherapies. {SILVI} development version is available at: github.com/{J}oana{P}issarra/{SILVI}2020 and https://doi.org/10.5281/zenodo.6865909.},
  keywords = {},
  booktitle = {},
  journal = {{PL}o{S} {O}ne},
  volume = {17},
  numero = {9},
  pages = {e0273494 [20 p.]},
  ISSN = {1932-6203},
  year = {2022},
  DOI = {10.1371/journal.pone.0273494},
  URL = {https://www.documentation.ird.fr/hor/fdi:010087414},
}