@inbook{e87c0b246b4249e98269bad9983cf83c,
title = "A Computational Pipeline for Predicting Cancer Neoepitopes",
abstract = "Mutant Peptide eXtractor and Informer (MuPeXI), by Bjerregaard et al. (Cancer Immunol Immunother CII 66:1123-1130, 2017), is a program which identifies tumor-specific peptides and assesses their potential to be neoepitopes. MuPeXI takes as input a VCF file and a list of human leukocyte antigen (HLA) types and optionally a gene expression profile to assess a peptide's potential to be a neoepitope. MuPeXI can be downloaded and run both locally and on a web server. Here, we describe a pipeline for processing the input data so that it can be used for MuPeXI and how to run MuPeXI both locally and as a web server.",
keywords = "Immunotherapy, Mutation, Neoantigens, Neoepitopes, Prediction, Sequencing, Variant calling",
author = "Schaap-Johansen, {Anna Lisa} and Paolo Marcatili",
note = "Publisher Copyright: {\textcopyright} 2023. Springer Science+Business Media, LLC, part of Springer Nature.",
year = "2023",
doi = "10.1007/978-1-0716-2609-2_27",
language = "English",
isbn = "978-1-0716-2608-5",
volume = "2552",
series = "Methods in molecular biology (Clifton, N.J.)",
publisher = "Humana Press",
pages = "475--488",
booktitle = "Computer-Aided Antibody Design",
}
