[HTML][HTML] Defining HLA-II ligand processing and binding rules with mass spectrometry enhances cancer epitope prediction

JG Abelin, D Harjanto, M Malloy, P Suri, T Colson… - Immunity, 2019 - cell.com
Increasing evidence indicates CD4+ T cells can recognize cancer-specific antigens and
control tumor growth. However, it remains difficult to predict the antigens that will be …

Immune epitope database analysis resource

Y Kim, J Ponomarenko, Z Zhu, D Tamang… - Nucleic acids …, 2012 - academic.oup.com
The immune epitope database analysis resource (IEDB-AR: http://tools. iedb. org) is a
collection of tools for prediction and analysis of molecular targets of T-and B-cell immune …

pVACtools: a computational toolkit to identify and visualize cancer neoantigens

J Hundal, S Kiwala, J McMichael, CA Miller, H Xia… - Cancer immunology …, 2020 - AACR
Identification of neoantigens is a critical step in predicting response to checkpoint blockade
therapy and design of personalized cancer vaccines. This is a cross-disciplinary challenge …

Best practices for bioinformatic characterization of neoantigens for clinical utility

MM Richters, H Xia, KM Campbell, WE Gillanders… - Genome medicine, 2019 - Springer
Neoantigens are newly formed peptides created from somatic mutations that are capable of
inducing tumor-specific T cell recognition. Recently, researchers and clinicians have …

A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction

S Mei, F Li, A Leier, TT Marquez-Lago… - Briefings in …, 2020 - academic.oup.com
Human leukocyte antigen class I (HLA-I) molecules are encoded by major histocompatibility
complex (MHC) class I loci in humans. The binding and interaction between HLA-I …

The role of neoantigens in naturally occurring and therapeutically induced immune responses to cancer

JP Ward, MM Gubin, RD Schreiber - Advances in immunology, 2016 - Elsevier
Definitive experimental evidence from mouse cancer models and strong correlative clinical
data gave rise to the Cancer Immunoediting concept that explains the dual host-protective …

TepiTool: a pipeline for computational prediction of T cell epitope candidates

S Paul, J Sidney, A Sette… - Current protocols in …, 2016 - Wiley Online Library
Computational prediction of T cell epitope candidates is currently being used in several
applications including vaccine discovery studies, development of diagnostics, and removal …

High-throughput prediction of MHC class I and II neoantigens with MHCnuggets

XM Shao, R Bhattacharya, J Huang… - Cancer immunology …, 2020 - AACR
Computational prediction of binding between neoantigen peptides and major
histocompatibility complex (MHC) proteins can be used to predict patient response to cancer …

Genomic landscape of high-grade meningiomas

WL Bi, NF Greenwald, M Abedalthagafi, J Wala… - NPJ genomic …, 2017 - nature.com
High-grade meningiomas frequently recur and are associated with high rates of morbidity
and mortality. To determine the factors that promote the development and evolution of these …

Systematically benchmarking peptide-MHC binding predictors: From synthetic to naturally processed epitopes

W Zhao, X Sher - PLoS computational biology, 2018 - journals.plos.org
A number of machine learning-based predictors have been developed for identifying
immunogenic T-cell epitopes based on major histocompatibility complex (MHC) class I and II …