Fundamentals and methods for T‐and B‐cell epitope prediction

JL Sanchez-Trincado… - Journal of …, 2017 - Wiley Online Library
Adaptive immunity is mediated by T‐and B‐cells, which are immune cells capable of
developing pathogen‐specific memory that confers immunological protection. Memory and …

T cell epitope predictions

B Peters, M Nielsen, A Sette - Annual Review of Immunology, 2020 - annualreviews.org
Throughout the body, T cells monitor MHC-bound ligands expressed on the surface of
essentially all cell types. MHC ligands that trigger a T cell immune response are referred to …

Mutational landscape determines sensitivity to PD-1 blockade in non–small cell lung cancer

NA Rizvi, MD Hellmann, A Snyder, P Kvistborg… - Science, 2015 - science.org
Immune checkpoint inhibitors, which unleash a patient's own T cells to kill tumors, are
revolutionizing cancer treatment. To unravel the genomic determinants of response to this …

Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes

J Racle, J Michaux, GA Rockinger, M Arnaud… - Nature …, 2019 - nature.com
Predictions of epitopes presented by class II human leukocyte antigen molecules (HLA-II)
have limited accuracy, restricting vaccine and therapy design. Here we combined unbiased …

Targeting of cancer neoantigens with donor-derived T cell receptor repertoires

E Strønen, M Toebes, S Kelderman, MM Van Buuren… - Science, 2016 - science.org
Accumulating evidence suggests that clinically efficacious cancer immunotherapies are
driven by T cell reactivity against DNA mutation–derived neoantigens. However, among the …

Properties of MHC class I presented peptides that enhance immunogenicity

JJA Calis, M Maybeno, JA Greenbaum… - PLoS computational …, 2013 - journals.plos.org
T-cells have to recognize peptides presented on MHC molecules to be activated and elicit
their effector functions. Several studies demonstrate that some peptides are more …

Tumor exome analysis reveals neoantigen-specific T-cell reactivity in an ipilimumab-responsive melanoma

N van Rooij, MM van Buuren, D Philips… - Journal of Clinical …, 2013 - ascopubs.org
Tumor Exome Analysis Reveals Neoantigen-Specific T-Cell Reactivity in an Ipilimumab-Responsive
Melanoma | Journal of Clinical Oncology Skip to main content ASCO Publications Publications …

Designing of interferon-gamma inducing MHC class-II binders

SK Dhanda, P Vir, GPS Raghava - Biology direct, 2013 - Springer
Background The generation of interferon-gamma (IFN-γ) by MHC class II activated CD4+ T
helper cells play a substantial contribution in the control of infections such as caused by …

Reliable B cell epitope predictions: impacts of method development and improved benchmarking

JV Kringelum, C Lundegaard, O Lund… - PLoS computational …, 2012 - journals.plos.org
The interaction between antibodies and antigens is one of the most important immune
system mechanisms for clearing infectious organisms from the host. Antibodies bind to …

Computational immunology meets bioinformatics: the use of prediction tools for molecular binding in the simulation of the immune system

N Rapin, O Lund, M Bernaschi, F Castiglione - PloS one, 2010 - journals.plos.org
We present a new approach to the study of the immune system that combines techniques of
systems biology with information provided by data-driven prediction methods. To this end …