Analysis of major histocompatibility complex (MHC) immunopeptidomes using mass spectrometry
The myriad of peptides presented at the cell surface by class I and class II major
histocompatibility complex (MHC) molecules are referred to as the immunopeptidome and …
histocompatibility complex (MHC) molecules are referred to as the immunopeptidome and …
A large peptidome dataset improves HLA class I epitope prediction across most of the human population
Prediction of HLA epitopes is important for the development of cancer immunotherapies and
vaccines. However, current prediction algorithms have limited predictive power, in part …
vaccines. However, current prediction algorithms have limited predictive power, in part …
Gapped sequence alignment using artificial neural networks: application to the MHC class I system
M Andreatta, M Nielsen - Bioinformatics, 2016 - academic.oup.com
Motivation: Many biological processes are guided by receptor interactions with linear
ligands of variable length. One such receptor is the MHC class I molecule. The length …
ligands of variable length. One such receptor is the MHC class I molecule. The length …
[HTML][HTML] Application of mass spectrometry-based MHC immunopeptidome profiling in neoantigen identification for tumor immunotherapy
X Zhang, Y Qi, Q Zhang, W Liu - Biomedicine & Pharmacotherapy, 2019 - Elsevier
One of the challenges for cancer vaccine and adoptive T-cell-based immunotherapy is to
identify the major histocompatibility complex (MHC)-associated non-self neoantigens …
identify the major histocompatibility complex (MHC)-associated non-self neoantigens …
NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets
M Nielsen, M Andreatta - Genome medicine, 2016 - Springer
Background Binding of peptides to MHC class I molecules (MHC-I) is essential for antigen
presentation to cytotoxic T-cells. Results Here, we demonstrate how a simple alignment step …
presentation to cytotoxic T-cells. Results Here, we demonstrate how a simple alignment step …
The length distribution of class I–restricted T cell epitopes is determined by both peptide supply and MHC allele–specific binding preference
HLA class I–binding predictions are widely used to identify candidate peptide targets of
human CD8+ T cell responses. Many such approaches focus exclusively on a limited range …
human CD8+ T cell responses. Many such approaches focus exclusively on a limited range …
Computationally optimized SARS-CoV-2 MHC class I and II vaccine formulations predicted to target human haplotype distributions
We present a combinatorial machine learning method to evaluate and optimize peptide
vaccine formulations for SARS-CoV-2. Our approach optimizes the presentation likelihood of …
vaccine formulations for SARS-CoV-2. Our approach optimizes the presentation likelihood of …
Quantification of epitope abundance reveals the effect of direct and cross-presentation on influenza CTL responses
The magnitude of T cell responses to infection is a function of the naïve T cell repertoire
combined with the context and duration of antigen presentation. Using mass spectrometry …
combined with the context and duration of antigen presentation. Using mass spectrometry …
Potential CD8+ T cell cross-reactivity against SARS-CoV-2 conferred by other coronavirus strains
While individuals infected with coronavirus disease 2019 (COVID-19) manifested a broad
range in susceptibility and severity to the disease, the pre-existing immune memory to …
range in susceptibility and severity to the disease, the pre-existing immune memory to …
Development of a novel clustering tool for linear peptide sequences
Epitopes identified in large‐scale screens of overlapping peptides often share significant
levels of sequence identity, complicating the analysis of epitope‐related data. Clustering …
levels of sequence identity, complicating the analysis of epitope‐related data. Clustering …