AIMC Topic: Antigen Presentation
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OnmiMHC: a machine learning solution for UCEC tumor vaccine development through enhanced peptide-MHC binding prediction.
Frontiers in immunology
Feb 28, 2025
The key roles of Major Histocompatibility Complex (MHC) Class I and II molecules in the immune system are well established. This study aims to develop a novel machine learning framework for predicting antigen peptide presentation by MHC Class I and I...
Identification of a gene score related to antigen processing and presentation machinery for predicting prognosis in head and neck squamous cell carcinoma and its potential implications for immunotherapy.
Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico
Dec 31, 2024
BACKGROUND: Despite its crucial role in immune surveillance and cell survival of tumors, the significance of MHC antigen processing and presentation machinery (APM) is still not fully understood in head and neck squamous cell carcinoma (HNSCC). We so...
LRMAHpan: a novel tool for multi-allelic HLA presentation prediction using Resnet-based and LSTM-based neural networks.
Frontiers in immunology
Nov 28, 2024
INTRODUCTION: The identification of peptides eluted from HLA complexes by mass spectrometry (MS) can provide critical data for deep learning models of antigen presentation prediction and promote neoantigen vaccine design. A major challenge remains in...
Identification of antigen-presentation related B cells as a key player in Crohn's disease using single-cell dissecting, hdWGCNA, and deep learning.
Clinical and experimental medicine
Aug 8, 2023
Crohn's disease (CD) arises from intricate intercellular interactions within the intestinal lamina propria. Our objective was to use single-cell RNA sequencing to investigate CD pathogenesis and explore its clinical significance. We identified a dist...
T cell immune responses deciphered.
Science (New York, N.Y.)
May 19, 2022
A machine-learning approach reveals antigen encoding that predicts T cell responses.
A simple pan-specific RNN model for predicting HLA-II binding peptides.
Molecular immunology
Sep 20, 2021
The prediction of human leukocyte antigen (HLA) class II binding peptides plays important roles in understanding the mechanism of immune recognition and developing effective epitope-based vaccines. In this work, gated recurrent unit (GRU)-based recur...
T Cell Epitope Prediction and Its Application to Immunotherapy.
Frontiers in immunology
Sep 15, 2021
T cells play a crucial role in controlling and driving the immune response with their ability to discriminate peptides derived from healthy as well as pathogenic proteins. In this review, we focus on the currently available computational tools for ep...
Computational Biology
Immunotherapy
Antigens, Neoplasm
Base Sequence
Sequence Analysis, DNA
Models, Molecular
Humans
Epitopes, T-Lymphocyte
Antigen Presentation
Mass Spectrometry
Histocompatibility Antigens Class I
Neural Networks, Computer
Peptides
T-Cell Antigen Receptor Specificity
Neoplasms
Receptors, Antigen, T-Cell
Improvement of Neoantigen Identification Through Convolution Neural Network.
Frontiers in immunology
May 25, 2021
Accurate prediction of neoantigens and the subsequent elicited protective anti-tumor response are particularly important for the development of cancer vaccine and adoptive T-cell therapy. However, current algorithms for predicting neoantigens are lim...
Unbiased Characterization of Peptide-HLA Class II Interactions Based on Large-Scale Peptide Microarrays; Assessment of the Impact on HLA Class II Ligand and Epitope Prediction.
Frontiers in immunology
Aug 5, 2020
Human Leukocyte Antigen class II (HLA-II) molecules present peptides to T lymphocytes and play an important role in adaptive immune responses. Characterizing the binding specificity of single HLA-II molecules has profound impacts for understanding ce...
Quantitative Prediction of the Landscape of T Cell Epitope Immunogenicity in Sequence Space.
Frontiers in immunology
Apr 16, 2019
Immunodominant T cell epitopes preferentially targeted in multiple individuals are the critical element of successful vaccines and targeted immunotherapies. However, the underlying principles of this "convergence" of adaptive immunity among different...
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