Structural basis for T cell recognition of cancer neoantigens and implications for predicting neoepitope immunogenicity

RA Mariuzza, D Wu, BG Pierce - Frontiers in Immunology, 2023 - frontiersin.org
Adoptive cell therapy (ACT) with tumor-specific T cells has been shown to mediate durable
cancer regression. Tumor-specific T cells are also the basis of other therapies, notably …

Breaking the performance ceiling for neoantigen immunogenicity prediction

H O'Brien, M Salm, LT Morton, M Szukszto, F O'Farrell… - Nature Cancer, 2023 - nature.com
Neoantigen immunogenicity prediction is a burgeoning field with vast potential; however, the
shortage of high-quality data and biases in current datasets limit model generalizability …

Transfer learning enables identification of multiple types of RNA modifications using nanopore direct RNA sequencing

Y Wu, W Shao, M Yan, Y Wang, P Xu, G Huang… - Nature …, 2024 - nature.com
Nanopore direct RNA sequencing (DRS) has emerged as a powerful tool for RNA
modification identification. However, concurrently detecting multiple types of modifications in …

Fragment-Fusion Transformer: Deep Learning-Based Discretization Method for Continuous Single-Cell Raman Spectral Analysis

Q Yu, X Shen, LL Yi, M Liang, G Li, Z Guan, X Wu… - ACS …, 2024 - ACS Publications
Raman spectroscopy has become an important single-cell analysis tool for monitoring
biochemical changes at the cellular level. However, Raman spectral data, typically …

ConvNeXt-MHC: improving MHC–peptide affinity prediction by structure-derived degenerate coding and the ConvNeXt model

L Zhang, W Song, T Zhu, Y Liu, W Chen… - Briefings in …, 2024 - academic.oup.com
Peptide binding to major histocompatibility complex (MHC) proteins plays a critical role in T-
cell recognition and the specificity of the immune response. Experimental validation such …

HLAIImaster: a deep learning method with adaptive domain knowledge predicts HLA II neoepitope immunogenic responses

Q Yang, L Xu, W Dong, X Li, K Wang… - Briefings in …, 2024 - academic.oup.com
While significant strides have been made in predicting neoepitopes that trigger autologous
CD4+ T cell responses, accurately identifying the antigen presentation by human leukocyte …

An integrated database of experimentally validated major histocompatibility complex epitopes for antigen-specific cancer therapy

S Kawakita, A Shen, CC Chao, Z Wang… - Antibody …, 2024 - academic.oup.com
Cancer immunotherapy represents a paradigm shift in oncology, offering a superior anti-
tumor efficacy and the potential for durable remission. The success of personalized vaccines …

Genesis: A modular protein language modelling approach to immunogenicity prediction

H O'Brien, M Salm, LT Morton, M Szukszto, F O'Farrell… - bioRxiv, 2024 - biorxiv.org
Neoantigen immunogenicity prediction is a highly challenging problem in the development
of personalised medicines. Low reactivity rates in called neoantigens result in a difficult …

Discovering and overcoming the bias in neoantigen identification by unified machine learning models

Z Zhang, W Wu, L Wei, X Wang - International Conference on Research in …, 2024 - Springer
Neoantigens, formed by genetic mutations in tumor cells, are abnormal peptides that can
trigger immune responses. Precisely identifying neoantigens from vast mutations is the key …

Predicting MHC-I ligands across alleles and species: How far can we go?

DM Tadros, J Racle, D Gfeller - bioRxiv, 2024 - biorxiv.org
CD8+ T-cell activation is initiated by the recognition of epitopes presented on class I major
histocompatibility complex (MHC-I) molecules. Identifying such epitopes is useful for …