Quantitative approaches for decoding the specificity of the human T cell repertoire

ZS Ghoreyshi, JT George - Frontiers in Immunology, 2023 - frontiersin.org
T cell receptor (TCR)-peptide-major histocompatibility complex (pMHC) interactions play a
vital role in initiating immune responses against pathogens, and the specificity of TCRpMHC …

Breast cancer dormancy: need for clinically relevant models to address current gaps in knowledge

GG Bushnell, AP Deshmukh, P den Hollander… - NPJ breast …, 2021 - nature.com
Breast cancer is the most commonly diagnosed cancer in the USA. Although advances in
treatment over the past several decades have significantly improved the outlook for this …

epiTCR: a highly sensitive predictor for TCR–peptide binding

MDN Pham, TN Nguyen, LS Tran, QTB Nguyen… - …, 2023 - academic.oup.com
Motivation Predicting the binding between T-cell receptor (TCR) and peptide presented by
human leucocyte antigen molecule is a highly challenging task and a key bottleneck in the …

Characterizing the interaction conformation between T-cell receptors and epitopes with deep learning

X Peng, Y Lei, P Feng, L Jia, J Ma, D Zhao… - Nature machine …, 2023 - nature.com
Computational modelling of the interactions between T-cell receptors (TCRs) and epitopes
is of great importance for immunotherapy and antigen discovery. However, current TCR …

Structure-based prediction of T cell receptor recognition of unseen epitopes using TCRen

VK Karnaukhov, DS Shcherbinin… - Nature Computational …, 2024 - nature.com
T cell receptor (TCR) recognition of foreign peptides presented by major histocompatibility
complex protein is a major event in triggering the adaptive immune response to pathogens …

Defining and studying B cell receptor and TCR interactions

CG Rappazzo, ML Fernández-Quintero… - The Journal of …, 2023 - journals.aai.org
Abstract BCRs (Abs) and TCRs (or adaptive immune receptors [AIRs]) are the means by
which the adaptive immune system recognizes foreign and self-antigens, playing an integral …

A transfer-learning approach to predict antigen immunogenicity and T-cell receptor specificity

B Bravi, A Di Gioacchino, J Fernandez-de-Cossio-Diaz… - ELife, 2023 - elifesciences.org
Antigen immunogenicity and the specificity of binding of T-cell receptors to antigens are key
properties underlying effective immune responses. Here we propose diffRBM, an approach …

RACER-m leverages structural features for sparse T cell specificity prediction

A Wang, X Lin, KN Chau, JN Onuchic, H Levine… - Science …, 2024 - science.org
Reliable prediction of T cell specificity against antigenic signatures is a formidable task,
complicated by the immense diversity of T cell receptor and antigen sequence space and …

Systems immunology of regulatory T cells: can one circuit explain it all?

S Tripathi, JS Tsang, K Park - Trends in Immunology, 2023 - cell.com
Regulatory T (Treg) cells play vital roles in immune homeostasis and response, including
discrimination between self-and non-self-antigens, containment of immunopathology, and …

DeepAIR: A deep learning framework for effective integration of sequence and 3D structure to enable adaptive immune receptor analysis

Y Zhao, B He, F Xu, C Li, Z Xu, X Su, H He, Y Huang… - Science …, 2023 - science.org
Structural docking between the adaptive immune receptors (AIRs), including T cell receptors
(TCRs) and B cell receptors (BCRs), and their cognate antigens are one of the most …