Can we predict T cell specificity with digital biology and machine learning?

D Hudson, RA Fernandes, M Basham, G Ogg… - Nature Reviews …, 2023 - nature.com
Recent advances in machine learning and experimental biology have offered breakthrough
solutions to problems such as protein structure prediction that were long thought to be …

[HTML][HTML] Challenges in neoantigen-directed therapeutics

L Lybaert, S Lefever, B Fant, E Smits, B De Geest… - Cancer Cell, 2023 - cell.com
A fundamental prerequisite for the efficacy of cancer immunotherapy is the presence of
functional, antigen-specific T cells within the tumor. Neoantigen-directed therapy is a …

NetTCR-2.0 enables accurate prediction of TCR-peptide binding by using paired TCRα and β sequence data

A Montemurro, V Schuster, HR Povlsen… - Communications …, 2021 - nature.com
Prediction of T-cell receptor (TCR) interactions with MHC-peptide complexes remains highly
challenging. This challenge is primarily due to three dominant factors: data accuracy, data …

DeepTCR is a deep learning framework for revealing sequence concepts within T-cell repertoires

JW Sidhom, HB Larman, DM Pardoll… - Nature communications, 2021 - nature.com
Deep learning algorithms have been utilized to achieve enhanced performance in pattern-
recognition tasks. The ability to learn complex patterns in data has tremendous implications …

Contribution of T cell receptor alpha and beta CDR3, MHC typing, V and J genes to peptide binding prediction

I Springer, N Tickotsky, Y Louzoun - Frontiers in immunology, 2021 - frontiersin.org
Introduction Predicting the binding specificity of T Cell Receptors (TCR) to MHC-peptide
complexes (pMHCs) is essential for the development of repertoire-based biomarkers. This …

TULIP: A transformer-based unsupervised language model for interacting peptides and T cell receptors that generalizes to unseen epitopes

B Meynard-Piganeau, C Feinauer… - Proceedings of the …, 2024 - National Acad Sciences
The accurate prediction of binding between T cell receptors (TCR) and their cognate
epitopes is key to understanding the adaptive immune response and developing …

[HTML][HTML] Benchmarking solutions to the T-cell receptor epitope prediction problem: IMMREP22 workshop report

P Meysman, J Barton, B Bravi, L Cohen-Lavi… - ImmunoInformatics, 2023 - Elsevier
Many different solutions to predicting the cognate epitope target of a T-cell receptor (TCR)
have been proposed. However several questions on the advantages and disadvantages of …

On TCR binding predictors failing to generalize to unseen peptides

F Grazioli, A Mösch, P Machart, K Li… - Frontiers in …, 2022 - frontiersin.org
Several recent studies investigate TCR-peptide/-pMHC binding prediction using machine
learning or deep learning approaches. Many of these methods achieve impressive results …

TCR-BERT: learning the grammar of T-cell receptors for flexible antigen-binding analyses

KE Wu, K Yost, B Daniel, J Belk, Y Xia… - Machine Learning …, 2024 - proceedings.mlr.press
The T-cell receptor (TCR) allows T-cells to recognize and respond to antigens presented by
infected and diseased cells. However, due to TCRs' staggering diversity and the complex …

[HTML][HTML] Mining adaptive immune receptor repertoires for biological and clinical information using machine learning

V Greiff, G Yaari, LG Cowell - Current Opinion in Systems Biology, 2020 - Elsevier
The adaptive immune system stores invaluable information about current and past immune
responses and may serve as an ultrasensitive biosensor. Given the immune system's critical …