Identification of neoantigens for individualized therapeutic cancer vaccines

F Lang, B Schrörs, M Löwer, Ö Türeci… - Nature reviews Drug …, 2022 - nature.com
Somatic mutations in cancer cells can generate tumour-specific neoepitopes, which are
recognized by autologous T cells in the host. As neoepitopes are not subject to central …

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 …

Deep learning-based prediction of the T cell receptor–antigen binding specificity

T Lu, Z Zhang, J Zhu, Y Wang, P Jiang, X Xiao… - Nature machine …, 2021 - nature.com
Neoantigens play a key role in the recognition of tumour cells by T cells; however, only a
small proportion of neoantigens truly elicit T-cell responses, and few clues exist as to which …

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 …

VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium

DV Bagaev, RMA Vroomans, J Samir… - Nucleic acids …, 2020 - academic.oup.com
Here, we report an update of the VDJdb database with a substantial increase in the number
of T-cell receptor (TCR) sequences and their cognate antigens. The update further provides …

TITAN: T-cell receptor specificity prediction with bimodal attention networks

A Weber, J Born, M Rodriguez Martínez - Bioinformatics, 2021 - academic.oup.com
Motivation The activity of the adaptive immune system is governed by T-cells and their
specific T-cell receptors (TCR), which selectively recognize foreign antigens. Recent …

T cell epitope predictions

B Peters, M Nielsen, A Sette - Annual Review of Immunology, 2020 - annualreviews.org
Throughout the body, T cells monitor MHC-bound ligands expressed on the surface of
essentially all cell types. MHC ligands that trigger a T cell immune response are referred to …

Predicting recognition between T cell receptors and epitopes with TCRGP

E Jokinen, J Huuhtanen, S Mustjoki… - PLoS computational …, 2021 - journals.plos.org
Adaptive immune system uses T cell receptors (TCRs) to recognize pathogens and to
consequently initiate immune responses. TCRs can be sequenced from individuals and …

TCRMatch: predicting T-cell receptor specificity based on sequence similarity to previously characterized receptors

WD Chronister, A Crinklaw, S Mahajan, R Vita… - Frontiers in …, 2021 - frontiersin.org
The adaptive immune system in vertebrates has evolved to recognize non-self antigens,
such as proteins expressed by infectious agents and mutated cancer cells. T cells play an …

Modern hopfield networks and attention for immune repertoire classification

M Widrich, B Schäfl, M Pavlović… - Advances in neural …, 2020 - proceedings.neurips.cc
A central mechanism in machine learning is to identify, store, and recognize patterns. How to
learn, access, and retrieve such patterns is crucial in Hopfield networks and the more recent …