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 …

Immunoinformatics: predicting peptide–MHC binding

M Nielsen, M Andreatta, B Peters… - Annual review of …, 2020‏ - annualreviews.org
Immunoinformatics is a discipline that applies methods of computer science to study and
model the immune system. A fundamental question addressed by immunoinformatics is how …

A framework for highly multiplexed dextramer map** and prediction of T cell receptor sequences to antigen specificity

W Zhang, PG Hawkins, J He, NT Gupta, J Liu… - Science …, 2021‏ - science.org
T cell receptor (TCR) antigen–specific recognition is essential for the adaptive immune
system. However, building a TCR-antigen interaction map has been challenging due to the …

Deep generative selection models of T and B cell receptor repertoires with soNNia

G Isacchini, AM Walczak, T Mora… - Proceedings of the …, 2021‏ - pnas.org
Subclasses of lymphocytes carry different functional roles to work together and produce an
immune response and lasting immunity. Additionally to these functional roles, T and B cell …

Explaining a black-box by using a deep variational information bottleneck approach

S Bang, P **e, H Lee, W Wu, E **ng - Proceedings of the AAAI …, 2021‏ - ojs.aaai.org
Interpretable machine learning has gained much attention recently. Briefness and
comprehensiveness are necessary in order to provide a large amount of information …

[HTML][HTML] Quantitative immunology for physicists

G Altan-Bonnet, T Mora, AM Walczak - Physics Reports, 2020‏ - Elsevier
The adaptive immune system is a dynamical, self-organized multiscale system that protects
vertebrates from both pathogens and internal irregularities, such as tumors. For these …

Population variability in the generation and selection of T-cell repertoires

Z Sethna, G Isacchini, T Dupic, T Mora… - PLOS Computational …, 2020‏ - journals.plos.org
The diversity of T-cell receptor (TCR) repertoires is achieved by a combination of two
intrinsically stochastic steps: random receptor generation by VDJ recombination, and …

Computational Methods for Predicting Key Interactions in T Cell–Mediated Adaptive Immunity

R Ehrlich, E Glynn, M Singh… - Annual Review of …, 2024‏ - annualreviews.org
The adaptive immune system recognizes pathogen-and cancer-specific features and is
endowed with memory, enabling it to respond quickly and efficiently to repeated encounters …

Predicting TCR-epitope binding specificity using deep metric learning and multimodal learning

AM Luu, JR Leistico, T Miller, S Kim, JS Song - Genes, 2021‏ - mdpi.com
Understanding the recognition of specific epitopes by cytotoxic T cells is a central problem in
immunology. Although predicting binding between peptides and the class I Major …

An overview of immunoinformatics approaches and databases linking T cell receptor repertoires to their antigen specificity

IV Zvyagin, VO Tsvetkov, DM Chudakov, M Shugay - Immunogenetics, 2020‏ - Springer
Recent advances in molecular and bioinformatic methods have greatly improved our ability
to study the formation of an adaptive immune response towards foreign pathogens, self …