Deep learning predictions of TCR-epitope interactions reveal epitope-specific chains in dual alpha T cells

G Croce, S Bobisse, DL Moreno, J Schmidt… - Nature …, 2024 - nature.com
T cells have the ability to eliminate infected and cancer cells and play an essential role in
cancer immunotherapy. T cell activation is elicited by the binding of the T cell receptor (TCR) …

Simultaneous analysis of pMHC binding and reactivity unveils virus-specific CD8 T cell immunity to a concise epitope set

NP Kristensen, E Dionisio, AK Bentzen, T Tamhane… - Science …, 2024 - science.org
CD8 T cells provide immunity to virus infection through recognition of epitopes presented by
peptide major histocompatibility complexes (pMHCs). To establish a concise panel of widely …

NetTCR 2.2-Improved TCR specificity predictions by combining pan-and peptide-specific training strategies, loss-scaling and integration of sequence similarity

MF Jensen, M Nielsen - bioRxiv, 2023 - biorxiv.org
The ability to predict binding between peptides presented by the Major Histocompatibility
Complex (MHC) class I molecules and T-cell receptors (TCR) is of great interest in areas of …

Enhancing TCR specificity predictions by combined pan-and peptide-specific training, loss-scaling, and sequence similarity integration

MF Jensen, M Nielsen - Elife, 2024 - elifesciences.org
Predicting the interaction between Major Histocompatibility Complex (MHC) class I-
presented peptides and T-cell receptors (TCR) holds significant implications for vaccine …

[HTML][HTML] Lessons learned from the IMMREP23 TCR-epitope prediction challenge

M Nielsen, A Eugster, MF Jensen, M Goel… - ImmunoInformatics, 2024 - Elsevier
Here, we present the findings from IMMREP23, the second benchmark competition focused
on predicting the specificity of TCR-pMHC interactions. The interaction of T cell receptors …

TSpred: a robust prediction framework for TCR–epitope interactions using paired chain TCR sequence data

HY Kim, S Kim, WY Park, D Kim - Bioinformatics, 2024 - academic.oup.com
Results We propose TSpred, a new deep learning approach for the pan-specific prediction
of TCR binding specificity based on paired chain TCR data. We develop a robust model that …

Herpes Virus Infections in Kidney Transplant Patients (HINT)–a prospective observational cohort study

SR Hamm, SK Saini, A Hald, AV Vaaben… - BMC Infectious …, 2023 - Springer
Background Kidney transplant recipients receive maintenance immunosuppressive therapy
to avoid allograft rejection resulting in increased risk of infections and infection-related …

Phage display enables machine learning discovery of cancer antigen specific TCRs

G Croce, R Lani, D Tardivon, S Bobisse, M de Tiani… - bioRxiv, 2024 - biorxiv.org
T cells targeting epitopes in infectious diseases or cancer play a central role in spontaneous
and therapy-induced immune responses. T-cell epitope recognition is mediated by the …

TSpred: a robust prediction framework for TCR-epitope interactions based on an ensemble deep learning approach using paired chain TCR sequence data

HY Kim, S Kim, WY Park, D Kim - bioRxiv, 2023 - biorxiv.org
Prediction of T-cell receptor (TCR)-epitope interactions is important for many applications
such as cancer immunotherapy. However, due to the scarcity of available data, it is known to …