Can we predict T cell specificity with digital biology and machine learning?
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 …
solutions to problems such as protein structure prediction that were long thought to be …
High-throughput and single-cell T cell receptor sequencing technologies
JA Pai, AT Satpathy - Nature methods, 2021 - nature.com
T cells express T cell receptors (TCRs) composed of somatically recombined TCRα and
TCRβ chains, which mediate recognition of major histocompatibility complex (MHC)–antigen …
TCRβ chains, which mediate recognition of major histocompatibility complex (MHC)–antigen …
[HTML][HTML] Multiple early factors anticipate post-acute COVID-19 sequelae
Post-acute sequelae of COVID-19 (PASC) represent an emerging global crisis. However,
quantifiable risk factors for PASC and their biological associations are poorly resolved. We …
quantifiable risk factors for PASC and their biological associations are poorly resolved. We …
Molecular signatures of antitumor neoantigen-reactive T cells from metastatic human cancers
The accurate identification of antitumor T cell receptors (TCRs) represents a major challenge
for the engineering of cell-based cancer immunotherapies. By mapping 55 neoantigen …
for the engineering of cell-based cancer immunotherapies. By mapping 55 neoantigen …
[HTML][HTML] Transcriptional programs of neoantigen-specific TIL in anti-PD-1-treated lung cancers
Abstract PD-1 blockade unleashes CD8 T cells, including those specific for mutation-
associated neoantigens (MANA), but factors in the tumour microenvironment can inhibit …
associated neoantigens (MANA), but factors in the tumour microenvironment can inhibit …
VDJdb in the pandemic era: a compendium of T cell receptors specific for SARS-CoV-2
M Goncharov, D Bagaev, D Shcherbinin, I Zvyagin… - Nature …, 2022 - nature.com
In 2016, we started a community effort to gather and curate publicly available sequence data
acquired from T cell receptor (TCRs) with defined antigen specificities, as well as …
acquired from T cell receptor (TCRs) with defined antigen specificities, as well as …
Pan-peptide meta learning for T-cell receptor–antigen binding recognition
The identification of the mechanisms by which T-cell receptors (TCRs) interact with human
antigens provides a crucial opportunity to develop new vaccines, diagnostics and …
antigens provides a crucial opportunity to develop new vaccines, diagnostics and …
Deep learning-based prediction of the T cell receptor–antigen binding specificity
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 …
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 …
challenging. This challenge is primarily due to three dominant factors: data accuracy, data …
[HTML][HTML] A blood atlas of COVID-19 defines hallmarks of disease severity and specificity
DJ Ahern, Z Ai, M Ainsworth, C Allan, A Allcock… - Cell, 2022 - cell.com
Treatment of severe COVID-19 is currently limited by clinical heterogeneity and incomplete
description of specific immune biomarkers. We present here a comprehensive multi-omic …
description of specific immune biomarkers. We present here a comprehensive multi-omic …