Computational strategies for dissecting the high-dimensional complexity of adaptive immune repertoires

E Miho, A Yermanos, CR Weber, CT Berger… - Frontiers in …, 2018 - frontiersin.org
The adaptive immune system recognizes antigens via an immense array of antigen-binding
antibodies and T-cell receptors, the immune repertoire. The interrogation of immune …

Using T cell receptor repertoires to understand the principles of adaptive immune recognition

P Bradley, PG Thomas - Annual review of immunology, 2019 - annualreviews.org
Adaptive immune recognition is mediated by antigen receptors on B and T cells generated
by somatic recombination during lineage development. The high level of diversity resulting …

Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases

P Barennes, V Quiniou, M Shugay, ES Egorov… - Nature …, 2021 - nature.com
Monitoring the T cell receptor (TCR) repertoire in health and disease can provide key
insights into adaptive immune responses, but the accuracy of current TCR sequencing …

BertTCR: a Bert-based deep learning framework for predicting cancer-related immune status based on T cell receptor repertoire

M Zhang, Q Cheng, Z Wei, J Xu, S Wu… - Briefings in …, 2024 - academic.oup.com
The T cell receptor (TCR) repertoire is pivotal to the human immune system, and
understanding its nuances can significantly enhance our ability to forecast cancer-related …

Machine learning approaches to TCR repertoire analysis

Y Katayama, R Yokota, T Akiyama… - Frontiers in …, 2022 - frontiersin.org
Sparked by the development of genome sequencing technology, the quantity and quality of
data handled in immunological research have been changing dramatically. Various data …

Comparing T cell receptor repertoires using optimal transport

BJ Olson, SA Schattgen, PG Thomas… - PLOS Computational …, 2022 - journals.plos.org
The complexity of entire T cell receptor (TCR) repertoires makes their comparison a difficult
but important task. Current methods of TCR repertoire comparison can incur a high loss of …

Methods for sequence and structural analysis of B and T cell receptor repertoires

S Teraguchi, DS Saputri… - Computational and …, 2020 - Elsevier
B cell receptors (BCRs) and T cell receptors (TCRs) make up an essential network of
defense molecules that, collectively, can distinguish self from non-self and facilitate …

Microbiota dictate T cell clonal selection to augment graft-versus-host disease after stem cell transplantation

AC Yeh, M Koyama, OG Waltner, SA Minnie, JR Boiko… - Immunity, 2024 - cell.com
Allogeneic T cell expansion is the primary determinant of graft-versus-host disease (GVHD),
and current dogma dictates that this is driven by histocompatibility antigen disparities …

sumrep: A Summary Statistic Framework for Immune Receptor Repertoire Comparison and Model Validation

BJ Olson, P Moghimi, CA Schramm… - Frontiers in …, 2019 - frontiersin.org
The adaptive immune system generates an incredible diversity of antigen receptors for B
and T cells to keep dangerous pathogens at bay. The DNA sequences coding for these …

TCR Repertoire Analysis Reveals Mobilization of Novel CD8+ T Cell Clones Into the Cancer-Immunity Cycle Following Anti-CD4 Antibody Administration

H Aoki, S Ueha, S Shichino, H Ogiwara… - Frontiers in …, 2019 - frontiersin.org
Depletion of CD4+ cells using an anti-CD4 monoclonal antibody (anti-CD4 mAb) induces
the expansion of tumor-reactive CD8+ T cells and strong antitumor effects in several murine …