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 …

Single-cell immune repertoire analysis

SE Irac, MSF Soon, N Borcherding, ZK Tuong - Nature Methods, 2024 - nature.com
Single-cell T cell and B cell antigen receptor-sequencing data analysis can potentially
perform in-depth assessments of adaptive immune cells that inform on understanding …

Observed Antibody Space: A diverse database of cleaned, annotated, and translated unpaired and paired antibody sequences

TH Olsen, F Boyles, CM Deane - Protein Science, 2022 - Wiley Online Library
The antibody repertoires of individuals and groups have been used to explore disease
states, understand vaccine responses, and drive therapeutic development. The arrival of B …

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 …

[HTML][HTML] SARS-CoV-2 epitopes are recognized by a public and diverse repertoire of human T cell receptors

AS Shomuradova, MS Vagida, SA Sheetikov… - Immunity, 2020 - cell.com
Understanding the hallmarks of the immune response to SARS-CoV-2 is critical for fighting
the COVID-19 pandemic. We assessed antibody and T cell reactivity in convalescent COVID …

Adaptive immune receptor repertoire analysis

V Mhanna, H Bashour, K Lê Quý, P Barennes… - Nature Reviews …, 2024 - nature.com
B cell and T cell receptor repertoires compose the adaptive immune receptor repertoire
(AIRR) of an individual. The AIRR is a unique collection of antigen-specific receptors that …

Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins

C Suo, K Polanski, E Dann, RGH Lindeboom… - Nature …, 2024 - nature.com
Assessment of single-cell gene expression (single-cell RNA sequencing) and adaptive
immune receptor (AIR) sequencing (scVDJ-seq) has been invaluable in studying …

Computational approaches to therapeutic antibody design: established methods and emerging trends

RA Norman, F Ambrosetti, AMJJ Bonvin… - Briefings in …, 2020 - academic.oup.com
Antibodies are proteins that recognize the molecular surfaces of potentially noxious
molecules to mount an adaptive immune response or, in the case of autoimmune diseases …

Observed antibody space: a resource for data mining next-generation sequencing of antibody repertoires

A Kovaltsuk, J Leem, S Kelm, J Snowden… - The Journal of …, 2018 - journals.aai.org
Abs are immune system proteins that recognize noxious molecules for elimination. Their
sequence diversity and binding versatility have made Abs the primary class of …

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 …