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 …

High-throughput analysis of the human thymic Vδ1+ T cell receptor repertoire

B Di Lorenzo, S Ravens, B Silva-Santos - Scientific Data, 2019 - nature.com
Abstract γδ T cells are a relatively rare subset of lymphocytes in the human peripheral blood,
but they play important roles at the interface between the innate and the adaptive immune …

Platypus: an open-access software for integrating lymphocyte single-cell immune repertoires with transcriptomes

A Yermanos, A Agrafiotis, R Kuhn… - NAR genomics and …, 2021 - academic.oup.com
High-throughput single-cell sequencing (scSeq) technologies are revolutionizing the ability
to molecularly profile B and T lymphocytes by offering the opportunity to simultaneously …

Comprehensive evaluation and optimization of amplicon library preparation methods for high-throughput antibody sequencing

U Menzel, V Greiff, TA Khan, U Haessler, I Hellmann… - PloS one, 2014 - journals.plos.org
High-throughput sequencing (HTS) of antibody repertoire libraries has become a powerful
tool in the field of systems immunology. However, numerous sources of bias in HTS …

Composition and variation analysis of the TCR β-chain CDR3 repertoire in systemic lupus erythematosus using high-throughput sequencing

W Sui, X Hou, G Zou, W Che, M Yang, C Zheng… - Molecular …, 2015 - Elsevier
The ability of T lymphocytes to mount an immune response against a diverse array of
pathogens is primarily conveyed by the amino acid (aa) sequence of the hypervariable …

Efficacy of a dual-epitope dendritic cell vaccine as part of combined immunotherapy for HER2-expressing breast tumors

BG Vincent, DM File, KP McKinnon… - The Journal of …, 2023 - journals.aai.org
Previous work from our group and others has shown that patients with breast cancer can
generate a T cell response against specific human epidermal growth factor 2 (HER2) …

Antibodies from dengue patients with prior exposure to Japanese encephalitis virus are broadly neutralizing against Zika virus

GM Salem, JU Galula, SR Wu, JH Liu, YH Chen… - Communications …, 2024 - nature.com
Exposure to multiple mosquito-borne flaviviruses within a lifetime is not uncommon;
however, how sequential exposures to different flaviviruses shape the cross-reactive …

Reconstructing antibody repertoires from error-prone immunosequencing reads

A Shlemov, S Bankevich, A Bzikadze… - The Journal of …, 2017 - journals.aai.org
Transforming error-prone immunosequencing datasets into Ab repertoires is a fundamental
problem in immunogenomics, and a prerequisite for studies of immune responses. Although …

Antibody isotype switching as a mechanism to counter HIV neutralization escape

C Scheepers, V Bekker, C Anthony, SI Richardson… - Cell reports, 2020 - cell.com
Neutralizing antibodies (nAbs) to highly variable viral pathogens show remarkable
diversification during infection, resulting in an" arms race" between virus and host. Studies of …

High‐throughput DNA sequencing analysis of antibody repertoires

SD Boyd, SA Joshi - Antibodies for Infectious Diseases, 2015 - Wiley Online Library
New high‐throughput DNA sequencing (HTS) technologies developed in the past decade
have rapidly increased the scale of data collection for all aspects of human genetics (1, 2) …