B cells, plasma cells and antibody repertoires in the tumour microenvironment

GV Sharonov, EO Serebrovskaya… - Nature Reviews …, 2020 - nature.com
Recent data show that B cells and plasma cells located in tumours or in tumour-draining
lymph nodes can have important roles in shaping antitumour immune responses. In tumour …

Co-evolution of immunity and seasonal influenza viruses

AX Han, SPJ de Jong, CA Russell - Nature Reviews Microbiology, 2023 - nature.com
Seasonal influenza viruses cause recurring global epidemics by continually evolving to
escape host immunity. The viral constraints and host immune responses that limit and drive …

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

T Smith, A Heger, I Sudbery - Genome research, 2017 - genome.cshlp.org
Unique Molecular Identifiers (UMIs) are random oligonucleotide barcodes that are
increasingly used in high-throughput sequencing experiments. Through a UMI, identical …

Rapid discovery of high-affinity antibodies via massively parallel sequencing, ribosome display and affinity screening

BT Porebski, M Balmforth, G Browne, A Riley… - Nature biomedical …, 2024 - nature.com
Developing therapeutic antibodies is laborious and costly. Here we report a method for
antibody discovery that leverages the Illumina HiSeq platform to, within 3 days, screen in the …

The promise and challenge of high-throughput sequencing of the antibody repertoire

G Georgiou, GC Ippolito, J Beausang, CE Busse… - Nature …, 2014 - nature.com
Efforts to determine the antibody repertoire encoded by B cells in the blood or lymphoid
organs using high-throughput DNA sequencing technologies have been advancing at an …

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 …

Memory B cell activation, broad anti-influenza antibodies, and bystander activation revealed by single-cell transcriptomics

F Horns, CL Dekker, SR Quake - Cell reports, 2020 - cell.com
Antibody memory protects humans from many diseases. Protective antibody memory
responses require activation of transcriptional programs, cell proliferation, and production of …

OLGA: fast computation of generation probabilities of B-and T-cell receptor amino acid sequences and motifs

Z Sethna, Y Elhanati, CG Callan Jr, AM Walczak… - …, 2019 - academic.oup.com
Motivation High-throughput sequencing of large immune repertoires has enabled the
development of methods to predict the probability of generation by V (D) J recombination of …

pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires

JA Vander Heiden, G Yaari, M Uduman… - …, 2014 - academic.oup.com
Driven by dramatic technological improvements, large-scale characterization of lymphocyte
receptor repertoires via high-throughput sequencing is now feasible. Although promising …

Molecular-level analysis of the serum antibody repertoire in young adults before and after seasonal influenza vaccination

J Lee, DR Boutz, V Chromikova, MG Joyce… - Nature medicine, 2016 - nature.com
Molecular understanding of serological immunity to influenza has been confounded by the
complexity of the polyclonal antibody response in humans. Here we used high-resolution …