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 …

Improving generalization of machine learning-identified biomarkers using causal modelling with examples from immune receptor diagnostics

M Pavlović, GS Al Hajj, C Kanduri, J Pensar… - Nature Machine …, 2024 - nature.com
Abstract Machine learning is increasingly used to discover diagnostic and prognostic
biomarkers from high-dimensional molecular data. However, a variety of factors related to …

Prime-seq, efficient and powerful bulk RNA sequencing

A Janjic, LE Wange, JW Bagnoli, J Geuder, P Nguyen… - Genome biology, 2022 - Springer
Cost-efficient library generation by early barcoding has been central in propelling single-cell
RNA sequencing. Here, we optimize and validate prime-seq, an early barcoding bulk RNA …

IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data

A Peres, WD Lees, OL Rodriguez, NY Lee… - Nucleic Acids …, 2023 - academic.oup.com
In adaptive immune receptor repertoire analysis, determining the germline variable (V) allele
associated with each T-and B-cell receptor sequence is a crucial step. This process is highly …

T-cell receptor repertoire sequencing and its applications: focus on infectious diseases and cancer

L Mazzotti, A Gaimari, S Bravaccini, R Maltoni… - International journal of …, 2022 - mdpi.com
The immune system is a dynamic feature of each individual and a footprint of our unique
internal and external exposures. Indeed, the type and level of exposure to physical and …

Individualized VDJ recombination predisposes the available Ig sequence space

A Slabodkin, M Chernigovskaya, I Mikocziova… - Genome …, 2021 - genome.cshlp.org
The process of recombination between variable (V), diversity (D), and joining (J)
immunoglobulin (Ig) gene segments determines an individual's naive Ig repertoire and …

Flairr-seq: A method for single-molecule resolution of near full-length antibody H chain repertoires

EE Ford, D Tieri, OL Rodriguez… - The Journal of …, 2023 - journals.aai.org
Abstract Current Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) using short-
read sequencing strategies resolve expressed Ab transcripts with limited resolution of the C …

Reading the repertoire: Progress in adaptive immune receptor analysis using machine learning

TJ O'Donnell, C Kanduri, G Isacchini, JP Limenitakis… - Cell Systems, 2024 - cell.com
The adaptive immune system holds invaluable information on past and present immune
responses in the form of B and T cell receptor sequences, but we are limited in our ability to …

Exploring T cell receptor repertoires in myocardial diseases

DED Ashour, K Le Gouge, PP Rainer… - Circulation …, 2024 - Am Heart Assoc
Mounting experimental and clinical evidence has revealed that adaptive immune
mechanisms targeting myocardial antigens are triggered by different forms of cardiac injury …

CD27 on human memory B cells–more than just a surface marker

O Grimsholm - Clinical and Experimental Immunology, 2023 - academic.oup.com
Immunological memory protects the human body from re-infection with an earlier recognized
pathogen. This memory comprises the durable serum antibody titres provided by long-lived …