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 …

Multi-omics analysis: Paving the path toward achieving precision medicine in cancer treatment and immuno-oncology

V Raufaste-Cazavieille, R Santiago… - Frontiers in Molecular …, 2022 - frontiersin.org
The acceleration of large-scale sequencing and the progress in high-throughput
computational analyses, defined as omics, was a hallmark for the comprehension of the …

Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire

OL Rodriguez, Y Safonova, CA Silver, K Shields… - Nature …, 2023 - nature.com
Variation in the antibody response has been linked to differential outcomes in disease, and
suboptimal vaccine and therapeutic responsiveness, the determinants of which have not …

The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires

M Pavlović, L Scheffer, K Motwani, C Kanduri… - Nature Machine …, 2021 - nature.com
Adaptive immune receptor repertoires (AIRR) are key targets for biomedical research as
they record past and ongoing adaptive immune responses. The capacity of machine …

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 …

Molecular big data in sports sciences: state-of-art and future prospects of OMICS-based sports sciences

M Sellami, MA Elrayess, L Puce… - Frontiers in molecular …, 2022 - frontiersin.org
Together with environment and experience (that is to say, diet and training), the biological
and genetic make-up of an athlete plays a major role in exercise physiology. Sports …

Biological controls for standardization and interpretation of adaptive immune receptor repertoire profiling

J Trück, A Eugster, P Barennes, CM Tipton… - Elife, 2021 - elifesciences.org
Use of adaptive immune receptor repertoire sequencing (AIRR-seq) has become
widespread, providing new insights into the immune system with potential broad clinical and …

TCR repertoire diversity in Multiple Sclerosis: High-dimensional bioinformatics analysis of sequences from brain, cerebrospinal fluid and peripheral blood

R Amoriello, M Chernigovskaya, V Greiff… - …, 2021 - thelancet.com
Background T cells play a key role in the pathogenesis of multiple sclerosis (MS), a chronic,
inflammatory, demyelinating disease of the central nervous system (CNS). Although several …

Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification

C Kanduri, M Pavlović, L Scheffer, K Motwani… - …, 2022 - academic.oup.com
Background Machine learning (ML) methodology development for the classification of
immune states in adaptive immune receptor repertoires (AIRRs) has seen a recent surge of …

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 …