Adaptive immune receptor repertoire analysis
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 …
(AIRR) of an individual. The AIRR is a unique collection of antigen-specific receptors that …
[HTML][HTML] T-cell repertoire analysis and metrics of diversity and clonality
J Chiffelle, R Genolet, MAS Perez, G Coukos… - Current opinion in …, 2020 - Elsevier
Highlights•Immune fitness in health and disease depends notably on the diversity of cellular
repertoires.•Single-cell sequencing is fostering the understanding of clonal diversity of T-cell …
repertoires.•Single-cell sequencing is fostering the understanding of clonal diversity of T-cell …
Hopfield networks is all you need
We introduce a modern Hopfield network with continuous states and a corresponding
update rule. The new Hopfield network can store exponentially (with the dimension of the …
update rule. The new Hopfield network can store exponentially (with the dimension of the …
A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding
Antibody-antigen binding relies on the specific interaction of amino acids at the paratope-
epitope interface. The predictability of antibody-antigen binding is a prerequisite for de novo …
epitope interface. The predictability of antibody-antigen binding is a prerequisite for de novo …
Neoantigen-specific CD8 T cells with high structural avidity preferentially reside in and eliminate tumors
J Schmidt, J Chiffelle, MAS Perez, M Magnin… - Nature …, 2023 - nature.com
The success of cancer immunotherapy depends in part on the strength of antigen
recognition by T cells. Here, we characterize the T cell receptor (TCR) functional (antigen …
recognition by T cells. Here, we characterize the T cell receptor (TCR) functional (antigen …
GIANA allows computationally-efficient TCR clustering and multi-disease repertoire classification by isometric transformation
Similarity in T-cell receptor (TCR) sequences implies shared antigen specificity between
receptors, and could be used to discover novel therapeutic targets. However, existing …
receptors, and could be used to discover novel therapeutic targets. However, existing …
T cell antigen discovery
AV Joglekar, G Li - Nature methods, 2021 - nature.com
T cells respond to threats in an antigen-specific manner using T cell receptors (TCRs) that
recognize short peptide antigens presented on major histocompatibility complex (MHC) …
recognize short peptide antigens presented on major histocompatibility complex (MHC) …
Modern hopfield networks and attention for immune repertoire classification
A central mechanism in machine learning is to identify, store, and recognize patterns. How to
learn, access, and retrieve such patterns is crucial in Hopfield networks and the more recent …
learn, access, and retrieve such patterns is crucial in Hopfield networks and the more recent …
Mapping the functional landscape of T cell receptor repertoires by single-T cell transcriptomics
Many experimental and bioinformatics approaches have been developed to characterize the
human T cell receptor (TCR) repertoire. However, the unknown functional relevance of TCR …
human T cell receptor (TCR) repertoire. However, the unknown functional relevance of TCR …
T cell repertoire profiling and the mechanism by which HLA-B27 causes ankylosing spondylitis
J Garrido-Mesa, MA Brown - Current rheumatology reports, 2022 - Springer
Abstract Purpose of Review Ankylosing spondylitis (AS) is strongly associated with the HLA-
B27 gene. The canonical function of HLA-B27 is to present antigenic peptides to CD8 …
B27 gene. The canonical function of HLA-B27 is to present antigenic peptides to CD8 …