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 …
Computational strategies for dissecting the high-dimensional complexity of adaptive immune repertoires
The adaptive immune system recognizes antigens via an immense array of antigen-binding
antibodies and T-cell receptors, the immune repertoire. The interrogation of immune …
antibodies and T-cell receptors, the immune repertoire. The interrogation of immune …
Optimization of therapeutic antibodies by predicting antigen specificity from antibody sequence via deep learning
The optimization of therapeutic antibodies is time-intensive and resource-demanding,
largely because of the low-throughput screening of full-length antibodies (approximately 1× …
largely because of the low-throughput screening of full-length antibodies (approximately 1× …
Deciphering the language of antibodies using self-supervised learning
An individual's B cell receptor (BCR) repertoire encodes information about past immune
responses and potential for future disease protection. Deciphering the information stored in …
responses and potential for future disease protection. Deciphering the information stored in …
In silico proof of principle of machine learning-based antibody design at unconstrained scale
Generative machine learning (ML) has been postulated to become a major driver in the
computational design of antigen-specific monoclonal antibodies (mAb). However, efforts to …
computational design of antigen-specific monoclonal antibodies (mAb). However, efforts to …
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 …
Single-cell BCR and transcriptome analysis after influenza infection reveals spatiotemporal dynamics of antigen-specific B cells
B cell responses are critical for antiviral immunity. However, a comprehensive picture of
antigen-specific B cell differentiation, clonal proliferation, and dynamics in different organs …
antigen-specific B cell differentiation, clonal proliferation, and dynamics in different organs …
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 …
Observed antibody space: a resource for data mining next-generation sequencing of antibody repertoires
Abs are immune system proteins that recognize noxious molecules for elimination. Their
sequence diversity and binding versatility have made Abs the primary class of …
sequence diversity and binding versatility have made Abs the primary class of …
The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires
Adaptive immune receptor repertoires (AIRR) are key targets for biomedical research as
they record past and ongoing adaptive immune responses. The capacity of machine …
they record past and ongoing adaptive immune responses. The capacity of machine …