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The immune system recognizes a myriad of invading pathogens and their toxic products. It does so with a finite repertoire of antibodies and T cell receptors. We here describe theories that quantify the immune system dynamics. We describe…
T-cell receptor (TCR) interactions with antigenic peptides underpin adaptive immunity and are pivotal for personalized immunotherapy and vaccine development. Despite recent progress, computational modeling of TCR-peptide specificity remains…
Despite the central role that antibodies play in the adaptive immune system and in biotechnology, much remains unknown about the quantitative relationship between an antibody's amino acid sequence and its antigen binding affinity. Here we…
We introduce Ibex, a pan-immunoglobulin structure prediction model that achieves state-of-the-art accuracy in modeling the variable domains of antibodies, nanobodies, and T-cell receptors. Unlike previous approaches, Ibex explicitly…
The classification of diabetes and prediabetes by static glucose thresholds obscures the pathophysiological dysglycemia heterogeneity, primarily driven by insulin resistance (IR), beta-cell dysfunction, and incretin deficiency. This review…
We analyse a minimal model for the primary response in the adaptive immune system comprising three different players: antigens, T and B cells. We assume B-T interactions to be diluted and sampled locally from heterogeneous degree…
The vertebrate immune system is a wonder of modern evolution. Occasionally, however, correlations within the immune system lead to inappropriate recruitment of preexisting T cells against novel viral diseases. We present a random energy…
Machine learning is increasingly used to discover diagnostic and prognostic biomarkers from high-dimensional molecular data. However, a variety of factors related to experimental design may affect the ability to learn generalizable and…
Envelope model also known as multivariate regression model was proposed to solve the multiple response regression problems. It measures the linear association between predictors and multiple responses by using the minimal reducing subspace…
The adaptive immune system of vertebrates can detect, respond to, and memorize diverse pathogens from past experience. While the clonal selection of T helper (Th) cells is the simple and established mechanism to better recognize new…
Antibodies are Y-shaped proteins that protect the host by binding to specific antigens, and their binding is mainly determined by the Complementary Determining Regions (CDRs) in the antibody. Despite the great progress made in CDR design,…
Immunology is the emerging research area which deals with the study of the immune system in any living organism. It is modelled through various computational and mathematical models to deal with the problem facing while to boost the immune…
Recent experimental studies have suggested the ratio between T-helper and T-suppressor lymphocytes as an index of immunosuppression in HIV, cancer, immunosenescence and inflammatory and auto-immune diseases. However, a quantitative…
T cells orchestrate adaptive immune responses upon activation. T cell activation requires sufficiently strong binding of T cell receptors on their surface to short peptides derived from foreign proteins bound to protein products of the…
Immune cells learn about their antigenic targets using tactile sense: during recognition, a highly organized yet dynamic motif, named immunological synapse, forms between immune cells and antigen-presenting cells (APCs). Via synapses,…
The efficient recognition of pathogens by the adaptive immune system relies on the diversity of receptors displayed at the surface of immune cells. T-cell receptor diversity results from an initial random DNA editing process, called VDJ…
Researching the specificity of TCR contributes to the development of immunotherapy and provides new opportunities and strategies for personalized cancer immunotherapy. Therefore, we established a TCR generative specificity detection…
The molecular recognition of T-cell receptors is the hallmark of the adaptive immunity. Given the finiteness of the T-cell repertoire, individual T-cell receptors are necessary to be cross-reactive to multiple antigenic peptides. In this…
Understanding the binding specificity between T-cell receptors (TCRs) and peptide-major histocompatibility complexes (pMHCs) is central to immunotherapy and vaccine development. However, current predictive models struggle with…
Studies of T cells and their clonally unique receptors have shown promise in elucidating the association between immune response and human disease. Methods to identify T-cell receptor clones which expand or contract in response to certain…