Related papers: How many different clonotypes do immune repertoire…
The human body is able to generate a diverse set of high affinity antibodies, the soluble form of B cell receptors (BCRs), that bind to and neutralize invading pathogens. The natural development of BCRs must be understood in order to design…
When our immune system encounters foreign antigens (i.e., from pathogens), the B cells that produce our antibodies undergo a cyclic process of proliferation, mutation, and selection, improving their ability to bind to the specific antigen.…
Cells often have tens of thousands of receptors, even though only a few activated receptors can trigger full cellular responses. Reasons for the overabundance of receptors remain unclear. We suggest that, in certain conditions, the large…
The diversity of the immune repertoire is initially generated by random rearrangements of the receptor gene during early T and B cell development. Rearrangement scenarios are composed of random events -- choices of gene templates, base pair…
Artificial intelligence (AI) is accelerating progress in modeling T and B cell receptors by enabling predictive and generative frameworks grounded in sequence data and immune context. This chapter surveys recent advances in the use of…
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…
B cells develop high affinity receptors during the course of affinity maturation, a cyclic process of mutation and selection. At the end of affinity maturation, a number of cells sharing the same ancestor (i.e. in the same "clonal family")…
B cell receptor sequences diversify through mutations introduced by purpose-built cellular machinery. A recent paper has concluded that a "templated mutagenesis" process is a major contributor to somatic hypermutation, and therefore…
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…
Recent advances in immunomics have shown that T-cell receptor (TCR) signatures can accurately predict active or recent infection by leveraging the high specificity of TCR binding to disease antigens. However, the extreme diversity of the…
It is known that the majority of the human genome consists of repeated sequences. Furthermore, it is believed that a significant part of the rest of the genome also originated from repeated sequences and has mutated to its current form. In…
We introduce a novel, multi-scale model for affinity maturation, which aims to capture the intra-clonal, inter-clonal and epitope-specific organization of the B cell population in a germinal center. We describe the evolution of the B cell…
A hallmark of the adaptive immune response is the proliferation of pathogen-specific lymphocytes that leave in their wake a long lived population of cells that provide lasting immunity. A subject of ongoing investigation is when during an…
Objectives: In this study, we quantify the growth variability of tumour cell clones from a human leukemia cell line. Materials and methods: We have used microplate spectrophotometry to measure the growth kinetics of hundreds of individual…
A stochastic model for the activation of T-cells is analysed. T-cells are part of the immune system and recognize foreign antigens against a background of the body's own molecules. The model under consideration is a slight generalization of…
We quantify the VDJ recombination and somatic hypermutation processes in human B-cells using probabilistic inference methods on high-throughput DNA sequence repertoires of human B-cell receptor heavy chains. Our analysis captures the…
Phenotypic variation is a hallmark of cellular physiology. Metabolic heterogeneity, in particular, underpins single-cell phenomena such as microbial drug tolerance and growth variability. Much research has focussed on transcriptomic and…
Reproducibility is central to the credibility of scientific findings, yet complete replication studies are costly and infrequent. However, many biological experiments contain internal replication, which is defined as repetition across…
We argue that immune system is an adaptive complex system. It is shown that it has emergent properties. Its network structure is of the small world network type. The network is of the threshold type, which helps in avoiding autoimmunity. It…
RNA virus populations will undergo processes of mutation and selection resulting in a mixed population of viral particles. High throughput sequencing of a viral population subsequently contains a mixed signal of the underlying clones. We…