Related papers: How a well-adapted immune system is organized
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…
In chemotaxis, cells are modulating their migration patterns in response to concentration gradients of a guiding substance. Immune cells are believed to use such chemotactic sensing for remotely detecting and homing in on pathogens.…
This paper describes a receiver that uses an innovative method to predict, according to history of receiver operating metrics (packet lost/well received), the optimum automatic gain control (AGC) index or most appropriate variable gain…
We develop a stochastic model to study the specific response of the immune system. The model is based on the dynamical interaction between Regulatory and Effector CD4+ T cells in the presence of Antigen Presenting Cells inside a lymphatic…
We introduce and analyze a within-host dynamical model of the coevolution between rapidly mutating pathogens and the adaptive immune response. Pathogen mutation and a homeostatic constraint on lymphocytes both play a role in allowing the…
As pathogens spread in a population of hosts, immunity is built up and the pool of susceptible individuals is depleted. This generates selective pressure, to which many human RNA viruses, such as influenza virus or SARS-CoV-2, respond with…
The toxins associated with infectious diseases are potential targets for inhibitors which have the potential for prophylactic or therapeutic use. Many antibodies have been generated for this purpose, and the objective of this study was to…
In this paper, we investigate game-theoretic strategies for containing spreading processes on large-scale networks. Specifically, we consider the class of networked susceptible-infected-susceptible (SIS) epidemics where a large population…
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…
Biological and artificial networks routinely make reliable distinctions between similar inputs, and the rules for making these distinctions are learned. In some ways, self/nonself discrimination in the immune system is similar, being both…
The vertebrate adaptive immune system provides a flexible and diverse set of molecules to neutralize pathogens. Yet, viruses such as HIV can cause chronic infections by evolving as quickly as the adaptive immune system, forming an…
One strategy for winning a coevolutionary struggle is to evolve rapidly. Most of the literature on host-pathogen coevolution focuses on this phenomenon, and looks for consequent evidence of coevolutionary arms races. An alternative…
High-throughput sequencing of B- and T-cell receptors makes it possible to track immune repertoires across time, in different tissues, and in acute and chronic diseases or in healthy individuals. However, quantitative comparison between…
We are frequently faced with a large collection of antibodies, and want to select those with highest affinity for their cognate antigen. When developing a first-line therapeutic for a novel pathogen, for instance, we might look for such…
The adaptive immune system responds to pathogens by selecting clones of cells with specific receptors. While clonal selection in response to particular antigens has been studied in detail, it is unknown how a lifetime of exposures to many…
Protein language models (PLMs) learn contextual representations from protein sequences and are profoundly impacting various scientific disciplines spanning protein design, drug discovery, and structural predictions. One particular research…
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…
We study how the interplay between the memory immune response and pathogen mutation affects epidemic dynamics in two related models. The first explicitly models pathogen mutation and individual memory immune responses, with contacted…
Diseases emerge, persist and vanish in an ongoing battle for available hosts. Hosts, on the other hand, defend themselves by developing immunity that limits the ability of pathogens to reinfect them. We here explore a multi-disease system…
In this chapter, we focus on the problem of containing the spread of diseases taking place in both temporal and adaptive networks (i.e., networks whose structure `adapts' to the state of the disease). We specifically focus on the problem of…