Related papers: How a well-adapted immune system is organized
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…
We study some simple mathematical models designed to test the following hypothesis: can a pathogen escape the immune system only because of its high probability of mutation? We propose both spatial and non-spatial models. In all of our…
The immune system provides an ideal metaphor for anomaly detection in general and computer security in particular. Based on this idea, artificial immune systems have been used for a number of years for intrusion detection, unfortunately so…
Contagious processes, such as spread of infectious diseases, social behaviors, or computer viruses, affect biological, social, and technological systems. Epidemic models for large populations and finite populations on networks have been…
The immune system normally protects the human host against death by infection. However, when an immune response is mistakenly directed at self antigens, autoimmune disease can occur. We describe a model of protein evolution to simulate the…
Efficient testing and vaccination protocols are critical aspects of epidemic management. To study the optimal allocation of limited testing and vaccination resources in a heterogeneous contact network of interacting susceptible, recovered,…
The coming 5G networks have been enabling the creation of a wide variety of new services and applications which demand a new network security architecture. Immunology is the study of the immune system in vertebrates (including humans) which…
T-cells play a key role in adaptive immunity by mounting specific responses against diverse pathogens. An effective binding between T-cell receptors (TCRs) and pathogen-derived peptides presented on Major Histocompatibility Complexes (MHCs)…
Zoonotic pathogens represent a growing global risk, yet the speed of adaptive immune activation across mammalian species remains poorly understood. Despite orders-of-magnitude differences in size and metabolic rate, we show that the time to…
Some bacteria and archaea possess an immune system, based on the CRISPR-Cas mechanism, that confers adaptive immunity against phage. In such species, individual bacteria maintain a "cassette" of viral DNA elements called spacers as a memory…
The mammalian adaptive immune system has evolved over millions of years to become an incredibly effective defense against foreign antigens. The adaptive immune system's humoral response creates plasma B cells and memory B cells, each with…
Many pathogens spread primarily via direct contact between infected and susceptible hosts. Thus, the patterns of contacts or contact network of a population fundamentally shapes the course of epidemics. While there is a robust and growing…
In this paper, we study the dynamics of epidemic processes taking place in temporal and adaptive networks. Building on the activity-driven network model, we propose an adaptive model of epidemic processes, where the network topology…
A persistent public health challenge is finding immunization schemes that are effective in combating highly mutable pathogens such as HIV and influenza viruses. To address this, we analyze a simplified model of affinity maturation, the…
Transforming error-prone immunosequencing datasets into antibody repertoires is a fundamental problem in immunogenomics, and a prerequisite for studies of immune responses. Although various repertoire reconstruction algorithms were released…
Mechanisms of immunity, and of the host-pathogen interactions in general are among the most fundamental problems of medicine, ecology, and evolution studies. Here, we present a microscopic, protein-level, sequence-based model of immune…
Despite being similar in structure, functioning, and size viral pathogens enjoy very different mostly well-defined ways of life. They occupy their hosts for a few days (influenza), for a few weeks (measles), or even lifelong (HCV), which…
The human immune system depends on a highly diverse collection of antibody-making B cells. B cell receptor sequence diversity is generated by a random recombination process called "rearrangement" forming progenitor B cells, then a Darwinian…
The dynamics of contact networks and epidemics of infectious diseases often occur on comparable time scales. Ignoring one of these time scales may provide an incomplete understanding of the population dynamics of the infection process. We…
During an epidemic outbreak, individuals often modify their behavior in response to global prevalence cues, using spatially mediated adaptations such as reduced mobility or transmission range. In this work, we investigate the impact of…