Related papers: Diversity against adversity: How adaptive immunity…
A new detailed mathematical model for dynamics of immune response to hepatitis B is proposed, which takes into account contributions from innate and adaptive immune responses, as well as cytokines. Stability analysis of different steady…
We discuss the origin of two classes of germinal centers that have been observed during humoral immune responses: Some germinal centers develop very well and give rise to a large number of high affinity antibody producing plasma cells.…
Antibodies, an essential part of our immune system, develop through an intricate process to bind a wide array of pathogens. This process involves randomly mutating DNA sequences encoding these antibodies to find variants with improved…
Existing approaches to modelling antibody concentration data are mostly based on finite mixture models that rely on the assumption that individuals can be divided into two distinct groups: seronegative and seropositive. Here, we challenge…
Classical population genetics a priori assigns fitness to alleles without considering molecular or functional properties of proteins that these alleles encode. Here we study population dynamics in a model where fitness can be inferred from…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
We present an SI epidemic model whereby a continuous variable captures variability in proliferative potential and resistance to infection among susceptibles. The occurrence of heritable, spontaneous changes in these phenotype and the…
We investigate the selective forces that promote the emergence of modularity in nature. We demonstrate the spontaneous emergence of modularity in a population of individuals that evolve in a changing environment. We show that the level of…
We consider the mutual interactions, via cytokine exchanges, among helper lymphocytes, B lymphocytes and killer lymphocytes, and we model them as a unique system by means of a tripartite network. Each part includes all the different clones…
Population dynamics and evolutionary genetics underly the structure of ecosystems, changing on the same timescale for interacting species with rapid turnover, such as virus (e.g. HIV) and immune response. Thus, an important problem in…
A cornerstone of the classical view of tolerance is the elimination of self-reactive T cells during negative selection in the thymus. However, high-throughput T-cell receptor sequencing data has so far failed to detect substantial…
A previously established multiscale population genetics model states that fitness can be inferred from the physical properties of proteins under the physiological assumption that a loss of stability by any protein confers the lethal…
RNA-based vaccination has been broadly applied in the COVID pandemic. A characteristic of the immunization was fast waning immunity. However, the time scale of this process varied considerable for virus subtypes and among individuals.…
An adaptive agent predicting the future state of an environment must weigh trust in new observations against prior experiences. In this light, we propose a view of the adaptive immune system as a dynamic Bayesian machinery that updates its…
Recent advances in diffusion models have shown remarkable potential for antibody design, yet existing approaches apply uniform generation strategies that cannot adapt to each antigen's unique requirements. Inspired by B cell affinity…
1. In recent years many studies have investigated the relationships between different aspects of the immune system and ecology in various organisms. Yet, it remains unclear why individuals differ in their ability to mount an immune response…
We study a well mixed SIR epidemic model with heterogeneous susceptibility and infectivity, allowing for an arbitrary joint distribution of these traits. Using an exact final size formulation and a branching process approximation for early…
Molecular phenotypes link genomic information with organismic functions, fitness, and evolution. Quantitative traits are complex phenotypes that depend on multiple genomic loci. In this paper, we study the adaptive evolution of a…
In this work we employ various methods of analysis (unfolding simulations and comparative analysis of structures and sequences of proteomes of thermophilic organisms) to show that organisms can follow two major strategies of thermophilic…
In this paper, we present a probabilistic analysis of a dynamical particle model for the self-adaptive immune response to cancer, as proposed by the first author in a previous work. The model is motivated by the interplay between immune…