Related papers: Multi-lineage evolution in viral populations drive…
In multi-cellular organisms, cells differentiate into multiple types as they divide. States of these cell types, as well as their numbers, are known to be robust to external perturbations; as conceptualized by Waddington's epigenetic…
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…
Common respiratory viruses cause seasonal epidemics in sequential patterns. The underlying mechanisms for this pattern have been debated for some time. For influenza, contenders include temperature, humidity, and vitamin D levels. While…
We propose a hybrid dynamical system approach to model the evolution of a pathogen that experiences different selective pressures according to a stochastic process. In every environment, the evolution of the pathogen is described by a…
We are interested in modeling some two-level population dynamics, resulting from the interplay of ecological interactions and phenotypic variation of individuals (or hosts) and the evolution of cells (or parasites) of two types living in…
Multiple viruses are widely studied because of their negative effect on the health of host as well as on whole population. The dynamics of coinfection is important in this case. We formulated a SIR model that describes the coinfection of…
Which factors govern the evolution of mutation rates and emergence of species? Here, we address this question using a first principles model of life where population dynamics of asexual organisms is coupled to molecular properties and…
The dynamics of a population undergoing selection is a central topic in evolutionary biology. This question is particularly intriguing in the case where selective forces act in opposing directions at two population scales. For example, a…
In an increasingly interconnected world, a key scientific challenge is to examine mechanisms that lead to the widespread propagation of contagions, such as misinformation and pathogens, and identify risk factors that can trigger large-scale…
We use a multitype continuous time Markov branching process model to describe the dynamics of the spread of parasites of two types that can mutate into each other in a common host population. Instead of using a single virulence…
Increasingly, experimentalists and modellers alike have come to recognise the important role of spatial structure in infection dynamics. Almost invariably, spatial computational models of viral infections - as with in vitro experimental…
We considered a {multi-block} molecular model of biological evolution, in which fitness is a function of the mean types of alleles located at different parts (blocks) of the genome. We formulated an infinite population model with selection…
During the recent pandemic, a rise in COVID-19 cases was followed by a decline in influenza. In the absence of cross-immunity, a potential explanation for the observed pattern is behavioral: non-pharmaceutical interventions (NPIs) designed…
Influenza virus contains two highly variable envelope glycoproteins, hemagglutinin (HA) and neuraminidase (NA). The structure and properties of HA, which is responsible for binding the virus to the cell that is being infected, change…
We develop a new structured compartmental model for the coevolutionary dynamics between susceptible and infectious individuals in heterogeneous SI epidemiological systems. In this model, the susceptible compartment is structured by a…
Microbial populations generally evolve in volatile environments, under conditions fluctuating between harsh and mild, e.g. as the result of sudden changes in toxin concentration or nutrient abundance. Environmental variability thus shapes…
Cooperation is a difficult proposition in the face of Darwinian selection. Those that defect have an evolutionary advantage over cooperators who should therefore die out. However, spatial structure enables cooperators to survive through the…
Given a sample of genome sequences from an asexual population, can one predict its evolutionary future? Here we demonstrate that the branching patterns of reconstructed genealogical trees contains information about the relative fitness of…
The theory of life history evolution provides a powerful framework to understand the evolutionary dynamics of pathogens in both epidemic and endemic situations. This framework, however, relies on the assumption that pathogen populations are…
In this study, we propose a novel model describing the coevolution between hosts and pathogens, based on a non-local partial differential equation formalism for populations structured by phenotypic traits. Our objective with this model is…