Related papers: Population genomics of intrapatient HIV-1 evolutio…
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…
Many mathematical models of evolution assume that all individuals experience the same environment. Here, we study the Moran process in heterogeneous environments. The population is of finite size with two competing types, which are exposed…
We will study a mathematical model of the human immunodeficiency virus (HIV) infection in the presence of combination therapy that includes within-host infectious dynamics. The deterministic model requires us to analyze asymptotic stability…
Intraspecific trait variation has been increasingly recognized as an important factor in determining species interaction and diversity. Eco-evolutionary models have studied the distribution of trait values within a population that changes…
Genotype networks are a method used in systems biology to study the "innovability" of a set of genotypes having the same phenotype. In the past they have been applied to determine the genetic heterogeneity, and stability to mutations, of…
Evolutionary dynamics and patterns of molecular evolution are strongly influenced by selection on linked regions of the genome, but our quantitative understanding of these effects remains incomplete. Recent work has focused on predicting…
Oxidative stress, a reaction caused by the imbalance between the reactive oxygen species of human organism and its ability to detoxify reactive intermediates and to repair the resulting damage plays an important role in HIV-infections. On…
Antigenic escape constitutes the main mechanism allowing rapidly evolving viruses to achieve endemicity. Beyond granting immune escape, empirical evidence also suggests that mutations of viruses might increase their inter-host…
Capturing the structured mixing within a population is key to the reliable projection of infectious disease dynamics and hence informed control. Both heterogeneity in the number of contacts and age-structured mixing have been repeatedly…
This research gives a thorough examination of an HIV infection model that includes quiescent cells and immune response dynamics in the host. The model, represented by a system of ordinary differential equations, captures the complex…
Understanding the processes that give rise to quantitative measurements associated with molecular sequence data remains an important issue in statistical phylogenetics. Examples of such measurements include geographic coordinates in the…
We explore the emergence of persistent infection in a patch of population, where the disease progression of the individuals is given by the SIRS model and an individual becomes infected on contact with another infected individual. We…
Men who have sex with men (MSM) remain disproportionately affected by HIV, yet optimizing Pre-exposure Prophylaxis (PrEP) distribution remains a public health challenge. Current guidelines and most modelling studies do not incorporate…
We study the evolution of large but finite asexual populations evolving in fitness landscapes in which all mutations are either neutral or strongly deleterious. We demonstrate that despite the absence of higher fitness genotypes, adaptation…
We explore how heterogeneity in the intensity of interactions between people affects epidemic spreading. For that, we study the susceptible-infected-susceptible model on a complex network, where a link connecting individuals $i$ and $j$ is…
Two species with similar resource requirements respond in a characteristic way to variations in their habitat -- their abundances rise and fall in concert. We use this idea to learn how bacterial populations in the microbiota respond to…
In this paper, we construct a model to describe the transmission of HIV in a homogeneous host population. By considering the specific mechanism of HIV, we derive a model structured in three successive stages: (i) primary infection, (ii)…
Population heterogeneity, especially in individuals' contact networks, plays an important role in transmission dynamics of infectious diseases. For vaccine-preventable diseases, outstanding issues like vaccine hesitancy and availability of…
Population genetics struggles to model extinction; standard models track the relative rather than absolute fitness of genotypes, while the exceptions describe only the short-term transition from imminent doom to evolutionary rescue. But…
Heterogeneity in physical and functional characteristics of cells (e.g. size, cycle time, growth rate, protein concentration) proliferates within an isogenic population due to stochasticity in intracellular biochemical processes and in the…