种群与进化
Effective public health decisions require early reliable inference of infectious disease properties. In this paper we assess the ability to infer infectious disease attributes from population-level stochastic epidemic trajectories. In…
Viruses present an amazing genetic variability. An ensemble of infecting viruses, also called a viral quasispecies, is a cloud of mutants centered around a specific genotype. The simplest model of evolution, whose equilibrium state is…
In stochastic population dynamics, stochastic wandering can produce transition to an absorbing state. In particular, under Allee effects, low densities amplify the possibility of population collapse. We investigate this in an…
Evolution occurs in populations of reproducing individuals. In stochastic descriptions of evolutionary dynamics, such as the Moran process, individuals are chosen randomly for birth and for death. If the same type is chosen for both steps,…
Multilevel selection occurs when short-term individual-level reproductive interests conflict with longer-term group-level fitness effects. Detecting and quantifying this phenomenon is key to understanding evolution of traits ranging from…
Living cells maintain size homeostasis by actively compensating for size fluctuations. Here, we present two stochastic maps that unify phenomenological models by integrating fluctuating single-cell growth rates and size-dependent noise…
We explore the connection between evolution and large-deviation theory. To do so, we study evolutionary dynamics in which individuals experience mutations, reproduction, and selection using variants of the Moran model. We show that, in the…
Phage display is a powerful laboratory technique used to study the interactions between proteins and other molecules, whether other proteins, peptides, DNA or RNA. The under-utilisation of this data in conjunction with deep learning models…
Cooperation in large groups and one-shot interactions is often hindered by freeloading. Punishment can enforce cooperation, but it is usually regarded as wasteful because the costs of punishing offset its benefits. Here, we analyze an…
Fitness consequence of dispersal depends on property of the entire landscape, which patches are available and what are the cost of moving. These are information that are not available locally when an organism make the decision to disperse.…
We propose a mathematical model of Antimicrobial Resistance in the host to predict the failure of two antagonists of bacterial growth: the immune response and a single-antibiotic therapy. After characterising the initial bacterial load that…
In this paper, we extend the demographic eco-evolutionary game approach, based on explicit birth and death dynamics instead of abstract "fitness" interpreted as an abstract "Malthusian parameter", by the introduction of the delay resulting…
Background: Antimicrobial resistance (AMR) is a major global public health problem, contributing to an estimated 4.95 million deaths in 2019 and projected to cause up to 10 million deaths annually and 100 trillion dollars in cumulative…
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…
Serine hydroxymethyltransferase is an essential enzyme in the Escherichia coli folate pathway, yet it has not been adopted as an antibacterial target, unlike DHFR, DHPS, or thymidylate synthase. To investigate this discrepancy, we applied a…
The survival of populations hinges on their ability to offset local extinctions through new colonizations. The dispersal area ($A$) plays a crucial role in this process, as it determines the probability of finding colonizable vacant sites.…
The perfect phylogeny mixture (PPM) model is useful due to its simplicity and applicability in scenarios where mutations can be assumed to accumulate monotonically over time. It is the underlying model in many tools that have been used, for…
We consider a multitype Galton-Watson process that allows for the mutation and reversion of individual types in discrete and continuous time. In this setting, we explicitly compute the time evolution of quantities such as the mean and…
A kernel density estimator (KDE) is one of the most popular non-parametric density estimators. In this paper we focus on a best bandwidth selection method for use in an analogue of a classical KDE using the tropical symmetric distance,…
Kinetic theory frameworks are widely used for modeling stochastic interacting systems, where the evolution primarily depends on binary interactions. Recently, in this framework the action of the external force field has been introduction in…