相关论文: A model for mutation in bacterial populations
The study of common heritability, or co-heritability, among multiple traits has been widely established in quantitative and molecular genetics. However, in bacteria, genome-based estimation of heritability has only been considered very…
We introduce a Markov model for the evolution of a gene family along a phylogeny. The model includes parameters for the rates of horizontal gene transfer, gene duplication, and gene loss, in addition to branch lengths in the phylogeny. The…
We study the backwards Markov chain for the Bak-Sneppen model of biological evolution and derive its corresponding reversibility equations. We show that, in contrast to the forwards Markov chain, the dynamics of the backwards chain…
This note works out an advection-diffusion approximation to the density of a population of E. coli bacteria undergoing chemotaxis in a one-dimensional space. Simulations show the high quality of predictions under a shallow-gradient regime.
The evolution of antimicrobial resistance generally occurs in an environment where antimicrobial concentration is variable, which has dramatic consequences on the microorganisms' fitness landscape, and thus on the evolution of resistance.…
Understanding the evolution of cooperation is pivotal in biology and social science. Public resources sharing is a common scenario in the real world. In our study, we explore the evolutionary dynamics of cooperation on a regular graph with…
We present a non-neutral stochastic model for the dynamics taking place in a meta-community ecosystems in presence of migration. The model provides a framework for describing the emergence of multiple ecological scenarios and behaves in two…
A variety of genome transformations can occur as a microbial population adapts to a large environmental change. In particular, genomic surveys indicate that, following the transition to an obligate, host-dependent symbiont, the density of…
We are interested in modelling Darwinian evolution, resulting from the interplay of phenotypic variation and natural selection through ecological interactions. Our models are rooted in the microscopic, stochastic description of a population…
We consider a nonlinear partial differential equation of conservation type to describe the dynamics of vesicular stomatitis virus observed in aliquots of fixed particle number taken from an evolving clone at periodic intervals of time…
We investigate a continuous time, probability measure-valued dynamical system that describes the process of mutation-selection balance in a context where the population is infinite, there may be infinitely many loci, and there are weak…
We have created a genome-scale network reconstruction of Escherichia coli metabolism. Existing reconstructions were improved in terms of annotation standards, to facilitate their subsequent use in dynamic modelling. The resultant network is…
Motile bacteria can migrate along chemical gradients in a process known as chemotaxis. When exposed to uniform environmental stress, Escherichia coli cells coordinate their chemotactic responses to form millimeter-sized condensates…
We present a theoretical as well as experimental investigation of a population of self-replicating segments of code subject to random mutation and survival of the fittest. Under the assumption that such a system constitutes a minimal system…
Spatial constraints such as rigid barriers affect the dynamics of cell populations, potentially altering the course of natural evolution. In this paper, we investigate the population genetics of Escherichia coli proliferating in…
The purpose of this note is to provide proofs for some facts about the NK model of evolution proposed by Kauffman and Levin. In the case of normally distributed fitness summands, some of these facts have been previously conjectured and…
We have simulated demographic changes in the human population using the Penna microscopic model, based on the simple Monte Carlo method. The results of simulations have shown that during a few generations changes in the genetic pool of a…
We consider integro-differential models describing the evolution of a population structured by a quantitative trait. Individuals interact competitively, creating a strong selection pressure on the population. On the other hand, mutations…
Epidemiological models describe the spread of an infectious disease within a population. They capture microscopic details on how the disease is passed on among individuals in various different ways, while making predictions about the state…
A number of studies have suggested using comparisons between DNA sequences of closely related bacterial isolates to estimate the relative rate of recombination to mutation for that bacterial species. We consider such an approach which uses…