Related papers: Some mathematical tools for the Lenski experiment
Kingman's model of selection and mutation studies the limit type value distribution in an asexual population of discrete generations and infinite size undergoing selection and mutation. This paper generalizes the model to analyse the…
We revisit the model by Wiser, Ribeck, and Lenski (Science \textbf{342} (2013), 1364--1367), which describes how the mean fitness increases over time due to beneficial mutations in Lenski's long-term evolution experiment. We develop the…
The Lenski experiment investigates the long-term evolution of bacterial populations. Its design allows the direct comparison of the reproductive fitness of an evolved strain with its founder ancestor. It was observed by Wiser et al. (2013)…
This chapter gives a synopsis of recent approaches to model and analyse the evolution of microbial populations under selection. The first part reviews two population genetic models of Lenski's long-term evolution experiment with Escherichia…
Taking into account an evolutionary model of mutations in term of Levy Fights that was previously constructed, we designed an algorithm to reproduce the evolutionary dynamics of the Long-Term Evolution Experiment (LTEE) with E. Coli…
Data from a long time evolution experiment with Escherichia Coli and from a large study on copy number variations in subjects with european ancestry are analyzed in order to argue that mutations can be described as Levy flights in the…
In this paper we develop and test algorithmic techniques to estimate genotypes fitnesses by analysis of observed daily frequency data monitoring the long-term evolution of bacterial populations. In particular, we develop a non-linear least…
Two powerful and complementary experimental approaches are commonly used to study the cell cycle and cell biology: One class of experiments characterizes the statistics (or demographics) of an unsynchronized exponentially-growing…
Laboratory experiments with bacterial colonies, under well-controlled conditions often lead to evolutionary diversification, where at least two ecotypes emerge from an initially monomorphic population. Empirical evidence suggests that such…
The data we analyze derives from the observation of numerous cells of the bacterium Escherichia coli (E. coli) growing and dividing. Single cells grow and divide to give birth to two daughter cells, that in turn grow and divide. Thus, a…
Levy flights in the space of mutations model time evolution of bacterial DNA. Parameters in the model are adjusted in order to fit observations coming from the Long Time Evolution Experiment with E. Coli.
Antibiotic resistance is a growing public health problem. To gain a fundamental understanding of resistance evolution, a combination of systematic experimental and theoretical approaches is required. Evolution experiments combined with…
Genetic interactions can strongly influence the fitness effects of individual mutations, yet the impact of these epistatic interactions on evolutionary dynamics remains poorly understood. Here we investigate the evolutionary role of…
The recent interest in human dynamics has led researchers to investigate the stochastic processes that explain human behaviour in various contexts. Here we propose a generative model to capture the dynamics of survival analysis,…
Recently, Lenski et al have carried out an experiment on bacterial evolution. Their findings support the theory of punctuated equilibrium in biological evolution. We show that the M=2 Bak-Sneppen model can explain some of the experimental…
Stochastic reaction networks are mathematical models with a wide range of applications in biochemistry, ecology, and epidemiology, and are often complex to analyze. Except for some special cases, it is generally difficult to predict how the…
Radical shifts in the genetic composition of large cell populations are rare events with quite low probabilities, which direct numerical simulations generally fail to evaluate accurately. In this paper, we develop a theoretical large…
This brief discusses evolutionary game theory as a powerful and unified mathematical tool to study evolution of collective behaviours. It summarises some of my recent research directions using evolutionary game theory methods, which include…
The variability in cell size of an isogenic population of Escherichia coli has been widely reported in experiment. The probability density function (PDF) of cell lengths has been variously described by exponential and lognormal functions.…
With the development of high throughput sequencing technology, it becomes possible to directly analyze mutation distribution in a genome-wide fashion, dissociating mutation rate measurements from the traditional underlying assumptions.…