Related papers: Recombination processes and non-linear Markov chai…
The bioinformatical methods to detect lateral gene transfer events are mainly based on functional coding DNA characteristics. In this paper, we propose the use of DNA traits not depending on protein coding requirements. We introduce several…
In bacterial populations, cells are able to cooperate in order to yield complex collective functionalities. Interest in population-level cellular behaviour is increasing, due to both our expanding knowledge of the underlying biological…
This theory seeks to define species and to explore evolutionary forces and genetic elements in speciation and species maintenance. The theory explains how speciation and species maintenance are caused by natural selection acting on…
More than ever, today we are left with the abundance of molecular data outpaced by the advancements of the phylogenomic methods. Especially in the case of presence of many genes over a set of species under the phylogeny question, more…
The dynamics of recombination in genetics leads to an interesting nonlinear differential equation, which has a natural generalization to a measure valued version. The latter can be solved explicitly under rather general circumstances. It…
In phylogenetic studies, the evolution of molecular sequences is assumed to have taken place along the phylogeny traced by the ancestors of extant species. In the presence of lateral gene transfer (LGT), however, this may not be the case,…
Many types of bacteria can survive under stress by switching stochastically between two different phenotypes: the "normals" who multiply fast, but are vulnerable to stress, and the "persisters" who hardly multiply, but are resilient to…
Historical sciences like evolutionary biology reconstruct past events by using the traces that the past has bequeathed to the present. The Markov Chain Convergence Theorem and the Data Processing Inequality describe how the mutual…
The structure of heterogeneous networks and human mobility patterns profoundly influence the spreading of endemic diseases. In small-scale communities, individuals engage in social interactions within confined environments, such as homes…
This paper introduces a stochastic adaptive dynamics model for the interplay of several crucial traits and mechanisms in bacterial evolution, namely dormancy, horizontal gene transfer (HGT), mutation and competition. In particular, it…
We investigate the interplay between two fundamental mechanisms of microbial population dynamics and evolution called dormancy and horizontal gene transfer. The corresponding traits come in many guises and are ubiquitous in microbial…
Large scale databases are available that contain homologous gene families constructed from hundreds of complete genome sequences from across the three domains of Life. Here we discuss approches of increasing complexity aimed at extracting…
Conjugation is the primary mechanism of horizontal gene transfer that spreads antibiotic resistance among bacteria. Although conjugation normally occurs in surface-associated growth (e.g., biofilms), it has been traditionally studied in…
It is known that the stationary distribution of the random walk process is dependent on the structure of the network. This could provide us a solution of the network reconstruction. However, the stationary distribution of the random walk…
We solve a simple model that supports a dynamic phase transition and show conditions for the existence of the transition. Using methods of large deviation theory we analytically compute the probability distribution for activity and entropy…
For a given permutation or set partition there is a natural way to assign a genus. Counting all permutations or partitions of a fixed genus according to cycle lengths or block sizes, respectively, is the main content of this article. After…
Competition between random genetic drift and natural selection plays a central role in evolution: Whereas non-beneficial mutations often prevail in small populations by chance, mutations that sweep through large populations typically confer…
Understanding flow and transport of bacteria in porous media is crucial to technologies such as bioremediation, biomineralization or enhanced oil recovery. While physicochemical bacteria filtration is well-documented, recent studies showed…
We consider random processes that are history-dependent, in the sense that the distribution of the next step of the process at any time depends upon the entire past history of the process. In general, therefore, the Markov property cannot…
We provide a detailed description of the structure of the transition probabilities and of the hitting distributions of boundary components of a manifold with corners for a degenerate strong Markov process arising in population genetics. The…