Related papers: Modeling gene's length distribution in genomes
Research in quantitative evolutionary genomics and systems biology led to the discovery of several universal regularities connecting genomic and molecular phenomic variables. These universals include the log-normal distribution of the…
We extend and develop our previous work on the evolution of a network of cosmic strings. The new treatment is based on an analysis of the probability distribution of the end-to-end distance of a randomly chosen segment of left-moving string…
Gene-sharing networks provide a powerful framework to study the evolution of viruses and mobile genetic elements. These bipartite networks, which link genes to the genomes that contain them, exhibit characteristic degree distributions: a…
The classification of life should be based upon the fundamental mechanism in the evolution of life. We found that the global relationships among species should be circular phylogeny, which is quite different from the common sense based upon…
We introduce a model for describing the defected growth of striped patterns. This model, while roughly related to the Swift-Hohenberg model, generates a quite different mixture of defects during phase ordering. We find two characteristic…
By introducing the notions of living and dead nodes a new model of random tree evolution with continuous time parameter has been constructed. It is assumed that two random variables, the lifetime and the offspring number of living nodes…
An important question in biology is how the relative size of different organs is kept nearly constant during growth of an animal. This property, called proportionate growth, has received increased attention in recent years. We discuss our…
Here we provide a detailed analysis, along with some extensions and additonal investigations, of a recently proposed self-organised model for the evolution of complex networks. Vertices of the network are characterised by a fitness variable…
A well-established model for the genealogy of a large population in equilibrium is Kingman's coalescent. For the population together with its genealogy evolving in time, this gives rise to a time-stationary tree-valued process. We study the…
We introduce a population dynamics model, where individual genomes are represented by bit-strings. Selection is described by death probabilities which depend on these genomes, and new individuals continuously replace the ones that die,…
For one-dimensional growth processes we consider the distribution of the height above a given point of the substrate and study its scale invariance in the limit of large times. We argue that for self-similar growth from a single seed the…
We have presented the basic knowledge on the structure of molecules coding the genetic information, mechanisms of transfer of this information from DNA to proteins and phenomena connected with replication of DNA. In particular, we have…
A mathematical model of interacting species filling ecological niches left by the extinction of others is introduced. Species organize themselves into genera of all sizes. The size of a genus on average grows linearly with its age,…
The number of extant individuals within a lineage, as exemplified by counts of species numbers across genera in a higher taxonomic category, is known to be a highly skewed distribution. Because the sublineages (such as genera in a clade)…
In this work we develop a microscopic physical model of early evolution, where phenotype,organism life expectancy, is directly related to genotype, the stability of its proteins in their native conformations which can be determined exactly…
This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include…
We study the phase-ordering kinetics of the one-dimensional Heisenberg model with conserved order parameter, by means of scaling arguments and numerical simulations. We find a rich dynamical pattern with a regime characterized by two…
The frequency distributions of DNA k-mers are shaped by fundamental biological processes and offer a window into genome structure and evolution. Inspired by analogies to natural language, prior studies have attempted to model genomic k-mer…
We describe the simulation method of modelling the population evolution using Monte Carlo based on the Penna model. Individuals in the populations are represented by their diploid genomes. Genes expressed after the minimum reproduction age…
This paper introduces a new way to define a genome rearrangement distance, using the concept of mean first passage time from probability theory. Crucially, this distance estimate provides a genuine metric on genome space. We develop the…