相关论文: Genetic Paralog Analysis and Simulations

We consider a probability distribution on the set of Boolean functions in n variables which is induced by random Boolean expressions. Such an expression is a random rooted plane tree where the internal vertices are labelled with connectives…

Qian, Luscombe and Gerstein [J. Molecular Biol. 313 (2001) 673--681] introduced a model of the diversification of protein folds in a genome that we may formulate as follows. Consider a multitype Yule process starting with one individual in…

Biological aging is characterized by an age-dependent increase in the probability of death and by a decrease in the reproductive capacity. Individual age-dependent rates of survival and reproduction have a strong impact on population…

The efficiency of Monte Carlo samplers is dictated not only by energetic effects, such as large barriers, but also by entropic effects that are due to the sheer volume that is sampled. The latter effects appear in the form of an entropic…

Although species longevity is subject to a diverse range of selective forces, the mortality curves of a wide variety of organisms are rather similar. We argue that aging and its universal characteristics may have evolved by means of a…

We deal with a random graph model where at each step, a vertex is chosen uniformly at random, and it is either duplicated or its edges are deleted. Duplication has a given probability. We analyse the limit distribution of the degree of a…

Correlations may affect propagation processes on complex networks. To analyze their effect, it is useful to build ensembles of networks constrained to have a given value of a structural measure, such as the degree-degree correlation $r$,…

Coalescent processes, including mutation, are derived from Moran type population models admitting large offspring numbers. Including mutation in the coalescent process allows for quantifying the turnover of alleles by computing the…

For two genotypes that have the same mean number of offspring but differ in the variance in offspring number, natural selection will favor the genotype with lower variance. The concept of fitness becomes cloudy under these conditions…

It is argued that the present log-normal distribution of language sizes is, to a large extent, a consequence of demographic dynamics within the population of speakers of each language. A two-parameter stochastic multiplicative process is…

We propose and study a class-expansion/innovation/loss model of genome evolution taking into account biological roles of genes and their constituent domains. In our model numbers of genes in different functional categories are coupled to…

A theoretical and experimental analysis is made of the effects of self-adaptation in a simple evolving system. Specifically, we consider the effects of coding the mutation and crossover probabilities of a genetic algorithm evolving in…

We numerically study the large deviation function of the total current, which is the sum of local currents over all bonds, for the symmetric and asymmetric simple exclusion processes with open boundary conditions. We estimate the generating…

This paper investigates the influence of genotype size on evolutionary algorithms' performance. We consider genotype compression (where genotype is smaller than phenotype) and expansion (genotype is larger than phenotype) and define…

Although the role of lateral gene transfer is well recognized in the evolution of bacteria, it is generally assumed that it has had less influence among eukaryotes. To explore this hypothesis we compare the dynamics of genome evolution in…

Populations can be genetically isolated both by geographic distance and by differences in their ecology or environment that decrease the rate of successful migration. Empirical studies often seek to investigate the relationship between…

With the number of sequenced genomes now over one hundred, and the availability of rough functional annotations for a substantial proportion of their genes, it has become possible to study the statistics of gene content across genomes. Here…

We show that simple stochastic models of genome evolution lead to power law asymptotics of protein domain family size distribution. These models, called Birth, Death and Innovation Models (BDIM), represent a special class of balanced…

We calculate the probability distribution of repetitions of ancestors in a genealogical tree for simple neutral models of a closed population with sexual reproduction and non-overlapping generations. Each ancestor at generation g in the…

A phylogenetic birth-and-death model is a probabilistic graphical model for a so-called phylogenetic profile, i.e., the size distribution for a homolog gene family at the terminal nodes of a phylogeny. Profile datasets are used in…