Related papers: The role of haplotype complementation and purifyin…
Surnames and nonrecombining alleles are inherited from a single parent in a highly similar way. A simple birth-death model with mutations can accurately describe this process. Exponentially growing and constant populations are investigated,…
When predicting the fate and consequences of recurring deleterious mutations in self-fertilising populations most models developed make the assumption that populations have discrete non-overlapping generations. This makes them biologically…
We examine the evolution of expression patterns and the organization of genetic information in populations of self-replicating digital organisms. Seeding the experiments with a linearly expressed ancestor, we witness the development of…
Transcription is a fundamental cellular process, and the first step of gene expression. In human cells, it depends on the binding to chromatin of various proteins, including RNA polymerases and numerous transcription factors (TFs).…
In this paper, we consider the evolution of an (infinitely large) population under recombination and additional evolutionary forces, modelled by a measure-valued ordinary differential equation. We provide a stochastic representation for the…
In this short communication, we shall explore a nonlinear discrete dynamical system that naturally occurs in population systems to describe a transmission of a trait from parents to their offspring. We consider a Mendelian inheritance for a…
The compartmentalization of distinct templates in protocells and the exchange of templates between them (migration) are key elements of a modern scenario for prebiotic evolution. Here we use the diffusion approximation of population…
We model and study the genetic evolution and conservation of a population of diploid hermaphroditic organisms, evolving continuously in time and subject to resource competition. In the absence of mutations, the population follows a 3-type…
How does the interplay between selection, mutation and horizontal gene transfer modify the phenotypic distribution of a bacterial or cell population? While horizontal gene transfer, which corresponds to the exchange of genetic material…
The combination of multiple classifiers using ensemble methods is increasingly important for making progress in a variety of difficult prediction problems. We present a comparative analysis of several ensemble methods through two case…
Identifying the complete set of functional elements within the human genome would be a windfall for multiple areas of biological research including medicine, molecular biology, and evolution. Complete knowledge of function would aid in the…
It has been a puzzling question why some organisms reproduce sexually. Fisher and Muller hypothesized that reproducing by sex can speed up the evolution. They explained that in the sexual reproduction, recombination can combine beneficial…
Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted…
We study a population of $N$ individuals evolving according to a biparental Moran model with two types, one being advantaged compared to the other. The advantage is conferred by a Mendelian mutation, which reduces the death probability of…
Gene expression programming, a genotype/phenotype genetic algorithm (linear and ramified), is presented here for the first time as a new technique for the creation of computer programs. Gene expression programming uses character linear…
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 introduce a model of molecular evolution in which the fitness of an individual depends both on its own and on the parent's genotype. The model can be solved by means of a nonlinear mapping onto the standard quasispecies model. The…
When biological populations expand into new territory, the evolutionary outcomes can be strongly influenced by genetic drift, the random fluctuations in allele frequencies. Meanwhile, spatial variability in the environment can also…
Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. We describe a…
We study the impact of a hard selective sweep on the genealogy of partially linked neutral loci in the vicinity of the positively selected allele. We consider a sexual population of stochastically varying size and, focusing on two…