相关论文: Genetic transfer in Staphylococcus: a case study o…
Cell signaling, gene expression, and metabolism are affected by cell-cell heterogeneity and random changes in the environment. The effects of such fluctuations on cell signaling and gene expression have recently been studied intensively…
Large populations may contain numerous simultaneously segregating polymorphisms subject to natural selection. Since selection acts on individuals whose fitness depends on many loci, different loci affect each other's dynamics. This leads to…
We introduce a Markov model for the evolution of a gene family along a phylogeny. The model includes parameters for the rates of horizontal gene transfer, gene duplication, and gene loss, in addition to branch lengths in the phylogeny. The…
A hybrid phase transition (HPT) that exhibits properties of continuous and discontinuous phase transitions at the same transition point has been observed in diverse complex systems. Previous studies of the HPTs on complex networks mainly…
The study of common heritability, or co-heritability, among multiple traits has been widely established in quantitative and molecular genetics. However, in bacteria, genome-based estimation of heritability has only been considered very…
The colonic mucus layer is a dynamic and complex structure formed by secreted and transmembrane mucins, which are high-molecular-weight and heavily glycosylated proteins. Colonic mucus consists of a loose outer layer and a dense…
We consider a single genetic locus with two alleles $A_1$ and $A_2$ in a large haploid population. The locus is subject to selection and two-way, or recurrent, mutation. Assuming the allele frequencies follow a Wright-Fisher diffusion and…
The haloarchaea are aerobic, heterotrophic, photophosphorylating prokaryotes, whose supposed closest relatives and ancestors, the methanogens, are CO2-reducing, anaerobic chemolithotrophs. Using two available haloarchaeal genomes we firstly…
We present a comparative analysis of large-scale topological and evolutionary properties of transcription networks in three species, the two distant bacteria E. coli and B. subtilis, and the yeast S. cerevisiae. The study focuses on the…
In the context of pharmacogenomics, whole genome sequencing provides a powerful approach for identifying correlations between response variability to specific drugs and genomic polymorphisms in a population, in an unbiased manner. In this…
Here we investigate translational regulation in bacteria by analyzing the distribution of start codons in fully assembled genomes. We report 36 genes (infC, rpoC, rnpA, etc.) showing a preference for non-AUG start codons in evolutionarily…
So far mutations analysis was performed in terms of transitions and trasversions, so on the basis of the molecule, or in terms of GC-content and isochors, through the quantification of GC->AT mutations over AT->GC mutations. We tried a…
We explore the interaction between two genetic incompatibilities (underdominant loci in diploid organisms) in a population occupying a one-dimensional space. We derive a system of partial differential equations describing the dynamics of…
Many methods have been developed for finding the commonalities between different organisms to study their phylogeny. The structure of metabolic networks also reveal valuable insights into metabolic capacity of species as well as into the…
Motivated by observations in sequence data of herpesviruses, we introduce a multi-locus model for the joint evolution of different genotypes in a virus population that is distributed across a population of hosts. In the model, virus…
A protocell model consisting of mutually catalyzing molecules is studied in order to investigate how chemical compositions are transferred recursively through cell divisions under replication errors. Depending on the path rate, the numbers…
We have analyzed DNA sequences of known genes from 16 yeast chromosomes (Saccharomyces cerevisiae) in terms of oligonucleotides. We have noticed that the relative abundances of oligonucleotide usage in the genome follow a long-tail…
Pattern analysis of tandem repeats in gene is an indispensable computational approach to the understanding of the gene expression and pathogenesis of diseases. This research applied a computational motif model and database techniques to…
Antimicrobial resistance (AMR) poses a significant threat to public health by increasing mortality, extending hospital stays, and increasing healthcare costs. It affects people of all ages and affects health services, veterinary medicine,…
Understanding the population structure and patterns of gene flow within species is of fundamental importance to the study of evolution. In the fields of population and evolutionary genetics, measures of genetic differentiation are commonly…