相关论文: Genetic transfer in Staphylococcus: a case study o…

Background: There is a 3-fold redundancy in the Genetic Code; most amino acids are encoded by more than one codon. These synonymous codons are not used equally; there is a Codon Usage Bias (CUB). This article will provide novel information…

Genotype networks are a method used in systems biology to study the "innovability" of a set of genotypes having the same phenotype. In the past they have been applied to determine the genetic heterogeneity, and stability to mutations, of…

Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…

In ecology and population dynamics, gene-flow refers to the transfer of a trait from one population to another. This phenomenon appears in studying the evolution of social features, such as languages. From the mathematical point of view,…

Molecular testing is rapidly becoming integral to the global tuberculosis (TB) control effort. Uncommon mechanisms of resistance can escape detection by these platforms and lead to the development of Multi-Drug Resistant (MDR) strains. This…

We investigate a multi-locus evolutionary model which is based on the DNA shuffling protocol widely applied in \textit{in vitro} directed evolution. This model incorporates selection, recombination and point mutations. The simplicity of the…

The topological data analysis method "concurrence topology" is applied to mutation frequencies in 69 genes in glioblastoma data. In dimension 1 some apparent "mutual exclusivity" is found. By simulation of data having approximately the same…

Gene conversion is a mechanism by which a double-strand break in a DNA molecule is repaired using a homologous DNA molecule as a template. As a result, one gene is 'copied and pasted' onto the other gene. It was recently reported that the…

The biological world, especially its majority microbial component, is strongly interacting and may be dominated by collective effects. In this review, we provide a brief introduction for statistical physicists of the way in which living…

Even closely related prokaryotes show an astounding diversity in their ability to grow in different nutritional environments. Mechanistically, this diversity arises predominantly through horizontal gene transfer, the exchange of DNA between…

We consider a population subdivided into two demes connected by migration in which selection acts in opposite direction. We explore the effects of recombination and migration on the maintenance of multilocus polymorphism, on local…

The pre-training paradigm fine-tunes the models trained on large-scale datasets to downstream tasks with enhanced performance. It transfers all knowledge to downstream tasks without discriminating which part is necessary or unnecessary,…

Research organisms provide invaluable insights into human biology and diseases, serving as essential tools for functional experiments, disease modeling, and drug testing. However, evolutionary divergence between humans and research…

Adaptation in response to selection on polygenic phenotypes may occur via subtle allele frequencies shifts at many loci. Current population genomic techniques are not well posed to identify such signals. In the past decade, detailed…

The phenomenon of gene conservation is an interesting evolutionary problem related to speciation and adaptation. Conserved genes are acted upon in evolution in a way that preserves their function despite other structural and functional…

Across all kingdoms of biological life, protein-coding genes exhibit unequal usage of synonmous codons. Although alternative theories abound, translational selection has been accepted as an important mechanism that shapes the patterns of…

Single gene mutations have been implicated in the pathogenesis of a form of diabetes mellitus (DM) known as the maturity-onset diabetes of the young (MODY). However, there are diverse opinions on the suspect genes and pathophysiology,…

Motivation: Genome rearrangement plays an important role in evolutionary biology and has profound impacts on phenotype in organisms ranging from microbes to humans. The mechanisms for genome rearrangement events remain unclear. Lots of…

Although traditional statistical techniques and machine learning methods have contributed significantly to genetics and, in particular, inherited disease diagnosis, they often struggle with complex, high-dimensional data, a challenge now…

The possibility of targeting the causal genes along with the mechanisms of pathogenically complex diseases has led to numerous studies on the genetic etiology of some diseases. In particular, studies have added more genes to the list of…