相关论文: "Junk" DNA as a genetic decoy

Many efforts have been done in order to explain the role of junk DNA, but its function remain to be elucidated. In addition the GC-content variations among species still represent an enigma. Both these two misteries can have a common…

Because genomes are products of natural processes rather than intelligent design, all genomes contain functional and nonfunctional parts. The fraction of the genome that has no biological function is called rubbish DNA. Rubbish DNA consists…

Point mutations can surely be dangerous but what is worst than to lose the reading frame?! Does DNA evolved a strategy to try to limit frameshift mutations?! Here we investigate if DNA sequences effectively evolved a system to minimize…

Most of the DNA that composes a complex organism is non-coding and defined as junk. Even the coding part is composed of genes that affect the phenotype differently. Therefore, a random mutation has an effect on the specimen fitness that…

Evolving genomes increase a number of their genes by gene duplications. To escape degradation in a functionless pseudogene, any gene duplicate needs to be guarded by negative (purifying) selection from otherwise inevitable fixation of…

We propose and apply a novel paradigm for characterization of genome data quality, which quantifies the effects of intentional degradation of quality. The rationale is that the higher the initial quality, the more fragile the genome and the…

Why is the genetic code the way it is? The most successful theory states that the codon assignments minimise the effects of errors arising in primordial living systems. Here a transversion is reported that leaves invariant degeneracy in the…

There are a number of vectors for attack when trying to link an individual to a certain DNA sequence. Phenotypic prediction is one such vector; linking DNA to an individual based on their traits. Current approaches are not overly effective,…

Understanding why we age is a long-lived open problem in evolutionary biology. Aging is prejudicial to the individual and evolutionary forces should prevent it, but many species show signs of senescence as individuals age. Here, I will…

In the near future, all the human genes will be identified. But understanding the functions coded in the genes is a much harder problem. For example, by using block entropy, one has that the DNA code is closer to a random code then written…

A mutation in a protein-coding gene in DNA can alter the protein structure coded by the same gene. Structurally altered proteins usually lose their functions and sometimes gain an undesirable function instead. These types of mutations and…

At any moment in time, evolution is faced with a formidable challenge: refining the already highly optimised design of biological species, a feat accomplished through all preceding generations. In such a scenario, the impact of random…

Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…

The modeling of time series is becoming increasingly critical in a wide variety of applications. Overall, data evolves by following different patterns, which are generally caused by different user behaviors. Given a time series, we define…

Significant fraction (about 98.5% in humans, 24% in microbe Rickettsia prowazekii) of most animal genomes is non-coding DNA. Although recent studies established functions of its certain portions, it remains genomic dark matter. The paper…

The premise of genetic analysis is that a causal link exists between phenotypic and allelic variation. Yet it has long been documented that mutant phenotypes are not a simple result of a single DNA lesion, but rather are due to interactions…

Mutations are typically classified by their effects on the nucleotide sequence and by their size. Here, we argue that if our main aim is to understand the effect of mutations on evolutionary outcomes (such as adaptation or speciation), we…

The current rate of species extinction is rapidly approaching unprecedented highs and life on Earth presently faces a sixth mass extinction event driven by anthropogenic activity, climate change and ecological collapse. The field of…

Mutations can arise from the chance misincorporation of nucleotides during DNA replication or from DNA lesions that are not repaired correctly. We introduce a model that relates the source of mutations to their accumulation with cell…

In this letter we study the full semi-conservative treatment of a model for the co-evolution of a virus and an adaptive immune system. Regions of viability are calculated for both conservatively and semi-conservatively replicating viruses…