Related papers: Evolutionary genomics of transposable elements in …
Global transposable characteristics in the complete DNA sequence of the Saccharomyces cevevisiae yeast is determined by using the metric representation and recurrence plot methods. In the form of the correlation distance of nucleotide…
The budding yeast Saccharomyces cerevisiae is important for human food production and as a model organism for biological research. The genetic diversity contained in the global population of yeast strains represents a valuable resource for…
Transposable elements can be categorised into DNA and RNA elements based on their mechanism of transposition. Tyrosine recombinase elements (YREs) are relatively rare and poorly understood, despite sharing characteristics with both DNA and…
MOTIVATION: A central goal of postgenomic biology is the elucidation of the regulatory relationships among all cellular constituents that together comprise the 'genetic network' of a cell or microorganism. Experimental manipulation of gene…
Transposable elements (TEs) constitute a significant portion of eukaryotic genomes, yet their role in chromatin organization remains poorly understood. This study investigates the distribution patterns of TEs around chromatin ligation…
Various genome evolutionary models have been proposed these last decades to predict the evolution of a DNA sequence over time, essentially described using a mutation matrix. By essence, all of these models relate the evolution of DNA…
Since the late `60s, various genome evolutionary models have been proposed to predict the evolution of a DNA sequence as the generations pass. Most of these models are based on nucleotides evolution, so they use a mutation matrix of size…
Gross chromosomal rearrangements have the potential to be evolutionarily advantageous to an adapting organism. The generation of a hybrid species increases opportunity for recombination by bringing together two homologous genomes. We sought…
BACKGROUND. Signal recognition and information processing is a fundamental cellular function, which in part involves comprehensive transcriptional regulatory (TR) mechanisms carried out in response to complex environmental signals in the…
Protein interaction networks aim to summarize the complex interplay of proteins in an organism. Early studies suggested that the position of a protein in the network determines its evolutionary rate but there has been considerable…
Background: Recent studies in a growing number of organisms have yielded accumulating evidence that a significant portion of the non-coding region in the genome is transcribed. We address this issue in the yeast Saccharomyces cerevisiae.…
We investigate the structural and dynamical properties of the transcriptional regulatory network of the yeast {\it Saccharomyces cerevisiae} and compare it with two unbiased ensembles: one obtained by reshuffling the edges and the other…
Background: Transposable elements (TEs) have played an important role in the diversification and enrichment of mammalian transcriptomes through various mechanisms such as exonization and intronization (the birth of new exons/introns from…
During evolution of microorganisms genomes underwork have different changes in their lengths, gene orders, and gene contents. Investigating these structural rearrangements helps to understand how genomes have been modified over time. Some…
Many important cellular functions are implemented by protein complexes that act as sophisticated molecular machines of varying size and temporal stability. Here we demonstrate quantitatively that protein complexes in the yeast,…
We investigate the cycles in the transcription network of S. cerevisiae. Unlike a similar network of E. coli, it contains many cycles. We characterize properties of these cycles and their place in the regulatory mechanism of the cell.…
Chromosomal rearrangements, particularly those mediated by transposable elements (TEs), can drive adaptive evolution by creating chimeric genes, inducing de novo gene formation, or altering gene expression. Here, we investigate…
In this article, we investigate the evolution of sexual diploid populations which are hosts for active TE families. Our purpose is to explore the relationship between the environmental change, that influences such population and activity of…
Transposed elements (TEs) are mobile genetic sequences. During the evolution of eukaryotes TEs were inserted into active protein-coding genes, affecting gene structure, expression and splicing patterns, and protein sequences. Genomic…
Despite its high and direct impact on nearly all biological processes, the underlying structure of gene-gene interaction networks is investigated so far according to pair connections. To address this, we explore the gene interaction…