Related papers: Genomic Sequence Diversity and Population Structur…
Many DNA sequence variants influence phenotypes by altering gene expression. Our understanding of these variants is limited by sample sizes of current studies and by measurements of mRNA rather than protein abundance. We developed a…
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…
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…
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: 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.…
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…
Saccharomyces cerevisiae is one of the premier model systems for studying the genomics and evolution of transposable elements. The availability of the S. cerevisiae genome led to many insights into its five known transposable element…
Estimates of the fraction of nucleotide substitutions driven by positive selection vary widely across different species. Accounting for different estimates of positive selection has been difficult, in part because selection on polymorphism…
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,…
Saccharomyces cerevisiae is increasingly recognised as a key source for single-cell protein (SCP) production, a rising solution to global protein-supply challenges. This study presents a computational framework combining the Yeast9…
Baker's yeast (Saccharomyces cerevisiae) is a model organism for studying the morphology that emerges at the scale of multi-cell colonies. To look at how morphology develops, we collect a dataset of time-lapse photographs of the growth of…
Background: Diversity estimates in cultivated plants provide a rationale for conservation strategies and support the selection of starting material for breeding programs. Diversity measures applied to crops usually have been limited to the…
The budding yeast {\it Saccharomyces cerevisiae} is the first eukaryote whose genome has been completely sequenced. It is also the first eukaryotic cell whose proteome (the set of all proteins) and interactome (the network of all mutual…
Growth rate is one of the most important and most complex phenotypic characteristics of unicellular microorganisms, which determines the genetic mutations that dominate at the population level, and ultimately whether the population will…
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…
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…
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…
The high-throughput data generated by microarray experiments provides complete set of genes being expressed in a given cell or in an organism under particular conditions. The analysis of these enormous data has opened a new dimension for…
Viroids are small circular single-stranded infectious RNAs that are characterized by a relatively high mutation level. Knowledge of their sequence heterogeneity remains largely elusive, and, as yet, no strategy attempting to address this…
Two processes can influence the evolution of protein interaction networks: addition and elimination of interactions between proteins, and gene duplications increasing the number of proteins and interactions. The rates of these processes can…