Related papers: Essentiality, conservation, evolutionary pressure …
Heterogeneity in physical and functional characteristics of cells (e.g. size, cycle time, growth rate, protein concentration) proliferates within an isogenic population due to stochasticity in intracellular biochemical processes and in the…
Due to the recent evolution of sequencing techniques, the number of available genomes is rising steadily, leading to the possibility to make large scale genomic comparison between sets of close species. An interesting question to answer is:…
Although the role of lateral gene transfer is well recognized in the evolution of bacteria, it is generally assumed that it has had less influence among eukaryotes. To explore this hypothesis we compare the dynamics of genome evolution in…
Selection pressures on proteins are usually measured by comparing homologous nucleotide sequences (Zuckerkandl and Pauling 1965). Recently we introduced a novel method, termed `volatility', to estimate selection pressures on protein…
Gene regulatory networks (GRNs) play a central role in cellular decision-making. Understanding their structure and how it impacts their dynamics constitutes thus a fundamental biological question. GRNs are frequently modeled as Boolean…
It is important to understand how protein folding and evolution influences each other. Several studies based on entropy calculation correlating experimental measurement of residue participation in folding nucleus and sequence conservation…
Convergent evolution provides powerful evidence for natural selection, yet its molecular basis is typically sought in protein-coding amino acid substitutions. Whether adaptive pressures can drive the convergent evolution of synonymous codon…
The problem of differentiating the informational content of coding (exons) and non-coding (introns) regions of a DNA sequence is one of the central problems of genomics. The introns are estimated to be nearly 95% of the DNA and since they…
This work illustrates potentials for recognition within {\em ad hoc} sensor networks if their nodes possess individual inter-related biologically inspired genetic codes. The work takes ideas from natural immune systems protecting organisms…
The inherent stochasticity of cellular processes leads to significant cell-to-cell variation in protein abundance. Although this noise has already been characterized and modeled, its broader implications and significance remain unclear. In…
RNA editing can be crucial for the expression of genetic information via inserting, deleting, or substituting a few nucleotides at specific positions in an RNA sequence. Within coding regions in an RNA sequence, editing usually occurs with…
Biological networks such as gene regulatory networks possess desirable properties. They are more robust and controllable than random networks. This motivates the search for structural and dynamical features that evolution has incorporated…
The nucleotide composition of human genes with a special emphasis on transcription-related strand asymmetries is analyzed. Such asymmetries may be associated with different mutational rates in two principal factors. The first one is…
Background: Gene regulatory networks coordinate the expression of genes across physiological states and ensure a synchronized expression of genes in cellular subsystems, critical for the coherent functioning of cells. Here we address the…
DNA supercoiling is central to many fundamental processes of living organisms. Its average level along the chromosome and over time reflects the dynamic equilibrium of opposite activities of topoisomerases, which are required to relax…
Bacteria, in contrast to eukaryotic cells contain two types of genes: chromosomal genes that are fixed to the cell, and plasmids that are mobile genes, easily shared to other cells. The sharing of plasmid genes between individual bacteria…
Biologists use random transposon mutagenesis to construct knockout libraries for bacteria. Random mutagenesis offers cost and efficiency benefits over the standard site directed mutagenesis, but one can no longer ensure that all the…
Evolving biomolecular networks have to combine the stability against perturbations with flexibility allowing their constituents to assume new roles in the cell. Gene duplication followed by functional divergence of associated proteins is a…
Among several quantitative invariants found in evolutionary genomics, one of the most striking is the scaling of the overall abundance of proteins, or protein domains, sharing a specific functional annotation across genomes of given size.…
Since protein mutations are the main driving force of evolution at the molecular level, a proper analysis of them (and the factors controlling them) will enable us to find a response to several crucial queries in evolutionary biology. Among…