相关论文: Statistical Approach to Gene Evolution
Living organisms are not just random collections of organic molecules. There is continuous information processing going on in the apparent bouncing around of molecules of life. Optimisation criteria in this information processing can be…
The present work is devoted to describe a set of rules explaining the discriminating versus non-discriminating behavior of the di-basic stages and to characterize the role of each base in determining such a behavior. Bases are analyze as…
Biologists have long sought a way to explain how statistical properties of genetic sequences emerged and are maintained through evolution. On the one hand, non-random structures at different scales indicate a complex genome organisation. On…
The gap in statistics between multi-variate and time-series analysis can be bridged by using entropy statistics and recent developments in multi-dimensional scaling. For explaining the evolution of the sciences as non-linear dynamics, the…
In special coordinates (codon position--specific nucleotide frequencies) bacterial genomes form two straight lines in 9-dimensional space: one line for eubacterial genomes, another for archaeal genomes. All the 348 distinct bacterial…
Statistical physics can describe the behavior of microbial populations consisting of many heterogeneous individuals. A direct consequence is the existence of phase transitions, where the behavior of a population changes discontinuously upon…
Gene expression is a stochastic process governed by the presence of specific transcription factors. Here we study the dynamics of gene expression in the presence of feedback, where a gene regulates its own expression. The nonlinear coupling…
In our paper selected linguistic features of genomes to study the statistics of the gene codes are considered. We present the information theory from which it follows that if the system is described by distributions of hyperbolic type it…
The problem of the directionality of genome evolution is studied. Based on the analysis of C-value paradox and the evolution of genome size we propose that the function-coding information quantity of a genome always grows in the course of…
Biological systems reach organizational complexity that far exceeds the complexity of any known inanimate objects. Biological entities undoubtedly obey the laws of quantum physics and statistical mechanics. However, is modern physics…
Research in quantitative evolutionary genomics and systems biology led to the discovery of several universal regularities connecting genomic and molecular phenomic variables. These universals include the log-normal distribution of the…
Several technological applications require the translation of a protein into a nucleic acid that codes for it (``backtranslation''). The degeneracy of the genetic code makes this translation ambiguous; moreover, not every translation is…
Much information is stored in amino acid composition of protein and base composition of DNA. We simulated the evolution of amino acid frequencies and genomic GC content by a linguistic model. It is showed that the evolution of genetic code…
A representation of the genetic code as a six-dimensional Boolean hypercube is described. This structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition. In this paper it is…
A macroscopic theory for describing cellular states during steady-growth is presented, which is based on the consistency between cellular growth and molecular replication, as well as the robustness of phenotypes against perturbations.…
The genetic code is the function from the set of codons to the set of amino acids by which a DNA sequence encodes proteins. Since the codons also influence the shape of the DNA molecule itself, the same sequence that encodes a protein also…
A number of signal processing and statistical methods can be used in analyzing either pieces of text or DNA sequences. These techniques can be used in a number of ways, such as determining authorship of documents, finding genes in DNA, and…
Gene expression is a central process to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular…
We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into…
Much evolutionary information is stored in the fluctuations of protein length distributions. The genome size and non-coding DNA content can be calculated based only on the protein length distributions. So there is intrinsic relationship…