Related papers: Law of Genome Evolution Direction : Coding Informa…
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…
We study complex networks in which the nodes of the network are tagged with different colors depending on the functionality of the nodes (colored graphs), using information theory applied to the distribution of motifs in such networks. We…
How mutations accumulate in genomes is the central question of molecular evolution theories, however our understanding of this process is far from complete. Drake's rule is a notoriously universal property of genomes from microbes to…
This paper discusses the benefits of describing the world as information, especially in the study of the evolution of life and cognition. Traditional studies encounter problems because it is difficult to describe life and cognition in terms…
The rules that specify how the information contained in DNA codes amino acids, is called "the genetic code". Using a simplified version of the Penna nodel, we are using computer simulations to investigate the importance of the genetic code…
The process of morphogenesis, which can be defined as an evolution of the form of an organism, is one of the most intriguing mysteries in the life sciences. It is clear, that gene expression patterns cannot explain the development of the…
Rich information on the prebiotic evolution is still stored in contemporary genomic data. The statistical mechanism at the sequence level may play a significant role in the prebiotic evolution. Based on statistical analysis of genome…
Background. The large-scale pattern of distribution of genes on the chromosomes in the known animal genomes is not well characterized. We hypothesized that individual genes will be distributed on chromosomes in a mathematically ordered…
We investigate the possibility of encoding multiple solutions of a problem in a single chromosome. The best solution encoded in an individual will represent (will provide the fitness of) that individual. In order to obtain some benefits the…
Sequence organizations are viewed from two points: one is from informational redundancy or informational correlation (IC) and another is from k-mer frequency statistics. Two problems are investigated. The first is how the ICs exceed the…
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 evolution of structure in biology is driven by accretion and change. Accretion brings together disparate parts to form bigger wholes. Change provides opportunities for growth and innovation. Here we review patterns and processes that…
This paper investigates the influence of genotype size on evolutionary algorithms' performance. We consider genotype compression (where genotype is smaller than phenotype) and expansion (genotype is larger than phenotype) and define…
Neural codes appear efficient. Naturally, neuroscientists contend that an efficient process is responsible for generating efficient codes. They argue that natural selection is the efficient process that generates those codes. Although…
The mean length and the variability of coding sequences for 48 genomes of bacteria and archaea were analyzed. It was found that the plotted data can be described by an angular area. This suggests the followings: a) The variability of a…
A representation of the genetic code as a six-dimensional Boolean hypercube is proposed. It is assumed here that this structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition.…
A fundamental question in the field of social studies of science is how research fields emerge, grow and decline over time and space. This study confronts this question here by developing an inductive analysis of emerging research fields…
The universal genetic code presents a fundamental paradox in molecular biology. Recent advances in synthetic biology have demonstrated that the code is remarkably flexible--organisms can survive with 61 codons instead of 64, natural…
Convolutional codes are error-correcting linear codes that utilize shift registers to encode. These codes have an arbitrary block size and they can incorporate both past and current information bits. DNA codes represent DNA sequences and…
The yearly global production of data is growing exponentially, outpacing the capacity of existing storage media, such as tape and disk, and surpassing our ability to store it. DNA storage - the representation of arbitrary information as…