相关论文: Statistical Approach to Gene Evolution
The codons, sixtyfour in number, are distributed over the coding parts of DNA sequences. The distribution function is the plot of frequency-versus-rank of the codons. These distributions are characterised by parameters that are almost…
The genetic code is profoundly shaped by an origin in ancient RNA-mediated interactions, needing an extended development to reach the Standard Genetic Code (SGC). That development can serially use RNA specificities, a ribonucleopeptide…
We recall the physical features of the parton distributions in the quantum statistical approach of the nucleon. Some predictions from a next-to-leading order QCD analysis are compared to recent experimental results. We also consider their…
Nature's many varied complex systems (including galaxies, stars, planets, life, and society) are islands of order within the increasingly disordered universe. All organized systems are subject to physical, biological or cultural evolution,…
The molecular biology revolution of the last seventy five years has transformed our view of living systems. Scientific explanations of biological phenomena are now synonymous with the identification of the genes, proteins, and signaling…
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…
Many transcription factors bind to DNA with a remarkable lack of specificity, so that regulatory binding sites compete with an enormous number of non-regulatory 'decoy' sites. For an auto-regulated gene, we show decoy sites decrease noise…
Sequencing by synthesis is used in many next-generation DNA sequencing technologies. Some of the technologies, especially those exploring the principle of single-molecule sequencing, allow incomplete nucleotide incorporation in each cycle.…
The distribution of most genes is not random, and functionally linked genes are often found in clusters. Several theories have been put forward to explain the emergence and persistence of operons in bacteria. Careful analysis of genomic…
The information contained in the genome is insufficient for the control of organism development. Thus, the whereabouts of actual operational directives and workings of the genome remain obscure. In this work, it is suggested that the genome…
Recent research has extended methods from the fields of thermodynamics and statistical mechanics into other disciplines. Most notably, one recent work creates a unified theoretical framework to understand evolutionary biology, machine…
The sequence of nucleotide bases occurring in an organism's DNA is often regarded as a codescript for its construction. However, information in a DNA sequence can only be regarded as a codescript relative to an operational biochemical…
Why is the genetic code the way it is? The most successful theory states that the codon assignments minimise the effects of errors arising in primordial living systems. Here a transversion is reported that leaves invariant degeneracy in the…
The modeling of time series is becoming increasingly critical in a wide variety of applications. Overall, data evolves by following different patterns, which are generally caused by different user behaviors. Given a time series, we define…
Cellular behavior is governed by gene regulatory processes that are intrinsically dynamic and nonlinear, and are subject to non-negligible amounts of random fluctuations. Such conditions are ubiquitous in physical systems, where they have…
Most of the DNA that composes a complex organism is non-coding and defined as junk. Even the coding part is composed of genes that affect the phenotype differently. Therefore, a random mutation has an effect on the specimen fitness that…
Languages and genes are both transmitted from generation to generation, with opportunity for differential reproduction and survivorship of forms. Here we apply a rigorous inference framework, drawn from population genetics, to distinguish…
A central question in developmental biology is how size and position are determined. The genetic code carries instructions on how to control these properties in order to regulate the pattern and morphology of structures in the developing…
As early indicated by Charles Darwin, languages behave and change very much like living species. They display high diversity, differentiate in space and time, emerge and disappear. A large body of literature has explored the role of…
The idea of the evolution of the genetic code from the CG to the CGUA alphabet has been developed further. The assumption of the originally triplet structure of the genetic code has been substantiated. The hypothesis of the emergence of…