Related papers: Long-range correlation in the whole human genome
The phenomenon of gene conservation is an interesting evolutionary problem related to speciation and adaptation. Conserved genes are acted upon in evolution in a way that preserves their function despite other structural and functional…
In this paper we analyse the fractal structure of long human-language records by mapping large samples of texts onto time series. The particular mapping set up in this work is inspired on linguistic basis in the sense that is retains {\em…
Sex chromosomes have independently evolved in species with separate sexes in most lineages across the tree of life. However, the well-accepted canonical model of sex chromosome evolution is not universally supported. There is no single…
We present a method to quantify spatial fluctuations of the substitution rate on different length scales throughout genomes of eukaryotes. The fluctuations on large length scales are found to be predominantly a consequence of a…
The multifractal detrended fluctuation analysis of time series is able to reveal the presence of long-range correlations and, at the same time, to characterize the self-similarity of the series. The rich information derivable from the…
Genetic interaction measures how different genes collectively contribute to a phenotype, and can reveal functional compensation and buffering between pathways under genetic perturbations. Recently, genome-wide screening for genetic…
An approach for approximately calculating the number of genes in a genome is presented, which takes into account the average protein length expected for the species. A number of virus, bacterial and eukaryotic genomes are scrutinized.…
The three dimensional structure of DNA in the nucleus (chromatin) plays an important role in many cellular processes. Recent experimental advances have led to high-throughput methods of capturing information about chromatin conformation on…
Large-scale dynamical properties of complete chromosome DNA sequences of eukaryotes are considered. By the proposed deterministic models with intermittency and symbolic dynamics we describe a wide spectrum of large-scale patterns inherent…
Based on a model first studied in [Physical Review A, vol. 43, 5240-5260,1991] properties of correlation function for expansion-modification systems are developed. The existence of several characteristic exponents is proved. The…
Characterizing the link between small-scale chromatin structure and large-scale chromosome folding during interphase is a prerequisite for understanding transcription. Yet, this link remains poorly investigated. Here, we introduce a simple…
We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions and insertion of random segments. These processes are found to generate long-range correlations…
A structural genetic model incorporating a modern understanding of the genome and common practice in genome-wide association studies is derived mathematically. The model shows the Haldane map distance as a direct consequence of the…
The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…
We show, that the specific distribution of gene's length, which is observed in natural genomes, might be a result of a growth process, in which a single length scale $L(t)$ develops that grows with time as $t^{1/3}$. This length scale could…
Understanding functional organization of genetic information is a major challenge in modern biology. Following the initial publication of the human genome sequence in 2001, advances in high-throughput measurement technologies and efficient…
The distribution of bases spacing in human genome was investigated. An analysis of the frequency of occurrence in the human genome of different sequence lengths flanked by one type of nucleotide was carried out showing that the distribution…
The problem of the directionality of genome evolution is studied from the information-theoretic view. We propose that the function-coding information quantity of a genome always grows in the course of evolution through sequence duplication,…
Modern genomics experiments measure functional behaviors for many thousands of DNA sequences. We suggest that, especially when these sequences are chosen at random, it is natural to compute correlation functions between sequences and…
We study the effects of interspecific correlations in a biological coevolution model in which organisms are represented by genomes of bitstrings. We present preliminary results for this model, indicating that these correlations do not…