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Symbolic Extensions Applied to Multiscale Structure of Genomes

A genome of a living organism consists of a long string of symbols over a finite alphabet carrying critical information for the organism. This includes its ability to control post natal growth, homeostasis, adaptation to changes in the surrounding environment, or to biochemically respond at the cell...

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Detalles Bibliográficos
Autores principales: Downarowicz, Tomasz, Travisany, Dante, Montecino, Martin, Maass, Alejandro
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Netherlands 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4012164/
https://www.ncbi.nlm.nih.gov/pubmed/24728912
http://dx.doi.org/10.1007/s10441-014-9215-y
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author Downarowicz, Tomasz
Travisany, Dante
Montecino, Martin
Maass, Alejandro
author_facet Downarowicz, Tomasz
Travisany, Dante
Montecino, Martin
Maass, Alejandro
author_sort Downarowicz, Tomasz
collection PubMed
description A genome of a living organism consists of a long string of symbols over a finite alphabet carrying critical information for the organism. This includes its ability to control post natal growth, homeostasis, adaptation to changes in the surrounding environment, or to biochemically respond at the cellular level to various specific regulatory signals. In this sense, a genome represents a symbolic encoding of a highly organized system of information whose functioning may be revealed as a natural multilayer structure in terms of complexity and prominence. In this paper we use the mathematical theory of symbolic extensions as a framework to shed light onto how this multilayer organization is reflected in the symbolic coding of the genome. The distribution of data in an element of a standard symbolic extension of a dynamical system has a specific form: the symbolic sequence is divided into several subsequences (which we call layers) encoding the dynamics on various “scales”. We propose that a similar structure resides within the genomes, building our analogy on some of the most recent findings in the field of regulation of genomic DNA functioning.
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spelling pubmed-40121642014-05-07 Symbolic Extensions Applied to Multiscale Structure of Genomes Downarowicz, Tomasz Travisany, Dante Montecino, Martin Maass, Alejandro Acta Biotheor Regular Article A genome of a living organism consists of a long string of symbols over a finite alphabet carrying critical information for the organism. This includes its ability to control post natal growth, homeostasis, adaptation to changes in the surrounding environment, or to biochemically respond at the cellular level to various specific regulatory signals. In this sense, a genome represents a symbolic encoding of a highly organized system of information whose functioning may be revealed as a natural multilayer structure in terms of complexity and prominence. In this paper we use the mathematical theory of symbolic extensions as a framework to shed light onto how this multilayer organization is reflected in the symbolic coding of the genome. The distribution of data in an element of a standard symbolic extension of a dynamical system has a specific form: the symbolic sequence is divided into several subsequences (which we call layers) encoding the dynamics on various “scales”. We propose that a similar structure resides within the genomes, building our analogy on some of the most recent findings in the field of regulation of genomic DNA functioning. Springer Netherlands 2014-04-13 2014 /pmc/articles/PMC4012164/ /pubmed/24728912 http://dx.doi.org/10.1007/s10441-014-9215-y Text en © The Author(s) 2014 https://creativecommons.org/licenses/by/4.0/ Open AccessThis article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited.
spellingShingle Regular Article
Downarowicz, Tomasz
Travisany, Dante
Montecino, Martin
Maass, Alejandro
Symbolic Extensions Applied to Multiscale Structure of Genomes
title Symbolic Extensions Applied to Multiscale Structure of Genomes
title_full Symbolic Extensions Applied to Multiscale Structure of Genomes
title_fullStr Symbolic Extensions Applied to Multiscale Structure of Genomes
title_full_unstemmed Symbolic Extensions Applied to Multiscale Structure of Genomes
title_short Symbolic Extensions Applied to Multiscale Structure of Genomes
title_sort symbolic extensions applied to multiscale structure of genomes
topic Regular Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4012164/
https://www.ncbi.nlm.nih.gov/pubmed/24728912
http://dx.doi.org/10.1007/s10441-014-9215-y
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