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Strategies for Reliable Exploitation of Evolutionary Concepts in High Throughput Biology

The recent availability of the complete genome sequences of a large number of model organisms, together with the immense amount of data being produced by the new high-throughput technologies, means that we can now begin comparative analyses to understand the mechanisms involved in the evolution of t...

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Detalles Bibliográficos
Autores principales: Levasseur, Anthony, Pontarotti, Pierre, Poch, Olivier, Thompson, Julie D.
Formato: Texto
Lenguaje:English
Publicado: Libertas Academica 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614184/
https://www.ncbi.nlm.nih.gov/pubmed/19204813
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author Levasseur, Anthony
Pontarotti, Pierre
Poch, Olivier
Thompson, Julie D.
author_facet Levasseur, Anthony
Pontarotti, Pierre
Poch, Olivier
Thompson, Julie D.
author_sort Levasseur, Anthony
collection PubMed
description The recent availability of the complete genome sequences of a large number of model organisms, together with the immense amount of data being produced by the new high-throughput technologies, means that we can now begin comparative analyses to understand the mechanisms involved in the evolution of the genome and their consequences in the study of biological systems. Phylogenetic approaches provide a unique conceptual framework for performing comparative analyses of all this data, for propagating information between different systems and for predicting or inferring new knowledge. As a result, phylogeny-based inference systems are now playing an increasingly important role in most areas of high throughput genomics, including studies of promoters (phylogenetic footprinting), interactomes (based on the presence and degree of conservation of interacting proteins), and in comparisons of transcriptomes or proteomes (phylogenetic proximity and co-regulation/co-expression). Here we review the recent developments aimed at making automatic, reliable phylogeny-based inference feasible in large-scale projects. We also discuss how evolutionary concepts and phylogeny-based inference strategies are now being exploited in order to understand the evolution and function of biological systems. Such advances will be fundamental for the success of the emerging disciplines of systems biology and synthetic biology, and will have wide-reaching effects in applied fields such as biotechnology, medicine and pharmacology.
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spelling pubmed-26141842009-02-09 Strategies for Reliable Exploitation of Evolutionary Concepts in High Throughput Biology Levasseur, Anthony Pontarotti, Pierre Poch, Olivier Thompson, Julie D. Evol Bioinform Online Review The recent availability of the complete genome sequences of a large number of model organisms, together with the immense amount of data being produced by the new high-throughput technologies, means that we can now begin comparative analyses to understand the mechanisms involved in the evolution of the genome and their consequences in the study of biological systems. Phylogenetic approaches provide a unique conceptual framework for performing comparative analyses of all this data, for propagating information between different systems and for predicting or inferring new knowledge. As a result, phylogeny-based inference systems are now playing an increasingly important role in most areas of high throughput genomics, including studies of promoters (phylogenetic footprinting), interactomes (based on the presence and degree of conservation of interacting proteins), and in comparisons of transcriptomes or proteomes (phylogenetic proximity and co-regulation/co-expression). Here we review the recent developments aimed at making automatic, reliable phylogeny-based inference feasible in large-scale projects. We also discuss how evolutionary concepts and phylogeny-based inference strategies are now being exploited in order to understand the evolution and function of biological systems. Such advances will be fundamental for the success of the emerging disciplines of systems biology and synthetic biology, and will have wide-reaching effects in applied fields such as biotechnology, medicine and pharmacology. Libertas Academica 2008-05-08 /pmc/articles/PMC2614184/ /pubmed/19204813 Text en Copyright © 2008 The authors. http://creativecommons.org/licenses/by/3.0 This article is published under the Creative Commons Attribution By licence. For further information go to: http://creativecommons.org/licenses/by/3.0. (http://creativecommons.org/licenses/by/3.0)
spellingShingle Review
Levasseur, Anthony
Pontarotti, Pierre
Poch, Olivier
Thompson, Julie D.
Strategies for Reliable Exploitation of Evolutionary Concepts in High Throughput Biology
title Strategies for Reliable Exploitation of Evolutionary Concepts in High Throughput Biology
title_full Strategies for Reliable Exploitation of Evolutionary Concepts in High Throughput Biology
title_fullStr Strategies for Reliable Exploitation of Evolutionary Concepts in High Throughput Biology
title_full_unstemmed Strategies for Reliable Exploitation of Evolutionary Concepts in High Throughput Biology
title_short Strategies for Reliable Exploitation of Evolutionary Concepts in High Throughput Biology
title_sort strategies for reliable exploitation of evolutionary concepts in high throughput biology
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614184/
https://www.ncbi.nlm.nih.gov/pubmed/19204813
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