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Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks

Over the last decade, a giant leap forward has been made in resolving the main bottleneck in metabolomics, i.e., the structural characterization of the many unknowns. This has led to the next challenge in this research field: retrieving biochemical pathway information from the various types of netwo...

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Detalles Bibliográficos
Autores principales: Desmet, Sandrien, Brouckaert, Marlies, Boerjan, Wout, Morreel, Kris
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Research Network of Computational and Structural Biotechnology 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7753198/
https://www.ncbi.nlm.nih.gov/pubmed/33384856
http://dx.doi.org/10.1016/j.csbj.2020.11.050
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author Desmet, Sandrien
Brouckaert, Marlies
Boerjan, Wout
Morreel, Kris
author_facet Desmet, Sandrien
Brouckaert, Marlies
Boerjan, Wout
Morreel, Kris
author_sort Desmet, Sandrien
collection PubMed
description Over the last decade, a giant leap forward has been made in resolving the main bottleneck in metabolomics, i.e., the structural characterization of the many unknowns. This has led to the next challenge in this research field: retrieving biochemical pathway information from the various types of networks that can be constructed from metabolome data. Searching putative biochemical pathways, referred to as biotransformation paths, is complicated because several flaws occur during the construction of metabolome networks. Multiple network analysis tools have been developed to deal with these flaws, while in silico retrosynthesis is appearing as an alternative approach. In this review, the different types of metabolome networks, their flaws, and the various tools to trace these biotransformation paths are discussed.
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spelling pubmed-77531982020-12-30 Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks Desmet, Sandrien Brouckaert, Marlies Boerjan, Wout Morreel, Kris Comput Struct Biotechnol J Review Over the last decade, a giant leap forward has been made in resolving the main bottleneck in metabolomics, i.e., the structural characterization of the many unknowns. This has led to the next challenge in this research field: retrieving biochemical pathway information from the various types of networks that can be constructed from metabolome data. Searching putative biochemical pathways, referred to as biotransformation paths, is complicated because several flaws occur during the construction of metabolome networks. Multiple network analysis tools have been developed to deal with these flaws, while in silico retrosynthesis is appearing as an alternative approach. In this review, the different types of metabolome networks, their flaws, and the various tools to trace these biotransformation paths are discussed. Research Network of Computational and Structural Biotechnology 2020-12-03 /pmc/articles/PMC7753198/ /pubmed/33384856 http://dx.doi.org/10.1016/j.csbj.2020.11.050 Text en © 2020 The Author(s) http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Review
Desmet, Sandrien
Brouckaert, Marlies
Boerjan, Wout
Morreel, Kris
Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks
title Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks
title_full Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks
title_fullStr Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks
title_full_unstemmed Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks
title_short Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks
title_sort seeing the forest for the trees: retrieving plant secondary biochemical pathways from metabolome networks
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7753198/
https://www.ncbi.nlm.nih.gov/pubmed/33384856
http://dx.doi.org/10.1016/j.csbj.2020.11.050
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