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

Sandrien Desmet (UGent) , Marlies Brouckaert (UGent) , Wout Boerjan (UGent) and Kris Morreel (UGent)
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Abstract
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.
Keywords
MASS-SPECTRAL DATA, NATURAL-PRODUCTS, STRUCTURAL-CHARACTERIZATION, MOLECULAR NETWORKING, FRAGMENTATION TREES, SPECTROMETRY DATA, IDENTIFICATION, ANNOTATION, ARABIDOPSIS, PREDICTION

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MLA
Desmet, Sandrien, et al. “Seeing the Forest for the Trees : Retrieving Plant Secondary Biochemical Pathways from Metabolome Networks.” COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, vol. 19, 2021, pp. 72–85, doi:10.1016/j.csbj.2020.11.050.
APA
Desmet, S., Brouckaert, M., Boerjan, W., & Morreel, K. (2021). Seeing the forest for the trees : retrieving plant secondary biochemical pathways from metabolome networks. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 19, 72–85. https://doi.org/10.1016/j.csbj.2020.11.050
Chicago author-date
Desmet, Sandrien, Marlies Brouckaert, Wout Boerjan, and Kris Morreel. 2021. “Seeing the Forest for the Trees : Retrieving Plant Secondary Biochemical Pathways from Metabolome Networks.” COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL 19: 72–85. https://doi.org/10.1016/j.csbj.2020.11.050.
Chicago author-date (all authors)
Desmet, Sandrien, Marlies Brouckaert, Wout Boerjan, and Kris Morreel. 2021. “Seeing the Forest for the Trees : Retrieving Plant Secondary Biochemical Pathways from Metabolome Networks.” COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL 19: 72–85. doi:10.1016/j.csbj.2020.11.050.
Vancouver
1.
Desmet S, Brouckaert M, Boerjan W, Morreel K. Seeing the forest for the trees : retrieving plant secondary biochemical pathways from metabolome networks. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL. 2021;19:72–85.
IEEE
[1]
S. Desmet, M. Brouckaert, W. Boerjan, and K. Morreel, “Seeing the forest for the trees : retrieving plant secondary biochemical pathways from metabolome networks,” COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, vol. 19, pp. 72–85, 2021.
@article{8686431,
  abstract     = {{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.}},
  author       = {{Desmet, Sandrien and Brouckaert, Marlies and Boerjan, Wout and Morreel, Kris}},
  issn         = {{2001-0370}},
  journal      = {{COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL}},
  keywords     = {{MASS-SPECTRAL DATA,NATURAL-PRODUCTS,STRUCTURAL-CHARACTERIZATION,MOLECULAR NETWORKING,FRAGMENTATION TREES,SPECTROMETRY DATA,IDENTIFICATION,ANNOTATION,ARABIDOPSIS,PREDICTION}},
  language     = {{eng}},
  pages        = {{72--85}},
  title        = {{Seeing the forest for the trees : retrieving plant secondary biochemical pathways from metabolome networks}},
  url          = {{http://dx.doi.org/10.1016/j.csbj.2020.11.050}},
  volume       = {{19}},
  year         = {{2021}},
}

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