Shrinking the metabolic solution space using experimental datasets.
Constraint-based models of metabolism have been used in a variety of studies on drug discovery, metabolic engineering, evolution, and multi-species interactions. These genome-scale models can be generated for any sequenced organism since their main parameters (i.e., reaction stoichiometry) are highl...
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2012
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oai:doaj.org-article:fcb5c40563fd4cb89a9e9eaeb26f656f2021-11-18T05:51:02ZShrinking the metabolic solution space using experimental datasets.1553-734X1553-735810.1371/journal.pcbi.1002662https://doaj.org/article/fcb5c40563fd4cb89a9e9eaeb26f656f2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22956899/pdf/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Constraint-based models of metabolism have been used in a variety of studies on drug discovery, metabolic engineering, evolution, and multi-species interactions. These genome-scale models can be generated for any sequenced organism since their main parameters (i.e., reaction stoichiometry) are highly conserved. Their relatively low parameter requirement makes these models easy to develop; however, these models often result in a solution space with multiple possible flux distributions, making it difficult to determine the precise flux state in the cell. Recent research efforts in this modeling field have investigated how additional experimental data, including gene expression, protein expression, metabolite concentrations, and kinetic parameters, can be used to reduce the solution space. This mini-review provides a summary of the data-driven computational approaches that are available for reducing the solution space and thereby improve predictions of intracellular fluxes by constraint-based models.Jennifer L ReedPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 8, Iss 8, p e1002662 (2012) |
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EN |
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Biology (General) QH301-705.5 |
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Biology (General) QH301-705.5 Jennifer L Reed Shrinking the metabolic solution space using experimental datasets. |
| description |
Constraint-based models of metabolism have been used in a variety of studies on drug discovery, metabolic engineering, evolution, and multi-species interactions. These genome-scale models can be generated for any sequenced organism since their main parameters (i.e., reaction stoichiometry) are highly conserved. Their relatively low parameter requirement makes these models easy to develop; however, these models often result in a solution space with multiple possible flux distributions, making it difficult to determine the precise flux state in the cell. Recent research efforts in this modeling field have investigated how additional experimental data, including gene expression, protein expression, metabolite concentrations, and kinetic parameters, can be used to reduce the solution space. This mini-review provides a summary of the data-driven computational approaches that are available for reducing the solution space and thereby improve predictions of intracellular fluxes by constraint-based models. |
| format |
article |
| author |
Jennifer L Reed |
| author_facet |
Jennifer L Reed |
| author_sort |
Jennifer L Reed |
| title |
Shrinking the metabolic solution space using experimental datasets. |
| title_short |
Shrinking the metabolic solution space using experimental datasets. |
| title_full |
Shrinking the metabolic solution space using experimental datasets. |
| title_fullStr |
Shrinking the metabolic solution space using experimental datasets. |
| title_full_unstemmed |
Shrinking the metabolic solution space using experimental datasets. |
| title_sort |
shrinking the metabolic solution space using experimental datasets. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2012 |
| url |
https://doaj.org/article/fcb5c40563fd4cb89a9e9eaeb26f656f |
| work_keys_str_mv |
AT jenniferlreed shrinkingthemetabolicsolutionspaceusingexperimentaldatasets |
| _version_ |
1718424766712381440 |