Genome scale models of yeast: towards standardized evaluation and consistent omic integration
Genome scale models (GEMs) have enabled remarkable advances in systems biology, acting as functional databases of metabolism, and as scaffolds for the contextualization of high-throughput data. In the case of Saccharomyces cerevisiae (budding yeast), several GEMs have been published and are currentl...
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| Veröffentlicht in: | Integrative biology (Cambridge) 2015-08, Vol.7 (8), p.846-858 |
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| creator | Sánchez, Benjamín J Nielsen, Jens |
| description | Genome scale models (GEMs) have enabled remarkable advances in systems biology, acting as functional databases of metabolism, and as scaffolds for the contextualization of high-throughput data. In the case of
Saccharomyces cerevisiae
(budding yeast), several GEMs have been published and are currently used for metabolic engineering and elucidating biological interactions. Here we review the history of yeast's GEMs, focusing on recent developments. We study how these models are typically evaluated, using both descriptive and predictive metrics. Additionally, we analyze the different ways in which all levels of omics data (from gene expression to flux) have been integrated in yeast GEMs. Relevant conclusions and current challenges for both GEM evaluation and omic integration are highlighted.
We review genome scale models of yeast, how are they typically evaluated, and how can they be integrated with omic data. |
| doi_str_mv | 10.1039/c5ib00083a |
| format | Article |
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Saccharomyces cerevisiae
(budding yeast), several GEMs have been published and are currently used for metabolic engineering and elucidating biological interactions. Here we review the history of yeast's GEMs, focusing on recent developments. We study how these models are typically evaluated, using both descriptive and predictive metrics. Additionally, we analyze the different ways in which all levels of omics data (from gene expression to flux) have been integrated in yeast GEMs. Relevant conclusions and current challenges for both GEM evaluation and omic integration are highlighted.
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Saccharomyces cerevisiae
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Saccharomyces cerevisiae
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| identifier | ISSN: 1757-9694 |
| ispartof | Integrative biology (Cambridge), 2015-08, Vol.7 (8), p.846-858 |
| issn | 1757-9694 1757-9708 1757-9708 |
| language | eng |
| recordid | cdi_crossref_primary_10_1039_C5IB00083A |
| source | MEDLINE; Royal Society Of Chemistry Journals 2008-; SWEPUB Freely available online; Oxford Journals |
| subjects | Computer Simulation Gene Expression Profiling - standards Genomics - standards Metabolic Flux Analysis - standards Metabolic Networks and Pathways - physiology Models, Biological Saccharomyces cerevisiae - metabolism Saccharomyces cerevisiae Proteins - metabolism Systems Integration |
| title | Genome scale models of yeast: towards standardized evaluation and consistent omic integration |
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