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Genome scale models of yeast: towards standardized evaluation and consistent omic integration

Benjamin Sánchez (Institutionen för biologi och bioteknik, Systembiologi) ; Jens B. Nielsen (Institutionen för biologi och bioteknik, Systembiologi)
Integrative Biology (1757-9694). Vol. 7 (2015), 8, p. 846-858.
[Artikel, refereegranskad vetenskaplig]

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.



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Denna post skapades 2015-08-18. Senast ändrad 2017-01-17.
CPL Pubid: 220773

 

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Institutioner (Chalmers)

Institutionen för biologi och bioteknik, Systembiologi

Ämnesområden

Livsvetenskaper
Biologiska vetenskaper

Chalmers infrastruktur