Genome scale models of yeast: towards standardized evaluation and consistent omic integration
Journal article, 2015

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.

Author

Benjamin José Sanchez Barja

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Jens B Nielsen

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Integrative Biology (United Kingdom)

1757-9694 (ISSN) 1757-9708 (eISSN)

Vol. 7 8 846-858

Subject Categories

Biological Sciences

Areas of Advance

Life Science Engineering (2010-2018)

DOI

10.1039/C5IB00083A

PubMed

26079294

More information

Created

10/8/2017