title: Genome scale models of yeast: towards standardized evaluation and consistent omic integration.
abstract: 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.
authors.affiliation: Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296 Gothenburg, Sweden. nielsenj@chalmers.se.
authors.forename: Benjamín J
authors.initials: BJ
authors.lastname: Sánchez
authors.forename: Jens
authors.initials: J
authors.lastname: Nielsen
mesh_terms: D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000592:standards; D023281:Genomics / Q000592:standards*; D064688:Metabolic Flux Analysis / Q000592:standards*; D053858:Metabolic Networks and Pathways / Q000502:physiology*; D008954:Models, Biological; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D018511:Systems Integration
chemical_list: D029701:Saccharomyces cerevisiae Proteins