Work

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

Year: 2015

Type: review

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.

Source: Integrative Biology

DOI: 10.1039/c5ib00083a

Authors: Benjamín J. Sánchez, Jens Nielsen

Institutions: Novo Nordisk Foundation, Chalmers University of Technology

Language: English

Topic: Microbial Metabolic Engineering and Bioproduction

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: hybrid

Estimated APC paid: $3,522

Funders: Knut och Alice Wallenbergs Stiftelse, Novo Nordisk, Novo Nordisk Fonden, Comisión Nacional de Investigación Científica y Tecnológica