%0 Journal Article %1 Kim2017Current %A Kim, Won J. %A Kim, Hyun U. %A Lee, Sang Y. %D 2017 %J Current Opinion in Systems Biology %K flux-analysis genome-scale in-silico metabolic-engineering review %P 9--17 %R 10.1016/j.coisb.2017.03.001 %T Current state and applications of microbial genome-scale metabolic models %U http://dx.doi.org/10.1016/j.coisb.2017.03.001 %V 2 %X Genome-scale metabolic models (GEMs) are important systems biology tools. Microbial GEMs have been successfully employed in metabolic engineering. High-quality GEMs need to be validated using more sophisticated experimental data. Reconstruction of GEMs for microbial communities is becoming important. Computational modeling resources and frameworks are critical for building GEMs. Genome-scale metabolic models (GEMs) are valuable in describing an organism's entire metabolism using genomic information and have made huge impact on systems biology and metabolic engineering. Here we review current state of microbial GEMs and their use in various applications. There has recently been much interest in reconstructing GEMs for microbial communities, reflecting the increasing importance of microbiome. Analyses of recent work suggest that the GEMs for the best studied microorganisms, new or less studied microorganisms, and also microbial communities need to be thoroughly validated with experimental data beyond simple gene essentiality and nutrient utilization capabilities. In this paper, computational modeling resources and frameworks developed recently for reconstructing GEMs of microorganisms and microbial communities together with their applications are reviewed.

@article{Kim2017Current, abstract = { Genome-scale metabolic models ({GEMs}) are important systems biology tools. Microbial {GEMs} have been successfully employed in metabolic engineering. High-quality {GEMs} need to be validated using more sophisticated experimental data. Reconstruction of {GEMs} for microbial communities is becoming important. Computational modeling resources and frameworks are critical for building {GEMs}. Genome-scale metabolic models ({GEMs}) are valuable in describing an organism's entire metabolism using genomic information and have made huge impact on systems biology and metabolic engineering. Here we review current state of microbial {GEMs} and their use in various applications. There has recently been much interest in reconstructing {GEMs} for microbial communities, reflecting the increasing importance of microbiome. Analyses of recent work suggest that the {GEMs} for the best studied microorganisms, new or less studied microorganisms, and also microbial communities need to be thoroughly validated with experimental data beyond simple gene essentiality and nutrient utilization capabilities. In this paper, computational modeling resources and frameworks developed recently for reconstructing {GEMs} of microorganisms and microbial communities together with their applications are reviewed.}, added-at = {2018-12-02T16:09:07.000+0100}, author = {Kim, Won J. and Kim, Hyun U. and Lee, Sang Y.}, biburl = {https://www.bibsonomy.org/bibtex/24b2bd4dc116a49810ed667307afa72a9/karthikraman}, citeulike-article-id = {14317988}, citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.coisb.2017.03.001}, doi = {10.1016/j.coisb.2017.03.001}, interhash = {0e36f2fe2671a01db96e748247cec6dd}, intrahash = {4b2bd4dc116a49810ed667307afa72a9}, issn = {24523100}, journal = {Current Opinion in Systems Biology}, keywords = {flux-analysis genome-scale in-silico metabolic-engineering review}, month = apr, pages = {9--17}, posted-at = {2017-03-24 05:56:34}, priority = {2}, timestamp = {2018-12-02T16:09:07.000+0100}, title = {Current state and applications of microbial genome-scale metabolic models}, url = {http://dx.doi.org/10.1016/j.coisb.2017.03.001}, volume = 2, year = 2017 }