Reconstruction and Validation of Saccharomyces cerevisiae iND750, a Fully Compartmentalized Genome-Scale Metabolic Model Export

@article{citeulike:323022, abstract = {10.1101/gr.2250904 A fully compartmentalized genome-scale metabolic model of that accounts for 750 genes and their associated transcripts, proteins, and reactions has been reconstructed and validated. All of the 1149 reactions included in this in silico model are both elementally and charge balanced and have been assigned to one of eight cellular locations (extracellular space, cytosol, mitochondrion, peroxisome, nucleus, endoplasmic reticulum, Golgi apparatus, or vacuole). When in silico predictions of 4154 growth phenotypes were compared to two published large-scale gene deletion studies, an 83\% agreement was found between iND750's predictions and the experimental studies. Analysis of the failure modes showed that false predictions were primarily caused by iND750's limited inclusion of cellular processes outside of metabolism. This study systematically identified inconsistencies in our knowledge of yeast metabolism that require specific further experimental investigation.}, address = {Department of Bioengineering, University of California-San Diego, La Jolla, California 92093-0412, USA.}, author = {Duarte, Natalie C. and Herrg\~{A}¥rd, Markus J. and Palsson, Bernhard}, booktitle = {Genome Research}, citeulike-article-id = {323022}, citeulike-linkout-0 = {http://dx.doi.org/10.1101/gr.2250904}, citeulike-linkout-1 = {http://genome.cshlp.org/content/14/7/1298.abstract}, citeulike-linkout-2 = {http://genome.cshlp.org/content/14/7/1298.full.pdf}, citeulike-linkout-3 = {http://www.genome.org/cgi/content/abstract/14/7/1298}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/15197165}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=15197165}, doi = {10.1101/gr.2250904}, issn = {1088-9051}, journal = {Genome Res}, keywords = {genome-scale, structural-model}, month = {July}, number = {7}, pages = {1298--1309}, posted-at = {2008-03-27 07:25:01}, priority = {2}, title = {Reconstruction and Validation of Saccharomyces cerevisiae iND750, a Fully Compartmentalized Genome-Scale Metabolic Model}, url = {http://dx.doi.org/10.1101/gr.2250904}, volume = {14}, year = {2004} }

TY - JOUR ID - citeulike:323022 L3 - citeulike-article-id:323022 N2 - 10.1101/gr.2250904 A fully compartmentalized genome-scale metabolic model of that accounts for 750 genes and their associated transcripts, proteins, and reactions has been reconstructed and validated. All of the 1149 reactions included in this in silico model are both elementally and charge balanced and have been assigned to one of eight cellular locations (extracellular space, cytosol, mitochondrion, peroxisome, nucleus, endoplasmic reticulum, Golgi apparatus, or vacuole). When in silico predictions of 4154 growth phenotypes were compared to two published large-scale gene deletion studies, an 83% agreement was found between iND750's predictions and the experimental studies. Analysis of the failure modes showed that false predictions were primarily caused by iND750's limited inclusion of cellular processes outside of metabolism. This study systematically identified inconsistencies in our knowledge of yeast metabolism that require specific further experimental investigation. IS - 7 JF - Genome Res SN - 1088-9051 AD - Department of Bioengineering, University of California-San Diego, La Jolla, California 92093-0412, USA. EP - 1309 TI - Reconstruction and Validation of Saccharomyces cerevisiae iND750, a Fully Compartmentalized Genome-Scale Metabolic Model VL - 14 T2 - Genome Research SP - 1298 KW - genome-scale KW - structural-model AU - Duarte, Natalie AU - Herrgård, Markus AU - Palsson, Bernhard PY - 2004/07// UR - http://dx.doi.org/10.1101/gr.2250904 ER -