{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"volume":["9"],"submitter":["Dinh HV"],"funding":["U.S. Department of Energy"],"pubmed_abstract":["<i>Rhodosporidium toruloides</i> is a red, basidiomycetes yeast that can accumulate a large amount of lipids and produce carotenoids. To better assess this non-model yeast's metabolic capabilities, we reconstructed a genome-scale model of <i>R. toruloides</i> IFO0880's metabolic network (<i>iRhto</i>1108) accounting for 2204 reactions, 1985 metabolites and 1108 genes. In this work, we integrated and supplemented the current knowledge with in-house generated biomass composition and experimental measurements pertaining to the organism's metabolic capabilities. Predictions of genotype-phenotype relations were improved through manual curation of gene-protein-reaction rules for 543 reactions leading to correct recapitulations of 84.5% of gene essentiality data (sensitivity of 94.3% and specific"],"journal":["Metabolic engineering communications"],"pagination":["e00101"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC6838544"],"repository":["biostudies-literature"],"pubmed_title":["A comprehensive genome-scale model for <i>Rhodosporidium toruloides</i> IFO0880 accounting for functional genomics and phenotypic data."],"pmcid":["PMC6838544"],"pubmed_authors":["Rabinowitz JD","Rao CV","Jagtap SS","Deewan A","Shen Y","Xiao T","Maranas CD","Dinh HV","Suthers PF","Chan SHJ","Zhao H"],"additional_accession":[]},"is_claimable":false,"name":"A comprehensive genome-scale model for <i>Rhodosporidium toruloides</i> IFO0880 accounting for functional genomics and phenotypic data.","description":"<i>Rhodosporidium toruloides</i> is a red, basidiomycetes yeast that can accumulate a large amount of lipids and produce carotenoids. To better assess this non-model yeast's metabolic capabilities, we reconstructed a genome-scale model of <i>R. toruloides</i> IFO0880's metabolic network (<i>iRhto</i>1108) accounting for 2204 reactions, 1985 metabolites and 1108 genes. In this work, we integrated and supplemented the current knowledge with in-house generated biomass composition and experimental measurements pertaining to the organism's metabolic capabilities. Predictions of genotype-phenotype relations were improved through manual curation of gene-protein-reaction rules for 543 reactions leading to correct recapitulations of 84.5% of gene essentiality data (sensitivity of 94.3% and specific","dates":{"release":"2019-01-01T00:00:00Z","publication":"2019 Dec","modification":"2026-07-14T13:38:33.997Z","creation":"2026-06-19T03:07:42.69Z"},"accession":"S-EPMC6838544","cross_references":{"pubmed":["31720216"],"doi":["10.1016/j.mec.2019.e00101"]}}