Dataset Information

Lu2019 - Genome scale metabolic model for Saccharomyces cerevisiae - yeastGEM8.5.0

ABSTRACT: yeast-GEM: The consensus genome-scale metabolic model of Saccharomyces cerevisiae. Further curations of this model will be tracked in the GitHub repository:https://github.com/SysBioChalmers/yeast-GEM For you use yeast-GEM, please cite the yeast8 paper: Lu, H. et al. A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. Nature Communications 10, 3586 (2019). https://doi.org/10.1038/s41467-019-11581-3. The FROG analysis was performed with the yeastGEM_rich_medium.mat, which is a rich medium setup.

SUBMITTER: feiran

PROVIDER: BIOMD0000001063 | BioModels | 2024-09-02

REPOSITORIES: BioModels

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Dataset's files

Source:

			Action	DRS
	BIOMD0000001063?filename=Description_miniFROG_yeastGEM.xlsx	Xlsx
	BIOMD0000001063?filename=FROG_Report_YeastGEM_rich_medium.zip	Other
	BIOMD0000001063?filename=Yeast_GEM_rich.mat	Other
	BIOMD0000001063?filename=yeast-GEM.omex	Other
	BIOMD0000001063?filename=yeast-GEM.xml	Xml

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Publications

A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism.

Lu Hongzhong H Li Feiran F Sánchez Benjamín J BJ Zhu Zhengming Z Li Gang G Domenzain Iván I Marcišauskas Simonas S Anton Petre Mihail PM Lappa Dimitra D Lieven Christian C Beber Moritz Emanuel ME Sonnenschein Nikolaus N Kerkhoven Eduard J EJ Nielsen Jens J

Nature communications 20190808 1

Genome-scale metabolic models (GEMs) represent extensive knowledgebases that provide a platform for model simulations and integrative analysis of omics data. This study introduces Yeast8 and an associated ecosystem of models that represent a comprehensive computational resource for performing simulations of the metabolism of Saccharomyces cerevisiae--an important model organism and widely used cell-factory. Yeast8 tracks community development with version control, setting a standard for how GEMs ...[more]

PMID: 31395883

Publication: 1/379

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Project description:This is genome-scale metabolic model of Yarrowia lipolytica as the representative yeast species for the clade Dipodascaceae_Trichomonascaceae. This model was generated through homology search using a fungal pan-GEM largely based on Yeast8 for Saccharomyces cerevisiae, in addition to manual curation. This model has been produced by the Yeast-Species-GEMs project from Sysbio (www.sysbio.se). This is model version 1.0.0 accompanying the publication (DOI: 10.15252/msb.202110427), currently hosted on BioModels Database and identified by MODEL2109130007. Further curations of this model will be tracked in the GitHub repository: https://github.com/SysBioChalmers/Yeast-Species-GEMs Models for species of the same clade includes: Blastobotrys adeninivorans; Starmerella apicola; Wickerhamiella infanticola; Wickerhamiella versatilis; Geotrichum candidum; Nadsonia fulvescens var. elongata; Saprochaete clavata; Starmerella bombicola; Sugiyamaella lignohabitans; Wickerhamiella domercqiae; Yarrowia deformans; Yarrowia keelungensis; Yarrowia lipolytica; Spencermartinsiella europaea; Nadsonia fulvescens var. fulvescens; Wickerhamiella cacticola; Diddensiella caesifluorescens; Dipodascus albidus; Blastobotrys serpentis; Blastobotrys raffinosifermentans; Blastobotrys proliferans; Blastobotrys peoriensis; Blastobotrys nivea; Blastobotrys muscicola; Blastobotrys mokoenaii; Blastobotrys americana; Deakozyma indianensis; Zygoascus ofunaensis; Zygoascus meyerae; Candida incommunis; Candida hispaniensis; Yarrowia bubula; Yarrowia divulgata; Middelhovenomyces tepae; Groenewaldozyma salmanticensis; Magnusiomyces tetraspermus; Dipodascus geniculatus. These models are available in the zip file. To cite BioModels, please use: V Chelliah et al; BioModels: ten-year anniversary. Nucleic Acids Res 2015; 43 (D1): D542-D548. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to MIT License for more information.