ArticleBMC systems biology2019
SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework.
Article in BMC systems biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
- Improvement of the production of biomass and lipid by Papiliotrema laurentii combining flux balance analysis and central composite rotational design.Bioprocess and biosystems engineering · 2026Article
- Constraint-based metabolic modeling reveals metabolic properties underpinning the unprecedented growth of Chlorella ohadii.The New phytologist · 2025Article
- A data-integrative modeling approach accurately characterizes the effects of mutations on Arabidopsis lipid metabolism.Plant physiology · 2025Article
- LipidSIM: Inferring mechanistic lipid biosynthesis perturbations from lipidomics with a flexible, low-parameter, Markov modeling framework.Metabolic engineering · 2024Article
- Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO Toolbox 3.0.Nature protocols · 2024Review
- Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism.Nature communications · 2023Article
- Genome-scale metabolic modeling reveals metabolic trade-offs associated with lipid production in Rhodotorula toruloides.PLoS computational biology · 2023Article
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- Reconstruction of Genome-Scale Metabolic Model for Hansenula polymorpha Using RAVEN.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Metabolic flux sampling predicts strain-dependent differences related to aroma production among commercial wine yeasts.Microbial cell factories · 2021Article
- Nitrogenous Compound Utilization and Production of Volatile Organic Compounds among Commercial Wine Yeasts Highlight Strain-Specific Metabolic Diversity.Microbiology spectrum · 2021Article
- Linking Gut Microbiome and Lipid Metabolism: Moving beyond Associations.Metabolites · 2021Review
- MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models.Nucleic acids research · 2021Article
- Advances in flux balance analysis by integrating machine learning and mechanism-based models.Computational and structural biotechnology journal · 2021Review
- An atlas of human metabolism.Science signaling · 2020Article
- A comprehensive genome-scale model forMetabolic engineering communications · 2019Article
- A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism.Nature communications · 2019Article
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4 authors.
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Abstract
backgroundA recurrent problem in genome-scale metabolic models (GEMs) is to correctly represent lipids as biomass requirements, due to the numerous of possible combinations of individual lipid species and the corresponding lack of fully detailed data. In this study we present SLIMEr, a formalism for correctly representing lipid requirements in GEMs using commonly available experimental data.
resultsSLIMEr enhances a GEM with mathematical constructs where we Split Lipids Into Measurable Entities (SLIME reactions), in addition to constraints on both the lipid classes and the acyl chain distribution. By implementing SLIMEr on the consensus GEM of Saccharomyces cerevisiae, we can represent accurate amounts of lipid species, analyze the flexibility of the resulting distribution, and compute the energy costs of moving from one metabolic state to another.
conclusionsThe approach shows potential for better understanding lipid metabolism in yeast under different conditions. SLIMEr is freely available at https://github.com/SysBioChalmers/SLIMEr .
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