ArticleMolecular systems biology2017
Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints.
Article in Molecular systems biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 219 papers.
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219 citing papers in PubMed.
- Strategies and applications for alleviating carbon catabolite repression.Synthetic and systems biotechnology · 2027Review
- EINN: An enzyme-informed neural network guided by an enzyme-constrained genome-scale metabolic model.Synthetic and systems biotechnology · 2027Article
- Katalyst: knowledge-guided semantic alignment via contrastive learning for enzyme turnover prediction.Bioinformatics (Oxford, England) · 2026Article
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- Towards the construction of a virtual yeast.Nature · 2026Review
- Nicotinamide Reverses the Warburg Effect in CHO Cell Culture.Biotechnology and bioengineering · 2026Article
- Model-driven analysis reveals oxidative stress adaptation enabling efficient energy utilization in a Crabtree-negative Saccharomyces cerevisiae.Scientific reports · 2026Article
- Predictive Algal Systems Biology: Integrating Omics, Genome-Scale Metabolic Models, and Machine Learning.Bioengineering (Basel, Switzerland) · 2026Review
- EnzymeTuning improves enzyme-constrained metabolic modeling and proteome abundance prediction through deep learning.Nature communications · 2026Article
- dAMN: a genome-scale neural-mechanistic hybrid model to predict bacterial growth dynamics.Bioinformatics (Oxford, England) · 2026Article
- Enzyme-constrained genome-scale modeling resolves growth-production trade-offs in fermentative biohydrogen production.Environmental science and ecotechnology · 2026Article
- Synergy and antagonism in a genome-scale model of metabolic hijacking by bacteriophages.Science advances · 2026Article
- The return of metabolism: biochemistry and physiology of glycolysis.Biological reviews of the Cambridge Philosophical Society · 2026Review
- Enzyme-constrained genome-scale model of Yarrowia lipolytica predicts growth-phase specific metabolic engineering targets.Applied microbiology and biotechnology · 2026Article
- Accurate prediction of flux distributions compatible with metabolite concentration effects in genome-scale metabolic networks.PLoS computational biology · 2026Article
- Advances in genome-scale metabolic modeling of Bacillus subtilis.Biotechnology letters · 2026Review
- Yeast Stress Response to Synthetic Constructs.ACS synthetic biology · 2026Review
- Whole-cell modeling predicts alternative proteome allocation strategies in the archaeon Methanococcus maripaludis.Scientific reports · 2026Article
- Model-driven exploration of lactose and galactose metabolism via an oxidoreductive pathway in Sungouiella intermedia for cell factory applications.Microbial cell factories · 2026Article
159 more citing papers are in PubMed but not listed here.
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6 authors.
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Abstract
Genome-scale metabolic models (GEMs) are widely used to calculate metabolic phenotypes. They rely on defining a set of constraints, the most common of which is that the production of metabolites and/or growth are limited by the carbon source uptake rate. However, enzyme abundances and kinetics, which act as limitations on metabolic fluxes, are not taken into account. Here, we present GECKO, a method that enhances a GEM to account for enzymes as part of reactions, thereby ensuring that each metabolic flux does not exceed its maximum capacity, equal to the product of the enzyme's abundance and turnover number. We applied GECKO to a
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