ArticleBioinformatics (Oxford, England)2014
FastPros: screening of reaction knockout strategies for metabolic engineering.
Article in Bioinformatics (Oxford, England), 2014. 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, 53 citations in OpenAlex.
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- In Silico Design Strategies for the Production of Target Chemical Compounds Using Iterative Single-Level Linear Programming Problems.Biomolecules · 2022Article
- Quantitative metabolic fluxes regulated by trans-omic networks.The Biochemical journal · 2022Review
- Dynamic Solution Space Division-Based Methods for Calculating Reaction Deletion Strategies for Constraint-Based Metabolic Networks for Substance Production: DynCubeProd.Frontiers in bioinformatics · 2021Article
- Adaptive laboratory evolution for growth coupled microbial production.World journal of microbiology & biotechnology · 2020Review
- Improving designer glycan production inMetabolic engineering communications · 2019Article
- Grid-based computational methods for the design of constraint-based parsimonious chemical reaction networks to simulate metabolite production: GridProd.BMC bioinformatics · 2018Article
- Growth-coupled overproduction is feasible for almost all metabolites in five major production organisms.Nature communications · 2017Article
- Selection Finder (SelFi): A computational metabolic engineering tool to enable directed evolution of enzymes.Metabolic engineering communications · 2017Article
- In Silico Constraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories.Microbiology and molecular biology reviews : MMBR · 2016Review
- Co-evolution of strain design methods based on flux balance and elementary mode analysis.Metabolic engineering communications · 2015Review
- Double and multiple knockout simulations for genome-scale metabolic network reconstructions.Algorithms for molecular biology : AMB · 2015Article
- Expanding Metabolic Engineering Algorithms Using Feasible Space and Shadow Price Constraint Modules.Metabolic engineering communications · 2014Article
- Increased 3-hydroxypropionic acid production from glycerol, by modification of central metabolism in Escherichia coli.Microbial cell factories · 2014Article
- Predictive sulfur metabolism - a field in flux.Frontiers in plant science · 2014Review
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationAlthough constraint-based flux analysis of knockout strains has facilitated the production of desirable metabolites in microbes, current screening methods have placed a limitation on the number knockouts that can be simultaneously analyzed.
resultsHere, we propose a novel screening method named FastPros. In this method, the potential of a given reaction knockout for production of a specific metabolite is evaluated by shadow pricing of the constraint in the flux balance analysis, which generates a screening score to obtain candidate knockout sets. To evaluate the performance of FastPros, we screened knockout sets to produce each metabolite in the entire Escherichia coli metabolic network. We found that 75% of these metabolites could be produced under biomass maximization conditions by adding up to 25 reaction knockouts. Furthermore, we demonstrated that using FastPros in tandem with another screening method, OptKnock, could further improve target metabolite productivity. AVAILABILITY AND IMPLEMENTATION: Source code is freely available at http://www-shimizu.ist.osaka-u.ac.jp/shimizu_lab/FastPros/, implemented in MATLAB and COBRA toolbox.
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