ArticleScientific reports2015
Designing overall stoichiometric conversions and intervening metabolic reactions.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Mechanism-informed rules tunably balance novelty and feasibility of predicted enzymatic reactions.bioRxiv : the preprint server for biology · 2026Article
- novoStoic2.0: An integrated framework for pathway synthesis, thermodynamic evaluation, and enzyme selection.PLoS computational biology · 2025Article
- Merging the computational design of chimeric type I polyketide synthases with enzymatic pathways for chemical biosynthesis.Nature communications · 2025Article
- minChemBio: Expanding Chemical Synthesis with Chemo-Enzymatic Pathways Using Minimal Transitions.ACS synthetic biology · 2025Article
- Current State, Challenges, and Opportunities in Genome-Scale Resource Allocation Models: A Mathematical Perspective.Metabolites · 2024Review
- Design and Assembly of a Biofactory for (2Biomolecules · 2023Article
- Functional Analysis of HApplied and environmental microbiology · 2022Article
- Minimal Pathway for the Regeneration of Redox Cofactors.JACS Au · 2021Article
- dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design.PLoS computational biology · 2021Article
- NetFlow: A tool for isolating carbon flows in genome-scale metabolic networks.Metabolic engineering communications · 2021Article
- Finding branched pathways in metabolic network via atom group tracking.PLoS computational biology · 2021Article
- Concerns with computational protein engineering programmes IPRO and OptMAVEn and metabolic pathway engineering programme optStoic.Open biology · 2021Article
- Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks.Computational and structural biotechnology journal · 2021Review
- novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model.Nucleic acids research · 2020Article
- MEMO: A Method for Computing Metabolic Modules for Cell-Free Production Systems.ACS synthetic biology · 2020Article
- A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory.Microbial cell factories · 2019Article
- Pareto Optimality Explanation of the Glycolytic Alternatives in Nature.Scientific reports · 2019Article
- Pathway design using de novo steps through uncharted biochemical spaces.Nature communications · 2018Article
- A Prospective Study on the Fermentation Landscape of Gaseous Substrates to Biorenewables UsingFrontiers in microbiology · 2018Article
- A review of computational tools for design and reconstruction of metabolic pathways.Synthetic and systems biotechnology · 2017Review
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2 authors.
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Abstract
Existing computational tools for de novo metabolic pathway assembly, either based on mixed integer linear programming techniques or graph-search applications, generally only find linear pathways connecting the source to the target metabolite. The overall stoichiometry of conversion along with alternate co-reactant (or co-product) combinations is not part of the pathway design. Therefore, global carbon and energy efficiency is in essence fixed with no opportunities to identify more efficient routes for recycling carbon flux closer to the thermodynamic limit. Here, we introduce a two-stage computational procedure that both identifies the optimum overall stoichiometry (i.e., optStoic) and selects for (non-)native reactions (i.e., minRxn/minFlux) that maximize carbon, energy or price efficiency while satisfying thermodynamic feasibility requirements. Implementation for recent pathway design studies identified non-intuitive designs with improved efficiencies. Specifically, multiple alternatives for non-oxidative glycolysis are generated and non-intuitive ways of co-utilizing carbon dioxide with methanol are revealed for the production of C2+ metabolites with higher carbon efficiency.
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