ArticleGenome research2004
OptStrain: a computational framework for redesign of microbial production systems.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 153 papers, 1 of them a synthesis that pooled it.
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Who cites it
153 citing papers in PubMed, 1 synthesis or guideline pooled it, 496 citations in OpenAlex.
- Pooled it
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- Metabolic growth-coupling strategies forMetabolic engineering communications · 2025Article
- Unveiling Metabolic Engineering Strategies by Quantitative Heterologous Pathway Design.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Systems biology approach for enhancing limonene yield by re-engineering Escherichia coli.NPJ systems biology and applications · 2024Article
- Regulatory-systemic approach in Aspergillus niger for bioleaching improvement by controlling precipitation.Applied microbiology and biotechnology · 2023Article
- Uses of Multi-Objective Flux Analysis for Optimization of Microbial Production of Secondary Metabolites.Microorganisms · 2023Review
- Integrating Omics Data in Genome-Scale Metabolic Modeling: A Methodological Perspective for Precision Medicine.Metabolites · 2023Review
- Metabolomics and modelling approaches for systems metabolic engineering.Metabolic engineering communications · 2022Review
- Genome-scale metabolic network models: from first-generation to next-generation.Applied microbiology and biotechnology · 2022Review
- OptDesign: Identifying Optimum Design Strategies in Strain Engineering for Biochemical Production.ACS synthetic biology · 2022Article
- Curating COBRA Models of Microbial Metabolism.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Application of the Metabolic Modeling Pipeline in KBase to Categorize Reactions, Predict Essential Genes, and Predict Pathways in an Isolate Genome.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Stoichiometric Modeling of Artificial String Chemistries Reveals Constraints on Metabolic Network Structure.Journal of molecular evolution · 2021Article
- GeneReg: a constraint-based approach for design of feasible metabolic engineering strategies at the gene level.Bioinformatics (Oxford, England) · 2021Article
- NetFlow: A tool for isolating carbon flows in genome-scale metabolic networks.Metabolic engineering communications · 2021Article
- Reaction lumping in metabolic networks for application with thermodynamic metabolic flux analysis.Scientific reports · 2021Article
- Finding branched pathways in metabolic network via atom group tracking.PLoS computational biology · 2021Article
- Opportunities and Challenges for Microbial Synthesis of Fatty Acid-Derived Chemicals (FACs).Frontiers in bioengineering and biotechnology · 2021Review
- Metabolic modelling approaches for describing and engineering microbial communities.Computational and structural biotechnology journal · 2021Review
93 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
This paper introduces the hierarchical computational framework OptStrain aimed at guiding pathway modifications, through reaction additions and deletions, of microbial networks for the overproduction of targeted compounds. These compounds may range from electrons or hydrogen in biofuel cell and environmental applications to complex drug precursor molecules. A comprehensive database of biotransformations, referred to as the Universal database (with >5700 reactions), is compiled and regularly updated by downloading and curating reactions from multiple biopathway database sources. Combinatorial optimization is then used to elucidate the set(s) of non-native functionalities, extracted from this Universal database, to add to the examined production host for enabling the desired product formation. Subsequently, competing functionalities that divert flux away from the targeted product are identified and removed to ensure higher product yields coupled with growth. This work represents an advancement over earlier efforts by establishing an integrated computational framework capable of constructing stoichiometrically balanced pathways, imposing maximum product yield requirements, pinpointing the optimal substrate(s), and evaluating different microbial hosts. The range and utility of OptStrain are demonstrated by addressing two very different product molecules. The hydrogen case study pinpoints reaction elimination strategies for improving hydrogen yields using two different substrates for three separate production hosts. In contrast, the vanillin study primarily showcases which non-native pathways need to be added into Escherichia coli. In summary, OptStrain provides a useful tool to aid microbial strain design and, more importantly, it establishes an integrated framework to accommodate future modeling developments.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.