ArticleBioinformatics (Oxford, England)2020
NIHBA: a network interdiction approach for metabolic engineering design.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- OptDesign: Identifying Optimum Design Strategies in Strain Engineering for Biochemical Production.ACS synthetic biology · 2022Article
- Picking the right metaphors for addressing microbial systems: economic theory helps understanding biological complexity.International microbiology : the official journal of the Spanish Society for Microbiology · 2021Article
- Opportunities and Challenges for Microbial Synthesis of Fatty Acid-Derived Chemicals (FACs).Frontiers in bioengineering and biotechnology · 2021Review
- Modelling microbial communities: Harnessing consortia for biotechnological applications.Computational and structural biotechnology journal · 2021Review
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4 authors.
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Abstract
motivationFlux balance analysis (FBA) based bilevel optimization has been a great success in redesigning metabolic networks for biochemical overproduction. To date, many computational approaches have been developed to solve the resulting bilevel optimization problems. However, most of them are of limited use due to biased optimality principle, poor scalability with the size of metabolic networks, potential numeric issues or low quantity of design solutions in a single run.
resultsHere, we have employed a network interdiction model free of growth optimality assumptions, a special case of bilevel optimization, for computational strain design and have developed a hybrid Benders algorithm (HBA) that deals with complicating binary variables in the model, thereby achieving high efficiency without numeric issues in search of best design strategies. More importantly, HBA can list solutions that meet users' production requirements during the search, making it possible to obtain numerous design strategies at a small runtime overhead (typically ∼1 h, e.g. studied in this article). AVAILABILITY AND IMPLEMENTATION: Source code implemented in the MATALAB Cobratoolbox is freely available at https://github.com/chang88ye/NIHBA. CONTACT: math4neu@gmail.com or natalio.krasnogor@ncl.ac.uk. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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