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Modeling the metabo...
Modeling the metabolic dynamics at the genome-scale by optimized yield analysis
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- Luo, Hao, 1992 (författare)
- Chalmers tekniska högskola,Chalmers University of Technology
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- Li, Peishun, 1988 (författare)
- Chalmers tekniska högskola,Chalmers University of Technology
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- Ji, Boyang, 1983 (författare)
- BioInnovation Institute (BII),Chalmers tekniska högskola,Chalmers University of Technology
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visa fler...
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- Nielsen, Jens B, 1962 (författare)
- BioInnovation Institute (BII),Chalmers tekniska högskola,Chalmers University of Technology
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visa färre...
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(creator_code:org_t)
- Elsevier BV, 2023
- 2023
- Engelska.
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Ingår i: Metabolic Engineering. - : Elsevier BV. - 1096-7176 .- 1096-7184. ; 75, s. 119-130
- Relaterad länk:
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https://research.cha... (primary) (free)
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https://research.cha...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- The hybrid cybernetic model (HCM) approach is a dynamic modeling framework that integrates enzyme synthesis and activity regulation. It has been widely applied in bioreaction engineering, particularly in the simulation of microbial growth in different mixtures of carbon sources. In a HCM, the metabolic network is decomposed into elementary flux modes (EFMs), whereby the network can be reduced into a few pathways by yield analysis. However, applying the HCM approach on conventional genome-scale metabolic models (GEMs) is still a challenge due to the high computational demands. Here, we present a HCM strategy that introduced an optimized yield analysis algorithm (opt-yield-FBA) to simulate metabolic dynamics at the genome-scale without the need for EFMs calculation. The opt-yield-FBA is a flux-balance analysis (FBA) based method that can calculate optimal yield solutions and yield space for GEM. With the opt-yield-FBA algorithm, the HCM strategy can be applied to get the yield spaces and avoid the computational burden of EFMs, and it can therefore be applied for developing dynamic models for genome-scale metabolic networks. Here, we illustrate the strategy by applying the concept to simulate the dynamics of microbial communities.
Ämnesord
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Datavetenskap (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Computer Sciences (hsv//eng)
- TEKNIK OCH TEKNOLOGIER -- Elektroteknik och elektronik -- Datorsystem (hsv//swe)
- ENGINEERING AND TECHNOLOGY -- Electrical Engineering, Electronic Engineering, Information Engineering -- Computer Systems (hsv//eng)
Nyckelord
- Genome-scale metabolic model
- Cybernetic modeling
- Elementary flux mode
- Yield space
- Flux-balance analysis
- Optimize yield
Publikations- och innehållstyp
- art (ämneskategori)
- ref (ämneskategori)
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