Advances in flux balance analysis - PubMed (original) (raw)
Advances in flux balance analysis
Kenneth J Kauffman et al. Curr Opin Biotechnol. 2003 Oct.
Abstract
Biology is going through a paradigm shift from reductionist to holistic, systems-based approaches. The complete genome sequence for a number of organisms is available and the analysis of genome sequence data is proving very useful. Thus, genome sequencing projects and bioinformatic analyses are leading to a complete 'parts catalog' of the molecular components in many organisms. The next challenge will be to reconstruct and simulate overall cellular functions based on the extensive reductionist information. Recent advances have been made in the area of flux balance analysis, a mathematical modeling approach often utilized by metabolic engineers to quantitatively simulate microbial metabolism.
Similar articles
- Mapping the landscape of metabolic goals of a cell.
Zhao Q, Stettner AI, Reznik E, Paschalidis ICh, Segrè D. Zhao Q, et al. Genome Biol. 2016 May 23;17(1):109. doi: 10.1186/s13059-016-0968-2. Genome Biol. 2016. PMID: 27215445 Free PMC article. - Toward metabolic phenomics: analysis of genomic data using flux balances.
Schilling CH, Edwards JS, Palsson BO. Schilling CH, et al. Biotechnol Prog. 1999 May-Jun;15(3):288-95. doi: 10.1021/bp9900357. Biotechnol Prog. 1999. PMID: 10356245 - Genome-scale in silico aided metabolic analysis and flux comparisons of Escherichia coli to improve succinate production.
Wang Q, Chen X, Yang Y, Zhao X. Wang Q, et al. Appl Microbiol Biotechnol. 2006 Dec;73(4):887-94. doi: 10.1007/s00253-006-0535-y. Epub 2006 Aug 23. Appl Microbiol Biotechnol. 2006. PMID: 16927085 - Metabolic ensemble modeling for strain engineers.
Tan Y, Liao JC. Tan Y, et al. Biotechnol J. 2012 Mar;7(3):343-53. doi: 10.1002/biot.201100186. Epub 2011 Oct 21. Biotechnol J. 2012. PMID: 22021171 Review. - Comparing methods for metabolic network analysis and an application to metabolic engineering.
Tomar N, De RK. Tomar N, et al. Gene. 2013 May 25;521(1):1-14. doi: 10.1016/j.gene.2013.03.017. Epub 2013 Mar 26. Gene. 2013. PMID: 23537990 Review.
Cited by
- Understanding flux switching in metabolic networks through an analysis of synthetic lethals.
Narasimha SM, Malpani T, Mohite OS, Nath JS, Raman K. Narasimha SM, et al. NPJ Syst Biol Appl. 2024 Sep 17;10(1):104. doi: 10.1038/s41540-024-00426-5. NPJ Syst Biol Appl. 2024. PMID: 39289347 Free PMC article. - Effect of microbial interactions on performance of community metabolic modeling algorithms: flux balance analysis (FBA), community FBA (cFBA) and SteadyCom.
Afarin M, Naeimpoor F. Afarin M, et al. Bioprocess Biosyst Eng. 2024 Nov;47(11):1833-1848. doi: 10.1007/s00449-024-03072-7. Epub 2024 Aug 24. Bioprocess Biosyst Eng. 2024. PMID: 39180547 - Construction of an enzyme-constrained metabolic network model for Myceliophthora thermophila using machine learning-based kcat data.
Wang Y, Mao Z, Dong J, Zhang P, Gao Q, Liu D, Tian C, Ma H. Wang Y, et al. Microb Cell Fact. 2024 May 15;23(1):138. doi: 10.1186/s12934-024-02415-z. Microb Cell Fact. 2024. PMID: 38750569 - Building blocks needed for mechanistic modeling of bioprocesses: A critical review based on protein production by CHO cells.
González-Hernández Y, Perré P. González-Hernández Y, et al. Metab Eng Commun. 2024 Feb 29;18:e00232. doi: 10.1016/j.mec.2024.e00232. eCollection 2024 Jun. Metab Eng Commun. 2024. PMID: 38501051 Free PMC article. Review. - Patterns of change in regulatory modules of chemical reaction systems induced by network modification.
Hishida A, Okada T, Mochizuki A. Hishida A, et al. PNAS Nexus. 2023 Dec 29;3(1):pgad441. doi: 10.1093/pnasnexus/pgad441. eCollection 2024 Jan. PNAS Nexus. 2023. PMID: 38292559 Free PMC article.
MeSH terms
LinkOut - more resources
Full Text Sources
Other Literature Sources