ArticleBioMed research international2014
OpenMebius: an open source software for isotopically nonstationary 13C-based metabolic flux analysis.
Article in BioMed research international, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers, 1 of them a synthesis that pooled it.
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Who cites it
42 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Preclinical techniques to investigate exercise training in vascular pathophysiology.American journal of physiology. Heart and circulatory physiology · 2021Pooled it
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- Methods and Guidelines for Metabolism Studies: Applications to Cancer Research.International journal of molecular sciences · 2025Review
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- FreeFlux: A Python Package for Time-Efficient Isotopically Nonstationary Metabolic Flux Analysis.ACS synthetic biology · 2023Article
- Yeast increases glycolytic flux to support higher growth rates accompanied by decreased metabolite regulation and lower protein phosphorylation.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Interpreting metabolic complexity via isotope-assisted metabolic flux analysis.Trends in biochemical sciences · 2023Review
- Isotope-Assisted Metabolic Flux Analysis: A Powerful Technique to Gain New Insights into the Human Metabolome in Health and Disease.Metabolites · 2022Review
- Metabolic flux analysis: a comprehensive review on sample preparation, analytical techniques, data analysis, computational modelling, and main application areas.RSC advances · 2022Review
- An integrated isotopic labeling and freeze sampling apparatus (ILSA) to support sampling leaf metabolomics at a centi-second scale.Plant methods · 2022Article
- Constitutive expression of the global regulator AbrB restores the growth defect of a genome-reduced Bacillus subtilis strain and improves its metabolite production.DNA research : an international journal for rapid publication of reports on genes and genomes · 2022Article
- Hot isopropanol quenching procedure for automated microtiter plate scaleMicrobial cell factories · 2022Article
- Isotope-assisted metabolic flux analysis as an equality-constrained nonlinear program for improved scalability and robustness.PLoS computational biology · 2022Article
- mfapy: An open-source Python package forMetabolic engineering communications · 2021Article
- Metabolic Flux Analysis-Linking Isotope Labeling and Metabolic Fluxes.Metabolites · 2020Review
- Systematic identification and elimination of flux bottlenecks in the aldehyde production pathway of Synechococcus elongatus PCC 7942.Metabolic engineering · 2020Article
- ScalaFlux: A scalable approach to quantify fluxes in metabolic subnetworks.PLoS computational biology · 2020Article
- Computational data mining method for isotopomer analysis in the quantitative assessment of metabolic reprogramming.Scientific reports · 2020Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The in vivo measurement of metabolic flux by (13)C-based metabolic flux analysis ((13)C-MFA) provides valuable information regarding cell physiology. Bioinformatics tools have been developed to estimate metabolic flux distributions from the results of tracer isotopic labeling experiments using a (13)C-labeled carbon source. Metabolic flux is determined by nonlinear fitting of a metabolic model to the isotopic labeling enrichment of intracellular metabolites measured by mass spectrometry. Whereas (13)C-MFA is conventionally performed under isotopically constant conditions, isotopically nonstationary (13)C metabolic flux analysis (INST-(13)C-MFA) has recently been developed for flux analysis of cells with photosynthetic activity and cells at a quasi-steady metabolic state (e.g., primary cells or microorganisms under stationary phase). Here, the development of a novel open source software for INST-(13)C-MFA on the Windows platform is reported. OpenMebius (Open source software for Metabolic flux analysis) provides the function of autogenerating metabolic models for simulating isotopic labeling enrichment from a user-defined configuration worksheet. Analysis using simulated data demonstrated the applicability of OpenMebius for INST-(13)C-MFA. Confidence intervals determined by INST-(13)C-MFA were less than those determined by conventional methods, indicating the potential of INST-(13)C-MFA for precise metabolic flux analysis. OpenMebius is the open source software for the general application of INST-(13)C-MFA.
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