ArticleBMC systems biology2015
FlexFlux: combining metabolic flux and regulatory network analyses.
Article in BMC systems biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Optimization-based framework with flux balance analysis (FBA) and metabolic pathway analysis (MPA) for identifying metabolic objective functions.PLoS computational biology · 2025Article
- New insights in metabolism modelling to decipher plant-microbe interactions.The New phytologist · 2025Review
- Modelling energy metabolism dysregulations in neuromuscular diseases: A case study of calpainopathy.Heliyon · 2024Article
- MetaLo: metabolic analysis of Logical models extracted from molecular interaction maps.Journal of integrative bioinformatics · 2024Article
- Genome-scale metabolic modelling of extremophiles and its applications in astrobiological environments.Environmental microbiology reports · 2024Review
- Synthetic lethality in large-scale integrated metabolic and regulatory network models of human cells.NPJ systems biology and applications · 2023Article
- Metabolic network reconstruction ofFrontiers in microbiology · 2023Review
- Hybrid computational modeling highlights reverse warburg effect in breast cancer-associated fibroblasts.Computational and structural biotechnology journal · 2023Article
- Metabolic reprogramming in Rheumatoid Arthritis Synovial Fibroblasts: A hybrid modeling approach.PLoS computational biology · 2022Article
- Multi-scale model suggests the trade-off between protein and ATP demand as a driver of metabolic changes during yeast replicative ageing.PLoS computational biology · 2022Article
- Construction of Multiscale Genome-Scale Metabolic Models: Frameworks and Challenges.Biomolecules · 2022Review
- Next-Generation Genome-Scale Metabolic Modeling through Integration of Regulatory Mechanisms.Metabolites · 2021Review
- A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism.PLoS computational biology · 2021Article
- MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics.PLoS computational biology · 2021Article
- Review
- Genome-Scale Investigation of the Metabolic Determinants Generating Bacterial Fastidious Growth.mSystems · 2020Article
- Intercellular cooperation in a fungal plant pathogen facilitates host colonization.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- MetExplore: collaborative edition and exploration of metabolic networks.Nucleic acids research · 2018Article
- Methanol-essential growth of Escherichia coli.Nature communications · 2018Article
- Control of primary metabolism by a virulence regulatory network promotes robustness in a plant pathogen.Nature communications · 2018Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundExpression of cell phenotypes highly depends on metabolism that supplies matter and energy. To achieve proper utilisation of the different metabolic pathways, metabolism is tightly regulated by a complex regulatory network composed of diverse biological entities (genes, transcripts, proteins, signalling molecules…). The integrated analysis of both regulatory and metabolic networks appears very insightful but is not straightforward because of the distinct characteristics of both networks. The classical method used for metabolic flux analysis is Flux Balance Analysis (FBA), which is constraint-based and relies on the assumption of steady-state metabolite concentrations throughout the network. Regarding regulatory networks, a broad spectrum of methods are dedicated to their analysis although logical modelling remains the major method to take charge of large-scale networks.
resultsWe present FlexFlux, an application implementing a new way to combine the analysis of both metabolic and regulatory networks, based on simulations that do not require kinetic parameters and can be applied to genome-scale networks. FlexFlux is based on seeking regulatory network steady-states by performing synchronous updates of multi-state qualitative initial values. FlexFlux is then able to use the calculated steady-state values as constraints for metabolic flux analyses using FBA. As input, FlexFlux uses the standards Systems Biology Markup Language (SBML) and SBML Qualitative Models Package ("qual") extension (SBML-qual) file formats and provides a set of FBA based functions.
conclusionsFlexFlux is an open-source java software with executables and full documentation available online at http://lipm-bioinfo.toulouse.inra.fr/flexflux/. It can be defined as a research tool that enables a better understanding of both regulatory and metabolic networks based on steady-state simulations. FlexFlux integrates well in the flux analysis ecosystem thanks to the support of standard file formats and can thus be used as a complementary tool to existing software featuring other types of analyses.
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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.