Constrained Allocation Flux Balance Analysis. [PDF]
PLoS Computational Biology, 2016 New experimental results on bacterial growth inspire a novel top-down approach to study cell metabolism, combining mass balance and proteomic constraints to extend and complement Flux Balance Analysis.
Matteo Mori +4 more
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‘Social’ versus ‘asocial’ cells—dynamic competition flux balance analysis [PDF]
npj Systems Biology and Applications, 2023 In multicellular organisms cells compete for resources or growth factors. If any one cell type wins, the co-existence of diverse cell types disappears. Existing dynamic Flux Balance Analysis (dFBA) does not accommodate changes in cell density caused by ...
Yanhua Liu, Hans V. Westerhoff
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Balancing biomass reaction stoichiometry and measured fluxes in flux balance analysis. [PDF]
Bioinformatics, 2023 Abstract Motivation Flux balance analysis (FBA) is widely recognized as an important method for studying metabolic networks. When incorporating flux measurements of certain reactions into an FBA problem, it is possible that the underlying linear program may become infeasible, e.g.
von Kamp A, Klamt S.
europepmc +5 more sources
Model validation and selection in metabolic flux analysis and flux balance analysis. [PDF]
Biotechnol Prog, 2023 Abstract 13C‐Metabolic Flux Analysis (13C‐MFA) and Flux Balance Analysis (FBA) are widely used to investigate the operation of biochemical networks in both biological and biotechnological research. Both methods use metabolic reaction network models of metabolism operating at steady state so that reaction rates ...
Kaste JAM, Shachar-Hill Y.
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Mitigating biomass composition uncertainties in flux balance analysis using ensemble representations [PDF]
Computational and Structural Biotechnology Journal, 2023 The biomass equation is a critical component in genome-scale metabolic models (GEMs): it is used as the de facto objective function in flux balance analysis (FBA).
Yoon-Mi Choi +6 more
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Advances in flux balance analysis by integrating machine learning and mechanism-based models [PDF]
Computational and Structural Biotechnology Journal, 2021 The availability of multi-omics data sets and genome-scale metabolic models for various organisms provide a platform for modeling and analyzing genotype-to-phenotype relationships.
Ankur Sahu +3 more
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Analyzing and Resolving Infeasibility in Flux Balance Analysis of Metabolic Networks [PDF]
Metabolites, 2022 Flux balance analysis (FBA) is a key method for the constraint-based analysis of metabolic networks. A technical problem may occur in FBA when known (e.g., measured) fluxes of certain reactions are integrated into an FBA scenario rendering the underlying
Steffen Klamt, Axel von Kamp
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Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells [PDF]
BMC Bioinformatics, 2022 Background Sophisticated methods to properly pre-process and analyze the increasing collection of single-cell RNA sequencing (scRNA-seq) data are increasingly being developed.
Bruno G. Galuzzi +2 more
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Optimization-based framework with flux balance analysis (FBA) and metabolic pathway analysis (MPA) for identifying metabolic objective functions. [PDF]
PLoS Computational BiologyMetabolic network modeling, especially Flux Balance Analysis (FBA), plays a critical role in systems biology by providing insights into cellular behaviors.
Ching-Mei Wen +2 more
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Community flux balance analysis for microbial consortia at balanced growth.
PLoS ONE, 2013 A central focus in studies of microbial communities is the elucidation of the relationships between genotype, phenotype, and dynamic community structure.
Ruchir A Khandelwal +4 more
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