Fluxes through plant metabolic networks: measurements, predictions, insights and challenges
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Title
Fluxes through plant metabolic networks: measurements, predictions, insights and challenges
Authors
Keywords
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Journal
BIOCHEMICAL JOURNAL
Volume 465, Issue 1, Pages 27-38
Publisher
Portland Press Ltd.
Online
2014-12-12
DOI
10.1042/bj20140984
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Note: Only part of the references are listed.- INCA: a computational platform for isotopically non-stationary metabolic flux analysis
- (2014) J. D. Young BIOINFORMATICS
- Advancing metabolic models with kinetic information
- (2014) Hannes Link et al. CURRENT OPINION IN BIOTECHNOLOGY
- Flux analysis in plant metabolic networks: increasing throughput and coverage
- (2014) Björn H Junker CURRENT OPINION IN BIOTECHNOLOGY
- Kinetic models in industrial biotechnology – Improving cell factory performance
- (2014) Joachim Almquist et al. METABOLIC ENGINEERING
- Elucidation of intrinsic biosynthesis yields using 13C-based metabolism analysis
- (2014) Arul M Varman et al. Microbial Cell Factories
- Flux profiling of photosynthetic carbon metabolism in intact plants
- (2014) Robert Heise et al. Nature Protocols
- Metabolic flux phenotype of tobacco hairy roots engineered for increased geraniol production
- (2014) Shyam K. Masakapalli et al. PHYTOCHEMISTRY
- Complete Proteomic-Based Enzyme Reaction and Inhibition Kinetics Reveal How Monolignol Biosynthetic Enzyme Families Affect Metabolic Flux and Lignin inPopulus trichocarpa
- (2014) Jack P. Wang et al. PLANT CELL
- The metabolic flux phenotype of heterotrophic Arabidopsis cells reveals a flexible balance between the cytosolic and plastidic contributions to carbohydrate oxidation in response to phosphate limitation
- (2014) Shyam K. Masakapalli et al. PLANT JOURNAL
- Bottom-up Metabolic Reconstruction of Arabidopsis and Its Application to Determining the Metabolic Costs of Enzyme Production
- (2014) A. Arnold et al. PLANT PHYSIOLOGY
- Elements Required for an Efficient NADP-Malic Enzyme Type C4 Photosynthesis
- (2014) Y. Wang et al. PLANT PHYSIOLOGY
- Metabolic Flux Analysis of Plastidic Isoprenoid Biosynthesis in Poplar Leaves Emitting and Nonemitting Isoprene
- (2014) A. Ghirardo et al. PLANT PHYSIOLOGY
- A Diel Flux Balance Model Captures Interactions between Light and Dark Metabolism during Day-Night Cycles in C3 and Crassulacean Acid Metabolism Leaves
- (2014) C. Y. M. Cheung et al. PLANT PHYSIOLOGY
- Can the Cyanobacterial Carbon-Concentrating Mechanism Increase Photosynthesis in Crop Species? A Theoretical Analysis
- (2014) J. M. McGrath et al. PLANT PHYSIOLOGY
- Multiscale digitalArabidopsispredicts individual organ and whole-organism growth
- (2014) Yin Hoon Chew et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- OpenMebius: An Open Source Software for Isotopically Nonstationary13C-Based Metabolic Flux Analysis
- (2014) Shuichi Kajihata et al. Biomed Research International
- The Spatial Organization of Metabolism Within the Plant Cell
- (2013) Lee J. Sweetlove et al. Annual Review of Plant Biology
- A metabolite-centric view on flux distributions in genome-scale metabolic models
- (2013) S Riemer et al. BMC Systems Biology
- Predicting C4 Photosynthesis Evolution: Modular, Individually Adaptive Steps on a Mount Fuji Fitness Landscape
- (2013) David Heckmann et al. CELL
- Isotopically non-stationary metabolic flux analysis: complex yet highly informative
- (2013) Wolfgang Wiechert et al. CURRENT OPINION IN BIOTECHNOLOGY
- Systems-integration of plant metabolism: means, motive and opportunity
- (2013) Mark Stitt CURRENT OPINION IN PLANT BIOLOGY
- Flux and reflux: metabolite reflux in plant suspension cells and its implications for isotope-assisted metabolic flux analysis
- (2013) Shilpa Nargund et al. Molecular BioSystems
- Transcriptional regulation is insufficient to explain substrate-induced flux changes in Bacillus subtilis
- (2013) V. Chubukov et al. Molecular Systems Biology
- A system dynamics model integrating physiology and biochemical regulation predicts extent of crassulacean acid metabolism (CAM) phases
- (2013) Nick A. Owen et al. NEW PHYTOLOGIST
- Metabolic Fluxes in an Illuminated Arabidopsis Rosette
- (2013) M. Szecowka et al. PLANT CELL
- Integration of Genome-Scale Modeling and Transcript Profiling Reveals Metabolic Pathways Underlying Light and Temperature Acclimation in Arabidopsis
- (2013) N. Topfer et al. PLANT CELL
- Seed Architecture Shapes Embryo Metabolism in Oilseed Rape
- (2013) Ljudmilla Borisjuk et al. PLANT CELL
- Analysis of metabolic flux using dynamic labelling and metabolic modelling
- (2013) A. R. FERNIE et al. PLANT CELL AND ENVIRONMENT
- Modelling metabolic CO2evolution - a fresh perspective on respiration
- (2013) LEE J. SWEETLOVE et al. PLANT CELL AND ENVIRONMENT
- A method for accounting for maintenance costs in flux balance analysis improves the prediction of plant cell metabolic phenotypes under stress conditions
- (2013) C. Y. Maurice Cheung et al. PLANT JOURNAL
- The metabolic flux phenotype of heterotrophic Arabidopsis cells reveals a complex response to changes in nitrogen supply
- (2013) Shyam K. Masakapalli et al. PLANT JOURNAL
- Metabolic flux analysis using13C peptide label measurements
- (2013) Dominic E. Mandy et al. PLANT JOURNAL
- Elucidating Rice Cell Metabolism under Flooding and Drought Stresses Using Flux-Based Modeling and Analysis
- (2013) M. Lakshmanan et al. PLANT PHYSIOLOGY
- Carbon and Nitrogen Provisions Alter the Metabolic Flux in Developing Soybean Embryos
- (2013) D. K. Allen et al. PLANT PHYSIOLOGY
- Multiscale Metabolic Modeling: Dynamic Flux Balance Analysis on a Whole-Plant Scale
- (2013) E. Grafahrend-Belau et al. PLANT PHYSIOLOGY
- Responses to Light Intensity in a Genome-Scale Model of Rice Metabolism
- (2013) M. G. Poolman et al. PLANT PHYSIOLOGY
- Functioning of a metabolic flux sensor in Escherichia coli
- (2013) K. Kochanowski et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- High-resolution metabolic mapping of cell types in plant roots
- (2013) A. Moussaieff et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Systems analysis of metabolic phenotypes: what have we learnt?
- (2013) Lee J. Sweetlove et al. TRENDS IN PLANT SCIENCE
- Flux Balance Analysis of Cyanobacterial Metabolism: The Metabolic Network of Synechocystis sp. PCC 6803
- (2013) Henning Knoop et al. PLoS Computational Biology
- Arabidopsis plants perform arithmetic division to prevent starvation at night
- (2013) Antonio Scialdone et al. eLife
- Mass Spectrometry Based Imaging Techniques for Spatially Resolved Analysis of Molecules
- (2013) Andrea Matros et al. Frontiers in Plant Science
- Photobioreactor design for isotopic non-stationary13C-metabolic flux analysis (INST13C-MFA) under photoautotrophic conditions
- (2012) Arnaud Martzolff et al. BIOTECHNOLOGY AND BIOENGINEERING
- A Whole-Cell Computational Model Predicts Phenotype from Genotype
- (2012) Jonathan R. Karr et al. CELL
- Plant genome-scale metabolic reconstruction and modelling
- (2012) Cristiana Gomes de Oliveira Dal’Molin et al. CURRENT OPINION IN BIOTECHNOLOGY
- Insights into metabolic efficiency from flux analysis
- (2012) Xuewen Chen et al. JOURNAL OF EXPERIMENTAL BOTANY
- Kinetic modelling of plant metabolic pathways
- (2012) Johann M. Rohwer JOURNAL OF EXPERIMENTAL BOTANY
- Metabolic cartography: experimental quantification of metabolic fluxes from isotopic labelling studies
- (2012) J. O'Grady et al. JOURNAL OF EXPERIMENTAL BOTANY
- Towards high throughput metabolic flux analysis in plants
- (2012) Jan Huege et al. Molecular BioSystems
- e-photosynthesis: a comprehensive dynamic mechanistic model of C3 photosynthesis: from light capture to sucrose synthesis
- (2012) XIN-GUANG ZHU et al. PLANT CELL AND ENVIRONMENT
- Isotope labelling of Rubisco subunits provides in vivo information on subcellular biosynthesis and exchange of amino acids between compartments
- (2012) DOUG K. ALLEN et al. PLANT CELL AND ENVIRONMENT
- Bacterial- and plant-type phosphoenolpyruvate carboxylase isozymes from developing castor oil seeds interact in vivo and associate with the surface of mitochondria
- (2012) Joonho Park et al. PLANT JOURNAL
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- Predictive Modeling of Biomass Component Tradeoffs in Brassica napus Developing Oilseeds Based on in Silico Manipulation of Storage Metabolism
- (2012) J. Schwender et al. PLANT PHYSIOLOGY
- On the Discordance of Metabolomics with Proteomics and Transcriptomics: Coping with Increasing Complexity in Logic, Chemistry, and Network Interactions Scientific Correspondence
- (2012) A. R. Fernie et al. PLANT PHYSIOLOGY
- Are we ready for genome-scale modeling in plants?
- (2012) Eva Collakova et al. PLANT SCIENCE
- Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis
- (2012) J. Nogales et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Subpopulation-Specific Metabolic Pathway Usage in Mixed Cultures as Revealed by Reporter Protein-Based13C Analysis
- (2011) Martin Rühl et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- An in silico compartmentalized metabolic model of Brassica napus enables the systemic study of regulatory aspects of plant central metabolism
- (2011) Eleftherios Pilalis et al. BIOTECHNOLOGY AND BIOENGINEERING
- Strategies for investigating the plant metabolic network with steady-state metabolic flux analysis: lessons from an Arabidopsis cell culture and other systems
- (2011) N. J. Kruger et al. JOURNAL OF EXPERIMENTAL BOTANY
- Mapping photoautotrophic metabolism with isotopically nonstationary 13C flux analysis
- (2011) Jamey D. Young et al. METABOLIC ENGINEERING
- Large-scale 13C-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli
- (2011) B. R. B. Haverkorn van Rijsewijk et al. Molecular Systems Biology
- Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism
- (2011) R. L. Chang et al. Molecular Systems Biology
- Dynamic 13C/1H NMR imaging uncovers sugar allocation in the living seed
- (2011) Gerd Melkus et al. PLANT BIOTECHNOLOGY JOURNAL
- Computational analysis of storage synthesis in developing Brassica napus L. (oilseed rape) embryos: flux variability analysis in relation to 13C metabolic flux analysis
- (2011) Jordan Hay et al. PLANT JOURNAL
- Metabolic network reconstruction and flux variability analysis of storage synthesis in developing oilseed rape (Brassica napus L.) embryos
- (2011) Jordan Hay et al. PLANT JOURNAL
- Capturing Metabolite Channeling in Metabolic Flux Phenotypes
- (2011) T. C. R. Williams et al. PLANT PHYSIOLOGY
- Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism
- (2011) Rajib Saha et al. PLoS One
- Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity
- (2011) S. Mintz-Oron et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- 13C Metabolic Flux Analysis Identifies an Unusual Route for Pyruvate Dissimilation in Mycobacteria which Requires Isocitrate Lyase and Carbon Dioxide Fixation
- (2011) Dany J. V. Beste et al. PLoS Pathogens
- Flux-Balance Modeling of Plant Metabolism
- (2011) Lee J. Sweetlove et al. Frontiers in Plant Science
- Understanding fatty acid synthesis in developing maize embryos using metabolic flux analysis
- (2010) Ana Paula Alonso et al. METABOLIC ENGINEERING
- Central metabolic fluxes in the endosperm of developing maize seeds and their implications for metabolic engineering
- (2010) Ana P. Alonso et al. METABOLIC ENGINEERING
- In folio isotopic tracing demonstrates that nitrogen assimilation into glutamate is mostly independent from current CO2 assimilation in illuminated leaves of Brassica napus
- (2010) Paul P. G. Gauthier et al. NEW PHYTOLOGIST
- AraGEM, a Genome-Scale Reconstruction of the Primary Metabolic Network in Arabidopsis
- (2010) C. G. de Oliveira Dal'Molin et al. PLANT PHYSIOLOGY
- C4GEM, a Genome-Scale Metabolic Model to Study C4 Plant Metabolism
- (2010) C. G. de Oliveira Dal'Molin et al. PLANT PHYSIOLOGY
- A Genome-Scale Metabolic Model Accurately Predicts Fluxes in Central Carbon Metabolism under Stress Conditions
- (2010) Thomas C.R. Williams et al. PLANT PHYSIOLOGY
- Not just a circle: flux modes in the plant TCA cycle
- (2010) Lee J. Sweetlove et al. TRENDS IN PLANT SCIENCE
- Insights into plant metabolic networks from steady-state metabolic flux analysis
- (2009) Nicholas J. Kruger et al. BIOCHIMIE
- Subcellular Flux Analysis of Central Metabolism in a Heterotrophic Arabidopsis Cell Suspension Using Steady-State Stable Isotope Labeling
- (2009) S. K. Masakapalli et al. PLANT PHYSIOLOGY
- Analysis of Metabolic Flux Phenotypes for Two Arabidopsis Mutants with Severe Impairment in Seed Storage Lipid Synthesis
- (2009) J. Lonien et al. PLANT PHYSIOLOGY
- A Genome-Scale Metabolic Model of Arabidopsis and Some of Its Properties
- (2009) M. G. Poolman et al. PLANT PHYSIOLOGY
- Predicting biological system objectives de novo from internal state measurements
- (2008) Erwin P Gianchandani et al. BMC BIOINFORMATICS
- Kinetic flux profiling for quantitation of cellular metabolic fluxes
- (2008) Jie Yuan et al. Nature Protocols
- Metabolic flux maps comparing the effect of temperature on protein and oil biosynthesis in developing soybean cotyledons
- (2008) VIDYA V. IYER et al. PLANT CELL AND ENVIRONMENT
- The role of light in soybean seed filling metabolism
- (2008) Doug K. Allen et al. PLANT JOURNAL
- Metabolic Network Fluxes in Heterotrophic Arabidopsis Cells: Stability of the Flux Distribution under Different Oxygenation Conditions
- (2008) T. C.R. Williams et al. PLANT PHYSIOLOGY
- An elementary metabolite unit (EMU) based method of isotopically nonstationary flux analysis
- (2007) Jamey D. Young et al. BIOTECHNOLOGY AND BIOENGINEERING
- Is maximization of molar yield in metabolic networks favoured by evolution?
- (2007) Stefan Schuster et al. JOURNAL OF THEORETICAL BIOLOGY
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