Advanced Stoichiometric Analysis of Metabolic Networks of Mammalian Systems

scientific article published on January 1, 2011

Advanced Stoichiometric Analysis of Metabolic Networks of Mammalian Systems is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.1615/CRITREVBIOMEDENG.V39.I6.30
P953full work available at URLhttps://dl.begellhouse.com/download/article/78bfa75c36235e19/CRB_3292_Orman_pp511-534_F.pdf
https://europepmc.org/articles/PMC3634616
https://europepmc.org/articles/pmc3634616?pdf=render
https://europepmc.org/articles/PMC3634616?pdf=render
P932PMC publication ID3634616
P698PubMed publication ID22196224

P2093author name stringFrancois Berthiaume
Mehmet A. Orman
Marianthi G. Ierapetritou
Ioannis P. Androulakis
P2860cites workComputational prediction of human metabolic pathways from the complete human genomeQ21092879
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)Q21194867
The ENZYME database in 2000Q22242849
KEGG: kyoto encyclopedia of genes and genomesQ24515297
Expansion of the BioCyc collection of pathway/genome databases to 160 genomesQ24535096
BRENDA, enzyme data and metabolic informationQ24548428
UniProt: the Universal Protein knowledgebaseQ24598826
Global reconstruction of the human metabolic network based on genomic and bibliomic dataQ24677060
Network-based analysis of metabolic regulation in the human red blood cellQ28212164
Analysis of optimality in natural and perturbed metabolic networksQ28213254
The antianginal drug trimetazidine shifts cardiac energy metabolism from fatty acid oxidation to glucose oxidation by inhibiting mitochondrial long-chain 3-ketoacyl coenzyme A thiolaseQ28373346
Metabolic flux analysis of mitochondrial uncoupling in 3T3-L1 adipocytesQ28476081
Regulatory on/off minimization of metabolic flux changes after genetic perturbationsQ28769658
A rational design approach for amino acid supplementation in hepatocyte cultureQ29392880
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growthQ29397612
In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental dataQ29618471
Dynamic analysis of integrated signaling, metabolic, and regulatory networksQ30441717
Compartmentalization of the Edinburgh Human Metabolic NetworkQ30986319
Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraintsQ31920157
Metabolic flux analysis of CHO cell metabolism in the late non-growth phase.Q51772488
Maximum entropy decomposition of flux distribution at steady state to elementary modesQ51782351
A metabolic control analysis of kinetic controls in ATP free energy metabolism in contracting skeletal muscleQ52075316
Metabolite-balancing techniques vs. 13C tracer experiments to determine metabolic fluxes in hybridoma cellsQ52219118
Stoichiometric analysis of animal cell growth and its application in medium designQ52377312
Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalismQ52425486
Mathematical analysis of isotope labeling in the citric acid cycle with applications to 13C NMR studies in perfused rat heartsQ52700131
What Controls Glycolysis in Bloodstream FormTrypanosoma brucei?Q57393902
Triosephosphate isomerase deficiency: predictions and factsQ71835515
Calculation of absolute metabolic flux and the elucidation of the pathways of glutamate labeling in perfused rat heart by 13C NMR spectroscopy and nonlinear least squares analysisQ72149299
Use of mathematical models for predicting the metabolic effect of large-scale enzyme activity alterations. Application to enzyme deficiencies of red blood cellsQ72221379
Mass flux balance-based model and metabolic flux analysis for collagen synthesis in the fibrogenesis process of human liverQ73047111
Multiple steady states with distinct cellular metabolism in continuous culture of mammalian cellsQ73226783
Metabolic flux analysis of postburn hepatic hypermetabolismQ73306352
A universal framework for 13C metabolic flux analysisQ74227987
Fluxes and enzyme activities in central metabolism of myeloma cells grown in chemostat cultureQ74660098
Metabolism of peptide amino acids by Chinese hamster ovary cells grown in a complex mediumQ74660866
Control of oxidative phosphorylation, gluconeogenesis, ureagenesis and ATP turnover in isolated perfused rat liver analyzed by top-down metabolic control analysisQ74750994
High cell density and high monoclonal antibody production through medium design and rational control in a bioreactorQ81646856
Energy metabolism and ATP balance in animal cell cultivation using a stoichiometrically based reaction networkQ81647024
Network-based prediction of human tissue-specific metabolismQ81798711
Genome-scale modeling and in silico analysis of mouse cell metabolic networkQ82298733
Metabolic flux analysis of hepatocyte function in hormone- and amino acid-supplemented plasmaQ44442836
Profiling of dynamic changes in hypermetabolic liversQ44473969
A critical perspective of the use of (13)C-isotopomer analysis by GCMS and NMR as applied to cardiac metabolism.Q44735612
Estimation of metabolic flux from dominant rate constants in vivo: application to brain and heartQ44735616
Quantitative effects of thermal injury and insulin on the metabolism of the skeletal muscle using the perfused rat hindquarter preparationQ45095296
Thermodynamic-based computational profiling of cellular regulatory control in hepatocyte metabolismQ45126764
Mechanistic model of cardiac energy metabolism predicts localization of glycolysis to cytosolic subdomain during ischemiaQ45244970
Enhanced antibody production following intermediate addition based on flux analysis in mammalian cell continuous culture.Q45933148
Quantification of statin effects on hepatic cholesterol synthesis by transient (13)C-flux analysis.Q45952866
Reconstructing metabolic flux vectors from extreme pathways: defining the alpha-spectrumQ46083927
Evolution of intrahepatic carbon, nitrogen, and energy metabolism in a D-galactosamine-induced rat liver failure modelQ46395411
Effects of dehydroepiandrosterone administration on rat hepatic metabolism following thermal injuryQ46481025
Novel quantitative tools for engineering analysis of hepatocyte cultures in bioartificial liver systemsQ46717379
Analysis of cellular metabolism of hybridoma cells at distinct physiological statesQ46760109
Monte Carlo sampling can be used to determine the size and shape of the steady-state flux spaceQ47417801
On the reconstruction of the Mus musculus genome-scale metabolic network model.Q47853955
Material balance studies on animal cell metabolism using a stoichiometrically based reaction networkQ47863148
Stirred vessel cultures of rat brain cells aggregates: characterization of major metabolic pathways and cell population dynamicsQ48106403
Modular decomposition of metabolic reaction networks based on flux analysis and pathway projectionQ48391295
A quadratic programming approach for decomposing steady-state metabolic flux distributions onto elementary modesQ48472250
Analysis of enzymopathies in the human red blood cells by constraint-based stoichiometric modeling approachesQ50720638
Integrated energy and flux balance based multiobjective framework for large-scale metabolic networksQ51036122
An interval approach for dealing with flux distributions and elementary modes activity patterns.Q51066980
Identification of flux regulation coefficients from elementary flux modes: A systems biology tool for analysis of metabolic networksQ51082383
Investigation of metabolic objectives in cultured hepatocytesQ51114910
Identification of distributed metabolic objectives in the hypermetabolic liver by flux and energy balance analysisQ51320677
Effects of glucose and insulin on HepG2-C3A cell metabolismQ39699721
Bayesian flux balance analysis applied to a skeletal muscle metabolic model.Q39776363
Effects of drugs in subtoxic concentrations on the metabolic fluxes in human hepatoma cell line Hep G2.Q39824671
Metabolic flux model for an anchorage-dependent MDCK cell line: characteristic growth phases and minimum substrate consumption flux distributionQ39958457
Comparison of metabolic flux distributions for MDCK cell growth in glutamine- and pyruvate-containing media.Q40021479
Identification of metabolic fluxes in hepatic cells from transient 13C-labeling experiments: Part II. Flux estimationQ40032706
Metabolic pathway analysis of enzyme-deficient human red blood cells.Q40466616
Metabolic-flux analysis of continuously cultured hybridoma cells using (13)CO(2) mass spectrometry in combination with (13)C-lactate nuclear magnetic resonance spectroscopy and metabolite balancingQ40787464
293SF metabolic flux analysis during cell growth and infection with an adenoviral vectorQ40850016
Metabolic flux analysis of hybridoma continuous culture steady state multiplicityQ40943461
Effects of glutamine supply on growth and metabolism of mammalian cells in chemostat cultureQ41110808
Intracellular flux analysis in hybridomas using mass balances and in vitro (13)C nmr.Q41368397
Elementary metabolite units (EMU): a novel framework for modeling isotopic distributionsQ41374953
Fed-batch cultivation of animal cells using different medium design concepts and feeding strategiesQ41468734
Metabolic engineering and human diseaseQ41496325
Applications of improved stoichiometric model in medium design and fed-batch cultivation of animal cells in bioreactorQ41505054
Metabolic flux determination in C6 glioma cells using carbon-13 distribution upon [1-13C]glucose incubationQ41525126
Network analysis of intermediary metabolism using linear optimization. II. Interpretation of hybridoma cell metabolismQ41639252
Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspectiveQ41724911
Soft constraints-based multiobjective framework for flux balance analysisQ41828147
Pathway analysis of liver metabolism under stressed conditionQ41833487
Computational reconstruction of tissue‐specific metabolic models: application to human liver metabolismQ41846171
Ivabradine reduces heart rate while preserving metabolic fluxes and energy status of healthy normoxic working heartsQ41906203
Metabolic-flux analysis of hybridoma cells under oxidative and reductive stress using mass balancesQ42326931
Modeling hybridoma cell metabolism using a generic genome-scale metabolic model of Mus musculusQ42657070
Flux profile and modularity analysis of time-dependent metabolic changes of de novo adipocyte formationQ42831228
Effects of amino acid transport limitations on cultured hepatocytesQ42913539
Metabolic flux determination in perfused livers by mass balance analysis: effect of fastingQ42956835
Transcriptional and metabolic flux profiling of triadimefon effects on cultured hepatocytesQ42957799
Tissue variation in the control of oxidative phosphorylation: implication for mitochondrial diseasesQ42996199
Metabolic flux analysis of CHO cells in perfusion culture by metabolite balancing and 2D [13C, 1H] COSY NMR spectroscopyQ43246624
From fluxes and isotope labeling patterns towards in silico cellsQ43421305
Intrahepatic amino acid and glucose metabolism in a D-galactosamine-induced rat liver failure modelQ43693286
The effect of thiamine supplementation on tumour proliferation. A metabolic control analysis studyQ43698055
Flux balance analysis of biological systems: applications and challenges.Q43740877
Glutamate-loading stimulates metabolic flux and improves cell recovery following chemical hypoxia in isolated cardiomyocytes.Q43816855
Analysis of CHO cells metabolic redistribution in a glutamate-based defined medium in continuous culture.Q43817062
Cardiac carbohydrate metabolism in Zucker diabetic fatty ratsQ44026484
Metabolic flux analysis of cultured hepatocytes exposed to plasmaQ44217005
Metabolic screening of mammalian cell cultures using well-platesQ44305861
Application of multivariate analysis to optimize function of cultured hepatocytesQ44390363
Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decompositionQ33236264
Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysisQ33238510
The topology of metabolic isotope labeling networksQ33295450
A procedure for the estimation over time of metabolic fluxes in scenarios where measurements are uncertain and/or insufficientQ33304395
Reconstruction of metabolic pathways for the cattle genomeQ33417923
Nontargeted elucidation of metabolic pathways using stable-isotope tracers and mass spectrometryQ33626814
Systems-level metabolic flux profiling identifies fatty acid synthesis as a target for antiviral therapyQ33675261
A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1.Q33722800
Advances in flux balance analysisQ33973453
Kinetic analysis of dynamic 13C NMR spectra: metabolic flux, regulation, and compartmentation in heartsQ34047635
13C metabolic flux analysisQ34084355
Regulation of Gene Expression in Flux Balance Models of MetabolismQ34101809
Transcriptional regulation in constraints-based metabolic models of Escherichia coliQ34128076
Extreme pathway analysis of human red blood cell metabolismQ34178460
HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiologyQ34240836
Assessment of Metabolic Phenotypes in Patients with Non-ischemic Dilated Cardiomyopathy Undergoing Cardiac Resynchronization TherapyQ34361776
Evaluation of 13C isotopic tracers for metabolic flux analysis in mammalian cellsQ34517790
Metabolic control analysis in drug discovery and diseaseQ34550535
Delineation of substrate selection and anaplerosis in tricarboxylic acid cycle of the heart by 13C NMR spectroscopy and mass spectrometry.Q34911991
Two approaches for metabolic pathway analysis?Q35062587
Metabolic response of perfused livers to various oxygenation conditionsQ35349814
Contribution of gene expression to metabolic fluxes in hypermetabolic livers induced through burn injury and cecal ligation and puncture in ratsQ35429254
In situ metabolic flux analysis to quantify the liver metabolic response to experimental burn injuryQ35751814
The Edinburgh human metabolic network reconstruction and its functional analysisQ36052649
Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutantsQ36217271
Predicting metabolic biomarkers of human inborn errors of metabolismQ37196179
Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolismQ37328003
MouseCyc: a curated biochemical pathways database for the laboratory mouseQ37350831
Impact of perturbed pyruvate metabolism on adipocyte triglyceride accumulationQ37438291
Effect of anaplerotic fluxes and amino acid availability on hepatic lipoapoptosisQ37446190
Metabolic flux analysis in mammalian cell cultureQ37615599
Metabolic flux analysis in eukaryotesQ37694051
13C metabolic flux analysis in complex systemsQ37787585
Genome‐scale metabolic networksQ37787963
Metabolic flux analysis of embryonic stem cells using three distinct differentiation protocols and comparison to gene expression patterns.Q39644329
P433issue6
P407language of work or nameEnglishQ1860
P921main subjectmetabolic pathwayQ68685
stoichiometryQ213185
metabolic networkQ2263094
P304page(s)511-534
P577publication date2011-01-01
P1433published inCritical Reviews in Biomedical EngineeringQ5186662
P1476titleAdvanced stoichiometric analysis of metabolic networks of mammalian systems
Advanced Stoichiometric Analysis of Metabolic Networks of Mammalian Systems
P478volume39

Reverse relations

cites work (P2860)
Q26772884Amino acids in the cultivation of mammalian cells
Q38637370Bioengineering solutions for manufacturing challenges in CAR T cells.
Q51590229Identification of active elementary flux modes in mitochondria using selectively permeabilized CHO cells.
Q31126202Identification of growth phases and influencing factors in cultivations with AGE1.HN cells using set-based methods
Q39082176Long-term maintenance of HepaRG cells in serum-free conditions and application in a repeated dose study.
Q52691899Metabolic flexibility as an adaptation to energy resources and requirements in health and disease
Q38058685Perspectives in Metabolic Engineering: Understanding Cellular Regulation Towards the Control of Metabolic Routes
Q39216749Quality by control: Towards model predictive control of mammalian cell culture bioprocesses.
Q40778167Reconstruction and validation of a constraint-based metabolic network model for bone marrow-derived mesenchymal stem cells
Q34903798Resuscitation of Ischemic Donor Livers with Normothermic Machine Perfusion: A Metabolic Flux Analysis of Treatment in Rats
Q37198583Towards high resolution analysis of metabolic flux in cells and tissues
Q38595074Understanding the cancer cell phenotype beyond the limitations of current omics analyses

Search more.