# Metabolism

- A Primer on Modular Mass Action Modelling with CellML
- A Primer on Modular Mass Action Modelling with CellML
- Acikgoz, Karim, Giri, Schmidt-Heck, Bader, 2009
- Two compartment model of diazepam biotransformation in an organotypical culture of primary human hepatocytes
- Acikgoz, Karim, Giri, Schmidt-Heck, Bader, 2009
- Two compartment model of diazepam biotransformation in an organotypical culture of primary human hepatocytes
- acikgoz_2009a.cellml
- acikgoz_2009a.cellml
- acikgoz_2009b.cellml
- acikgoz_2009b.cellml
- Aon, Cortassa, 2002
- Coherent and robust modulation of a metabolic network by cytoskeletal organization and dynamics
- Bakker, Mensonides, Teusink, van Hoek, Michels, Westerhoff, 2000
- Compartmentation protects trypanosomes from the dangerous design of glycolysis
- Bakker, Michels, Opperdoes, Westerhoff, 1997
- Glycolysis in Bloodstream Form Trypanosoma brucei Can Be Understood in Terms of the Kinetics of the Glycolytic Enzymes
- Beard, 2005
- A biophysical model of the mitochondrial respiratory system and oxidative phosphorylation
- Bertram, Pedersen, Luciani, Sherman, 2006
- A simplified model for mitochondrial ATP production
- Bertram, Satin, Pedersen, Luciani, Sherman, 2007
- Intra- and inter-islet synchronization of metabolically driven insulin secretion
- Bertram, Satin, Zhang, Smolen, Sherman, 2004
- Calcium and Glycolysis Mediate Multiple Bursting Modes in Pancreatic Islets (glycolytic bursting model)
- Bertram, Satin, Zhang, Smolen, Sherman, 2004
- Calcium and Glycolysis Mediate Multiple Bursting Modes in Pancreatic Islets (compound bursting model)
- Bertram, Smolen, Sherman, Mears, Atwater, Martin, Soria, 1995
- A role for calcium release-activated current (CRAC) in cholinergic modulation of electrical activity in pancreatic beta-cells
- Chassagnole, Rais, Quentin, Fell, Mazat, 2001
- An integrated study of Threonine-pathway enzyme kinetics in Escherichia coli
- Cloutier, Bolger, Lowry, Wellstead, 2009
- An integrative dynamic model of brain energy metabolism using in vivo neurochemical measurements
- Cloutier, Wellstead, 2009
- The control systems structures of energy metabolism (Version A)
- Cloutier, Wellstead, 2009
- The control systems structures of energy metabolism (Version B)
- Cloutier, Wellstead, 2009
- The control systems structures of energy metabolism (Version C)
- Cloutier, Wellstead, 2009
- The control systems structures of energy metabolism (Version D)
- Cloutier, Wellstead, 2009
- The control systems structures of energy metabolism (Version E)
- Cloutier, Wellstead, 2009
- The control systems structures of energy metabolism (Version F)
- Cortassa, Aon, Marban, Winslow, O'Rourke, 2003
- An Integrated Model of Cardiac Mitrochondrial Energy Metabolism and Calcium Dynamics
- Cortassa, Aon, Winslow, O'Rourke, 2004
- A mitochondrial oscillator dependent on reactive oxygen species
- Cronwright, Rohwer, Prior, 2002
- Metabolic Control Analysis of Glycerol Synthesis in Saccharomyces cerevisiae
- Curien, Ravanel, Dumas, 2003
- A kinetic model of the branch-point between the methionine and threonine biosynthesis pathways in Arabidopsis thaliana
- Dash, Bassingthwaighte, 2004
- Blood HbO2 and HbCO2 dissociation curves at varied O2, CO2, pH, 2,3-DPG and temperature levels
- Dijkstra, Neal, Beever, France, 1992
- Simulation of nutrient digestion, absorption and outflow in the rumen: model description
- Goldbeter,
- A model for the dynamics of human weight cycling
- Grange, Holford, Guentert, 2001
- A pharmacokinetic model to predict the PK interaction of L-dopa and benserazide in rats (L-dopa)
- Grange, Holford, Guentert, 2001
- A pharmacokinetic model to predict the PK interaction of L-dopa and benserazide in rats (L-dopa + Benserazide)
- Gupta, Maurya, Stephens, Dennis, Subramaniam, 2009
- An integrated model of eicosanoid metabolism and signaling based on lipidomics flux analysis
- Gupta, Maurya, Stephens, Dennis, Subramaniam, 2009
- An integrated model of eicosanoid metabolism and signaling based on lipidomics flux analysis
- Heyd, Drew, 2003
- A mathematical model for elongation of a peptide chain
- Hoefnagel, Starrenburg, Martens, Hugenholtz, Kleerebezem, Van Swam, Bongers, Westerhoff, Snoep, 2002
- Metabolic engineering of lactic acid bacteria, the combined approach: kinetic modelling, metabolic control and experimental analysis
- Hynne, Dano, Sorensen, 2001
- Full-scale model of glycolysis in Saccharomyces cerevisiae
- Keener, 2001
- Diffusion Induced Oscillatory Insulin Secretion
- Kongas, van Beek, 2001
- Creatine kinase in energy metabolic signaling in muscle
- Korzeniewski, Zoladz, 2001
- A model of oxidative phosphorylation in mammaliam skeletal muscle
- Lambeth, Kushmerick, 2002
- A computational model for glycogenolysis in skeletal muscle
- Martinov, Vitvitsky, Mosharov, Banerjee, Ataullakhanov, 2000
- A Substrate Switch: A New Mode of Regulation in the Methionine Metabolic Pathway
- Martins, Mendes, Coreiro, Freire, 2001
- In situ kinetic analysis of glyoxalase I and glyoxalase II in Saccharomyces cerevisiae
- Michailova, McCulloch, 2001
- Model study of ATP and ADP buffering, transport of Ca2+ and Mg2+, and regulation of ion pumps in ventricular myocyte
- Michailova, Saucerman, Belik, McCulloch, 2005
- Modeling regulation of cardiac KATP and L-type Ca2+ currents by ATP, ADP, and Mg2+
- Mijailovich, Butler, Fredburg, 2000
- Perturbed Equilibria of Myosin Binding in Airway Smooth Muscle: Bond-Length Distributions, Mechanics and ATP Metabolism
- Mitochondrial energetic metabolism: a simplified model of TCA cycle with ATP production (scaled version)
- Mitochondrial energetic metabolism: a simplified model of TCA cycle with ATP production (scaled version)
- Mitochondrial energetic metabolism: a simplified model of TCA cycle with ATP production (unscaled version)
- Mitochondrial energetic metabolism: a simplified model of TCA cycle with ATP production (unscaled version)
- Novak, Tyson, 1993
- Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte extracts and intact embryos: parameter values have been taken from the original published paper to reproduce figure 4A.
- Novak, Tyson, 1993
- Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte extracts and intact embryos: parameter values have been taken from the SBML model in the BioModels Database and the model simulates the synthesis and degradation of cyclin.
- Novak, Tyson, 1993
- Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte extracts and intact embryos: parameter values have been taken from the original published paper to reproduce figure 4A.
- Novak, Tyson, 1993
- Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte extracts and intact embryos: parameter values have been taken from the SBML model in the BioModels Database and the model simulates the synthesis and degradation of cyclin.
- Olsen, Hauser, Kummer, 2003
- Mechanism of protection of peroxidase activity by oscillatory dynamics
- Overgaard, Holford, Rytved, Madsen, 2007
- PKPD model of interleukin-21 effects on thermoregulation in monkeys (Baseline)
- Overgaard, Holford, Rytved, Madsen, 2007
- PKPD model of interleukin-21 effects on thermoregulation in monkeys (Pharmacodynamic)
- Ralser, Lehrach, Krobitsch, Wamelink, Kowald, Gerisch, Heeren, Struys, Klipp, Jakobs, Breitenbach, 2007
- Dynamic rerouting of the carbohydrate flux is key to counteracting oxidative stress
- Reed, Nijhout, Sparks, Ulrich, 2004
- A mathematical model of the methionine cycle
- Salem, Saidel, Stanley, Cabrera, 2002
- Mechanistic Model of Myocardial Energy Metabolism Under Normal and Ischemic Conditions
- Saucerman, Brunton, Michailova, McCulloch, 2003
- Modeling beta-adrenergic control of cardiac myocyte contractility in silico
- Saucerman, McCulloch, 2004
- Mechanistic systems models of cell signaling networks: a case study of myocyte adrenergic regulation
- Sedaghat, Sherman, Quon, 2002
- A mathematical model of metabolic insulin signaling pathways (without feedback)
- Sedaghat, Sherman, Quon, 2002
- A mathematical model of metabolic insulin signaling pathways (with feedback)
- Surkis, Peskin, Tranchina, Leonard, 1998
- Recovery of Cable Properties Through Active and Passive Modeling of Subthreshold Membrane Responses From Laterodorsal Tegmental Neurons
- Teusink, Westerhoff, Snoep, Passarge, Reijenga, Esgalhado, van der Weijden, Schepper, Walsh, Bakker, van Dam, 2000
- Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry.
- Tolic, Mosekilde, Sturis, 2000
- Modelling the Insulin-Glucose Feedback System: The Significance of Pulsatile Insulin Secretion
- Topp, Promislow, de Vries, Miura, Finegood, 2000
- A Model of Beta-Cell Mass, Insulin, and Glucose Kinetics: Paythways to Diabetes
- Tran, Smith, Loiselle, Crampin, 2009
- A metabolite-sensitive, thermodynamically-constrained model of cardiac cross-bridge cycling: Implications for force development during ischemia
- Tran, Smith, Loiselle, Crampin, 2010
- A metabolite-sensitive, thermodynamically-constrained model of cardiac cross-bridge cycling: Implications for force development during ischemia
- van Beek, 2007
- Adenine nucleotide-creatine-phosphate module in myocardial metabolic system explains fast phase of dynamic regulation of oxidative phosphorylation
- Vaseghi, Baumeister, Rizzi, Reuss, 1999
- In Vivo Dynamics of the Pentose Phosphate Pathway in Saccharomyces cerevisiae
- Vinnakota, Kemp, Kushmeric, 2006
- Dynamics of Muscle Glycogenolysis Modeled with pH Time Course Computation and pH-Dependent Reaction Equilibria and Enzyme Kinetics (Experiment 29, 0.2% Glycogen Phosphorylase A)
- Vinnakota, Kemp, Kushmeric, 2006
- Dynamics of Muscle Glycogenolysis Modeled with pH Time Course Computation and pH-Dependent Reaction Equilibria and Enzyme Kinetics (Experiment 29, 40% Glycogen Phosphorylase A)
- Vinnakota, Kemp, Kushmeric, 2006
- Dynamics of Muscle Glycogenolysis Modeled with pH Time Course Computation and pH-Dependent Reaction Equilibria and Enzyme Kinetics (Experiment 45)
- Vinnakota, Rusk, Palmer, Shankland, Kushmeric, 2010
- Common Phenotype of Resting Mouse EDL and SOL Muscles: EDL
- Vinnakota, Rusk, Palmer, Shankland, Kushmeric, 2010
- Common Phenotype of Resting Mouse EDL and SOL Muscles: SOL
- Westermark, Lansner, 2003
- A Model of Phosphofructokinase and Glycolytic Oscillations in the Pancreatic Beta-cell
- Wierschem, Bertram,
- Complex bursting in pancreatic islets: a potential glycolytic mechanism
- Wolf, Heinrich, 2000
- Effect of cellular interaction on glycolytic oscillations in yeast: a theoretical investigation
- Wolf, Passarge, Somsen, Snoep, Heinrich, Westerhoff, 2000
- Transduction of Intracellular and Intercellular Dynamics in Yeast Glycolytic Oscillations
- Wolf, Sohn, Heinrich, Kuriyama, 2001
- Mathematical analysis of a mechanism for autonomous metabolic oscillations in continuous culture of Saccharomyces cerevisae
- Wu, Jeneson, Beard, 2006
- Oxidative ATP Synthesis in Skeletal Muscle is Controlled by Substrate Feedback
- Wu, Yang, Vinnakota, Beard, 2007
- Computer Modeling of Mitochondrial Tricarboxylic Acid Cycle, Oxidative Phosphorylation, Metabolite Transport, and Electrophysiology
- Yang, Tong, McCarver, Hines, Beard, 2006
- Population-Based Analysis of Methadone Distribution and Metabolism Using an Age-Dependent Physiologically Based Pharmacokinetic Model