Assays
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Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Srimani et al (2017) Molecular Systems Biology
A model for the PGK reaction of yeast in presence or absence of the ATP recycling reactions
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: PGK-30C
BPG stability analysis
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: BPG stability
PGK 70C model
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: PGK-70C
PGK - GAPDH models
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: PGK-GAPDH 30C & 70C
We have developed a method for comparative analysis of pairs of complex networks based on gene co-expression analysis. We apply this modeling analysis to data set for gene expressions in multiple tissues of mus musculus and homo sapiens.
Submitter: Eivind Almaas
Biological problem addressed: Model Analysis Type
Investigation: Development of methods for comparing gene co-ex...
Submitter: Matthias König
Biological problem addressed: Model Analysis Type
Investigation: MM-PLF: Multiscale modeling for personalized li...
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Adlung et al (2017) Molecular Systems Biology
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model analysis
Inhibition of lactate flux due to glucose transport inhibitor
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model analysis
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model analysis
Genome scale metabolic model of Sulfolobus solfataricus specific scenario: modelling of L-fucose degradation pathways
Submitter: Jacqueline Wolf
Biological problem addressed: Metabolic Network
Investigation: L-fucose degradation in Sulfolobus solfataricus P2
The multi-compartmental metabolic network of Arabidopsis thaliana was reconstructed and optimized in order to explain growth stoichiometry of the plant both in light and in dark conditions. Balances and turnover of energy (ATP/ADP) and redox (NAD(P)H/NAD(P)) metabolites as well as proton in different compartments were estimated. The model showed that in light conditions, the plastid ATP balance depended on the relationship between fluxes through photorespiration and photosynthesis including both ...
Submitter: Maksim Zakhartsev
Biological problem addressed: Metabolic Network
Investigation: Metabolic analysis of effects of sucrose transl...
SED-ML simulation: https://jjj.bio.vu.nl/models/experiments/bachmann2011/simulate
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Bachmann et al (2011) Molecular Systems Biology...
SED-ML simulation: https://jjj.bio.vu.nl/models/experiments/bachmann2011/simulate
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Kolodkin et al (2010) Molecular Systems Biology...
Submitter: Ron Henkel
Biological problem addressed: Cell Cycle
Investigation: Hands-on: Model Management in SEEK
Submitter: Katy Wolstencroft
Biological problem addressed: Model Analysis Type
Investigation: Yeast Glycolytic Oscillations
Mathematical model for PGK kinetics, saturation with ADP, ATP, 3PG and BPG.
Submitter: Jacky Snoep
Biological problem addressed: Enzymology
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model Gluconeogenesis
In vitro reconstitution of the PGK, GAPHD, TPI and FBPAase enzymes from S. solfataricus
Submitter: Jacky Snoep
Biological problem addressed: Metabolic Network
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model Gluconeogenesis
Model prediction of the conversion of 3PG to fructose-6-phosphate and the gluconeogenic pathway intermediates. https://jjj.bio.vu.nl/models/experiments/kouril3_experiment-user/simulate
Submitter: Jacky Snoep
Biological problem addressed: Metabolic Network
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Mathematical model for GAPDH kinetics, saturation with BPG, NADPH, NADP, GAP and Pi
Submitter: Jacky Snoep
Biological problem addressed: Enzymology
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model Gluconeogenesis
Mathematical model for TPI kinetics, saturation with GAP and DHAP, and inhibition by 3PG and PEP
Submitter: Jacky Snoep
Biological problem addressed: Enzymology
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model Gluconeogenesis
Mathematical model for FBPAase kinetics, saturation with DHAP and GAP
Submitter: Jacky Snoep
Biological problem addressed: Enzymology
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model Gluconeogenesis
Modelling the degradation of BPG, GAP and DHAP at high temperature
Submitter: Jacky Snoep
Biological problem addressed: Metabolism
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model Gluconeogenesis
The stressosome is an important sensor of environmental stresses in B. subtilis. It is formed by three protein types that form an icosahedral geometric protein complex. There are uncertanties how protein interactions take place, what the effects on the response behaviour of activation and inhibition of phosphorylation among proteins is, and what kind of proximal signal activates the stressosome in the first place. To answer these questions a computational modelling approach was developed. This ...
Submitter: Ulf Liebal
Biological problem addressed: Signal Induction
Investigation: The transition from growing to non-growing Baci...
Despite high similarity in sequence and catalytic properties, the L-lactate dehydrogenases (LDH) in lactic acid bacteria (LAB) display differences in their regulation which may arise from their adaptation to different habitats. We combined experimental and computational approaches to investigate the effects of fructose-1,6-bisphosphate (FBP), phosphate (Pi) and ionic strength (NaCl concentration) on 6 LDHs from 4 LABs studied at pH 6 and pH 7. We find: (1) The extent of activation by FBP (Kact) ...
Submitter: Anna Feldman-Salit
Biological problem addressed: Metabolism
Investigation: Investigation of glycolysis and pyruvate branch...
We here create a kinetic model for a single enzyme within the T. brucei trypanothione synthesis pathway, the enzyme trypanothione synthetase based on the insights from the laboratory experiments
Submitter: Jurgen Haanstra
Biological problem addressed: Enzymology
Investigation: Kinetic understanding of the T. brucei trypanot...
The RNAseq data on mRNA processing and mRNA decay were used to update a previously published model and to interrogate which process should be dependent on mRNA length
Submitter: Jurgen Haanstra
Biological problem addressed: Model Analysis Type
Investigation: Gene expression in Trypanosoma brucei
Kinetic characterisation en mathematical modelling of HK.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Kinetic characterisation en mathematical modelling of PGI.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction