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- Jacky Snoep
SEEK ID: https://fairdomhub.org/people/49
Locations:
United Kingdom
,
South Africa
Expertise: Not specified
Tools: Not specified
ORCID: Not specified
PSYSMO (Manchester Centre for Integrative Systems Biology, University of Manchester) ; MOSES (Manchester Centre for Integrative Systems Biology, University of Manchester) ; SysMO DB (Manchester Centre for Integrative Systems Biology, University of Manchester) ; SysMO-LAB (University of Stellenbosch) ; SulfoSys (Manchester Centre for Integrative Systems Biology, University of Manchester) ; SulfoSys - Biotec (Manchester Centre for Integrative Systems Biology, University of Manchester) ; Whole body modelling of glucose metabolism in malaria patients (University of Stellenbosch) ; FAIRDOM (University of Manchester - Department of Computer Science) ; Molecular Systems Biology (Manchester Centre for Integrative Systems Biology, University of Manchester) ; COMBINE Multicellular Modelling (Stellenbosch University) ; HOTSOLUTE (University of Stellenbosch) ; Steroid biosynthesis (Stellenbosch University) ; Yeast glycolytic oscillations (Stellenbosch University) ; Computational pathway design for biotechnological applications (Stellenbosch University)
Related items
- Projects (14)
- Institutions (4)
- Investigations (14)
- Studies (30)
- Assays (58)
- Data files (63+8)
- Models (86+10)
- SOPs (20)
- Publications (28)
- Presentations (10)
- Events (1)
FAIRDOM will establish a support and service network for European Systems Biology. We will serve projects in standardising, managing and disseminating data and models in a FAIR manner: Findable, Accessible, Interoperable and Reusable.
Organisms: Not specified
Background- Thermophilic organisms are composed of both bacterial and archaeal species. The enzymes isolated from these species and from other extreme habitats are more robust to temperature, organic solvents and proteolysis. They often have unique substrate specificities and originate from novel metabolic pathways. Thermophiles as well as their stable enzymes (‘thermozymes’) are receiving increased attention for biotechnological applications.
The proposed project will establish thermophilic in
...
Programme: Era CoBioTech
Public web page: https://www.cobiotech.eu/call-information
Programme: COMBINE (Computational Modeling in Biology Network)
Public web page: https://multicellml.org/
Organisms: Not specified
The goal of the project is to establish a new biotechnological platform for the production of hydroxy-amino acids, since the current production of these important building blocks is very expensive. Enzyme engineering, systems biotechnology and metabolic engineering will be used in a synthetic biology approach.
Programme: SARCHI: Mechanistic modelling of health and epidemiology
Public web page: Not specified
Organisms: Caulobacter
The main objectives of SysMO-DB are to: facilitate the web-based exchange of data between research groups within- and inter- consortia, and to provide an integrated platform for the dissemination of the results of the SysMO projects to the scientific community. We aim to devise a progressive and scalable solution to the data management needs of the SysMO initiative, that:
* facilitates and maximises the potential for data exchange between SysMO research groups;
* maximises the ‘shelf life’ and
...
Programme: SysMO
Public web page: http://www.sysmo-db.org/
Organisms: Not specified
Programme: SARCHI: Mechanistic modelling of health and epidemiology
Public web page: Not specified
Organisms: Saccharomyces cerevisiae
Programme: SARCHI: Mechanistic modelling of health and epidemiology
Public web page: Not specified
Organisms: Homo sapiens
The Molecular Systems Biology project holds information for reproducing simulation figures in the journal. This can include experimental data files, model files and manuscript information.
Programme: Journals
Public web page: http://msb.embopress.org
Organisms: Not specified
Within the e:Bio - Innovationswettbewerb Systembiologie (Federal Ministry of Education and Research (BMBF)), the SulfoSYSBIOTECH consortium (10 partners), aim to unravel the complexity and regulation of the carbon metabolic network of the thermoacidophilic archaeon Sulfolobus solfataricus (optimal growth at 80°C and pH 3) in order to provide new catalysts ‘extremozymes’ for utilization in White Biotechnology.
Based on the available S. solfataricus genome scale metabolic model (Ulas et al., 2012)
...
Programme: e:Bio
Public web page: http://www.sulfosys.com/
Organisms: Sulfolobus solfataricus
Hypoglycaemia and lactic acidosis are key diagnostics for poor chances of survival in malaria patients. In this project we aim to test to what extent the metabolic activity of Plasmodium falciparum contributes to a changed glucose metabolism in malaria patients. The approach is to start with detailed bottom up models for the parasite and then merge these with more coarse grained models at the whole body level.
Programme: SARCHI: Mechanistic modelling of health and epidemiology
Public web page: Not specified
Organisms: Plasmodium falciparum, Homo sapiens
Comparative Systems Biology: Lactic Acid Bacteria
Programme: SysMO
Public web page: http://www.sysmo.net/index.php?index=57
Systems analysis of process-induced stresses: towards a quantum increase in process performance of Pseudomonas putida as the cell factory of choice for white biotechnology.
The specific goal of this project is to exploit the full biotechnological efficacy of Pseudomonas putida KT2440 by developing new optimization strategies that increase its performance through a systems biology understanding of key metabolic and regulatory parameters that control callular responses to key stresses generated
...
Programme: SysMO
Public web page: http://www.psysmo.org/
Organisms: Pseudomonas putida
MOSES (Micro Organism Systems biology: Energy and Saccharomyces cerevisiae) develops a new Systems Biology approach, which is called 'domino systems biology'. It uses this to unravel the role of cellular free energy ('ATP') in the control and regulation of cell function. MOSES operates though continuous iterations between partner groups through a new systems-biology driven data-management workflow. MOSES also tries to serve as a substrate for three or more other SYSMO programs.
Programme: SysMO
Public web page: http://www.moses.sys-bio.net/
Organisms: Saccharomyces cerevisiae
Silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation
Programme: SysMO
Public web page: http://sulfosys.com/
Organisms: Sulfolobus solfataricus
The oxidative Weimberg pathway for the five-step pentose degradation to α ketoglutarate from Caulobacter crescentus is a key route for sustainable bioconversion of lignocellulosic biomass to added-value products and biofuels. Here, we developed a novel iterative approach involving initial rate kinetics, progress curves, and enzyme cascades, with high resolution NMR analysis of intermediate dynamics, and multiple cycles of kinetic modelling analyses to construct and validate a quantitative model
...
Snapshots: Snapshot 1, Snapshot 2
Studies: Cell free extract, Initial rate kinetics, One pot cascade, Progress curves
Assays: Cell free extract, with Mn and NAD recycling, Cell free extract, with Mn, no NAD recycling, Cell free extract, without added Mn, with NAD recycling, KDXD, KGSADH, One pot cascade 10, One pot cascade 12, One pot cascade 13, One pot cascade 16, Progress curve KDXD, Progress curve KGSADH, Progress curve XAD, Progress curve XDH, Progress curve XLA, Progress curves combined, Steady state cell free extract, with Mn and NAD recycling, XAD, XDH, XLA
Biphasic response as a mechanism against mutant takeover in tissue homeostasis circuits
Snapshots: No snapshots
Studies: Figure 1C: Biphasic control can resist mutant invasion of feedback circu..., Figure 1D: Biphasic control can resist mutant invasion of feedback circu..., Figure 1G: Biphasic control can resist mutant invasion of feedback circu..., Figure 1H: Biphasic control can resist mutant invasion of feedback circu..., Figure 2: Frequency-dependent selection of mutant pancreatic beta cells., Figure 4C: Biphasic control can provide mutant resistance to stem-cell h..., Figure 4D: Biphasic control can provide mutant resistance to stem-cell h...
Assays: Biphasic control can provide mutant resistance to stem-cell homeostatic ..., Biphasic control can provide mutant resistance to stem-cell homeostatic ..., Biphasic control can resist mutant invasion of feedback circuits., Biphasic control can resist mutant invasion of feedback circuits., Biphasic control can resist mutant invasion of feedback circuits., Biphasic control can resist mutant invasion of feedback circuits., Frequency-dependent selection of mutant pancreatic beta cells.
Frequency doubling in the cyanobacterial circadian clock
Snapshots: No snapshots
Snapshots: No snapshots
Snapshots: No snapshots
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Studies: Entrainment of heterogeneous glycolytic oscillations in single cells
Assays: No Assays
Snapshots: No snapshots
Studies: Substrate preferences for AKR1C3, and implications of varying AKR1C3:17B...
Assays: No Assays
The gluconeogenic conversion of 3-phosphoglycerate via 1,3-bisphosphoglycerate to glyceraldehyde-3-phosphate was compared at 30 C and at 70 C. At 30 C it was possible to produce 1,3-bisphosphoglycerate from 3-phosphoglycerate with phosphoglycerate kinase, but at 70 C, 1,3- bisphosphoglycerate was dephosphorylated rapidly to 3-phosphoglycerate, effectively turning the phosphoglycerate kinase into a futile cycle. At both temperatures it was possible to convert 3-phosphoglycerate to glyceraldehyde
...
Snapshots: No snapshots
Drug detoxification dynamics explain the postantibiotic effect
Snapshots: No snapshots
Protein abundance of AKT and ERK pathway components governs cell-type- specific regulation of proliferation
Snapshots: No snapshots
The investigation entails the construction and validation of a detailed mathematical model for glycolysis of the malaria parasite Plasmodium falciparum in the blood stage trophozoite form.
Snapshots: Snapshot 1
Studies: Model analysis, Model construction, Model validation
Assays: ALD, ATPASE, Culturing and synchronisation of P. falciparum, ENO, G3PDH, GAPDH, GLC incubation, GLCtr, GLYtr, HK, Inhibition of glucose transport, Inhibition of lactate flux, LACtr, LDH, PFK, PGI, PGK, PGM, PK, PYRtr, Steady state, Supply-demand analysis, TPI, Trophozoite Isolation and Lysate Preparation
Design principles of nuclear receptor signaling: how complex networking improves signal transduction
Snapshots: No snapshots
Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range
Snapshots: No snapshots
An investigation in the central carbon metabolism of S. solfataricus with a focus on the unique temperature adaptations and regulation; using a combined modelling and experimental approach.
Snapshots: No snapshots
Studies: Carbon Loss at High Temperature, Model Gluconeogenesis
Assays: Experimental Validation Gluconeogenesis in S. solfataricus, FBPAase, FBPAase Modelling, GAPDH, GAPDH Modelling, Model Validation Gluconeogenesis in S. solfataricus, Modelling Metabolite Degradation at High Temperature, PGK, PGK Modelling, Reconstituted Gluconeogenesis System, TPI, TPI Modelling, Temperature Degradation of Gluconeogenic Intermediates
One pot cascade - pathway analysis for the purified Caulinobacter crescentus Weimberg pathway enzymes. Effect of co-factor recycling, removal of XLA, and optimisation on Xylose to aKG is studied.
https://jjj.bio.vu.nl/models/experiments/shen2020_fig3a/simulate
https://jjj.bio.vu.nl/models/experiments/shen2020_fig3b/simulate
https://jjj.bio.vu.nl/models/experiments/shen2020_fig3c/simulate
https://jjj.bio.vu.nl/models/experiments/shen2020_fig3d/simulate
Person responsible: Jacky Snoep
Snapshots: No snapshots
Investigation: Caulobacter crescentus Weimberg pathway
Assays: One pot cascade 10, One pot cascade 12, One pot cascade 13, One pot cascade 16
Initial rate kinetics for the purified Caulinobacter crescentus Weimberg pathway enzymes, including substrate dependence, and product inhibition.
Person responsible: Jacky Snoep
Snapshots: No snapshots
Progress curves for the purified Caulinobacter crescentus Weimberg pathway enzymes. Each reaction is followed up to completion and then the next enzyme in the pathway is added, i.e. XDH-XLA-XAD-KDXD and finally KGSADH
Person responsible: Jacky Snoep
Snapshots: No snapshots
Cell free extract - pathway analysis for Caulinobacter crescentus Weimberg pathway enzymes. Effect of co-factor recycling, and Mn2+ on Xylose to aKG conversion is studied.
Person responsible: Jacky Snoep
Snapshots: No snapshots
D Biphasic control of stem-cell expansion, where stem-cell expansion is low both at high and low concentrations of y. The system has a stable fixed point at the concentration of y where pr = 0.5 and an unstable fixed point at some lower concentration of y.
SED-ML simulation
https://jjj.bio.vu.nl/models/experiments/karin2017_fig4d/simulate
Person responsible: Jacky Snoep
Snapshots: No snapshots
C A mutated stem cell with a strong inactivation of the sensing of y has a
growth advantage (differentiates less), and therefore, it invades the stem- cell population. As a result, both the stem-cell pool and the number of terminally differentiated cells increase.
SED-ML simulation
https://jjj.bio.vu.nl/models/experiments/karin2017_fig4c/simulate
Person responsible: Jacky Snoep
Snapshots: No snapshots
Mathematical simulation of a tamoxifen-induced conditional knock-in of a sixfold activating GCK mutant in beta cells. (C) The percentage of beta cells with mutated GCK increases to ~25% after 3 days, but then decreases and is eliminated after a few weeks. (D) Glucose levels initially decrease after the tamoxifen injection, but return to normal after a few weeks. Insets: Experimental results of Tornovsky-Babeay et al (2014).
SED-ML simulation
https://jjj.bio.vu.nl/models/experiments/karin2017_fig2/simulate
...
Person responsible: Jacky Snoep
Snapshots: No snapshots
C Trajectories of Z from different initial concentrations of cells (Z) (i) or y (ii) for the circuit of (B). The healthy concentration Z = ZST is reached regardless of initial
concentration of Z, as long as it is nonzero, and regardless of the initial concentration of y.
SED-ML simulation
https://jjj.bio.vu.nl/models/experiments/karin2017_fig1c/simulate
Person responsible: Jacky Snoep
Snapshots: No snapshots
D An arrow marks the time when a mutant with a strong activation of the sensing of y arises (for the circuit depicted in B). This mutant has a selective advantage and
takes over the population.
SED-ML simulation
https://jjj.bio.vu.nl/models/experiments/karin2017_fig1d/simulate
Person responsible: Jacky Snoep
Snapshots: No snapshots
G Trajectories of Z from different initial concentrations of Z (i) or y (ii) for the circuit depicted in (F). The healthy concentration Z = ZST is not reached for small values of
Z (Z << ZST) or large values of y (y >> yUST).
SED-ML simulation
https://jjj.bio.vu.nl/models/experiments/karin2017_fig1g/simulate
Person responsible: Jacky Snoep
Snapshots: No snapshots
H The arrows mark the times when a mutant with a strong activation of the sensing of y arises (for the biphasic circuit depicted in F). This mutant has a selective
disadvantage and is thus eliminated.
SED-ML simulation
https://jjj.bio.vu.nl/models/experiments/karin2017_fig1h/simulate
Person responsible: Jacky Snoep
Snapshots: No snapshots
C Numerical simulations of the RpoD6 wild-type network show a shoulder of expression trailing the main peak (red line). All the parameters describing the clock and
SigC are as in Fig 4B, and only the threshold of activation of the rpoD6 promoter by the clock was modified. Numerical simulations of a SigC knock-out model (in
which the terms representing the regulation of RpoD6 by SigC are set to zero) show only single-peaked oscillations (blue line).
D The incoherent feedforward loop circuit that
...
Person responsible: Jacky Snoep
Snapshots: No snapshots
Numerical simulations of the wild-type network show double peaks of expression (red line), and numerical simulations of a SigC knock-out model (in which the terms representing the regulation of PsbAI by SigC are set to zero) show only single-peaked oscillations (blue line)..
SED-ML simulation
https://jjj.bio.vu.nl/models/experiments/martins2016_fig4b/simulate
Person responsible: Jacky Snoep
Snapshots: No snapshots
Person responsible: Dawie van Niekerk
Snapshots: No snapshots
Investigation: From steady-state to synchronized yeast glycoly...
Assays: No Assays
Person responsible: Dawie van Niekerk
Snapshots: No snapshots
Investigation: From steady-state to synchronized yeast glycoly...
Assays: No Assays
Person responsible: Dawie van Niekerk
Snapshots: No snapshots
Investigation: Glycolytic oscillations in individual isolated ...
Assays: gustavsson1-4 models
Person responsible: Dawie van Niekerk
Snapshots: No snapshots
Investigation: Glycolytic oscillations in individual isolated ...
Assays: No Assays
Person responsible: Dawie van Niekerk
Snapshots: No snapshots
Investigation: Glycolytic oscillations in individual isolated ...
Assays: gustavsson5 model
Person responsible: Dawie van Niekerk
Snapshots: No snapshots
Investigation: Phase shift responses in isolated yeast glycoly...
Assays: No Assays
Person responsible: Jacky Snoep
Snapshots: No snapshots
Investigation: Prostate cancer
Assays: No Assays
Conversion of XYL to KG in a cell free extract of Caulobacter crescentus, without Mn2+ added, but with NAD recycling, metabolites measured enzymatically.
https://jjj.bio.vu.nl/models/experiments/shen2020_fig4d/simulate
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Snapshots: Snapshot 1, Snapshot 2
Investigation: Caulobacter crescentus Weimberg pathway
Study: Cell free extract
Organisms: No organisms
Models: CFE analysis (shen2), CFE no Mn, with NADrec
SOPs: No SOPs
Data files: CFE no-Mn but with NADrec data
Conversion of XYL to KG in a cell free extract of Caulobacter crescentus, with 0.15 mM Mn2+ added, but no NAD recycling, metabolites measured enzymatically.
https://jjj.bio.vu.nl/models/experiments/shen2020_fig4c/simulate
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Snapshots: Snapshot 1, Snapshot 2
Investigation: Caulobacter crescentus Weimberg pathway
Study: Cell free extract
Organisms: No organisms
Models: CFE Mn noNADrec, CFE analysis (shen2)
SOPs: No SOPs
Data files: CFE Mn no-NADrec data
Conversion of XYL to KG in a cell free extract of Caulobacter crescentus, with 0.15 mM Mn2+ added, and with NAD recycling, metabolites measured enzymatically.
https://jjj.bio.vu.nl/models/experiments/shen2020_fig4b/simulate
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Snapshots: Snapshot 1, Snapshot 2
Investigation: Caulobacter crescentus Weimberg pathway
Study: Cell free extract
Organisms: No organisms
Models: CFE Mn NADrec, CFE analysis (shen2)
SOPs: No SOPs
Data files: CFE Mn NADrec data
Conversion of XYL to KG in one pot cascade of Weimberg pathway enzymes of Caulobacter crescentus, using old enzymes with optimal protein distribution, with NAD recycling, measured in NMR.
https://jjj.bio.vu.nl/models/experiments/shen2020_fig3d/simulate
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Snapshots: Snapshot 1, Snapshot 2
Investigation: Caulobacter crescentus Weimberg pathway
Study: One pot cascade
Organisms: No organisms
Models: Cascade analysis (shen2), One pot cascade 16
SOPs: No SOPs
Data files: One-Pot-Cascade 16 data
Conversion of XYL to KG in one pot cascade of Weimberg pathway enzymes of Caulobacter crescentus, with NAD recycling, measured in NMR.
https://jjj.bio.vu.nl/models/experiments/shen2020_fig3b/simulate
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Snapshots: Snapshot 1, Snapshot 2
Investigation: Caulobacter crescentus Weimberg pathway
Study: One pot cascade
Organisms: No organisms
Models: Cascade analysis (shen2), One-Pot-Cascade 13
SOPs: No SOPs
Data files: One-Pot-Cascade 13 data
Conversion of XYL to KG in one pot cascade of Weimberg pathway enzymes of Caulobacter crescentus, omitting XLA, measured in NMR.
https://jjj.bio.vu.nl/models/experiments/shen2020_fig3c/simulate
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Snapshots: Snapshot 1, Snapshot 2
Investigation: Caulobacter crescentus Weimberg pathway
Study: One pot cascade
Organisms: No organisms
Models: Cascade analysis (shen2), One pot cascade 12
SOPs: No SOPs
Data files: One-Pot-Cascade 12 data
Conversion of XYL to KG in one pot cascade of Weimberg pathway enzymes of Caulobacter crescentus, measured in NMR.
https://jjj.bio.vu.nl/models/experiments/shen2020_fig3a/simulate
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Snapshots: Snapshot 1, Snapshot 2
Investigation: Caulobacter crescentus Weimberg pathway
Study: One pot cascade
Organisms: No organisms
Models: Cascade analysis (shen2), One-Pot-Cascade 10
SOPs: No SOPs
Data files: One-Pot-Cascade 10 data
Conversion of XYL to KG by sequential addition of Weimberg pathway enzymes of Caulobacter crescentus, measured in NMR.
https://jjj.bio.vu.nl/models/experiments/shen2020_fig2c/simulate
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Snapshots: Snapshot 1, Snapshot 2
Investigation: Caulobacter crescentus Weimberg pathway
Study: Progress curves
Organisms: No organisms
Models: Progress curve analysis (shen1), Progress curve analysis combined
SOPs: No SOPs
Data files: Progress curve analysis data
Investigation: Caulobacter crescentus Weimberg pathway
Study: Cell free extract
Organisms: No organisms
Models: CFE steady state analysis (shen3)
SOPs: No SOPs
Data files: No Data files
Kinetic characterisation and mathematical modelling of XDH.
Investigation: Caulobacter crescentus Weimberg pathway
Study: Initial rate kinetics
Organisms: No organisms
Models: XDH model
SOPs: No SOPs
Data files: XDH-initial rate kinetics data
Kinetic characterisation and mathematical modelling of XLA.
Investigation: Caulobacter crescentus Weimberg pathway
Study: Initial rate kinetics
Organisms: No organisms
Models: XLA model
SOPs: No SOPs
Data files: XLA-initial rate kinetics data
Kinetic characterisation and mathematical modelling of XAD.
Investigation: Caulobacter crescentus Weimberg pathway
Study: Initial rate kinetics
Organisms: No organisms
Models: XAD model
SOPs: No SOPs
Data files: XAD-initial rate kinetics data
Kinetic characterisation and mathematical modelling of KDXD.
Investigation: Caulobacter crescentus Weimberg pathway
Study: Initial rate kinetics
Organisms: No organisms
Models: KDXD model
SOPs: No SOPs
Data files: KDXD-initial rate kinetics data
Kinetic characterisation and mathematical modelling of KGSADH.
Investigation: Caulobacter crescentus Weimberg pathway
Study: Initial rate kinetics
Organisms: No organisms
Models: KGSADH model
SOPs: No SOPs
Data files: KGSADH-initial rate kinetics data
Conversion of Xyl to XLAC by Caulobacter crescentus XDH, measured in NMR.
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Snapshots: Snapshot 1, Snapshot 2
Investigation: Caulobacter crescentus Weimberg pathway
Study: Progress curves
Organisms: No organisms
Models: Progress curve analysis (shen1), Progress curve analysis XDH
SOPs: No SOPs
Data files: Progress curve analysis data
Conversion of XLAC to XA by Caulobacter crescentus XLA, measured in NMR.
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Snapshots: Snapshot 1, Snapshot 2
Investigation: Caulobacter crescentus Weimberg pathway
Study: Progress curves
Organisms: No organisms
Models: Progress curve analysis (shen1), Progress curve analysis XLA
SOPs: No SOPs
Data files: Progress curve analysis data
Conversion of XA to KDX by Caulobacter crescentus XAD, measured in NMR.
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Snapshots: Snapshot 1, Snapshot 2
Investigation: Caulobacter crescentus Weimberg pathway
Study: Progress curves
Organisms: No organisms
Models: Progress curve analysis (shen1), Progress curve analysis XAD
SOPs: No SOPs
Data files: Progress curve analysis data
Conversion of KDX to KGSA by Caulobacter crescentus KDXD, measured in NMR.
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Snapshots: Snapshot 1, Snapshot 2
Investigation: Caulobacter crescentus Weimberg pathway
Study: Progress curves
Organisms: No organisms
Models: Progress curve analysis (shen1), Progress curve analysis KDXD
SOPs: No SOPs
Data files: Progress curve analysis data
Conversion of KGSA to KG by Caulobacter crescentus KGSADH, measured in NMR.
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Snapshots: Snapshot 1, Snapshot 2
Investigation: Caulobacter crescentus Weimberg pathway
Study: Progress curves
Organisms: No organisms
Models: Progress curve analysis (shen1), Progress curve analysis KGSADH
SOPs: No SOPs
Data files: Progress curve analysis data
Investigation: Karin et al (2017) Molecular Systems Biology
Study: Figure 4D: Biphasic control can provide mutant ...
Organisms: No organisms
Models: 1 hidden item
SOPs: No SOPs
Data files: No Data files
Data files for the conversion of XYL to KG, via the sequential addition of the Caulobacter crescentus Weimberg pathway enzymes, XDH, XLA, XAD, KDXD, KGSADH.
Creators: Jacky Snoep, Lu Shen
Submitter: Jacky Snoep
Investigations: Caulobacter crescentus Weimberg pathway
Studies: Progress curves
Assays: Progress curve KDXD, Progress curve KGSADH, Progress curve XAD, Progress curve XDH, Progress curve XLA, Progress curves combined
Initial rate kinetics for the α-ketoglutarate semialdehyde dehydrogenase of Caulobacter crescentus, α-ketoglutarate semialdehyde and NAD saturation, and α-ketoglutarate, NADH and 2-keto-3-deoxy-D-xylonate inhibition.
Creators: Jacky Snoep, Lu Shen
Submitter: Jacky Snoep
Investigations: Caulobacter crescentus Weimberg pathway
Studies: Initial rate kinetics
Assays: KGSADH
Initial rate kinetics for the 2-keto-3-deoxy-D-xylonate dehydrates of Caulobacter crescentus, 2-keto-3-deoxy-D-xylonate saturation and inhibitor titrations.
Creators: Jacky Snoep, Lu Shen
Submitter: Jacky Snoep
Initial rate kinetics for the xylonate dehydratase of Caulobacter crescentus, xylonate saturation.
Creators: Jacky Snoep, Lu Shen
Submitter: Jacky Snoep
Initial rate kinetics for the xylonolactonase reaction of Caulobacter crescentus, xylonolactone saturation for the enzyme catalysed reaction, and for the non-enzymatic reaction.
Creators: Jacky Snoep, Lu Shen
Submitter: Jacky Snoep
Initial rate kinetics for xylose dehydrogenase of Caulobacter crescentus, saturation with xylose and NAD, and inhibition by NADH and xylonolactone.
Data files for the conversion of XYL to KG, via the Caulobacter crescentus Weimberg pathway, using old enzymes: XDH, XLA, XAD, KDXD, KGSADH, with NAD recycling, and optimal protein distribution.
Creators: Jacky Snoep, Lu Shen
Submitter: Jacky Snoep
Investigations: Caulobacter crescentus Weimberg pathway
Studies: One pot cascade
Assays: One pot cascade 16
Data files for the conversion of XYL to KG, in Caulobacter crescentus cell free extract, with NAD recycling, and additional Mn2+ (0.15 mM) added.
Creators: Jacky Snoep, Lu Shen
Submitter: Jacky Snoep
Investigations: Caulobacter crescentus Weimberg pathway
Studies: Cell free extract
Data files for the conversion of XYL to KG, in Caulobacter crescentus cell free extract, without NAD recycling, but with additional Mn2+ (0.15 mM) added.
Creators: Jacky Snoep, Lu Shen
Submitter: Jacky Snoep
Investigations: Caulobacter crescentus Weimberg pathway
Studies: Cell free extract
Data files for the conversion of XYL to KG, in Caulobacter crescentus cell free extract, with NAD recycling, but without additional Mn2+ added.
Creators: Jacky Snoep, Lu Shen
Submitter: Jacky Snoep
Investigations: Caulobacter crescentus Weimberg pathway
Studies: Cell free extract
Data files for the conversion of XYL to KG, via the Caulobacter crescentus Weimberg pathway enzymes, XDH, XLA, XAD, KDXD, KGSADH.
Creators: Jacky Snoep, Lu Shen
Submitter: Jacky Snoep
Investigations: Caulobacter crescentus Weimberg pathway
Studies: One pot cascade
Assays: One pot cascade 10
Data files for the conversion of XYL to KG, via the Caulobacter crescentus Weimberg pathway enzymes, omitting XLA: XDH, XAD, KDXD, KGSADH.
Creators: Jacky Snoep, Lu Shen
Submitter: Jacky Snoep
Investigations: Caulobacter crescentus Weimberg pathway
Studies: One pot cascade
Assays: One pot cascade 12
Data files for the conversion of XYL to KG, via the Caulobacter crescentus Weimberg pathway enzymes: XDH, XLA, XAD, KDXD, KGSADH, with NAD recycling.
Creators: Jacky Snoep, Lu Shen
Submitter: Jacky Snoep
Investigations: Caulobacter crescentus Weimberg pathway
Studies: One pot cascade
Assays: One pot cascade 13
Creators: Theresa Kouril, Jacky Snoep
Submitters: Jacky Snoep, Theresa Kouril
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-70C
Assays: PGK 70 data
Experimental data for 3PG conversion to fructose-6-phosphase in reconstituted systems of gluconeogenesis of S. solfataricus
Creators: Jacky Snoep, Theresa Kouril
Submitter: Jacky Snoep
Simulation results of TPI experimental data for GAP and DHAP saturation.
Creators: Jacky Snoep, Theresa Kouril
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model Gluconeogenesis
Assays: TPI Modelling
Simulation results of temperature degradation of gluconeogenic intermediates
Creators: Jacky Snoep, Theresa Kouril
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model Gluconeogenesis
Simulation results of experimental data of the reconstituted gluconeogenic system
Creators: Jacky Snoep, Theresa Kouril
Submitter: Jacky Snoep
Simulation results of PGK experimental data for ADP, ATP, 3PG and BPG saturation.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model Gluconeogenesis
Assays: PGK Modelling
Simulation results of FBPAase of experimental data for DHAP and GAP saturation
Creator: Jacky Snoep
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model Gluconeogenesis
Assays: FBPAase Modelling
Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the progress curves will be reproduced.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Algebraic equations
Model format: Mathematica
Environment: Mathematica
Organism: Not specified
Investigations: Caulobacter crescentus Weimberg pathway
Studies: Progress curves
Modelling analyses: Progress curve KGSADH
Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the progress curves will be reproduced.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Algebraic equations
Model format: Mathematica
Environment: Mathematica
Organism: Not specified
Investigations: Caulobacter crescentus Weimberg pathway
Studies: Progress curves
Modelling analyses: Progress curve KDXD
Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the progress curves will be reproduced.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Algebraic equations
Model format: Mathematica
Environment: Mathematica
Organism: Not specified
Investigations: Caulobacter crescentus Weimberg pathway
Studies: Progress curves
Modelling analyses: Progress curve XAD
Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the progress curves will be reproduced.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Algebraic equations
Model format: Mathematica
Environment: Mathematica
Organism: Not specified
Investigations: Caulobacter crescentus Weimberg pathway
Studies: Progress curves
Modelling analyses: Progress curve XLA
Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the progress curves will be reproduced.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Algebraic equations
Model format: Mathematica
Environment: Mathematica
Organism: Not specified
Investigations: Caulobacter crescentus Weimberg pathway
Studies: Progress curves
Modelling analyses: Progress curve XDH
Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the progress curves will be reproduced.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Algebraic equations
Model format: Mathematica
Environment: Mathematica
Organism: Not specified
Investigations: Caulobacter crescentus Weimberg pathway
Studies: Progress curves
Modelling analyses: Progress curves combined
Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG in cell free extract. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the cell free extract with added Mn, but no NAD rec, will be reproduced.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Algebraic equations
Model format: Mathematica
Environment: Mathematica
Organism: Not specified
Investigations: Caulobacter crescentus Weimberg pathway
Studies: Cell free extract
Modelling analyses: Cell free extract, with Mn, no NAD recycling
Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for cascade 12 will be reproduced.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Algebraic equations
Model format: Mathematica
Environment: Mathematica
Organism: Not specified
Investigations: Caulobacter crescentus Weimberg pathway
Studies: One pot cascade
Modelling analyses: One pot cascade 12
Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG in cell free extract. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the cell free extract with no added Mn, but with NAD rec, will be reproduced.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Algebraic equations
Model format: Mathematica
Environment: Mathematica
Organism: Not specified
Investigations: Caulobacter crescentus Weimberg pathway
Studies: Cell free extract
Modelling analyses: Cell free extract, without added Mn, with NAD r...
Steady state model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG. Protein levels need to be adapted to CFE levels, see SED-ML scripts.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Caulobacter
Investigations: Caulobacter crescentus Weimberg pathway
Studies: Cell free extract
Modelling analyses: Steady state cell free extract, with Mn and NAD...
Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG, with NAD recycling. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for cascade 13 will be reproduced.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Algebraic equations
Model format: Mathematica
Environment: Mathematica
Organism: Not specified
Investigations: Caulobacter crescentus Weimberg pathway
Studies: One pot cascade
Modelling analyses: One pot cascade 13
Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for cascade 10 will be reproduced.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Algebraic equations
Model format: Mathematica
Environment: Mathematica
Organism: Not specified
Investigations: Caulobacter crescentus Weimberg pathway
Studies: One pot cascade
Modelling analyses: One pot cascade 10
Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG, using old enzymes, with optimal protein distribution. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for cascade 16 will be reproduced.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Algebraic equations
Model format: Mathematica
Environment: Mathematica
Organism: Not specified
Investigations: Caulobacter crescentus Weimberg pathway
Studies: One pot cascade
Modelling analyses: One pot cascade 16
Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Caulobacter crescentus Weimberg pathway
Studies: One pot cascade
Modelling analyses: One pot cascade 10, One pot cascade 12, One pot cascade 13, One pot cascade 16
Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG in cell free extract. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the cell free extract with added Mn and NAD rec will be reproduced.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Algebraic equations
Model format: Mathematica
Environment: Mathematica
Organism: Not specified
Investigations: Caulobacter crescentus Weimberg pathway
Studies: Cell free extract
Modelling analyses: Cell free extract, with Mn and NAD recycling
Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG. Protein levels need to be adapted to CFE levels, see SED-ML scripts
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Caulobacter crescentus Weimberg pathway
Studies: Cell free extract
Modelling analyses: Cell free extract, with Mn and NAD recycling, Cell free extract, with Mn, no NAD recycling, Cell free extract, without added Mn, with NAD r...
Model for the Caulobacter crescentus α-ketoglutarate semialdehyde dehydrogenase, describing the initial rate kinetics for substrate dependence and product inhibition. If the Mathematica notebook is downloaded and the data file for the XAD kinetics is downloaded in the same directory, then the notebook can be evaluated. The model in the notebook will then be parameterised and the figures in the manuscript for KGSADH will be reproduced.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Algebraic equations
Model format: Mathematica
Environment: Mathematica
Organism: Not specified
Investigations: Caulobacter crescentus Weimberg pathway
Studies: Initial rate kinetics
Modelling analyses: KGSADH
Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG, with sequential addition of purified enzymes.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Caulobacter crescentus Weimberg pathway
Studies: Progress curves
Modelling analyses: Progress curve KDXD, Progress curve KGSADH, Progress curve XAD, Progress curve XDH, Progress curve XLA, Progress curves combined
Model for the Caulobacter crescentus xylose dehydrogenase, describing the initial rate kinetics including substrate dependence and product inhibition. If the Mathematica notebook is downloaded and the data file for the XDH kinetics is downloaded in the same directory, then the notebook can be evaluated. The model in the notebook will then be parameterised and the figures in the manuscript for XDH will be reproduced.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Algebraic equations
Model format: Mathematica
Environment: Mathematica
Organism: Not specified
Investigations: Caulobacter crescentus Weimberg pathway
Studies: Initial rate kinetics
Modelling analyses: XDH
Model for the Caulobacter crescentus xylonolactonase, describing the initial rate kinetics and substrate dependence. If the Mathematica notebook is downloaded and the data file for the XLA kinetics is downloaded in the same directory, then the notebook can be evaluated. The model in the notebook will then be parameterised and the figures in the manuscript for XLA will be reproduced.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Algebraic equations
Model format: Mathematica
Environment: Mathematica
Organism: Not specified
Investigations: Caulobacter crescentus Weimberg pathway
Studies: Initial rate kinetics
Modelling analyses: XLA
SOP for the determination of external metabolites (Glc, Pyr, Gly, Lac) in intact trophozoite incubations, and for the determination of intracellular metabolite concentrations.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model validation
Assays: GLC incubation, Steady state
SOP for the cultivation conditions of Plasmodium falciparum, including the protocol for synchronisation.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
SOP for measurement of G3PDH activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: G3PDH
SOP for measurement of ALD activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: ALD
SOP for measurement of glucose transport activity in intact trophozoites.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
SOP for measurement of GAPDH activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: GAPDH
SOP for measurement of ENO activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: ENO
SOP for measurement of HK activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: HK
SOP for measurement of PFK activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: PFK
SOP for measurement of LDH activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: LDH
SOP for measurement of PGK activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: PGK
SOP for measurement of PK activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: PK
SOP for measurement of PGM activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
SOP for measurement of PGI activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: PGI
SOP for measurement of PGM activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: PGM
SOP for measurement of TPI activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: TPI
SOP for the isolation of intact Plasmodium falciparum trophozoites from infected red blood cells and the preparation of a cell free extract that can be used for kinetic analyses.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Preparation of cell free extracts of the recombinant E. coli strains expressing the gluconeogenic S. solfataricus enzymes.
Creators: Jacky Snoep, Theresa Kouril
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model Gluconeogenesis
Cloning and heterologous expression of gluconeogenic enzymes from S. solfataricus in E. coli
Creators: Jacky Snoep, Theresa Kouril
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model Gluconeogenesis
Purification of gluconeogenic enzymes from S. solfataricus in recombinant E.coli extracts
Creators: Jacky Snoep, Theresa Kouril
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model Gluconeogenesis
Abstract (Expand)
Authors: Lu Shen, Martha Kohlhaas, Junichi Enoki, Roland Meier, Bernhard Schönenberger, Roland Wohlgemuth, Robert Kourist, Felix Niemeyer, David van Niekerk, Christopher Bräsen, Jochen Niemeyer, Jacky Snoep, Bettina Siebers
Date Published: 1st Dec 2020
Publication Type: Not specified
DOI: 10.1038/s41467-020-14830-y
Citation: Nat Commun 11(1) : 82
Abstract (Expand)
Authors: N. J. Stanford, M. Scharm, P. D. Dobson, M. Golebiewski, M. Hucka, V. B. Kothamachu, D. Nickerson, S. Owen, J. Pahle, U. Wittig, D. Waltemath, C. Goble, P. Mendes, J. Snoep
Date Published: 12th Oct 2019
Publication Type: Journal
PubMed ID: 31602618
Citation: Methods Mol Biol. 2019;2049:285-314. doi: 10.1007/978-1-4939-9736-7_17.
Abstract (Expand)
Authors: Maxwell Lewis Neal, Matthias König, David Nickerson, Göksel Mısırlı, Reza Kalbasi, Andreas Dräger, Koray Atalag, Vijayalakshmi Chelliah, Michael T Cooling, Daniel L Cook, Sharon Crook, Miguel de Alba, Samuel H Friedman, Alan Garny, John H Gennari, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nick Juty, Chris Myers, Brett G Olivier, Herbert M Sauro, Martin Scharm, Jacky L Snoep, Vasundra Touré, Anil Wipat, Olaf Wolkenhauer, Dagmar Waltemath
Date Published: 1st Mar 2019
Publication Type: Journal
DOI: 10.1093/bib/bby087
Citation: Briefings in Bioinformatics 20(2):540-550
Abstract (Expand)
Authors: Monique Barnard, Jonathan L. Quanson, Elahe Mostaghel, Elzette Pretorius, Jacky L. Snoep, Karl-Heinz Storbeck
Date Published: 1st Oct 2018
Publication Type: Not specified
DOI: 10.1016/j.jsbmb.2018.06.013
Citation: The Journal of Steroid Biochemistry and Molecular Biology 183 : 192
Abstract (Expand)
Authors: T. Kouril, J. J. Eicher, B. Siebers, J. L. Snoep
Date Published: 7th Oct 2017
Publication Type: Not specified
PubMed ID: 28982396
Citation: Microbiology. 2017 Nov;163(11):1604-1612. doi: 10.1099/mic.0.000542. Epub 2017 Oct 6.
Abstract (Expand)
Authors: Omer Karin, Uri Alon
Date Published: 26th Jun 2017
Publication Type: Not specified
Citation: Mol Syst Biol 13(6) : 933
Abstract (Expand)
Authors: K. Wolstencroft, O. Krebs, J. L. Snoep, N. J. Stanford, F. Bacall, M. Golebiewski, R. Kuzyakiv, Q. Nguyen, S. Owen, S. Soiland-Reyes, J. Straszewski, D. D. van Niekerk, A. R. Williams, L. Malmstrom, B. Rinn, W. Muller, C. Goble
Date Published: 4th Jan 2017
Publication Type: Journal
PubMed ID: 27899646
Citation: Nucleic Acids Res. 2017 Jan 4;45(D1):D404-D407. doi: 10.1093/nar/gkw1032. Epub 2016 Nov 28.
Abstract (Expand)
Authors: K. Wolstencroft, O. Krebs, J. L. Snoep, N. J. Stanford, F. Bacall, M. Golebiewski, R. Kuzyakiv, Q. Nguyen, S. Owen, S. Soiland-Reyes, J. Straszewski, D. D. van Niekerk, A. R. Williams, L. Malmstrom, B. Rinn, W. Muller, C. Goble
Date Published: 4th Jan 2017
Publication Type: Journal
PubMed ID: 27899646
Citation: Nucleic Acids Res. 2017 Jan 4;45(D1):D404-D407. doi: 10.1093/nar/gkw1032. Epub 2016 Nov 28.
Abstract (Expand)
Authors: Bruno MC Martins, Arijit K Das, Liliana Antunes, James CW Locke
Date Published: 22nd Dec 2016
Publication Type: Not specified
Citation: Mol Syst Biol 12(12) : 896
Abstract (Expand)
Authors: David D. van Niekerk, Gerald P. Penkler, Francois du Toit, Jacky L. Snoep
Date Published: 1st Feb 2016
Publication Type: Not specified
DOI: 10.1111/febs.13615
Citation: FEBS J 283(4) : 634
Abstract (Expand)
Authors: J. L. Snoep, K. Green, J. Eicher, D. C. Palm, G. Penkler, F. du Toit, N. Walters, R. Burger, H. V. Westerhoff, D. D. van Niekerk
Date Published: 27th Nov 2015
Publication Type: Not specified
DOI: 10.1042/BST20150145
Citation: Biochemical Society Transactions 43(6) : 1157
Abstract (Expand)
Authors: Gerald Penkler, Francois du Toit, Waldo Adams, Marina Rautenbach, Daniel C. Palm, David D. van Niekerk, Jacky L. Snoep
Date Published: 1st Apr 2015
Publication Type: Not specified
DOI: 10.1111/febs.13237
Citation: FEBS J 282(8) : 1481
Abstract
Authors: Anna-Karin Gustavsson, David D. van Niekerk, Caroline B. Adiels, Bob Kooi, Mattias Goksör, Jacky L. Snoep
Date Published: 1st Jun 2014
Publication Type: Not specified
DOI: 10.1111/febs.12820
Citation: FEBS J 281(12) : 2784
Abstract
Authors: Anna-Karin Gustavsson, David D. van Niekerk, Caroline B. Adiels, Mattias Goksör, Jacky L. Snoep
Date Published: 3rd Jan 2014
Publication Type: Not specified
DOI: 10.1016/j.febslet.2013.11.028
Citation: Heterogeneity of glycolytic oscillatory behaviour in individual yeast cells 588(1) : 3
Abstract (Expand)
Authors: , Dominik Esser, Julia Kort, , ,
Date Published: 20th Jul 2013
Publication Type: Not specified
PubMed ID: 23865479
Citation:
Abstract (Expand)
Authors: , , Matthew Horridge, Simon Jupp, , , , , Robert Stevens,
Date Published: 1st Feb 2013
Publication Type: Journal
DOI: 10.1002/cpe.2941
Citation: Concurrency Computat.: Pract. Exper. 25(4):467-480
Abstract
Authors: Anna-Karin Gustavsson, David D. van Niekerk, Caroline B. Adiels, Franco B. du Preez, Mattias Goksör, Jacky L. Snoep
Date Published: 1st Aug 2012
Publication Type: Not specified
DOI: 10.1111/j.1742-4658.2012.08639.x
Citation: Sustained glycolytic oscillations in individual isolated yeast cells 279(16) : 2837
Abstract (Expand)
Authors: , David D van Niekerk, Bob Kooi, Johann M Rohwer,
Date Published: 21st Jun 2012
Publication Type: Not specified
PubMed ID: 22712534
Citation:
Abstract (Expand)
Authors: , David D van Niekerk,
Date Published: 13th Jun 2012
Publication Type: Not specified
PubMed ID: 22686585
Citation:
Abstract (Expand)
Authors: Anna-Karin Gustavsson, David D van Niekerk, Caroline B Adiels, , Mattias Goksör,
Date Published: 23rd May 2012
Publication Type: Not specified
PubMed ID: 22607453
Citation:
Talk given by Olga Krebs at EmPowerPutida project meeting in Bruxeles 23rd November 2016
Creators: Olga Krebs, Carole Goble, Rostyslav Kuzyakiv, Wolfgang Müller, Quyen Nguyen, Stuart Owen, Bernd Rinn, Jacky Snoep, Natalie Stanford
Submitter: Olga Krebs
Presentation of data management concepts for ERASysAPP projects at IMOMESIC kick off meeting on 8 th of May 2015 in Heidelberg. Part I presented by Olga Krebs
Creators: Olga Krebs, Caterina Barillari, Carole Goble, Peter Kunszt, Rostyslav Kuzyakiv, Wolfgang Müller, Quyen Nguyen, Stuart Owen, Bernd Rinn, Jacky Snoep, Natalie Stanford, Jakub Straszewski
Submitter: Olga Krebs
Creators: Olga Krebs, Caterina Barillari, Carole Goble, Peter Kunszt, Rostyslav Kuzyakiv, Wolfgang Müller, Quyen Nguyen, Stuart Owen, Bernd Rinn, Jacky Snoep, Natalie Stanford, Jakub Straszewski
Submitter: Olga Krebs
Carole Goble's talk at ERASysAPP - EXCHANGE Networking and Info Day for research projects of the first ERASysAPP call (a day before PALs meeting)
Creators: Olga Krebs, Carole Goble, Wolfgang Müller, Peter Kunszt, Bernd Rinn, Stuart Owen, Natalie Stanford, Jacky Snoep
Submitter: Olga Krebs
Poster presented at SWAT4LS - Semantic web applications and tools for life science- in Berlin at 10 of december 2014 by Olga Krebs
Creators: Olga Krebs, Carole Goble, Bernd Rinn, Wolfgang Müller, Quyen Nguyen, Jacky Snoep, Stuart Owen, Natalie Stanford, Peter Kunszt
Submitter: Olga Krebs
Presentation by Carole Goble at the International Semantic Web Conference 2013 in Sydney Australia about the use of semantic web technology in SEEK and RightField.
Creators: Stuart Owen, Carole Goble, Katy Wolstencroft, Jacky Snoep, Wolfgang Müller, Olga Krebs, Quyen Nguyen
Submitter: Stuart Owen
SEEK at ICSB 2012 (presented by Olga Krebs)
Creators: Olga Krebs, Katy Wolstencroft, Carole Goble, Wolfgang Müller, Quyen Nguyen, Stuart Owen, Jacky Snoep, Franco du Preez, Martin Golebiewski, Andreas Weidemann
Submitter: Olga Krebs
Start Date: 6th Feb 2013
End Date: 8th Feb 2013
Event Website: Not specified
Country: Germany
City: Berlin