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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
SEEK ID: https://fairdomhub.org/projects/39
Public web page: http://msb.embopress.org
Organisms: No Organisms specified
FAIRDOM PALs: No PALs for this Project
Project created: 3rd Mar 2016
Related items
- People (3)
- Institutions (2)
- Investigations (6)
- Studies (13)
- Assays (15)
- Data files (9)
- Models (11+7)
- Publications (4)
Projects: Molecular Systems Biology
Institutions: Stellenbosch University
Projects: PSYSMO, MOSES, SysMO DB, SysMO-LAB, SulfoSys, SulfoSys - Biotec, Whole body modelling of glucose metabolism in malaria patients, FAIRDOM, Molecular Systems Biology, COMBINE Multicellular Modelling, HOTSOLUTE, Steroid biosynthesis, Yeast glycolytic oscillations, Computational pathway design for biotechnological applications
Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester, University of Stellenbosch, University of Manchester - Department of Computer Science, Stellenbosch University
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
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
Design principles of nuclear receptor signaling: how complex networking improves signal transduction
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Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range
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
After the removal of the extracellular antibiotic, efflux and inhibition dynamics combine to delay the synthesis of ribosomes in a concentration-dependent manner (panel ii). Colors indicate increasing antibiotic concentration, as shown in panel ii.
SED-ML simulation
https://jjj.bio.vu.nl/models/experiments/srimani2017_fig2cii/simulate
Person responsible: Dawie van Niekerk
Snapshots: No snapshots
Growth-factor deprived mCFU-E cells (5x106 cells per condition) and BaF3-EpoR cells (1x107 cells per condition) were stimulated with different Epo doses and absolute concentrations were determined for pEpoR (B), pAKT (C), ppERK (D). The scale for pS6 (E) was estimated in arbitrary units. GTP-Ras (F) and ppERK were determined upon stimulation with indicated, color-coded Epo doses. pEpoR was analyzed by immunoprecipitation followed by immunoblotting, GTP-Ras was analyzed after pulldown using a
...
Person responsible: Dawie van Niekerk
Snapshots: No snapshots
Transcriptional response to a sudden increase in extracellular ligand (hormone), for the six network designs of (A). The transcriptional response is taken to equal the ratio ReNrL/Retotal, i.e., the fraction of REs attaching ligand-bound NR. The ligand concentration was increased from 0 to 0.005 nM and maintained constant at the latter level. The observation that design 6 is higher than all other designs at long times is robust for parameter changes up to a factor of 3.
Person responsible: Dawie van Niekerk
Snapshots: No snapshots
Investigation: Kolodkin et al (2010) Molecular Systems Biology...
For all experiments, primary CFU-E cells were starved and stimulated with 5 U/ml Epo. At the indicated time points, samples were subjected to quantitative immunoblotting. Experimental data (black circles) with estimated standard errors and trajectories of the best fit (solid lines) are represented. Mass spectrometry data represent replicates of four independent experiments.
Person responsible: Dawie van Niekerk
Snapshots: No snapshots
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
Investigation: Karin et al (2017) Molecular Systems Biology
Study: Figure 4C: Biphasic control can provide mutant ...
Organisms: No organisms
Models: 1 hidden item
SOPs: No SOPs
Data files: No Data files
Investigation: Karin et al (2017) Molecular Systems Biology
Study: Figure 2: Frequency-dependent selection of muta...
Organisms: No organisms
Models: 1 hidden item
SOPs: No SOPs
Data files: No Data files
Investigation: Karin et al (2017) Molecular Systems Biology
Study: Figure 1G: Biphasic control can resist mutant i...
Organisms: No organisms
Models: 1 hidden item
SOPs: No SOPs
Data files: No Data files
Investigation: Karin et al (2017) Molecular Systems Biology
Study: Figure 1H: Biphasic control can resist mutant i...
Organisms: No organisms
Models: 1 hidden item
SOPs: No SOPs
Data files: No Data files
Investigation: Karin et al (2017) Molecular Systems Biology
Study: Figure 1D: Biphasic control can resist mutant i...
Organisms: No organisms
Models: 1 hidden item
SOPs: No SOPs
Data files: No Data files
Investigation: Karin et al (2017) Molecular Systems Biology
Study: Figure 1C: Biphasic control can resist mutant i...
Organisms: No organisms
Models: 1 hidden item
SOPs: No SOPs
Data files: No Data files
Investigation: Martins et al (2016) Molecular Systems Biology
Study: Figure 4B: A minimal mathematical model, contai...
Organisms: No organisms
Models: Frequency doubling in the cyanobacterial circad...
SOPs: No SOPs
Data files: No Data files
Investigation: Martins et al (2016) Molecular Systems Biology
Study: Figure 6C and D: The clock-sigC circuit represe...
Organisms: No organisms
Models: Frequency doubling in the cyanobacterial circad...
SOPs: No SOPs
Data files: No Data files
Submitter: Dawie van Niekerk
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Adlung et al (2017) Molecular Systems Biology
Study: Figure 2: Model calibration with time-resolved ...
Organisms: No organisms
SOPs: No SOPs
Data files: Source data for Figure 2B, Source data for Figure 2C, Source data for Figure 2D, Source data for Figure 2E, Source data for Figure 2F BaF3, Source data for Figure 2F mCFU-E, Source data for Figure 2G BaF3, Source data for Figure 2G mCFU-E
Submitter: Dawie van Niekerk
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Bachmann et al (2011) Molecular Systems Biology...
Study: Figure 3A: Model calibration with experimental ...
Organisms: No organisms
SOPs: No SOPs
Data files: Source data for Figure 3A: Experimental quantit...
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Investigation: Srimani et al (2017) Molecular Systems Biology
Study: Figure 2C Panel ii: After the removal of the ex...
Organisms: No organisms
Models: Kinetic model of antibiotic-mediated inhibition...
SOPs: No SOPs
Data files: No Data files
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Investigation: Adlung et al (2017) Molecular Systems Biology
Study: Figure 2: Model calibration with time-resolved ...
Organisms: No organisms
Models: BaF3 model, mCFU-E model
SOPs: No SOPs
Data files: No Data files
SED-ML simulation: https://jjj.bio.vu.nl/models/experiments/bachmann2011/simulate
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Investigation: Bachmann et al (2011) Molecular Systems Biology...
Study: Figure 3A: Model calibration with experimental ...
Organisms: No organisms
Models: JAK2/STAT5 model
SOPs: No SOPs
Data files: No Data files
SED-ML simulation: https://jjj.bio.vu.nl/models/experiments/bachmann2011/simulate
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Investigation: Kolodkin et al (2010) Molecular Systems Biology...
Study: Figure 2B: Transcriptional response to a sudde...
Organisms: No organisms
Models: NR model 1, NR model 2, NR model 3, NR model 4, NR model 5, NR model 6
SOPs: No SOPs
Data files: No Data files
See 'Figure 3 legend' and 'Materials and methods - Time course experiments, cell lysis and quantitative immunoblotting' for details.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Martins et al (2016) Molecular Systems Biology
Studies: Figure 4B: A minimal mathematical model, contai..., Figure 6C and D: The clock-sigC circuit represe...
Modelling analyses: Frequency doubling in the cyanobacterial circad..., Frequency doubling in the cyanobacterial circad...
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Srimani et al (2017) Molecular Systems Biology
Studies: Figure 2C Panel ii: After the removal of the ex...
Modelling analyses: Kinetic model of antibiotic-mediated inhibition...
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Organism: Not specified
Investigations: Adlung et al (2017) Molecular Systems Biology
Studies: Figure 2: Model calibration with time-resolved ...
Modelling analyses: Mathematical models of the Epo-induced AKT, ERK...
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Organism: Not specified
Investigations: Adlung et al (2017) Molecular Systems Biology
Studies: Figure 2: Model calibration with time-resolved ...
Modelling analyses: Mathematical models of the Epo-induced AKT, ERK...
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Kolodkin et al (2010) Molecular Systems Biology...
Studies: Figure 2B: Transcriptional response to a sudde...
Modelling analyses: Model nuclear receptor (NR) signaling
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Kolodkin et al (2010) Molecular Systems Biology...
Studies: Figure 2B: Transcriptional response to a sudde...
Modelling analyses: Model nuclear receptor (NR) signaling
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Kolodkin et al (2010) Molecular Systems Biology...
Studies: Figure 2B: Transcriptional response to a sudde...
Modelling analyses: Model nuclear receptor (NR) signaling
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Kolodkin et al (2010) Molecular Systems Biology...
Studies: Figure 2B: Transcriptional response to a sudde...
Modelling analyses: Model nuclear receptor (NR) signaling
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Kolodkin et al (2010) Molecular Systems Biology...
Studies: Figure 2B: Transcriptional response to a sudde...
Modelling analyses: Model nuclear receptor (NR) signaling
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Kolodkin et al (2010) Molecular Systems Biology...
Studies: Figure 2B: Transcriptional response to a sudde...
Modelling analyses: Model nuclear receptor (NR) signaling
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Bachmann et al (2011) Molecular Systems Biology...
Studies: Figure 3A: Model calibration with experimental ...
Modelling analyses: Model for JAK2/STAT5 signaling
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: 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: J. Bachmann, A. Raue, M. Schilling, M. E. Bohm, C. Kreutz, D. Kaschek, H. Busch, N. Gretz, W. D. Lehmann, J. Timmer, U. Klingmuller
Date Published: 2011
Publication Type: Not specified
DOI: 10.1038/msb.2011.50
Citation: Molecular Systems Biology 7(1) : 516
Abstract (Expand)
Authors: Alexey N Kolodkin, Frank J Bruggeman, Nick Plant, Martijn J Moné, Barbara M Bakker, Moray J Campbell, Johannes P T M van Leeuwen, Carsten Carlberg, Jacky L Snoep, Hans V Westerhoff
Date Published: 21st Dec 2010
Publication Type: Not specified
DOI: 10.1038/msb.2010.102
Citation: Mol Syst Biol 6