Jacky Snoep
SEEK ID: https://fairdomhub.org/people/49
Locations:
United Kingdom, 
South Africa
Disciplines: Not specified
Expertise: Not specified
Tools: Not specified
ORCID: Not specified
Project roles
Jacky's tagsPSYSMO (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 (School of Computer Science, University of Manchester) ; 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)
Related items
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.
Programme: FAIRDOM
Public web page: http://fair-dom.org/
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/
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: SARCHI: Mechanistic modelling of health and epidemiology
Public web page: Not specified
Programme: SARCHI: Mechanistic modelling of health and epidemiology
Public web page: Not specified
Programme: COMBINE (Computational Modeling in Biology Network)
Public web page: Not specified
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
Biphasic response as a mechanism against mutant takeover in tissue homeostasis circuits
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Frequency doubling in the cyanobacterial circadian clock
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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
...
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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
Simulation results of TPI experimental data for GAP and DHAP saturation.
Creators: Jacky Snoep, Theresa Kouril
Contributor: Jacky Snoep
DownloadSimulation results of temperature degradation of gluconeogenic intermediates
Creators: Jacky Snoep, Theresa Kouril
Contributor: Jacky Snoep
Simulation results of experimental data of the reconstituted gluconeogenic system
Creators: Jacky Snoep, Theresa Kouril
Contributor: Jacky Snoep
Simulation results of PGK experimental data for ADP, ATP, 3PG and BPG saturation.
Creator: Jacky Snoep
Contributor: Jacky Snoep
Simulation results of FBPAase of experimental data for DHAP and GAP saturation
Creator: Jacky Snoep
Contributor: Jacky Snoep
Simulation results of GAPDH experimental data for BPG, NADPH, NADP, GAP, and Pi
Creators: Jacky Snoep, Theresa Kouril
Contributor: Jacky Snoep
Creator: Jacky Snoep
Contributor: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
PGK-GAPDH model Sulfolobus kouril8
Creator: Jacky Snoep
Contributor: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
PGK-GAPDH model yeast kouril7
Creator: Jacky Snoep
Contributor: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
PGK-GAPDH models yeast and Sulfolobus Fig. 4 in manuscript
Creator: Jacky Snoep
Contributor: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Mathematica
PGK 70C model, Fig 3 in manuscript
Creator: Jacky Snoep
Contributor: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Mathematica
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
Contributor: Dawie Van Niekerk
SOP for the cultivation conditions of Plasmodium falciparum, including the protocol for synchronisation.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
SOP for measurement of G3PDH activity in extracts.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
SOP for measurement of ALD activity in extracts.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
SOP for measurement of glucose transport activity in intact trophozoites.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
SOP for measurement of GAPDH activity in extracts.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
SOP for measurement of ENO activity in extracts.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Abstract (Expand)
Author: Karin Omer,Alon Uri
Date Published: 26th Jun 2017
Journal: Mol Syst Biol
Abstract (Expand)
Author: Martins Bruno MC,Das Arijit K,Antunes Liliana,Locke James CW
Date Published: 22nd Dec 2016
Journal: Mol Syst Biol
Abstract (Expand)
Authors: Dawie Van Niekerk, Jacky Snoep, du Preez F. B.,Kooi B.,Rohwer J. M.
Date Published: No date defined
Journal: FEBS J
Abstract (Expand)
Authors: Dawie Van Niekerk, Jacky Snoep, du Preez F. B.
Date Published: No date defined
Journal: FEBS J
Abstract:
Authors: Dawie Van Niekerk, Jacky Snoep, Gustavsson Anna-Karin,Adiels Caroline B.,du Preez Franco B.,Goksör Mattias
Date Published: 1st Aug 2012
Journal: Not specified
Abstract:
Authors: Dawie Van Niekerk, Jacky Snoep, Gustavsson Anna-Karin,Adiels Caroline B.,Goksör Mattias
Date Published: 3rd Jan 2014
Journal: Not specified
Abstract:
Authors: Dawie Van Niekerk, Jacky Snoep, Gustavsson Anna-Karin,Adiels Caroline B.,Kooi Bob,Goksör Mattias
Date Published: 1st Jun 2014
Journal: FEBS J
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
Contributor: 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
Contributor: 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
Contributor: 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
Contributor: 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
Contributor: 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
Contributor: Stuart Owen
Start Date: 6th Feb 2013
End Date: 8th Feb 2013
Event Website: Not specified
Country: 
Germany
City: Berlin
