Jacky Snoep
SEEK ID: https://fairdomhub.org/people/49
Locations:
United Kingdom, 
South Africa
Expertise: Not specified
Tools: Not specified
ORCID: Not specified
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) ; Computational pathway design for biotechnological applications (Stellenbosch University)
Related items
Programme: COMBINE (Computational Modeling in Biology Network)
Public web page: 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
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Programme: Era CoBioTech
Public web page: https://www.cobiotech.eu/call-information
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
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.
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
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Programme: SysMO
Public web page: http://www.sysmo-db.org/
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
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
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/
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
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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Drug detoxification dynamics explain the postantibiotic effect
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Protein abundance of AKT and ERK pathway components governs cell-type- specific regulation of proliferation
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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
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
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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
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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
Contributor: Dawie Van Niekerk
Biological problem addressed: Model Analysis Type
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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
incubations with yeast enzymes at 30C
Creators: Theresa Kouril, Jacky Snoep
Contributor: Theresa Kouril
BPG stability notebook
Creator: Jacky Snoep
Contributor: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Mathematica
PGK model for S. solfataricus
Creator: Jacky Snoep
Contributor: Jacky Snoep
Model type: Algebraic equations
Model format: Mathematica
Environment: Mathematica
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 SBML
Creator: Jacky Snoep
Contributor: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
PGK yeast Fig1a
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
SOP for measurement of HK activity in extracts.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
SOP for measurement of PFK activity in extracts.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
SOP for measurement of LDH activity in extracts.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Abstract (Expand)
Authors: Theresa Kouril, J. J. Eicher, Bettina Siebers, Jacky Snoep
Date Published: 7th Oct 2017
Journal: Microbiology
Abstract:
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, Mike Hucka, Nick Juty, Chris Myers, Brett G Olivier, Herbert M Sauro, Martin Scharm, Jacky Snoep, Vasundra Toure, Anil Wipat, Olaf Wolkenhauer, Dagmar Waltemath
Date Published: 21st Nov 2018
Journal: Not specified
Abstract (Expand)
Authors: Omer Karin, Uri Alon
Date Published: 26th Jun 2017
Journal: Mol Syst Biol
Abstract (Expand)
Authors: Bruno MC Martins, Arijit K Das, Liliana Antunes, James CW Locke
Date Published: 22nd Dec 2016
Journal: Mol Syst Biol
Abstract (Expand)
Authors: F. B. du Preez, Dawie Van Niekerk, B. Kooi, J. M. Rohwer, Jacky Snoep
Date Published: No date defined
Journal: FEBS J
Abstract (Expand)
Authors: F. B. du Preez, Dawie Van Niekerk, Jacky Snoep
Date Published: No date defined
Journal: FEBS J
Abstract:
Authors: Anna-Karin Gustavsson, Dawie Van Niekerk, Caroline B. Adiels, Franco B. du Preez, Mattias Goksör, Jacky Snoep
Date Published: 1st Aug 2012
Journal: Not specified
Abstract:
Authors: Anna-Karin Gustavsson, Dawie Van Niekerk, Caroline B. Adiels, Mattias Goksör, Jacky Snoep
Date Published: 3rd Jan 2014
Journal: Not specified
Abstract:
Authors: Anna-Karin Gustavsson, Dawie Van Niekerk, Caroline B. Adiels, Bob Kooi, Mattias Goksör, Jacky Snoep
Date Published: 1st Jun 2014
Journal: FEBS J
Abstract (Expand)
Authors: Katy Wolstencroft, Stuart Owen, Matthew Horridge, Wolfgang Müller, Finn Bacall, Jacky Snoep, Franco du Preez, Quyen Nguyen, Olga Krebs, Carole Goble
Date Published: 2012
Journal: Knowledge Engineering and Knowledge Management
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
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
Contributor: Olga Krebs
Start Date: 6th Feb 2013
End Date: 8th Feb 2013
Event Website: Not specified
Country: 
Germany
City: Berlin
