GROUP LEADER: Dr Dawie van Niekerk
Office: A107 JC Smuts Building
Educational and Professional Background
PhD, Theoretical Nuclear Physics, Stellenbosch University, South Africa, 2010
Postdoctoral fellow, Department of Biochemistry, Stellenbosch University, South Africa, 2011-2012
Lecturer, Department of Biochemistry, Stellenbosch University, South Africa, 2013-
Mathematical and Computational Systems Biology, Dynamical Systems, Pharmacometrics
Successful treatment of malaria and HIV/AIDS, and combatting side effects of the relevant drugs are of major importance to the African continent. Increasingly, mathematical modelling is used to identify drug targets in molecular pathways, analyse drug effects on the level of the patient physiology and treatment interventions on the level of populations. Traditional modelling approaches have been disjointed with approximations used for the missing detail. This has limited achievements at every level since the description of the disease, its epidemiology and how it responds to drugs has been incomplete.
Our work focusses on constructing unified frameworks for analyses of pharmacological effects of drugs and disease response in patients and populations. This is accomplished by combining detailed mechanistic mathematical models of metabolism and signal transduction with statistical and phenomenological models of disease, pharmacology and epidemiology. As such it involves combining work from a variety of fields in health and life sciences and applying mathematical, computational and experimental techniques to construct the formalism, to code, simulate and analyse the models, and to do additional biochemical characterisation of the relevant metabolic pathways.
Martin Peters, Johann J. Eicher, David D. van Niekerk, Dagmar Waltemath, Jacky L. Snoep (2017) The JWS online simulation database. Bioinformatics btw831.
van Niekerk, D. D., Penkler, G. P., du Toit, F. and Snoep, J. L. (2016), Targeting glycolysis in the malaria parasite Plasmodium falciparum. FEBS J, 283: 634- 646.
Snoep JL, Green K, Eicher J, Palm DC, Penkler G, Toit Du F, Walters N, Burger R, Westerhoff H & van Niekerk DD (2015) Quantitative analysis of drug effects at the whole-body level: a case study for glucose metabolism in malaria patients. Biochemical Society Transactions 43, 1157-1163.
Penkler, G., du Toit, F., Adams, W., Rautenbach, M., Palm, D. C., van Niekerk, D. D. and Snoep, J. L. (2015), Construction and validation of a detailed kinetic model of glycolysis in Plasmodium falciparum. FEBS J, 282: 1481-1511.
Gustavsson, A.-K., van Niekerk, D. D., Adiels, C. B., Kooi, B., Goksor, M. and Snoep, J. L. (2014), Allosteric regulation of phosphofructokinase controls the emergence of glycolytic oscillations in isolated yeast cells. FEBS J, 281: 2784-2793.
Gustavsson A-K, van Niekerk DD, Adiels CB, Goksor M & Snoep JL (2014) Heterogeneity of glycolytic oscillatory behaviour in individual yeast cells. FEBS Letters 588, 3-7.
Gustavsson, A.-K., van Niekerk, D. D., Adiels, C. B., du Preez, F. B., Gokor, M. and Snoep, J. L. (2012), Sustained glycolytic oscillations in individual iso- lated yeast cells. FEBS Journal, 279: 2837-2847.
du Preez, F. B., van Niekerk, D. D. and Snoep, J. L. (2012), From steady- state to synchronized yeast glycolytic oscillations II: model validation. FEBS Journal, 279: 2823-2836.
du Preez, F. B., van Niekerk, D. D., Kooi, B., Rohwer, J. M. and Snoep, J. L. (2012), From steady-state to synchronized yeast glycolytic oscillations I: model construction. FEBS Journal, 279: 2810-2822.
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