I am a Professor in Medical Systems Biology and the University Medical Centre Groningen. The research in my lab is focused on complex regulation of mammalian lipid and carbohydrate metabolism, eventually aiming at network-based therapies. We combine dynamic computer simulations with quantitative metabolomics, 13C fluxomics, proteomics and transcriptome analysis, and in depth biochemical analysis. This allows to predict and understand ‘emergent’ properties, those properties that are counterintuitive when just looking at static pictures of pathways. We apply this approach to (i) inherited metabolic disease, (ii) the interplay between intestinal microbiota and host metabolism, (iii) the role of metabolism in ageing, and (iv) selective targeting of parasites or tumours without harming host metabolic function.
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PoLiMeR is funded through the EU Marie Skłodowska-Curie Innovative Training Network (ITN), which drives scientific excellence and innovation. ITNs bring together universities, research institutes, industry and clinical partners from across the world to train researchers to doctorate level.
Metabolic diseases are a burden on the European population and health care system. It is increasingly recognised that individual differences with respect to history, lifestyle, and genetic make-up affect disease
MESI-STRAT: Systems Medicine of Metabolic-Signaling Networks -A New Concept for Breast Cancer Patient Stratification.
Breast cancer is a complex disease with high prevalence in the European Union and world-wide. 75%-80 of the patients have estrogen receptor-positive (ER)-positive tumors and are treated with endocrine therapies. Endocrine therapies, which block ER-driven tumor growth, show high efficacy. Yet, a significant proportion of the patients will eventually relapse with metastatic breast
Short-chain fatty-acids (SCFA) are produced from dietary fibres by the intestinal microbiota. They protect humans against obesity. The fate of SCFA and their impact on human fat metabolism is complex and dynamic. To optimally apply prebiotic (fibre) and probiotic (microbial) supplements, a better understanding of their mode of action is required. Our aim is to construct, infer, and analyse a dynamic, multiscale computational model predicting how dietary fibres affect the balance between fat intake
Programme: Independent Projects
Organisms: Not specified
The SilicoTryp project aims at the creation of a “Silicon Trypanosome”, a comprehensive, experiment-based, multi-scale mathematical model of trypanosome physiology.
Trypanosomes are blood-stream parasites transmitted by tsetse flies; they cause African sleeping sickness in humans and livestock. Currently available drugs have severe side effects, and the parasites are rapidly developing resistance.
In this project, we collect a wide range of new experimental data on the parasite in its various
SBML file supplementary material of the publication.
Contributor: Fiona Achcar
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Organism: Trypanosoma brucei
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
Authors: Karen Van Eunen, C. M. Volker-Touw, A. Gerding, A. Bleeker, J. C. Wolters, W. J. van Rijt, A. M. Martines, K. E. Niezen-Koning, R. M. Heiner, H. Permentier, A. K. Groen, D. J. Reijngoud, Terry G.J. Derks, Barbara Bakker
Date Published: 7th Dec 2016
Journal: BMC Biol
PubMed ID: 27927213
Citation: BMC Biol. 2016 Dec 7;14(1):107. doi: 10.1186/s12915-016-0327-5.
Authors: J. C. Wolters, J. Ciapaite, K. van Eunen, K. E. Niezen-Koning, A. Matton, R. J. Porte, P. Horvatovich, Barbara Bakker, R. Bischoff, H. P. Permentier
Date Published: No date defined
Journal: J Proteome Res
PubMed ID: 27447838
Citation: J Proteome Res. 2016 Sep 2;15(9):3204-13. doi: 10.1021/acs.jproteome.6b00419. Epub 2016 Aug 5.
Date Published: 26th Aug 2014
Journal: Mol Microbiol
PubMed ID: 25145465
Date Published: 8th May 2012
Journal: Int J Parasitol
PubMed ID: 22580731
Date Published: 17th Jan 2013
Journal: PLoS Negl Trop Dis
PubMed ID: 23350008
Date Published: 5th Dec 2013
Journal: PLoS Comput Biol
PubMed ID: 24339766
Authors: Fiona Achcar, Abeer Fadda, Jurgen Haanstra, Eduard Kerkhoven, Dong-Hyun Kim, Alejandro Leroux, T. Papamarkou, Federico Rojas, Barbara Bakker, Mike Barrett, Christine Clayton, Mark Girolami, Luise Krauth-Siegel, Keith Matthews, Rainer Breitling
Date Published: 7th May 2014
Journal: Adv Microb Physiol
PubMed ID: 24797926
Date Published: 3rd Jul 2013
Journal: J. Biol. Chem.
PubMed ID: 23814051
Date Published: 19th Jan 2012
Journal: PLoS Comput Biol
Date Published: 17th Feb 2010
PubMed ID: 20158937
Date Published: 6th May 2010
PubMed ID: 20444304