Publications of Van Riel and co-workers

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Internal reports 


  • v (2010)



  • van Dooren, F. (2009) insulin signaling pathway. Master Thesis (BME)

  • Rios Velazquez, E. (2009) Decoding biologic phenotypes from non-invasive CT-PET imaging

  • Wu, W. (2009) spatio-temporal model of carcinoma (epithelial cancer). Master Thesis (BME)

  • Niesen, M. (2009) Synthetic Biology. Master Thesis (BME)

  • Vanlier, J. (2009) A versatile MATLAB toolbox for the quantification of MRS data. Master Thesis (BME)

  • Vanlier, J. (2009) The Biochemical Simulation Environment for Mitochondrial Energetics. external traineeship (BME)


  • Tiemann, C.A. (2008) Dynamic Modeling of the Hypoxia Induced HIF-1 Response. Master Thesis (BME)

  • Schmitz, J.P.J. (2008) Human skeletal muscle metabolism; 31P NMR spectroscopy and computational modeling. Master Thesis (BME)

  • Rios Velazquez, E. (2008) The hypothalamic-pituitary-adrenal system activity and its relation with metabolic syndrome. internship report (BME)

  • Wei, W. (2008) Implementation and analysis of a mathematical model of tumour invasion. internship report (BME)

  • Tiemann, C.A. (2008) Analysis of time course microarray data; a systems biology approach. external traineeship (BME)


  • Groenendaal, G. (2007) Biomarker analysis and target identification in Rheumatoid Arthritis; an in silico investigation. Master Thesis (BME)

  • Tiemann, C.A. (2007) Development of the first differential equation model of the mammalian Unfolded Protein Response. internship report (BME)

  • van Ooijen, H.J. (2007) Towards an In Silico Disease Model for Coagulopathies. Master Thesis (BME)

  • van Stiphout, R.G.P.M. (2007) Multistep feed-forward activation by calcium in the energy buffered skeletal muscle cell. Master Thesis (BME)

  • Verhoog, P.J. (2007) Prediction of the local dynamic [Ca2+] in mouse EDL muscle fibers at physiological temperature. Master Thesis (BME)

  • Verhoog, P.J. (2007) Spatio-temporal modeling of calcium handling and energy metabolism in skeletal muscle cells; setting the framework. internship report (BME)

  • Verhoog, P.J. (2007) Repositioning of an optical probe on the skin with image processing. external traineeship (BME)


  • Groenendaal, W. (2006) Glucose and Water Dynamics in Human Skin. Master Thesis (BME)

  • Sander van Boxtel  (2006) Improved reliability in parameter estimation of dynamic nonlinear systems with sparse data incorporating a priori information; a myocardial calcium handling case study. Master Thesis (E)

  • Daniel Lindenaar (2006) A hybrid systems approach to identification of nonlinear biochemical processes. Master Thesis report no. 06A/04 (E)





Hugo Aerts (2005) Towards optimal experimental conditions in dynamic contrast-enhanced MRI: the influence of injection parameters. report no. 05A/08 (E)


Alfonso Puras (2005) Analysis of bioregulatory networks as monotone systems. internship report no. 05A/05 (E)



Eric Zijlstra (2004) Validation of the use of a minimal model of glucose metabolism during an oral test from both a physiological and an identification point of view. report no. 04/BMT/A03 (BME)


Evelien Hermeling (2004) An exploration of two dynamic functions of the kidneys: autoregulation and control of arterial pressure. report no. 04/BMT/A02 (BME)


Richard Lopata (2004) Identifiability and optimal experiment design of the standard pharmacokinetic models for dynamic contrast-enhanced imaging of large tumour volumes. report no. 04/BMT/A01 (BME)



Ward van Vlimmeren (2003) Surface electromyography and action potential propagation; measuring and modeling. report no. 03A/11 (E)


Koen Koene (2003) Identification of non-linear closed loop systems; analysis of the human respiratory system in hyperoxia. report no. 03A/10 (E)


Jorn op den Buijs (2003) Telomere shortening in endothelial and progenitor cells likely to play a crucial role in the development of vascular disease. report no. 03/BMT/A02 (BME)
Mark Musters (2003) Computational modeling of cardiac fatty acid uptake and utilization. report no. 03/BMT/A01 (BME)
grant from Dutch Heart Foundation



Joep Kierkels (2002) Muscle motor unit conduction velocity; measurements and modelling. report no. 02-BMT-A01 (BME)




overview of reports


Recent presentations and invited lectures

  • 'Model-based hypothesis testing of key mechanisms in insulin signaling', Kickoff meeting BEAZ, Dec. 10, 2009, Alderley Park, UK

  • 'Silencing of glycolysis in skeletal muscle', Meeting Comparative systems biology of glycolysis Oct. 19, 2009, VU, Amsterdam

  • 'Systems Biology: mechanistic models of biochemical networks', PREDICCt meeting, June 17, 2009, Utrecht

  • 'Experimental Design: making it work', Lorentz workshop Experimental design in systems biology; Data analysis and parameter identification, June 2-5, 2009, Leiden

  • 3rd FEBS Advanced Course on Systems Biology: From Molecular Biology to Biological Function. March 7-13, 2009, Alpbach, Austria.
    Systems Physiology

  • Medical Biochemistry and Molecular Systems Biology course University of Amsterdam, February 13, 2009
    Computational Modeling & Computation: the ‘dry’ part of Systems Biology

  • Biomedical Engineering Society Annual Meeting, October 2-4, 2009, St. Louis
    A multi-scale model of human skeletal muscle metabolism

  • 9th International Conference on Systems Biology, August 22-28, 2009, Gothenburg, Sweden
    Modeling the glycolytic pathway in human skeletal muscle tissue; understanding the regulation of its hundredfold dynamic range

  • Course 'Voeding' University of Amsterdam, May 14, 2008
    An introduction to Systems Biology

  • Medical Biochemistry and Molecular Biology course University of Amsterdam, Febr. 15, 2008
    Physiological modelling; mechanism-based models and model-based experiments

  • BioSim workshop 'Diabetes and Modeling', January 10-11, 2008, Lund University, Malmö Sweden

  • NDNS+ workshop "Control Theory for Systems Biology", University of Groningen, Nov. 12-14, 2007
    Parameter identification in biochemical networks; the identifiability versus robustness paradox

  • Birmingham Ageing Network Symposium, University of Birmingham, Sept. 21, 2007
    Integrative Systems Biology and Ageing

  • Second FEBS Advanced Course on Systems Biology: from molecules to life. March 10-16, 2007, Gosau, Austria.
    Physiological Modeling

  • Medical Biochemistry and Molecular Biology course University of Amsterdam, May 30, 2007
    Physiological modelling; mechanism-based models and model-based experiments

  • ‘Computational Cell Biology and Simulation of Biological Systems’, Computational Life Sciences summer school, June 19 - 22, 2006, The Netherlands


CMMSE 2005, Alicante, Spain, June 27-30, 2005

In silico biology for physiological understanding of heart metabolism


MBI workshop Quantitative mathematical modeling of gene regulatory networks, Mathematical Biosciences Institute, Ohio State University, December 2-4, 2004.

Systems biology of yeast central nitrogen metabolism


Oncology seminar, University Hospital Maastricht, July 30, 2004.

Systems biology; a top-down approach.


School of Sport and Exercise Sciences, University of Birmingham, June 14, 2004.


Karolinska Institutet, University Hospital Huddinge, Stockholm, April 14, 2004.

Inference of physiological fluxes from tracer experiments.


Dept. of Movement Sciences, University of Maastricht, February 17, 2004.

Biological insights from computational modeling of cardiac fatty acid uptake and utilization.


CARIM Donald Bers master class Excitation-contraction coupling in the heart, January 21, 2004, Maastricht.

System biology of calcium transients in the heart.


FASEB Experimental Biology, San Francisco, April 1-5, 2006
Identification of sources and functions of metabolic capacitance in the ATP metabolic network in muscle


ICSB 2005 Boston, MA, Oct. 19-21, 2005
Improved graphical analysis for reducing the parameter search space of a model of the extracellular matrix


FASEB Experimental Biology San Diego, CA, April 2-6, 2005

Lack of unique parameter values in databased modeling of calcium-contraction coupling; consequences for the analysis of contractile performance of the diabetic heart


49th Biophysical Society Annual Meeting, Long Beach, CA, February 12-16, 2005

Transmembrane diffusion of unbound fatty acids is insufficient for cardiac energy requirements: model analysis

Numerical method for databased modeling of switching characteristics of calcium handling in the intact heart







Van Riel N.A.W. (2000)  "A cybernetic modelling approach for cell biology; case study of the Central Nitrogen Metabolism in Saccharomyces cerevisiae " PhD thesis, Utrecht University, The Netherlands



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Last update: May 2010


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