The Bruggeman lab

Bruggeman info


Short CV:

  • BSc degree in Biotechnology in 1997 (HR&O, Delft, The Netherlands)
  • MSc degree in Biology (Cum Laude) in 1999 at Leiden University (The Netherlands)
  • 1999-2004 PhD studies in the lab of Prof Dr Hans Westerhoff
  • 2004-2005 Van Rijn Talent Grant at the VU University
  • 2005 PhD degree (Cum Laude) at VU University (Amsterdam, The Netherlands)
  • 2005-2007 Postdoctoral researcher (30%) in European Network of Excellence BioSim
  • 2006 Lecturer (70%) at the School of Chemical Engineering and Analytical Science, University of Manchester, Manchester, UK. I was localised in the Manchester Interdisciplinary Biocentre of the  University of Manchester.
  • 2007 Postdoctoral researcher (70%) at the department for Multiscale modelling and nonlinear dynamics,  Centre for Mathematics and Computer Science (CWI) in Amsterdam, The Netherlands
  • 2007-2012 Junior Group Leader in the Netherlands Institute for Systems Biology (NISB). Collaboration between AMOLF, VU University, University of Amsterdam and CWI.
  • 2012 Associate Professor in the section Systems Bioinformatics at the VU University, Amsterdam, The Netherlands
  • 2009-2014 Managing director of the VU participation in the international master student program CanSys, involving the University of Luxembourg (Prof Dr Thomas Sauter) and the Roswell Park Cancer Institute (Buffalo, NY, USA; Prof Dr Moray Campbell).
  • 2013-2017 Teaching director of the NWO Graduate Program STAR (Scientific Top Training in Antimicrobial Research). In this program, we award four PhD studentship in total. The awardees are all master students of one VU-Life Science master program who wrote the best PhD research project, under supervision of a principle investigator of the Amsterdam Institute for Molecules, Medicine, and Systems. I am responsible for the overal organisation of the program, together with a team of executives.
  • 2012-2015 Extraordinary professor in Mathematics for Systems Biology at the Mathematics Department of the VU University, Amsterdam, The Netherlands. (This contract ended when I started with the URC appointment as Januari 1, 2015.)
  • Januari 1, 2015-2020 University Research Chair at the VU University (see link)

Long CV:
I grew up in Sommelsdijk in the South of the Netherlands (link to Google Maps) where I did primary, secondary, and high school. I obtained a bachelor degree in Biotechnology (HLO, HR&O) in Delft. I did an internship, working with yeast fermentations in Prof Dr Jack Pronk’s lab at the Technical University of Delft. Next, I moved to Leiden University to study Biology in a master program. This study I finished Cum Laude. At that time, I had developed a strong interest in the molecular working of living cells. To pursue this interest, I required much more knowledge of mathematics and physics in a cell biology setting. I decided to pursue a PhD project in Prof Dr Hans Westerhoff’s lab in Amsterdam (NL) at the VU University. He is one of the pioneers of the systems biology field and used mathematical models and experimentation throughout his career. During my PhD studies, I focussed on: i. extending metabolic control analysis, ii. the molecular control mechanism of ammonium assimilation in Escherichia coli, iii. MAPK signal transduction in collaboration (with my room mate, Jorrit Hornberg, now Dr of course), and several philosophical aspects of complex systems biology (such as limitations of reductionism). During my PhD project, the VU University, the University of Amsterdam, and the Humboldt University in Berlin (Germany) had a shared Graduate School. This gave me the opportunity to meet many scientists with similar interests. They were mostly members of the Theoretical Biophysics Dept headed by Prof Dr Reinhart Heinrich, who died at a much too young age in 2006. In this graduate school, Thomas Höfer, Edda Klipp, Stefan Schuster, Oliver Ebenhöh, Wolfram Liebermeister, and Nils Blüthgen were all active; now all original systems biologists in Europe.  Their research and discussions has had a strong influence on me. During my PhD studies, I also visited Prof Dr Kholodenko and Prof Dr Jan Hoek at the Thomas Jefferson Medical College in Philadelphia (PA, USA) to work on extensions of metabolic control analysis from a modular perspective and an emphasis on eukaryotic signal transduction. I feel very fortunate to have worked with all those great scientists. They were often already using mathematical models in their research, decades before systems biology was picked up the mainstream cell biology community. The Biothermokinetics meetings are also a great example of early systems biology research in Europe – I regrettably only visited a few of them. In 2005, I finished my PhD studies Cum Laude at the VU University in Amsterdam. Next, I obtained a Talent Grant of the VU University that allowed me to stay for a short time. After this, I became a postdoctoral researcher on a large EU project called BioSim. All of these placements were still in the Westerhoff lab. In 2006, I held a 70% lecturer position at the University of Manchester in the Manchester Interdisciplinary Biocentre and 30% postdoc position in Amsterdam. I decided not to stay in Manchester for personal reasons and moved back to Amsterdam. In Amsterdam, I was offered in Oct 2007 a 5-year Junior Group Leader position at the NISB (a systems biology collaboration between AMOLF, VU, UVA and CWI). During this time, I divided my time between the UvA, VU, and the CWI. The CWI (Centre for Mathematics and Computer Science) initiated the Life Sciences section during this period. It is now full of extremely interesting science at the edges of the mathematics, computer science and biology. My interests proved more on the experimental biological side than on the mathematical side. So, I decided to move back to the VU where I was offered an Associate Professor position in the Systems Bioinformatics Section in Oct 2012. This section is headed by Prof Dr Bas Teusink. In May 2012, I was offered a 5-year professor position in the Mathematics department of the VU University to strengthen the contacts between mathematics and systems biology. Also in 2012, I was awarded a VIDI grant by NWO-ALW that enabled me to pursue my research. In the next years, I will be setting up the experimental methods to study single-cell physiology and develop theory to understand how single cells make adaptive decisions given biochemical and physical constraints. As of Januari 1, 2015, I have a five year appointment as University Research Chair at the VU University.