Systems biology of molecular regulatory networks

This group is a subgroup of Life Sciences.Coordinator of this subgroup: Frank Bruggeman

This group is a subgroup of Life Sciences.
Coordinator of this subgroup: Frank Bruggeman

Present-day molecular techniques allow for the monitoring and perturbation of the dynamics of the molecular regulatory networks that drive emergent cellular dynamics, such as physiological adaptation and cell differentiation.  One of the major aims of those studies is to develop approaches to specifically alter the dynamics of molecular networks by precise molecular perturbations of cells for the benefit of biotechnology and medicine.  Besides quantitative experimentation, the development of predictive kinetic models and insightful theory will be necessary to guide experimentation, formulate/test hypotheses and offer understanding in terms of realistic molecular mechanisms.

In this group, we develop:

  • Kinetic models of molecular regulatory networks.
  • Control and stochastic theory to better understand the action of molecular regulatory networks at the level of individual cells populations thereof (eukaryotic and prokaryotic) and microbial ecosystems.

The majority of the projects are intense collaborations with experimental groups. Current projects deal with:

  • Stochastic and control theory for eukaryotic gene regulation and nuclear receptor signaling.
  • Prokaryotic metabolism and signaling.
  • Flux balance analysis for multicellular systems and microbial ecosystems. 

This group is a part of the Netherlands Institute for Systems Biology (NISB),  Frank Bruggeman (group leader) is a part time member of the group of Bas Teusink (Integrative Bioinformatics, Vrije Universiteit, Amsterdam, The Netherlands).

Master student projects on modeling and theory development for molecular networks are in principle always available. Combined experimental and theoretical projects as collaborations with experimental groups are also possible. Please sent an email to:

Many of the group members also work in other groups and are co-workers on collaborative projects.

  • Systems of Nuclear Receptors (NucSys; Marie Curie Network 2006; Prof Dr Carsten Carlberg (University of Luxembourg), project leader)
    a. Alexey Kolodkin (PhD student, co-supervisor/promotor: Prof Dr Hans Westerhoff), Kinetic modeling and theory development for nucleocytoplasmic shuttling and signaling by nuclear receptors.
    b. Katja Rybakova (PhD student, co-supervisor.promotor: Prof Dr Hans Westerhoff), Kinetic modeling and theory development for transcriptional regulation of genes by nuclear receptors. 
  • MEMESA project (NWO-CLS 2008; Dr Frank Bruggeman, project leader, co-applicants Dr W Roling, Prof Dr L Stougie, Prof Dr H Westerhoff), open position (PhD student, co-supervisor: Dr Wilfred Roling, VU), Steven Kelk (postdoctoral student, in Prof Dr Leen Stougie's group, CWI), Stoichiometric analysis of microorganisms in microbial communities (mathematics, Brett Ollivier (postdoctoral student, co-supervisor Dr Wilfred Roling, VU), Stoichiometric analysis of microorganisms in microbial communities (models and software).
  • Stochastic modeling and theory for molecular networks (NWO-CLS project 2005)
    Maciej Dobrzynski (PhD student, co-supervisor: Drs Joke Blom, CWI)
    Theory and measures for burst in transcription and translation. Optimal two-component signaling by prokaryotes and the impact of: (i) noise deriving from diffusion and fluctuations in molecule copy numbers and (ii) operon organization of two-component signaling proteins on reliability and response time of signaling.
  • Eukaryotic gene regulation (NISB funded PhD project)
    Anne Schwabe (PhD student)
    Stochastic theory and kinetic models of mammalian gene transcription with a focus on molecular mechanisms for quality control, noise suppression and transcription bursts.
  • Noise in microbial physiology (NISB funded glue project)
    To be filled (PhD student, co-supervisors: Dr S Tans, Prof Dr K Hellingwerf, Dr PR ten Wolde, Dr D Crommelin)
  • Synthetic eukaryotic gene networks (NISB funded glue project)
    To be filled (PhD student, co-supervisor: Dr P Verschure)
  • Impact of stochasticity and chromatin regulation on mammalian transcription regulation (NWO Meervoud project; applicant Dr P Verschure, Bruggeman as co-applicant/modeling advisor), Lisette Annink (PhD student).