Biomodeling and Biosystems Analysis
 
The Biomodeling and Biosystems Analysis group is based at CWI and the Netherlands Institute for Systems Biology. We are part of CWI’s Life Sciences Cluster, and we are the “core modeling group” of the Netherlands Consortium for Systems Biology. In collaboration with systems biology groups at participating institutes, we develop quantitative and predictive models and multiscale computer simulations, with a primary focus on multiscale, cell-based modeling of biological form and function.
 
 
Multiscale, cell-based modeling
One of the most central questions in biology is how the sequential information in the genome translates to biological form and function.
    We need two logical steps to explain how genetics drives biological development, which put the cell in the center of the explanation. First we ask how genes define the cell’s behavior, then we ask how collective cell behavior drives the formation of patterns, shapes, and physiological and pathological functionality at the tissue and organ level.
    We have applied this cell-centered approach to de novo and sprouting blood vessel growth (angiogenesis and vasculogenesis) and to auxin-flux-driven patterning problems in plant development.
 
Contact: Roeland Merks
 
 
Biomodeling & Biosystems Analysis
Research & Publications
 
 
Blood vessel growth
Cell-based modeling
 
 
Plant development
 
 
 
Coral growth
 
 
 
Simulation techniques and frameworks
 
 
Ph.D and M.Sc. Theses
 
 
 
 
Events
  1. •3rd Annual NCSB Symposium, 3-4 November 2011
  2. • CWI’s Life Sciences seminar, Fridays, 13:00-14:00, CWI, Science Park 123, Amsterdam
 
Group members
  1. • Roeland Merks (PI)
  2. • Milan van Hoek (postdoc) - simulation of metabolizing microbial communities
  3. • Margriet Palm (Ph.D student) - cell-based modeling of angiogenesis
  4. • Michael Guravage (scientific programmer) - VirtualLeaf simulation environment
  5. •Sonja Boas (Ph.D student) - modeling cell-ECM interactions in angiogenesis cell cultures
  6. •András Szabó (postdoc) - computational biophysics of tumor growth and evolution

    Vacancies

    Former group members
  7. • Josephine Daub (M.Sc. student) - cell-based modeling of angiogenesis (now at Swiss Institute of Bioinformatics -  Universität Bern)
  8. • Frederik Van Parijs (Research assistant) - modeling lignin polymerization, plant development  (now at Universiteit Antwerpen)
  9. •Ioana Niculescu (M.Sc. student @UvA/SCS): modeling in-stent restenosis (now at Utrecht University)
  10. •Erik van Dijk (M.Sc. student) - modeling endothelial cell signaling during angiogenesis
 
Links
  1. •www.sysbio.nl
  2. •www.cwi.nl