[Socbin] PhD position in biomodeling at NISB and CWI

[Roeland Merks]

The Netherlands Institute for Systems Biology (NISB) and Centrum  
Wiskunde & Informatica (CWI) invite applications for the position of a:

PhD student (OIO): Cell-based modeling of in vitro angiogenesis: role  
of tip cell selection, cross-talk between diffusive and contact- 
dependent signaling, and endothelial cell-matrix interactions.

The opening is a research position within the field of computational  
biology

Research background

Angiogenesis, the outgrowth of sprouts from existing blood vessels, is  
essential for many biomedical phenomena, including tumor growth and  
tissue engineering. A detailed understanding of its mechanisms will  
help identify specific targets for therapeutical intervention. The key  
players of angiogenesis are endothelial cells (ECs), the cells lining  
the inner walls of mature blood vessels, and the surrounding matrix  
proteins. We have previously built simple models of the ECs’ self- 
organization into angiogenic sprouts. In this project we aim to refine  
our understanding of angiogenic sprouting, by including the selection  
of “tip cells”—the leading cells of blood vessel sprouts—and the  
interactions between the ECs and the protein matrix they live in. The  
final goal of this project is to develop a multiscale, explanatory  
model of angiogenesis.

Job description

The PhD student will further develop and analyze cell-based models of  
angiogenesis and, depending on interest, validate the cell-based  
models using mean-field approaches. Techniques include ordinary  
differential equations (ECs’ regulatory networks), the Cellular Potts  
Model (cell behavior) and PDEs (protein matrix).  Model insights and  
predictions will be interpreted and validated in close collaboration  
with our experimental collaborators.


Location

The work will be embedded in the Biomodeling and Biosystems Analysis  
group of the Netherlands Institute for Systems Biology (NISB) and  
within the Life Sciences group of the Center for Mathematics and  
Computer Science (CWI) in Amsterdam. As the “core modeling group” of  
the Netherlands Consortium for Systems Biology, the Biomodeling and  
Biosystems Analysis group develops quantitative and predictive models  
and multiscale computer simulations in collaboration with systems  
biology groups at participating institutes.


Profile

Candidates ideally fulfill the following criteria:

-       M.Sc. in theoretical biology, computer science, mathematics or  
a related discipline
-       able to communicate with scientists in biology and mathematics
-       good programming skills in C++ and Python or equivalent


Conditions of employment

The vacancy concerns a temporary research position for four years. The  
salary and terms of employment are in accordance with the "CAO- 
onderzoekinstellingen". Besides the salary, CWI offers attractive and  
flexible terms of employment, like a collective health insurance,  
pension-fund, and initial help with housing for foreigners.


Websites
http://www.sysbio.nl and http://www.cwi.nl

Applications and requests for information

Direct requests for information or applications before 1 December 2008  
to:

Dr. Roeland Merks, Roeland.Merks at sysbio.nl
phone +31 20 592 4117, skype: roelandmerks
Centrum Wiskunde & Informatica (CWI) and Netherlands Institute for  
Systems Biology (NISB)
Kruislaan 413, 1098SJ Amsterdam, The Netherlands

Applications should include a motivation letter, a curriculum vitae,  
list of publications, and the names and addresses of at least two  
persons that can be approached to obtain further information.

Application deadline

1 December 2008

Literature

Roeland M. H. Merks, Sergey V. Brodsky, Michael S. Goligorksy, Stuart  
A. Newman, James A. Glazier (2006). Cell elongation is key to in  
silico replication of in vitro vasculogenesis and subsequent  
remodeling. Developmental Biology 289, 44-54. doi:10.1016/j.ydbio. 
2005.10.003

Roeland M. H. Merks, Erica D Perryn, Abbas Shirinifard, James A  
Glazier (2008). Contact-inhibited chemotaxis in de novo and sprouting  
blood-vessel growth. PloS Computational Biology 4 (9), e1000163. doi:  
10.1371/journal.pcbi.1000163