[Socbin] PhD position: modeling in vitro angiogenesis
Roeland Merks
roeland.merks at sysbio.nl
Tue Mar 24 14:00:22 CET 2009
The Netherlands Institute for Systems Biology (NISB) and Centrum
Wiskunde & Informatica (CWI) invite applications for the position of a
PhD position (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 therapeutic 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
You will further develop and analyze cell-based models of angiogenesis
and, depending on your 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 May 2009 to:
Dr. Roeland Merks, Roeland.Merks at sysbio.nl
phone +31 20 592 4117
Netherlands Institute for Systems Biology (NISB)
and Centrum Wiskunde & Informatica (CWI)
P.O. Box 94079, 1090 GB 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.
Closing time
1 May 2009
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
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Roeland M. H. Merks
Netherlands Institute for Systems Biology (NISB)
and Centrum Wiskunde & Informatica (CWI)
Science Park 123, 1098 XG Amsterdam, The Netherlands
Mailing address: P.O. Box 94079, 1090 GB Amsterdam
CWI Office Room M136
Roeland.Merks at sysbio.nl / Roeland.Merks at cwi.nl
http://www.roelandmerks.nl
Phone +31 20 592 4117
Fax +31 20 592 4199
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