[BBC] OIO and postdoc positions in biomodeling at NISB and CWI
Roeland Merks
roeland.merks at psb.ugent.be
Tue Nov 4 19:23:16 CET 2008
Vacancy
The Netherlands Institute for Systems Biology (NISB) and Centrum
Wiskunde & Informatica (CWI) invite applications for the position of a
Postdoc (two years, with possibility for extension): Computational
modeling of structural genomic variation in hierarchically-regulated
gene networks
The opening is a research position within the field of computational
biology
Research background
Structural variation of the genome, including translocation of DNA
chunks across chromosomes, inversions, and deletions can have enormous
impact on gene expression and consequently on cell function.
Hierarchical regulation mechanisms, including conditional DNA folding
and nuclear lamina interactions, can switch gene clusters between a
state rendering the genes inaccessible to transcription and a
“permissive” state in which gene transcription is possible.
The consequences of hierarchical network organization for the dynamics
and evolution of gene networks are poorly understood. The project will
develop computational and mathematical modeling approaches to explore
the effects that structural genomic variation can have on gene
expression in hierarchically-structured gene networks at single-organism
and evolutionary time scales.
Job description
The postdoc will develop and analyze theoretical, evolutionary models of
hierarchical gene network regulation using discrete and/or continuous
modeling approaches. Model insights and predictions based on artificial
and actual regulatory networks will be interpreted in close
collaboration with two functional genomics groups that participate in
the NCSB: the Edwin Cuppen group at the Hubrecht laboratory, Utrecht and
the Lodewyk Wessels group at the Netherlands Cancer Institute in Amsterdam.
Location
The work will be embedded in the Biomodeling and Biosystems Analysis
group of the Netherlands Institute for Systems Biology (NISB;
www.sysbio.nl) 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:
- Ph.D. theoretical biology, computer science, mathematics or a related
discipline
- able to communicate with scientists in biology and mathematics
- good programming skills in C++ or equivalent
Conditions of employment
The vacancy concerns a temporary research position for two years, with
possibility of extension. The salary and terms of employment are in
accordance with the "CAO-onderzoekinstellingen" and are based on
qualifications. Besides the salary and excellent working conditions, CWI
offers attractive and flexible terms of employment, like a collective
health insurance, pension-fund, and initial help with housing for
foreigners. The position is at postdoc level for 38 hrs/week.
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
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Vacancy
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.
Closing time
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
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Note: from September 1st 2008 I will move to the Netherlands Institute
for systems biology (www.sysbio.nl) and to CWI, the National Center for
Mathematics and Computer Science (www.cwi.nl) in Amsterdam. However,
I will be in Ghent until September 5th 2008 for our plant modeling
summer school: www.psb.ugent.be/plantmodels.
My current e-mail address will still be operational for a while, but
it will soon change to: Roeland.Merks at cwi.nl and Roeland.Merks at sysbio.nl.
If any of these addresses does not (yet) work, please use my personal
e-mail address: post at roelandmerks.nl.
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Roeland Merks
Group Leader "Plant Systems Modeling"
Tel:32 (0)9 3313823 Fax:32 (0)9 3313809
VIB DEPARTMENT OF PLANT SYSTEMS BIOLOGY, UGent
Technologiepark 927, 9052 Gent, BELGIUM
roeland.merks at psb.ugent.be http://www.psb.ugent.be
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