[Coral-List] PhD student in Computational Biology of cnidarians at the University of Amsterdam

Jaap Kaandorp J.A.Kaandorp at uva.nl
Fri Oct 9 08:42:45 EDT 2009

PhD student in Computational Biology of cnidarians at the University of Amsterdam

The Section computational Science (University of Amsterdam) has a vacancy
for a PhD Student for the project ``Genetic and Cellular Mechanisms
for Controlled Growth'' (38 hours per week).

The project is funded by the Honda Research Institute Europe. In this
project the candidate will collaborate with researchers from the Honda
Research Institute Europe and should be willing to spend 1-2 months each
year at this institute in Offenbach (Germany). The candidate is expected
to collaborate extensively with molecular developmental biologists.

The main target of the project is to develop computational models for
cellular development to achieve a controlled growth. By controlled growth,
we mean three mutually related properties. First, the morphological growth
should stop within a limited time. This does not necessarily mean that cells
should stop dividing, rather, a balance between cell proliferation and cell
death should be achieved. Second, it should achieve a desired shape with a
sufficient complexity. Third, it should show a certain capability of
self-repairing, i.e., when a small number of the cells are destroyed, the
balanced cell growth process should be able to re-generate these cells at
the right place. Cellular interaction mechanisms that facilitate a structured
growth will be studied. Second, evidence indicating mechanisms for controlled
growth found in biology, such as the role of negative and positive feedback
loops in gene regulatory networks, will be evaluated and related to those
network motifs found in the computational model. Based on the understanding
of the structure, dynamics and cellular behaviour of the gene regulatory
network model, we will perform a case study of a GRN model for the development
of cnidarians Nematostella vectensis and Acropora millepora using biological
data, including spatio-temporal gene expression data (in situ hybridisations)
and morphological data.

Candidates should have a master's degree (or equivalent) in scientific
computing or computational science, (computational) physics, (computational)
chemistry or a comparable expertise.  Candidates are expected to have
expertise in modelling and scientific programming and an active interest in
life science applications.  Candidate should be able to work in an international
research team. Fluency in oral and written English is required. Motivation to
travel to a different country and integrate efficiently in a new research team
is fundamental.

More information
Further information can be obtained from Dr J. A. Kaandorp, Section
Computational Science, University of Amsterdam, Kruislaan 403, 1098 SJ,
Amsterdam, The Netherlands, +31 20 525 7539, J.A.Kaandorp at uva.nl and Dr
Y. Jin, Honda Research Institute Europe, Germany, yaochu.jin at honda-ri.de.
More information (application procedure, deadlines etc.) is available on
the website http://www.uva.nl/vacatures

Dr. Jaap A. Kaandorp
Section Computational Science
Faculty of Science
University of Amsterdam
Science Park 107 (new address name from 1-1-2009) 
1098 XG Amsterdam
The Netherlands
Phone: +31 20 5257539 / +31 20 5257462
email: J.A.Kaandorp at uva.nl (please note new email address from 20-5-2008)
fax: +31 20 525.7419
URL: http://www.science.uva.nl/~jaapk/

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