[Coral-List] Postdoc in Computational Biology Universiteit van Amsterdam

Jaap Kaandorp J.A.Kaandorp at uva.nl
Thu Jan 13 10:03:53 EST 2011

Postdoc in Computational Biology at the Section Computational
Science of the Universiteit van Amsterdam

Project: ‘Multi-objective optimization for modeling developmental gene regulatory networks'
The project is financed by the NWO research programme Interdisciplinary Challenges
for Complexity Science (Complexity-Net). The project is a collaboration with the
research groups from Dr J. Jaeger (Centre for Genomic Regulation, Barcelona, Spain)
and Dr F. Alves (Center for Developmental Biology, Lisbon, Portugal). The candidate
is expected to collaborate extensively with system biologists and molecular
developmental biologists.  In this project, we propose to compare distinct network
modeling formalisms applied to the study of real-world developmental gene regulatory
networks. An important challenge is the determination of model parameters.. Even models
of moderately sized networks contain a large number of (unknown) parameters. We propose
to use multi-objective optimization for the network inference and estimation of unknown
model parameters. Models will be optimized both with regard to their ability to fit the
data, as well as their robustness towards molecular fluctuations and changes in parameter
values. In this part of the project we will use qualitative and quantitative spatial gene
expression data from the sea anemone Nematostella vectensis. We want to test systematically
under which circumstances each formalism is best able to reproduce the observed expression
patterns and which one is the most suited for prediction of network topology and perturbed
gene expression, and is able to reproduce the robustness of pattern forming gene regulatory

More information about the job and application procedure
can be found at http://www.uva.nl/vacatures (postdoc computational biology)
or contact Dr. Jaap A. Kaandorp, E-mail J.A.Kaandorp at uva.nl

Dr. Jaap A. Kaandorp
Section Computational Science
Faculty of Science
University of Amsterdam
Postal address: 
PO Box  94216
1090 GE Amsterdam
The Netherlands
Visiting address:  
Science Park 904 (room C3.147)
1098 XH Amsterdam
The Netherlands
Phone: +31 20 5257539 / +31 20 5257463
email: J.A.Kaandorp at uva.nl 
fax: +31 20 525.7419
URL: http://www.science.uva.nl/~jaapk/

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