Postdoctoral Position in Computational Biology -Multi-objective optimization for modeling developmental gene regulatory networks

Description: 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 networks..

Requirements

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 modeling and scientific programming and an active interest in life science applications. The Candidate should be able to work in an international research team. A strong research record, evidenced by a PhD thesis and papers published in peer-reviewed journals is needed. 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.
Contact: Dr J. A. Kaandorp, Informatics Institute, University of Amsterdam, Kruislaan 403, 1098 SJ, Amsterdam, The Netherlands; +31 20 525 7539 +31 20 525 7539 
Email:  J.A.Kaandorp@uva.nl.

Appointment

This full-time appointment will be on a temporary basis for a maximum period of two years. The salary is in accordance with the university regulations for academic personnel, and will range from €2,379 before tax, up to a maximum of €3,755 per month (scale 10). The holiday allowance is 8% of the annual gross income. Furthermore, there will be an annual bonus of 8.3% of the annual gross income. The Collective Employment Agreement of the Dutch Universities applies.

 Application:

Applications should include a letter of motivation, pdfs of most relevant publications and a Curriculum Vitae. Please include the names and contact information of two references. Applications should be sent by e-mail to Mrs J.C. Knaap-Cabi at application-science@uva.nl.The application period will remain open until the position is filled; however, review of applications will commence on 13 February 2011
Deadline: 13 February 2011
Links: For more details click here
University of Amsterdam,Netherlands,deadline-13-02-2011,Postdoc,Biology