PhD Positions Delft University of Technology The Netherlands

July 7, 2008

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PhD Positions The Vrije Universiteit Amsterdam and Delft University of Technology

Title 2 PhD positions in Understanding hierarchical and metabolic regulation of
metabolic networks through Bayesian constraint modeling f/m (4 years, 1,0 fte)
Vacancy number 1.2008.00183
Description The Vrije Universiteit Amsterdam and Delft University of Technology are searching for two
PhD students in a project funded by NWO Computational Life Sciences:

Description of the project – Living cells are able to carry out a large number of reactions,
which are all connected within a metabolic network. Recently, our understanding of how
such a network is regulated at the different levels of cellular organization (genes, proteins,
metabolites), has increased substantially. Yet, there is still a surprising lack of knowledge as
to why steps in a pathway are regulated the way they are. In this project, we will combine
kinetic modeling with machine learning techniques to investigate different regulation
scenarios and their impact on metabolism, providing a context for interpreting
experimentally observed regulation in Saccharomyces cerevisiae and Lactococcus lactis.
These two organisms are intensively studied within the Kluyver Center in which the research
groups participate, and kinetic models of primary metabolism have been developed. One
PhD student (based in Amsterdam) will focus on the extension of existing kinetic models to
encompass other levels of regulation and constraints. The other PhD student (based in
Delft) will focus on machine learning, parameter uncertainty propagation and dynamic
constraints.

Organisation – This project will be carried out at the Centre for Integrative Bioinformatics
of the Vrije Universiteit Amsterdam (IBIVU), and at the Information & Communication
Theory Group at Delft University of Technology. IBIVU focuses on integrating theory,
bioinformatics and modeling with experimental, quantitative biology. The Bioinformatics
section of the Information & Communication Theory Group specialises in data-driven
bioinformatics research in collaboration with researchers in medicine, molecular biology and
biotechnology.

Both groups are partners in the Kluyver Centre for Genomics of Industrial Fermentation, one
of the Centres of Excellence of the Netherlands Genomics Initiative. It employs microbial
genomics to improve microorganisms for use in industrial fermentation processes. The IBIVU
group participates in the recently founded Netherlands Institute of Systems Biology (NISB)
which seeks to understand the integrated functioning of metabolic, signal-transduction and
genetic networks via a systems biology approach.

Job requirements – For this ambitious project, we are looking for two excellent, highly
motivated and ambitious PhD candidates. For the Amsterdam part we are looking for a
candidate with a MSc degree in (micro)biology, biochemistry, systems biology, engineering,
physics or mathematics. Affinity with mathematical models applied to biological systems is
essential. For the Delft part we are looking for a candidate experienced in machine learning
and/or optimisation, with an MSc degree in bioinformatics, computer science, engineering,
physics or mathematics. Experience with or affinity for biological applications is an asset.
Both PhD candidates need to be able to work independently but as part of a multidisciplinary
team, and are expected to deliver a PhD thesis and a number of scientific publications within
a period of 4 years.

Conditions of employment – We offer a full-time PhD position for 12 months. After a
successful evaluation the contract will be prolonged with 36 months. Our fringe benefits of
employment can be found at www.vu.nl/vacatures.
Salary – The salary is according to the standards for PhD positions and is starting at €
2000,- in the first year to € 2.558,- in the last year of appointment, based on a fulltime
employment.

Information

Information about this position can be obtained from: Dr. Bas Teusink
(bas.teusink@nizo.nl, 06-21835201) or Dr. Barbara Bakker (barbara.bakker@falw.vu.nl, 020
5987196), Amsterdam; Dr. ir. Dick de Ridder (d.deridder@tudelft.nl, 015 2785114) or Prof.
dr. ir. Marcel Reinders (m.j.t.reinders@tudelft.nl, 015 2786424), Delft.
Written applications in English should be sent to the Vrije Universiteit, Dr. J.M.R.M.
Neutelings, Managing Director, Faculty of Earth and Life Sciences, De Boelelaan 1085, 1081
HV Amsterdam, The Netherlands or by e-mail to falw-vacatures@falw.vu.nl, with the
vacancy number on the letter and the envelope, or in the e-mail subject line. Deadline for
application is August 1, 2008.

Scholarship Tags: Delft, PhD, positions, The Netherlands, University of Technology