Basic cancer research through the development of appropriate model systems such as mice, rats and cell lines is a field of special interest within the Netherlands Cancer Institute. Ultimately, the goal is to combine this information with human tumor data in order to deliver personalised treatment to patients.
Recent developments in high-throughput genomic technologies have made it possible to significantly further this research by unraveling the role of large numbers of genes in important cellular processes. These technologies include, amongst other, high-throughput high content screening (HTHCS) and insertional mutagenesis screens.
In HTHCS, a large RNAi library in combination with cell-based assays, fluorescence- based reagents, automated fluorescence microscopy and image analysis are employed to study complex cellular phenotypes. In HTHCS one can study the consequence of inactivation of large numbers of individual genes, in a collection of individual cells, measured by multiple cellular parameters.
In retroviral insertional mutagenesis, retroviruses integrate in the genome of (genetically manipulated) mice, causing tumors by either activating oncogenes of de-activating tumor suppressors. By studying the genomic distribution patterns of the viral integration sites and the gene expression of associated tumors, valuable information about genes and pathways involved in tumorigenesis can be obtained.
Each of these technologies generates large, heterogeneous, complex datasets.
Currently, many of these datasets are simply employed to extract an interesting new hit (e.g. a putative new oncogene) from a screen. By performing an integrative analysis of the data we want to work towards developing a 'systems level' understanding of the pathways and processes involved in tumorigenesis. The computational challenges that need to be addressed include the development of: 1) integrative models for 'experiment specific' data and 'experiment independent' data to identify pathways and interactions between pathways relevant to tumor development; 2) approaches to associate (perturbations to) the identified pathways to phenotypic outcomes; 3) cross-species comparisons to translate findings from model systems (cell lines and mouse models) to the human system, and integration of the findings from model systems with data from human tumors to predict outcome and therapy response.
About the candidate - requirements:
Ph.D in a relevant computational discipline such as Computer Science, Statistics, Engineering, Applied Mathematics or Physics with experience in Bioinformatics and/or Machine learning. Applicants that hold a Ph.D in the life sciences, but with substantial experience in bioinformatics are also encouraged to apply. The researcher appointed in this position will function as a liaison between the Bioinformatics group and the research groups within the Netherlands Cancer Institute performing the screens.
About the employer:
The position is embedded within the Bioinformatics and statistics group lead by Dr Lodewyk Wessels (http://bioinformati cs.nki.nl). This group closely collaborates with the groups of Drs Rene Bernards, Roderick Beijerbergen, Anton Berns, Maarten van Lohuizen and Laura van 't Veer on the topics listed above. The candidate will also be closely interacting with these groups on the relevant topics. Research in the Netherlands Cancer Institute covers all major areas of cancer research, with special emphasis on mouse models, mouse (reverse) genetics, cell biology, immunology, translational research requiring close collaboration between clinical and basic scientists and epidemiology and psychosocial cancer research.
Employment conditions:
The employment conditions follow general employment rules as laid down in the 'CAO' for hospitals. The salary will be determined depending on education and experience.
Want to find out more?
For further information about the position please contact Dr. Lodewyk Wessels, tel. +31 20 512 7987 or e-mail: l.wessels@nki. nl
How to apply:
Applications for this position should include a Curriculum Vita with the names and contact information of two professional references that can be contacted for further information.
Send applications to:
The Personnel Department
The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital
Plesmanlaan 121
1066 CX Amsterdam
The Netherlands, or via email to work@nki.nl.
L.F.A.Wessels, Ph.D
Bioinformatics and Statistics
The Netherlands Cancer Institute
Plesmanlaan 121, 1066 CX Amsterdam
The Netherlands
Tel: +31 (0)20 5127987
Fax: +31 (0)20 6691383
Mobile: +31 (0)634485714
http://bioinformati cs.nki.nl/
Setia Pramana
Bioinformatics Research Group
Center for Statistics
Hasselt University
Agoralaan - building D
3590 Diepenbeek
Belgium
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