[BBC] Postdoc position: Integrative cancer bioinformatics

[Lodewyk Wessels]

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Integrative cancer bioinformatics: Postdoc position.
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About the position:
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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:
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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:
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The position is embedded within the Bioinformatics and statistics group lead 
by Dr Lodewyk Wessels (http://bioinformatics.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:
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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?
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For further information about the position please contact Dr. Lodewyk 
Wessels, tel. +31 20 512 7987 or e-mail: l.wessels at nki.nl

How to apply:
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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 at 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://bioinformatics.nki.nl/