[SocBiN] Computational cancer biology for personalized medicine

[Lodewyk Wessels]

CombatCancer: Computational cancer biology for personalized medicine

For an ambitious joint Synergy-ERC program the Netherlands Cancer Institute (NKI, Amsterdam, The Netherlands) and the Wellcome Trust Sanger Institute (WTSI, Hinxton, UK) invite excellent and ambitious postdocs and PhD students with expertise in computational biology to apply. It is the ambition of this international team to unravel the genomic and phenotypic complexity of human cancers in order to identify optimal drug combinations for personalized cancer therapy that will be further explored in our existing clinical trial networks. The expected duration of the project is 6 years. The computational biologists will collaborate closely with experimentalists and will focus on the following tasks:

Mapping the mutational landscape of tumors. 
We will employ exome sequencing data from over 5000 tumors from 12 different tumor types to identify recurrently mutated, recurrently co-mutated and mutually exclusively mutated genes as well as frequently mutated pathways or sub-networks. Employing results from mouse forward genetic screens we will characterize the mutational landscape in mice and overlay this landscape with the human mutational landscape in order to produce a filtered, high confidence map of the cancer mutational landscape. This landscape will reveal putative cancer vulnerabilities (e.g. frequently mutated pathways) that can be attacked in an orchestrated fashion by targeted (combination) therapies.

Leveraging data from large scale molecular and drug sensitivity characterization of cell lines.  
The CGP program with the WTSI recently completed the molecular (RNAseq, DNAseq, methylation) and pharmacological (400 anti-cancer drugs) profiling of 1000 cancer cell lines. In addition, drug combination screens are being performed for a subset of the 400 drugs. We will leverage this data to map the cancer vulnerabilities identified in tumors to drug response using, amongst other, logic rules. These logic rules will aid the discovery of novel combination treatments that will be validated in cell lines and mouse models.

Requirements
•	Degree in bioinformatics, computer science, mathematics or physics 
•	A strong cancer biology interest and/or background 
•	Strong documented experience in analyzing patient and preferable high throughput data. 
•	Strong background in computer hard- and software systems 
•	Proficiency in programming languages such as Java, Perl or Python, as well as Linux systems.
•	Experience in liaising between computational and molecular biologists as well as clinicians
•	Fluency in spoken and written English is a strong requirement

Contact details. 
Please contact Lodewyk Wessels, tel. +31 20 512 7987 or e-mail: l.wessels at nki.nl. When applying, please ensure you include a CV, list of publications and the names and addresses of at least two persons that can be approached as references. Also see bioinformatics.nki.nl for further information.

Closing date: 1 October 2013