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Bioinformatics Jobs Germany | PhD Position @ DKFZ

Bioinformatics Jobs Germany | PhD Position @ DKFZ

Bioinformatics Jobs Germany | PhD Position @ DKFZ: The German Cancer Research Center (DKFZ) in Heidelberg is Germany’s largest biomedical research institute. As part of the Helmholtz Association, the largest research organization in Germany, the DKFZ has an international and dynamic work environment, providing scientists with access to state-of-the-art research facilities and exceptional resources.

More than 2,800 employees in over 90 divisions and research groups carry out research to unravel the causes and mechanisms of cancer development and to identify novel tools for diagnosis, treatment and prevention. With Harald zur Hausen (2008) and Stefan Hell (2014), two researchers of the DKFZ have been awarded the Nobel Prize.

Bioinformatics Jobs Germany | PhD Position @ DKFZ

Department: Pediatric Neurooncology

Designation: PhD Student

Code: 132/2016

Your tasks: The division “Pediatric Neurooncology” (Head: Prof. Stefan Pfister) at the German Cancer research Center (DKFZ) in Heidelberg studies pediatric brain tumors using high-throughput genomic and epigenomic profiling with the aim to translate molecular findings into clinical practice. This is desperately needed from a clinical perspective, since brain tumors have become the number one cause of cancer related mortality of children. Over the years our division has generated a large amount of high-throughput genomic data of several pediatric brain tumors. Tumors have been analyzed by whole genome DNA and RNA sequencing, DNA methylation, and gene expression profiling. This has led to the identification of multiple molecular subtypes that are not only biologically but also clinically very different. Identification of these molecular subtypes may lead to new treatment strategies, but for that we have to understand better the genes, pathways and processes that are dysregulated in these tumors and how they can be targeted.

In this project we want to investigate whether alternative splicing of mRNA plays a role in the tumorigenesis of ependymomas. The clinical behavior of these tumors is highly variable and approximately 40% of patients are incurable owing to the paucity of effective treatment options available. Recently, we have used DNA methylation to classify ependymal tumors and have identified nine distinct molecular subgroups (Pajtler et al., Cancer Cell 2015). Notably, the vast majority of high-risk patients (mostly children), for whom novel therapeutic concepts are desperately needed, were restricted to just two of the identified molecular subgroups, indicating the clinical relevance of this molecular classification. However, recurrent genetic aberrations have only been identified in three of the subgroups, suggesting that epigenetic or structural alterations or other alternative mechanisms like alternative splicing of mRNA drive the disease in other subgroups.

Existing and new to generate RNA-seq data of ependymal tumors will be analyzed for alternative splicing events of mRNAs and identification of under- or overexpressed splicing factors. In addition, epigenetic factors that could influence splicing will be evaluated using whole genome DNA methylation data and ChIP-seq data for various histone marks. Tumor cell lines will be used to validate any potential downstream effects of identified splicing and epigenetic factors.

The project will be a close collaboration between the Pediatric Neurooncology Division (Marcel Kool) and the Bioinformatics Group in the Core Facility Genomics and Proteomics (Agnes Hotz-Wagenblatt) at the DKFZ. It is part of a DKFZ-Israel-Project which involves the collaboration with the group of Gil Ast in Tel Aviv, who have developed specific algorithms to perform regulatory splicing network analyses. Joined project meetings will take place every year in March either in Heidelberg or in Israel.

Further information can be found on our website: www.pediatric-neurooncology.com.

Bioinformatics Jobs Germany | PhD Position @ DKFZ

Your profile:

The successful candidate is a highly motivated, ambitious, hard-working individual with excellent grades who enjoys working in an international team and is passionate about making a difference through cancer research. Applicants should hold a university degree in bioinformatics, biology, biochemistry, biotechnology, or a related field. The ideal candidate has expertise in bioinformatic analyses of genomic data, R and/or Perl programming, a strong interest in cancer biology, is highly self-motivated, and able to pursue research projects independently. Excellent communication skills and proficiency in English are mandatory. Applications should include a CV, cover letter, certificates, expected availability date, and 2-3 references.

We offer:

  • Interesting, varied position
  • International environment
  • Compensation to TV-L
  • Opportunities for part-time work
  • Flexible working hours
  • Good education and training

Starts: as soon as possible

Expiration: The position is limited for 3 years.

Application deadline: June 27, 2016

Further information: Dr. Marcel Kool

phone 06221 42-4636

Apply Online

Bioinformatics Jobs Germany | PhD Position @ DKFZ

View original notification: http://www.dkfz.de/en/stellenangebote/index.php?id=132/2016

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