PhD Student / bioinformatics: Non-Coding DNA in genetics of neurodevelopmental disorders

Project “Non-Coding DNA in genetics of neurodevelopmental disorders”

Job description                       
Many genetic disorders are still incompletely understood, and there might be a large role for genetic alterations in non-coding DNA elements, such as enhancers, in the pathogenesis of these disorders. My lab focusses on the role of alterations in these elements in neurodevelopmental disorders, such as malformations of cortical brain development. The PhD candidate will analyze data from the latest state-of-the-art techniques produced in our lab including next generation sequencing, massively parallel reporter assays (https://doi.org/10.1101/146696), RNA-seq and ChIP-seq in cell culture models and patient materials, to decipher the functional parts of the non-coding genome involved in brain development. The identified functional elements will be tested for alterations in a large, existing cohort of patients with structural neurodevelopmental disorders. Using patient specific induced pluripotent stem (iPS) cells and in vitro 3D/organoid culture systems, these identified alterations will be further functionally characterized.

Work environment
A healthy population and excellence in healthcare through research and education. This is what Erasmus MC stands for, in Rotterdam, The Netherlands. Conducting groundbreaking work, pushing boundaries and leading the way. In research, education, and healthcare. We are practical people with a high level of expertise, working hard to improve and renew the healthcare of today and the public health of tomorrow. The project will take place in the Department of Clinical Genetics, in the laboratory of Dr. Stefan Barakat. The focus of our group is to unravel the role of alterations in the non-coding DNA in the pathogenesis of genetic disorders. There is a strong interdisciplinary link between research, diagnostics and patient care, and in particular for this project, the candidate is expected to closely work together with wet-lab biologist, different collaborators and our diagnostics department. Research in our group is supported by grants from NWO/ZonMW, the Brain and Behaviour Research foundation and the Erasmus MC.

Qualifications and skills  
We are looking for a highly motivated candidate with a MSc Degree in Bioinformatics or a related computational field. You are interested in Genetics, and brain disorders in particular. You are a creative and actively participating team player with strong problem solving skills and broad interests. Your English language skills are excellent. You have prior experience with next generation sequencing data analysis and are interested in developing novel approaches to decipher the role of the non-coding DNA, including but not limited to the application of massively-parallel-reporter systems and data mining. Any additional wet-lab experience and previous publications would be highly appreciated.

Terms of employment     
We offer an employment for a period of 4 years, fulltime, 36 hours a week. The gross monthly salary, depending on previous education and expertise equals a maximum of € 2.874,- (scale OIO). The conditions of employment are in accordance with the Collective Bargaining Agreement for University Medical Centers (CAO UMC).

Information
For more information about this position, please contact Stefan Barakat, M.D., Ph.D., Principal Investigator, by e-mail: stefanbarakat@gmail.com. Review of candidates will occur till the position is filled. More information can be found at https://www.erasmusmc.nl/klinische_genetica/research/introduction/stefan-barakat/

Application
Please send your application directly by e-mail to: stefanbarakat@gmail.com. Your application should include: motivation letter, Curriculum Vitae, list of courses and obtained grades during BSc and MSc, any written publications (e.g. MSc thesis), and a minimum of two reference letters.