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Computational scientist at postdoc level

Would you like to work in a highly dynamic environment between the interphase of fundamental science and applied human clinical genetics, directly benefiting patients?
  • Closing date 17-10-2022
  • 38.06.22.TS
  • 36 hours
  • PhD
  • Research & Education
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Questions? Contact our recruiter

  • Closing date 17-10-2022
  • 38.06.22.TS

Job description

Are you interested in the non-coding genome and how alterations of it can cause human disease? Are you interested in neurodevelopment and brain diseases such as epileptic encephalopathies? Would you like to work in a highly dynamic environment between the interphase of fundamental science and applied human clinical genetics, directly benefiting patients? And all of that in a fun, young and international team at a top university? Then join our expanding research team as a computational postdoc!

The current position is funded by a ZonMw Vidi project, which aims to solve missing heritability in epileptic encephalopathies. These are severely devastating disorders that present with intractable epileptic seizures at early age, severely affecting brain development of affected individuals and thereby imposing a large burden on patients, their families and the health care system. Many epileptic encephalopathies are caused by mutations in a large number of coding genes, but still around 50% of patients cannot be genetically diagnosed despite the high suspicion that it must be a genetic disorder. We hypothesis that some of this “missing heritability” is caused by genetic alterations in the non-coding genome, which contains important gene regulatory elements, such as enhancers. Our previous work, using computational analysis and massively parallel reporter assays has resulted in an atlas of such regulatory elements, of which we find many to regulate medically relevant human genes. In this project, we will explore how mutations in these regulatory elements might cause epileptic encephalopathy and other neurodevelopmental disorders. For this we will use analysis of patient whole genome sequencing data (both from our local patient cohort, our large network of international collaborators as well as from the Genomics England 100,000 Genomes Project), patient derived RNA-seq data, and data obtained in the wet-lab including massively parallel reporter assays, single cell analysis and chromatin conformation capture analysis in various cell models including brain organoids and zebrafish, combined with computational approaches including machine learning. Tight interplay with the wet-lab will allow functional validation of the various obtained findings, and close links to clinic and diagnostics will ensure immediate translation of findings to improve patient care. 

Work environment

You will be part of a highly international working environment in an inspiring, dynamic and productive team at the Barakat lab at the Clinical Genetics department of Erasmus MC, with access to a broad range of high-throughput next generation sequencing data, both from wet lab experiments as well as patient samples (https://www.erasmusmc.nl/en/research/groups/barakat-lab-non-coding-genome-in-clinical-genetics).

The Barakat lab was established in 2017 at Erasmus MC, and focusses on deciphering molecular mechanisms leading to neurodevelopmental disorders, with a particular interest in the role of the non-coding genome. Using functional-genomics and computational approaches we aim to understand the gene-regulatory-landscape in cells representing neurodevelopment. Our long-term goal is to translate our research findings to the clinic, where we aim to develop novel diagnostics and therapies focusing on the so far, so often, neglected non-coding regions of the human genome. Next to our interest in fundamental gene-regulation, we apply disease-modelling for neurodevelopmental disorders using genome-engineering, induced pluripotent stem-cells, brain-organoids, and zebrafish. Our group, currently consisting of 10 members, is strongly embedded in the department, and forms an important bridge between research and clinic, ultimately leading to advancements for patients. Since 2017, we have published 33 papers (majority in top-10 journals) describing new disease entities and mechanisms, have obtained > 3 million euro funding (including competitive grants from CURE Epilepsy, EpilepsieNL, ZonMw Veni, ZonMw Vidi) and have been awarded a number of prizes, including an KNAW Early Career Award 2021.

Full publication record of the PI (incl. previous publications in Cell, Nature and Cell Stem Cell) can be found here:
https://orcid.org/0000-0003-1231-1562    https://pubmed.ncbi.nlm.nih.gov/?term=tahsin%20stefan%20barakat&sort=date&page=3     

Qualifications and skills

  • You are a highly motivated, creative and actively participating, hardworking team player with strong problem solving skills and broad interests.
  • You have successfully obtained a PhD (or will shortly graduate), in the field of Medicine, Health Science, Life Science, Neuro Science, Biology, Bioinformatics or related field, in which you have applied computational analysis of multiple types of next generation sequencing data, including whole genome sequencing, RNA-seq and ChIP-seq.
  • Next to computational skills, you have a solid understanding of (molecular) biology and affinity to the field of human genetics.
  • Prior skills in machine learning, analysis of massively parallel reporter assay analysis or analysis of clinical human genetics data would be a strong pre. 
  • You have an excellent early career track-record (as testified for example by obtained prizes, scholar- and fellowships, (internship) experience abroad etc.) and have at least published two first-author publications in peer-reviewed, international journals.
  • You are highly communicative with outstanding verbal and written English language skills (minimal IELTS 7.0, TOEFL 100 or equivalent) and you are willing to share your knowledge with other group members.
  • You are preferably available from January 2023 onwards.

Before you apply please check our conditions for employment.

Terms of employment

  • Postdoc position (1.0 fte) for 32 months funded by a ZonMw Vidi project, with options to further extend this position based on ongoing funding applications.
  • The gross monthly salary amounts a maximum of € 4.800,- (scale 10), depending on your level of education and relevant experience, based on a full-time working week of 36 hours.
  • Excellent fringe benefits, such as a 13th month that is already paid out in November and an individual travel expense package.
  • Pension insurance with ABP, we take care of approximately 2/3 of the monthly contribution.
  • Special benefits, such as an incompany physiotherapist and bicycle repairer. There is also a gym where you can work on your fitness after work.

More information

For more information about this position, please mail Dr. Stefan Barakat, Principal Investigator t.barakat@erasmusmc.nl 

In case of other requirements to apply:
Your application should include: motivation letter, Curriculum Vitae, list of courses and obtained grades during BSc, MSc and PhD program, a publication list, and a minimum of two reference letters.

If you are excited by the thought of this position and would like to apply, please do so by using the application form on our website.

No agencies please.

Application proces

Step 1 - Apply

Did we get you excited about this position? Submit your application through the application button. You will receive a confirmation of receipt from our recruiter right away.

Step 2 - Selection

Based on your application, we check to see if there is a fit between us. We will let you know as soon as possible whether you are invited for an interview.

Step 3 - Interview

You have been invited for an interview, great! In this first meeting we get to know each other and see if You can form an idea of the position, the department and Erasmus MC. If the interview goes well usually a second interview follows.

Step 4 - Offer and terms

It’s a match! Your future manager will discuss your salary and employment with you. You will also receive more information about our other terms of employment.

Step 5 - Getting started

Your first working day has come! We are more than happy to have you. Your new department will give you a warm welcome and provide you with all the information you need. Enjoy your job at Erasmus MC!

Contact me

Alexandra Goud
Recruiter

Alexandra Goud
Erasmus MC

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