Bioinformatician in Multimodal Data Analysis of Organoids (f/m/d)

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The mission of the Berlin Institute of Health (BIH) is medical translation: transferring biomedical research findings into novel approaches to personalized prediction, prevention, diagnostics and therapy and, conversely, using clinical observations to develop new research ideas. The aim is to deliver relevant medical benefits to patients and the population at large. The BIH is also committed to establishing a comprehensive translational ecosystem as translational research area at Charité – one that places emphasis on a system-wide understanding of health and disease and that promotes change in the biomedical research culture. The BIH is funded 90 percent by the Federal Ministry of Education and Research (BMBF) and 10 percent by the State of Berlin. The two founding institutions, Charité – Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), were independent member entities within the BIH until 2020. As of 2021, the BIH has been integrated into Charité as the so-called third pillar; the MDC is privileged partner of the BIH.
The Stem Cell Core Facility and the Core Unit Bioinformatics (CUBI) of the BIH are looking for a 
Bioinformatician in Multimodal Data Analysis of Organoids (f/m/d)

to work in the field of analysis of 2D and 3D cellular models of liver, heart and brain derived from human pluripotent stem cells (hPSC). We are looking for a highly motivated dedicated candidate to work in the field of analysis of 2D and 3D cellular models of liver, heart and brain. The candidate will work for a central technology provision project in the Collaborative Research Centre/Transregio 296 LocoTact funded by the DFG. The LocoTact CRC-TR aims to dissect the local control of thyroid hormone action in physiology and pathophysiology ( The interdisciplinary research consortium will take advantage of sophisticated in vitro tools such as 3D organoids derived from hPSC to facilitate the studies on the local control of thyroid hormone action in translationally relevant human model systems. The candidate will be expected set up state-of-the-art methods for analysis of 3D organoids (single cell RNA sequencing, 3D high content imaging).

Job description:

  • Analyze project needs and translate biomedical questions into bioinformatics projects,
  • Design, implement and deploy data analysis workflows,
  • Select and benchmark methods and tools, define and perform appropriate QC measures,
  • Develop innovative analysis approaches when standard methods are not adequate,
  • Contribute to automation of processing and results reporting,
  • Interpret and present analysis results to coworkers and collaborators.
  • participation in the training and supervision of new colleagues (e.g. doctoral students) in addition to the scientific work.
Depending on the employment relationship, sufficient time is given for one’s own academic work.


  • PhD in bioinformatics or comparable skills,
  • In depth understanding of computational methods for NGS analysis and the usage of public data resources,
  • Experience with single cell data analysis is a plus, good understanding of NGS wet-lab protocols is a plus,
  • Sound experience im multi-modal data integration and statistical data analysis is a strong plus,
  • Experience in multidimensional microscopy and (automated) data analysis is a strong plus,
  • Demonstrated ability to work with and troubleshoot academic open source software packages,
  • Excellent programming skills in R and Python or similar, good git knowledge needed,
  • Demonstrate ability to create reproducible and reusable analysis workflows,
  • Sound experience with HPC environments, pipelines and large scale data management,
  • Ability to work in a highly interdisciplinary environment both independently and as part of the team is essential
  • Excellent communication skills in written and spoken English

We offer:

  • A collaborative research environment that encourages and supports scientific curiosity, innovation, and development of its team members,
  • Remuneration according to E13 TVöD VKA-K: The grouping takes into consideration the qualifications and the personal circumstances of the candidate,
  • A full-time position (39h/week),
  • Appointment duration: until 30.06.2024,
  • Family - friendly, flexible working hours

We live diversity!

BIH strongly encourages qualified women to apply. Severely disabled applicants and those with equal status will be given preferential consideration in cases of equal suitability.
Please submit your application via the BIH Career portal by 05.12.2021, quoting the reference number BIH-99.21. We are looking forward to hear from you!
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