Position: Data Scientist in 3D Imaging of High-Content Screening Experiments

Department: Signaling and Functional Genomics

Code number: 2022-0267

The German Cancer Research Center is the largest biomedical research institution in Germany. With more than 3,000 employees, we operate an extensive scientific program in the field of cancer research.

The Division "Signaling and Functional Genomics", headed by Prof. Dr. Michael Boutros at the German Cancer Research Center (DKFZ) in Heidelberg, is studying oncogenic signaling pathways and develops high-throughput functional genomic approaches for target discovery. We are seeking a highly motivated data scientist to join an EIC transition project team (European Innovation Council, https://eic.ec.europa.eu). The EIC is Europe’s flagship innovation programme to identify, develop and scale up breakthrough technologies. In the EIC project we are developing and validating a new drug discovery platform based on patient-derived organoids (PDOs) and machine learning-assisted phenotypic target validation. The project will target critical, cell-specific vulnerabilities in cancer and is based on technologies and approaches developed previously during an ERC project in our group. The EIC project is a close collaboration with Prof. Dr. Matthias Ebert (Director, II. Medical Clinic, University Hospital Mannheim and Heidelberg University). Initially, this platform will be used to identify therapeutics to target stem cell signaling pathways in colorectal cancer (see also Betge et al., 2022, https://www.nature.com/articles/s41467-022-30722-9). The platform technology as well as validated targets will serve as basis for a new spin-off company to be founded during the course of the project.

Job description:

As part of the project, you will optimize the analysis pipeline performance towards 3D imaging. You will establish a software that registers all images, insert resulting phenotypic profiles into a database as aggregated and single-cell profiles. Reports will be generated as interactive web pages and communicated to the other scientists in the team. You will set up a microscopy image segmentation pipeline which will be optimized for the analysis of large-scale 3D image recordings. The analysis pipeline will be deployed to a cloud domain and a web-suite for orchestration will be implemented. Resulting profiles will be analyzed and reports including visualizations will be generated.


We are looking for a highly motivated, entrepreneur-spirited scientist with a strong background in 3D image analysis, high-performance computing, database software, statistics, and machine learning tools. Knowledge of cloud computing and software engineering is of advantage. Candidates should have an advanced academic degree (Master's and Ph.D.) in bioinformatics or a related field and have published previously in peer-reviewed journals. You should be able to work independently and also have excellent team working skills. Curiosity and ability to work in interdisciplinary projects is expected. The position further requires organizational qualifications and the ability to communicate effectively with internal and external collaborators. An excellent written and oral command of English is essential.

The application shall include a CV, a letter of motivation, degree certificates and names and contact information of at least two references.

We offer:

  • Interesting, versatile workplace
  • International, attractive working environment
  • Campus with modern state-of-the-art infrastructure
  • Salary according to TV-L including social benefits
  • Possibility to work part-time
  • Flexible working hours
  • Comprehensive further training program

Important notice:

The DKFZ is subject to the regulations of the Infection Protection Act (IfSG). As a consequence, only persons who present proof of immunity against measles as well as against COVID-19 may work at the DKFZ.

Earliest Possible Start Date: 01.11.2022

Duration: The position is initially limited to 2 years with the possibility of prolongation.

The position can in principle be part-time.

Application Deadline: 07.09.2022


Prof. Dr. Michael Boutros
Phone +49 (0)6221/42-1950

Please note that we do not accept applications submitted via email.

The DKFZ is committed to increase the proportion of women in all areas and positions in which women are underrepresented. Qualified female applicants are therefore particularly encouraged to apply.

Among candidates of equal aptitude and qualifications, a person with disabilities will be given preference.

To apply for a position please use our online application portal (https://www.dkfz.de/en/stellenangebote/index.php).

We ask for your understanding that we cannot return application documents that are sent to us by post (Deutsches Krebsforschungszentrum, Personalabteilung, Im Neuenheimer Feld 280, 69120 Heidelberg) and that we do not accept applications submitted via email. We apologize for any inconvenience this may cause.