Position: Bioinformatician for Spatial and Single Cell Genomics

Department: Artificial Intelligence in Oncology

Code number: 2021-0035

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.

In the newly established lab of Dr. Moritz Gerstung (Division of Artificial Intelligence in Oncology), which works at the interface of AI and cancer evolution together with the Omics IT and Data Management Core Facility (ODCF),  is a joint position as postdoc / bioinformatician for spatial and single-cell genomics analyses available.


Job description:

We are looking for a (senior) bioinformatician to guide our efforts in spatial and single cell genomics analyses of tumour samples. These involve handling and analysis of hundreds to thousands of 10-30Gb microscopy images as well as associated sequencing data and also clinical metadata. You will also be responsible for creating and running analysis workflows on these raw data sets to extract molecular information about the molecular nature and spatial composition of tumour samples.

In particular your tasks will be:

  • Establishment of a data management systems for large imaging data sets such as OMERO
  • Creation and running of analysis workflows for image based spatial transcriptomics based on existing algorithms, involving image registration, fluorescent feature extraction and decoding of molecular barcodes.
  • Data management and analysis of single cell sequencing data
  • Running and trouble shooting of analysis workflows and reporting results and QC metrics

The fellow will be jointly affiliated with the Gerstung Lab and the Omics IT and Data Management Core Facility and collaborate with clinical partners at DKFZ and elsewhere.



You will hold at least a master’s degree in computer science, statistics, mathematics, physics, and/or engineering, or a degree in biological science with demonstrated experience in computational biology / bioinformatics.

Previous experience in developing and applying computational methods applied to large datasets is expected. We especially seek candidates with prior experience in the analysis and management of microscopy imaging and/or NGS data.

Proficiency with relevant scripting languages, and statistical data analysis tools such as Python (or equivalent) as well as workflow scripting languages (e.g. CWL or Nextflow) and container technologies such as docker or singularity is required.

The ideal applicant should have demonstrated the ability to work independently and creatively. You should have excellent communications skills and be able to articulate clearly the scientific and technical needs, set clear goals and work within an interdisciplinary setting, communicating with other partners.

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
  • Access to the DKFZ  International Postdoc Program

Earliest possible start date: as soon as possible

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

The position can in principle be part-time.

Application deadline: 06.03.2021


Silvia Fuchs
Phone +49 (0)6221/42-2747

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.