The German Cancer Research Center (DKFZ) is one of Europe’s largest cancer research centers. “Research for a life without cancer" is the mission of our world-class scientists and all our team members.
We investigate how cancer develops, identify cancer risk factors and search for new cancer prevention strategies. We develop new methods with which tumors can be diagnosed more precisely and cancer patients can be treated more successfully. Every contribution counts – whether in research, administration or infrastructure. This is what makes our daily work so meaningful and exciting.
The Division of Computational Genomics and Systems Genetics develops and applies computational approaches to study molecular variations and their phenotypic consequences.
To strengthen our team, we are seeking for the next possible date a
Software Developer - Interoperability for Single-Cell and Spatial Omics Methods
Reference number: 2025-0331
The research group of Prof. Dr. is seeking a software developer to advance interoperability for single-cell and spatial omics across the (Python) and (R) ecosystems. The project focuses on enhancing the FAIR capabilities of, a modern Python framework for spatial omics, across platforms, and on strengthening its language-agnostic file format based on the open standard. You will help ensure seamless cross-language usage, robust data exchange, and clear specifications that serve both communities.
You will be part of a vibrant open-source environment at the interface of software development and biomedical research - specifically within the global scverse community. You will have the opportunity to shape widely used, FAIR-by-design tools that accelerate single-cell and spatial omics research across both Python and R ecosystems. We also offer substantial opportunities for professional growth, learning, and leadership, including mentorship, structured code reviews, participation in conferences and hackathons, and visibility through community calls and cross-consortium initiatives. Recent community events include the Scverse Hackathon in Paris (2025) and the NGFF Hackathon in Zurich (2025); previous hackathons have taken place in Boston, Cambridge, Heidelberg, Innsbruck, and Munich.
The Stegle group is jointly based at DKFZ and EMBL and embedded in Heidelberg’s vibrant ecosystem for data science, machine learning, and computational biology. We collaborate closely with research groups across Germany and worldwide, and we actively engage with open-source communities through coordinated development, cross-consortium events, and hackathons.
Your Tasks
* Expand the bridge between the scverse and R/Bioconductor ecosystems through interoperable software development focused on the OME-Zarr file format and the SpatialData framework
* Build and automate an infrastructure to ensure continued interoperability of SpatialData across R/Python, including robust converters, I/O layers, and validation tests
* Improve the documentation of the SpatialData format with clear tutorials, examples, and contributor guides that lower the barrier to entry
* Contribute to the NGFF specification and help support the incoming versions, in particular and, via updates to the SpatialData codebase, but also by contributing to the NGFF codebase
* Engage with the open-source scverse and NGFF communities: triage issues; review PRs; collaborate in public forums and with the possibility to participate in cross-consortium events, sprints, and hackathons
Your Profile
Required Qualifications:
* An M.Sc. or equivalent in computer science, statistics, mathematics, physics, engineering, or a biological science with demonstrated experience in statistics and software development
* Software development skills in Python and familiarity with the data science and geospatial Python stack (e.g., xarray, dask; GeoPandas/Shapely a plus)
* Open-source development practices: Git/GitHub, code review, testing (e.g., pytest), packaging, CI/CD (e.g., GitHub Actions), and documentation (e.g., Sphinx)
* Excellent collaboration and communication skills; motivation to contribute to a scientific, community-driven project as a supportive, creative, and responsible team member
Preferred Qualifications:
* Experience with R/Bioconductor, AnnData/SummarizedExperiment, Zarr/NGFF, or designing cross-language APIs and data schemas
* Research experience implementing statistical learning or machine learning (e.g., Bayesian inference, deep learning), ideally connected to spatial omics, and experience with frameworks like PyTorch, Keras, Pyro, or TensorFlow
Application process:
* Interested candidates should submit a cover letter, a CV, and the contact details of 2 referees via our online application tool. Please elaborate in your cover letter on your (open-source) software development experience, or willingness to contribute. Ideally, please provide links to Git repositories where you made significant contributions.
* We will conduct two rounds of interviews. In the first round, taking place online, you will be asked to bring and comment on a code sample/project of your choice that you previously wrote, for approximately 15-30 minutes. You can also choose to bring a newly written short code sample (100-500 lines of code). The rest of the interview will follow with general and technical questions related to the job description.
* In the second round, we will ask you to perform a spoken code review on a short sample code that we will prepare, and you will also meet the team (either online or in person).
* You are encouraged to ask questions, whether technical or related to team culture, at any stage of the interview process.
* Applications will be reviewed on a rolling basis, so you are encouraged to apply before the deadline.
If you’re excited about building interoperable, well-documented, and community-aligned software that advances spatial omics, we’d love to hear from you.
Recent relevant publications:
* Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and universal data framework for spatial omics. Nat Methods 22, 58–62 (2025).
* Crowell, H. L., Dong Y., Billato I. et al. Orchestrating Spatial Transcriptomics Analysis with Bioconductor. bioRxiv 2025.11.20.688607; doi:
* Moore, J., Basurto-Lozada, D., Besson, S. et al. OME-Zarr: a cloud-optimized bioimaging file format with international community support. Histochem Cell Biol 160, 223–251 (2023).
* Virshup, I., Bredikhin, D., Heumos, L. et al. The scverse project provides a computational ecosystem for single-cell omics data analysis. Nat Biotechnol 41, 604–606 (2023).
We Offer
* Excellent framework conditions: state-of-the-art equipment and opportunities for international networking at the highest level
* 30 days of vacation per year
* Flexible working hours
* Remuneration according to TV-L incl. occupational pension plan and capital-forming payments
* Possibility of mobile work and part-time work
* Family-friendly working environment
* Sustainable travel to work: subsidized Germany job ticket
* Unleash your full potential: targeted offers for your personal development promote your talents
* Our Corporate Health Management Program offers a holistic approach to your well-being
Contact:
Prof. Dr. Oliver Stegle
Phone:
The position is limited until 31.12.2026.
Application Deadline: 13.01.2026
Applications by e-mail cannot be accepted.
Are you interested?
Then become part of the DKFZ and join us in contributing to a life without cancer!
We are convinced that an innovative research and working environment thrives on the diversity of its employees. Therefore, we welcome applications from talented people, regardless of gender, cultural background, nationality, ethnicity, sexual identity, physical ability, religion and age. People with severe disabilities are given preference if they have the same aptitude.
Notice: We are subject to the regulations of the Infection Protection Act (IfSG). Therefore, all our employees must provide proof of immunity against measles.
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Deutsches Krebsforschungszentrum | Im Neuenheimer Feld 280 | 69120 Heidelberg |
Company
About the German Cancer Research Center (DKFZ)
The German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ) is Germany’s largest biomedical research institute and a member of the Helmholtz Association of German Research Centers. Over 3,200 staff members from 88 nations are dedicated to performing and driving cutting edge research for a life without cancer. Organized in more than 100 divisions and research groups, the focus of our 1,400 scientists is to unravel the causes and mechanisms of cancer development and progression, and to develop novel strategies for the diagnosis, early detection, prevention and treatment of cancer though innovative translational research.
Scientists at the DKFZ have received the most prestigious academic awards, including Prof. Harald zur Hausen, awarded the Nobel Prize in Physiology or Medicine in 2008 for his pioneering work on Human Papilloma Viruses (HPV),and Prof. Stefan Hell, who received the Nobel Prize in Chemistry for his research on super-resolution imaging.
The DKFZ core site is located in Heidelberg, the “ City of Science ”, which is considered one of the most beautiful cities in Germany with a highly international community: An estimated 56,000 of Heidelberg’s 160,000 inhabitants have an international background – many of whom are scientists or students.
Research Topics and Scientific Collaborations
The DKFZ is an international leader in a number of research areas including stem cell research, bioinformatics and systems biology, cancer genomics, neurooncology, pediatric oncology, cancer prevention, tumor immunology, virology, radiooncology and medical image analysis. The interdisciplinary and collaborative research environment at the DKFZ also results in excellent opportunities for computational and data scientists with interest in biomedical applications.
Research at the DKFZ is organized into six research programs :
On the mission for a life without cancer, the DKFZ collaborates with renowned clinical and research institutions at the local, national and international level. A key goal is to continuously strengthen translational research activities with the aim of sustainably advancing state-of-the-art clinical cancer research in Germany and thereby improving the treatment outcomes and quality of life of cancer patients. Together with University Hospital partners across Germany, the DKFZ established the National Centers for Tumor Diseases (NCT) as leading Comprehensive Cancer Centers in Germany, as well as the Hopp Childrens’ Tumor Center (KiTZ) in Heidelberg with a specific focus on pediatric oncology. Within the German Cancer Consortium for Translational Cancer Research (DKTK), research institutions and university hospitals at eight partner locations collaborate with the DKFZ, the core center of the DKTK, to speed up the transfer of successful cancer research into clinical practice. Furthermore, the HI-TRON in Mainz is a cooperative effort to make full use of the potential of individualized immunotherapy.
Training Programs and Career Development
Talent management and career development are central parts of DKFZ’s mission to maintain scientific excellence. The DKFZ places strong emphasis on the international recruitment and comprehensive training of excellent scientists, specifically welcoming diverse and international backgrounds.
Dedicated programs train young scientists and clinicians and prepare them for their next career step:
The DKFZ has developed programs to support the reconciliation of family and careers at all levels and international employees are supported by the International Staff Services in the planning, preparation and realization of their stay in Heidelberg.
Innovation Management
The DKFZ builds on strong Innovation Management to foster the development of innovative preventive, diagnostic and therapeutic products for maximum societal benefit. It facilitates technology transfer through licensing and support of spin-off companies. Recent examples include iOmx Therapeutics, Apogenix and mtm laboratories. The DKFZ also has strong collaborations with industry partners, such as Bayer Healthcare, Bosch, SAP and Siemens .
Company info
Telephone
+49 (0) 6221 420
Location
Im Neuenheimer Feld 280
Heidelberg
Baden-Württemberg
D-69120
Germany