PhD position in Cancer Research; Heinzelmann​/Jacob Lab

The Department of Biomedicine is a joint effort between the University of Basel and the University Hospitals Basel. It unites basic and clinical scientists to advance our understanding of health and disease and to develop pioneering therapies benefiting the lives of patients in areas of unmet need. With more than 70 research groups and 800 employees, the Department of Biomedicine is the largest department at the University.

We are located in the heart of Basel at 6 different locations. Be part of our future! The Ovarian Cancer Research (OCR) Group, led by Viola Heinzelmann-Schwarz and Francis Jacob, offers a PhD position focused on high-throughput single-cell analysis, computational biology, and ex vivo models to study ovarian cancer. The project aims to dissect transcriptional programs in the tumor microenvironment associated with homologous recombination deficiency, with a strong emphasis on isoform-resolved, long-read single-cell transcriptomics.

Your position

The successful candidate will have the opportunity to leverage cutting‑edge long‑read single‑cell RNA sequencing technologies (Pac Bio) and apply computational methods to explore full‑length transcriptomes from human cancer tissue samples. The project will involve the statistical analysis of large‑scale, high‑throughput datasets and offers strong opportunities to further develop computational and analytical expertise.

Relevant resources include access to the Basel Ovarian Biobank, state‑of‑the‑art sequencing platforms, high‑performance scientific computing (Sci Core+), multiplex immunofluorescence, and an ex vivo drug‑response platform (DRUGSENS). The project is embedded in a strong collaborative environment, with close interaction with international project partners, partners from the Swiss Tumor Profiler consortium, DBM Bioinformatics and IT, and the DBM Microscopy Facility.

The candidate should have a strong background in computational analysis and a keen interest in long‑read sequencing technologies. Excellent teamwork and communication skills in English are required. The PhD candidate will be expected to take an active role in shaping and leading the project, supported by senior lab members and close collaboration partners, within an environment that encourages academic freedom and scientific independence.

In line with the values of the University of Basel (https://(Use the "Apply for this Job" box below).), we are committed to fostering an inclusive and diverse working environment that promotes equal opportunities and mutual respect. We are seeking a highly motivated PhD candidate eager to develop innovative strategies to gain novel insights into single‑cell transcriptomes within the tumor microenvironment.

Your main tasks will be:

• Conducting wet‑lab (30%) and dry‑lab (70%) research activities
• Performing tissue processing, including quality control, for library preparation and single‑cell RNA sequencing
• Applying and further developing computational tools to analyze and visualize long‑read sequencing data
• Performing and analyzing ex‑vivo culture experiments to test and validate cell‑type–specific isoforms
• Contributing to the co‑supervision of Bachelor's and Master's student projects
• Willingness to undertake research visits abroad within this collaborative project (computational analysis and spatial proteomics for immune cell subtyping and isoform localization)
• Supporting the preparation of grant proposals, scientific reports, and peer‑reviewed publications

Your profile

• Highly motivated candidate driven by scientific curiosity and a strong commitment to addressing biologically and clinically relevant research questions.
• Master's degree in Bioinformatics/Computational Biology, (Bio)
  Physics, Biological Sciences, Systems Biology, Molecular Biology, or a related field.
• Experience in wet‑lab work, including cell culture work.
• Experience in statistical approaches for the analysis of datasets.
• Strong motivation to work in an international research environment.
• Strong experience with programming languages (e.g. R or Python).
• Excellent communication skills and scientific curiosity.
• Plus:
  Experience with analysis of single‑cell technologies.

We offer you

…

Application / Contact

Please send your application to francis.jacob and submit the following documents:

A) a cover letter,

B) a complete curriculum vitae,

C) the PhD application form, and

D) references from at least two referees.