Website University of Basel
Last date to apply: 31.01.2026
Number of Positions: 01
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 (PacBio) 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 (SciCore+), 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://www.unibas.ch/en/Research/Values-Ethics/Diversity-and-Inclusion.html), 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
■ You will have access to state-of-the-art research equipment in RNA sequencing, cell biology, computational resources, and microscopy.
■ You will work in a dynamic and highly interdisciplinary team including computer scientists, experimentalists and clinicians.
■ You will be involved in cross-disciplinary collaborations and have training opportunities to further develop and grow your scientific interests.
■ Access to a large consortium of experts in different disciplines, such as cancer research, cell biology, computational biology, gynaecological oncology, and immunology.
■ Opportunity to work in close contact with other basic- and clinical-research groups at the Department of Biomedicine and the Biozentrum in Basel.
■ Support from highly competent, experienced team members and potential to lead projects with a high degree of academic freedom.