PhD position in systems biology

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 Zampieri group offers a PhD research opportunity in the context of systems pharmacology, computational biology and metabolic regulation. The mission of the group is to understand fundamental mechanisms regulating short- and long-term metabolic adaptation to genetic and chemical perturbations to find new and unconventional therapeutic strategies, ranging from antibacterial to anti-cancer drugs. To this end, we develop new ways to combine state-of-the-art technologies in metabolomics with mathematical modeling.

The candidate will have the opportunity to exploit some of the cutting-edge experimental and computational methods, comprising constraint-based and kinetic modeling, statistical analysis of large datasets, high-throughput metabolomics, time-lapse microscopy, to investigate how to pharmacologically interfere with fundamental mechanisms in the regulation of cancer metabolism. Available resources at the department include a mouse facility, high-end FACS, IT and microscopy facilities, the Life Sciences Training Facility (for gene expression and proteome profiling) and much more.

The candidate is expected to have a strong background and interest in quantitative disciplines, excellent teamwork and communication skills in English. The candidate will have the opportunity to develop the following project with a lot of academic freedom and strong support from senior members in the lab, and at the same time to play an active role in shaping and creating inspiring research and working environment.

In line with our and Uni Basel values ), we are committed to sustain and promote an inclusive culture, ensure equal opportunities and value diversity and respect in our working and learning environment.

We are looking for a highly motivated doctoral researcher to develop new metabolomics strategy to advance and speed up anti-cancer drug discovery.

Your main tasks will be:

• Developing new strategies to combine high-throughput metabolomics with 3D cell culture models
• Perform large chemical and genetic studies in cancer cell lines derived spheroids
• Develop predictive model of drug response by comparing 2D to 3D cellular systems
• Testing and validating the relevance of such models in patient tumour specimens
• Support and preparation of scientific reports and journal articles

• Master's degree in (Bio-)Physics, (Bio-)Engineering, Biological Sciences, Microbiology, Biochemistry, Systems Biology, Molecular Biology, Bioinformatics/Computational Biology, or related fields.
• Experience in designing and running experiments with 2D and 3D (organoids, spheroids) cell cultures in the laboratory.
• Experience in basic statistical approaches for the analysis of large datasets.
• Hands-on experience with key biochemical and molecular biological methods.
• Motivation to work in an international research environment.
• Experience with and/or motivation to learn systems biology approaches, high-throughput methodologies, analysis of single cell imaging data.
• Experience with programming language (e.g. Matlab, R or Python).
• Excellent communication skills.
• Any of the following will be a plus: Experience with mass spectrometry.
• Experience with the analysis of metabolomics data.
• Interest in mathematical modelling of metabolic and regulatory/signalling network.

• You will have access to state-of-the-art research equipment in metabolomics, cell biology, time-lapse microscopy and single cell analysis.
• 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 chemistry, engineering, clinics, computational biology and Micro-, Cell- and Immunobiology.
• 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.

Key References

Laurentz Schuhknecht, Karin Ortmayr, Jürgen Jänes, Martina Bläsi, Eleni Panoussis, Sebastian Bors, Terézia Dorčáková, Tobias Fuhrer, Pedro Beltrao, Mattia Zampieri. A human metabolic map of pharmacological perturbations reveals drug modes of action. Nature Biotechnology (2025)

Anglada-Girotto, M., Handschin, G., Ortmayr, K. et al. Combining CRISPRi and metabolomics for functional annotation of compound libraries. Nat Chem Biol 18, 482–

Campos A. and Zampieri M. Metabolomics-Driven Exploration of the Chemical Drug Space to Predict Combination Antimicrobial Therapies. Molecular Cell 74,

Application

Please use the link below to apply and submit the following documents: A) a cover letter, B) a complete curriculum vitae C) the PhD application form (D) references from at least two referees.

Apply