Post-Doc position in quantitative 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 post-doctoral 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 anticancer 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 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 an 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.

The key aim of this project is to systematically map the metabolic profile of a large biobank of lung tumor specimens and link specific metabolic signatures to tumor characteristics, prognosis, and treatment response using high throughput metabolomics integrated with clinical data. The project seeks to identify drugs that can target and potentially reverse disease-associated metabolic alterations. We are looking for a highly motivated Post-Doc researcher to study lung tumor metabolism (60% wet lab and 40% computational).

Your main tasks will be:

• Adapting existing and developing improved experimental protocols for the high-throughput metabolomics analysis of complex clinical samples.
• Coordinate and perform large-scale metabolomics profiling in lung tumor specimens.
• Apply and develop model-based and statistical approaches to analyze and interpret large compendia of metabolome profiling.
• Integrate diverse large-scale omics profiles to derive experimentally testable hypotheses on patient-specific metabolic vulnerabilities and drug sensitivity.
• Design and implement experimental validation of metabolome-based predictions.
• Support and preparation of scientific reports and journal articles.

Essential:

• PhD in (Bio)Physics, (Bio)engineering, Biological Sciences, Microbiology, Biochemistry, Systems Biology, Molecular Biology, Bioinformatics/Computational Biology, or related fields.
• Hands-on experience with mass spectrometry.
• Experience with statistical analysis of large-scale datasets, especially metabolomics and transcriptomics.
• Experience with programming language (e.g. Matlab, R or Python) and statistics.
• Motivation to work in an international research environment.

Highly desirable:

• Experience in cell culture
• Hands-on experience with key biochemical and molecular biological methods.
• Experience with and/or motivation to learn systems biology approaches, high-throughput methodologies.
• Excellent communication skills.
• Interest in mathematical modeling of metabolic and regulatory/signaling network.

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

Ortmayr, K., de la Cruz Moreno, R. & Zampieri, M. Expanding the search for small-molecule antibacterials by multidimensional profiling. Nat Chem Biol 18, 584–

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

Application / Contact

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