PhD position in systems biology (Zampieri 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 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.

Your position

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.

n line with our and Uni Basel values (https://www.unibas.ch/en/Research/Values-Ethics/Diversity.html), 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 seeking a highly motivated doctoral researcher to investigate how metabolic programs enable cancer cells to metastasize and colonize distant tissues using mouse models, in close collaboration with the Bentires Lab at the University of Basel. This project is fundamentally driven by hands-on experimental in vivo mouse work, including the use of CRISPR-engineered cancer cell lines and metastatic models. In addition, the project integrates high-throughput metabolic profiling of genetic perturbations, computational data analysis, and next-generation sequencing (NGS) of pooled CRISPR libraries, providing a unique opportunity to combine rigorous in vivo experimentation with systems-level approaches.

Your main tasks will be:

A strong interest in and commitment to animal experimentation is essential.
Perform in vivo mouse studies using CRISPR-engineered cancer cell lines
Design, perform, and analyse in vivo CRISPR pooled screens
Perform high throughput metabolomics profiling using a unique framework developed in the lab.
Analyze and interpret metabolomics data to derive experimentally testable hypotheses
Support and preparation of scientific reports and journal articles

Your profile

Essential:

Master's degree in (Bio-)Physics, (Bio-)Engineering, Biological Sciences, Microbiology, Biochemistry, Systems Biology, Molecular Biology, Bioinformatics/Computational Biology, or related fields
Hands-on experience with mouse experiments gained in previous work (i.e. Master's thesis) and LTK-1 certification

Desirable:

Experience with intracardiac injections and monitoring cancer cells using bioluminescence imaging techniques
Experience with basic statistical approaches
Motivation to work in an international research environment
Motivation to learn systems biology approaches, high-throughput methodologies, and programming languages (e.g., MATLAB, R, or Python)
Excellent communication skills

We offer you

You will have in-building access to mouse laboratories as well as 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)

Karin Ortmayr, Meret Ringwald, Laurentz Schuhknecht, Sébastien Dubuis, Eleni Paunossis, Martina Blaesi, Charly Jehanno, Sarah D Grieder, Mohamed Bentires-Alj, Moritz Mall, Mattia Zampieri. The glutamine-aspartate metabolic tradeoff between fast growth and metabolic flexibility. BioRxiv (2025)

Application / Contact

Please send your application via the University of Basel Recruiting-Portal, by submitting the following requested documents: A) a cover letter, B) a complete curriculum vitae C) the PhD application form (see https://www.zampierilab.org/join-us/) (D) references from at least two referees.

Apply