Postdoc position in quantitative 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 post-doctoral research opportunity in the context of systems pharmacology, computational biology and metabolic regulation.

This position will be based in the Department of Biomedicine (https : / / biomedizin.unibas.ch / en / ) in Basel, one of the world’s leading locations for life sciences, home to several companies and institutions.

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, 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 in creating inspiring research and working environment.

In 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..

Project Combine mathematical models of metabolism with time resolved metabolic profiling of drug effects to characterize drug Mode of Action and unravel fundamental principle of metabolic regulation in cancer cells.

We are looking for a highly motivated Post-Doc researcher to study how chemical perturbations interfere with metabolism (40% wet lab and 60% computational, can be adapted based on the candidate).

Your position

• Apply and develop model-based and statistical approaches to analyze and interpret large scale dynamic profiles of small molecules effects on cancer cell metabolism.
• Adapting existing and possibly developing improved experimental protocols for the high-throughput metabolomics analysis of drug-perturbed cells.
• Unravel the hidden potential of apparently inactive molecules in interfering with cellular metabolism.
• Support and preparation of scientific reports and journal articles

Your profile

Essential :

• PhD in (Bio)Physics, (Bio)engineering, Systems Biology, Bioinformatics / Computational Biology, or related fields.
• Solid experience in data analysis
• Experience with programming language (e.g. Matlab, R or Python) Motivation to work in an international research environment

Highly desirable :

• Experience in kinetic modeling and / or hands-on laboratory experience
• Good communication skills
• Interest in mathematical modeling of metabolic and regulatory / signaling network

We offer you

• You will have access to state-of-the-art research equipment in metabolomics and computational biology.
• You will work in a dynamic and highly interdisciplinary team including computer scientists, experimentalists.
• You will be involved in cross-disciplinary collaborations and have training opportunities to further develop and grow your scientific interests.
• 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

Application / Contact

Please use the link below to apply and submit the following documents : A) a cover letter, B) a complete curriculum vitae C) at least two reference letters

Key References :

Ortmayr, K., de la Cruz Moreno, R. & Zampieri, M. Expanding the search for small-molecule antibacterials by multidimensional profiling.

Nat Chem Biol 18, 584 595 (2022)

Anglada-Girotto, M., Handschin, G., Ortmayr, K. et al. Combining CRISPRi and metabolomics for functional annotation of compound libraries.

Nat Chem Biol 18, 482 491 (2022)

Zampieri, M., Hörl, M., Hotz, F. et al. Regulatory mechanisms underlying coordination of amino acid and glucose catabolism in Escherichia coli. Nat Commun 10, 3354 (2019)

Øyås O., Borrell S., Trauner A., et al. Model-based integration of genomics and metabolomics reveals SNP functionality in Mycobacterium tuberculosis. PNAS 117 (2020)

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

Molecular Cell 74, 1291-1303 (2020)