PhD Position in Computational Biology

University of Basel

PhD position in computational biology (Zampieri Lab)

100%, starting date any time (to be discussed). Applications need to be sent by end of June at the latest.

The Zampieri group offers a PhD research opportunity in the context of systems pharmacology, computational biology and metabolic regulation. This position will be based in the Department of Biomedicine ( 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, time-lapse microscopy, to investigate how to pharmacologically interfere with fundamental mechanisms in the regulation of bacterial 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.

Your position

  • Apply and develop model-based and statistical approaches to analyze and interpret large compendia of dynamic metabolome profiling of small molecules effects.
  • Infer and validate mechanisms of actions for naïve molecules.
  • Unravel fundamental regulatory mechanisms to survive drug action and predict mechanisms of drug resistance.
  • Support and preparation of scientific reports and journal articles

Your profile


  • Master's degree and/or PhD in (Bio)Physics, (Bio)engineering, Biochemistry, Systems Biology, Bioinformatics/Computational Biology, or related fields.
  • Experience with programming language (e.g. Matlab, R or Python).
  • Motivation to work in an international research environment.
Highly desirable:
  • Experience with mathematical modeling of metabolic and regulatory/signaling network.
  • Experience with and/or motivation to learn systems biology approaches, high-throughput methodologies.
  • Good communication skills.

We offer you

  • 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.
  • 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:

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)
Application / Contact

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.

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 ( )
D) references from at least two referees