Phd Position in computational biology (Zampieri Lab)
100 %
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 900 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. 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, 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.
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 Description In the framework of the NCCR AntiResist (https://www.nccr-antiresist.ch/en/), we are looking for a highly motivated doctoral researcher to uncover the role of the central metabolism in mediating antibiotic tolerance. This project will be conducted in collaboration with Prof. Sarah Tschudin Sutter at the University hospital of Basel and Prof. Urs Jenal at the Biozentrum (60% wet lab and 40% computational).
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Key References:
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).
Fuentes, D.A.F., Manfredi, P., Jenal, U. et al. Pareto optimality between growth-rate and lag-time couples metabolic noise to phenotypic heterogeneity in Escherichia coli. Nat Commun 12, 3204 (2021).
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
Please use the link to submit 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.
The PhD Application form consists of the below questions. The candidate should address these question in a word document of max 1 page and attach it to the application.
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