PhD position in systems biology

Project description: Cell growth and division are fundamental cellular processes whose proper coordination is essential for cell viability and organismal health. For this reason, the growth and cell division cycle of all eukaryotic cells, from baker’s yeast to mammalian cells, are tightly regulated by several conserved signaling pathways that interact with each other. However, we still do not fully understand how the pathways that control cell growth are coupled to the cell cycle machinery that controls DNA replication and division. In particular, we still lack an overview of i) which pathway components are implicated in this coupling and ii) which cell cycle phases and processes they affect.
Using budding yeast as a model organism, our goal in this project is to systematically identify and characterize components of the main growth-regulatory pathways (TORC1, TORC2, PKA and AMPK) that have the strongest effects on cell cycle progression. To this end, we will use a combination of targeted perturbations of protein abundances, time-lapse microscopy and statistical modelling. Our work will elucidate a largely unexplored aspect of growth regulators, and contribute to our understanding of fundamental cellular processes which are intimately linked with human health.
Tools and methods: microscopy, microfluidics, CRISPR genome editing, auxin-mediated protein depletion, generalized linear models.

Organisation
The Molecular Systems Biology (MSB) group at the University of Groningen (NL) has an opening for a 4-year PhD position. The University of Groningen, located in the north of The Netherlands, enjoys an international reputation as one of the oldest and leading research universities in Europe. The MSB group, part of the Groningen Biomolecular Sciences and Biotechnology Institute (GBB), aims at generating a systems-level understanding of cellular metabolism (Prof. Matthias Heinemann), growth regulation by signaling pathways (Prof. Andreas Milias-Argeitis) and the regulation of cell division mechanisms (Dr Julia Kamenz). Towards these goals, the group members combine experimental approaches using state-of-the-art single-cell technologies such as microfluidics and optogenetics, and develop new methods to address the computational challenges that arise. Together, the members of the international and interdisciplinary team (PhD students and postdocs with backgrounds in biology, engineering, physics and mathematics) create an inspiring and highly collaborative research atmosphere. The description for the currently open position is provided below. The project will be supervised by Prof. A. Milias-Argeitis.

• a Master’s degree with a background in systems biology, molecular biology, biochemistry, biophysics or engineering, and ideally some undergraduate research experience. Familiarity with yeast genetic engineering and fluorescence microscopy is a plus. Candidates with only wet lab experience should be willing to familiarize themselves with coding and image analysis techniques; candidates with only computational experience should be willing to carry out wet lab work
• good knowledge of a high-level programming language (e.g. Matlab, Python or R)
• good command of English (oral and written) and possess excellent communication and collaboration skills.

We offer you in accordance with the Collective Labour Agreement for Dutch Universities:

• a salary of € 2,770 gross per month in the first year, up to a maximum of € 3,539 gross per month (based on fulltime employment) in the fourth and final year
• a full-time position (1.0 FTE)
• a holiday allowance of 8% gross annual income
• an 8.3% end-of-year bonus and participation in a pension scheme for employees.

The successful candidate will first be offered a temporary position of one year with the option of renewal for another three years. Prolongation of the contract is contingent on sufficient progress in the first year to indicate that successful completion of the PhD thesis within the next three years is to be expected. A PhD training program is part of the agreement and the successful candidate will be enrolled in the Graduate School of Science and Engineering.

Starting date: as soon as possible