PhD position in computational systems biology (1.0 FTE)

Department

Faculty of Science and Engineering

Organisation

University of Groningen

The Molecular Systems Biology group at the University of Groningen (Netherlands) has an opening for an enthusiastic and talented PhD student. 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 Molecular Systems Biology group aims at generating a systems-level understanding about the functioning of metabolism (Prof. Matthias Heinemann) and of growth regulation by TOR in budding yeast (Dr. Andreas Milias-Argeitis). Towards these goals, the group members combine classical and systems biology approaches exploiting latest state-of-the-art single cell technologies such as microfluidics and optogenetics. 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 project description for the currently open position is provided below.

Job description

Uncertainty is encountered in every aspect of biochemical network modeling: intracellular noise leads to cellular heterogeneity, low-quality experimental data lead to parametric uncertainties, while incomplete mechanistic knowledge results in structural ambiguities in models. Consequently, model predictions typically display large variability that complicates further inference and analysis steps.

Our group is currently developing computationally efficient methods for carrying out uncertainty propagation and quantification in ODE-based systems, using a range of statistical approaches such as surrogate models (Gaussian processes) and moment-based techniques. At the same time, we are generating a wealth of single-cell, time-lapse microscopy data on the dynamics of the TORC1 signaling pathway in budding yeast upon various perturbations and during the cell cycle.

In this project, we will use our developed methods as a basis for the construction of parameter estimation and model selection algorithms for biochemical networks affected by cell-to-cell variability. The developed algorithms will be employed to evaluate the effects of different dynamic input perturbations, with the goal of determining experiments that can maximize the information on particular aspects of a given system. Our ultimate goal is to generate dynamical models for the regulation of key targets of the yeast TORC1 signaling pathway, making use of our rich single-cell microscopy data.

Requirements

- you have a background in systems biology, applied mathematics, (control) engineering or physics, and ideally have some undergraduate research experience
- you have good knowledge of programming languages (e.g. Matlab, Python or C++) and sufficient experience with dynamical system simulation; familiarity with the basics of probability theory, Bayesian statistics and/or uncertainty quantification methods is also highly desirable
- you have a good command of English (oral and written) and possess excellent communication and collaboration skills.

Job tags:
Dynamical systems theory, probability theory, Bayesian inference, Monte Carlo methods, mathematical modeling, biochemical networks, systems biology

Conditions of employment

Contract length: 12 months.

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

- a salary of € 2.395 gross per month in the first year, up to a maximum of € 3.061 gross per month in the fourth and final year,
- a full-time position (1.0 FTE)
- a holiday allowance of 8% gross annual income
- an 8.3% year-end bonus
- minimum of 29 holidays and additional 12 holidays in case of full-time employment.

Job Application

Do you meet our qualification criteria? If yes, your application should include:

1) CV
2) information about grades and other measures of success
3) two letters of recommendation (these can also be emailed directly)
4) statement of prior experience/expertise could be connected to the project.

You can submit your application until 31 August 11.59pm 2020/ before 1 September 2020 Dutch local time (CET) by means of the application form (click on "Apply" below on the advertisement on the university website).

The preferred starting date is as soon as possible.

We are an equal opportunity employer and value diversity at our University. We are committed to building a diverse faculty so you are encouraged to apply. Our selection procedure follows the guidelines of the Recruitment code (NVP), https://nvp-plaza.nl/download/?id=7714 and European Commission's European Code of Conduct for recruitment of researchers, https://euraxess.ec.europa.eu/jobs/charter/code

Unsolicited marketing is not appreciated.

Additional information

For additional information, please contact:

Dr Andreas Millias
+31 50 - 36 36 225
a.milias.argeitis@rug.nl

In your application, please always include the job opening ID 220244

Extra informatie kan worden verkregen via een van de volgende links:

About the group About Groningen

Digital application form