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PhD position - Optogenetics and computational methods for system identification
Published(1117 days ago)
Deadline for applications(1065 days ago)
University of GroningenGröningen (Niederlande)
PhD position Optogenetics and computational methods for system identification
Vacancy number 216251
The Molecular Systems Biology group at the University of Groningen has a number of openings for enthousiastic and
talented PhD students. 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 lab hosts the group of Prof Matthias Heinemann and the group of Dr Andreas
Milias-Argeitis. Prof Heinemann is mainly interested in generating a quantitative understanding about core (microbial)
metabolism, and Dr. Milias-Argeitis focuses on developing combined computational/experimental methods for the design
of dynamic external input signals, which can potentially extract more information from a system interest in comparison
to constant perturbations. The positions described below are provided by Dr Milias-Argeitis.
The ability of optogenetic tools to induce fast, targeted and reversible perturbations to cellular systems makes them
ideal for interrogating complex biochemical networks in a minimally disruptive and dynamic fashion. Coupling of optogenetic
stimulation with patterned illumination through the microscope (e.g. through a Digital Micromirror Device) and fast optical
readouts will enable addressing single cells with light inputs and monitoring their responses in real time. In this way, the
behaviour of intracellular networks can be studied great detail and time resolution. Our goal in this project is to develop
and apply online system identification methods that will adaptively stimulate a given network in closed-loop, in order
to estimate parameters with higher precision, or to discriminate among competing model structures. The combined computational
and experimental methods should exploit the ability to apply cell-specific dynamic light inputs, to increase the amount of
information provided by a single experiment run and guide the development of accurate models of cellular behaviour at the
Tools and methods that candidates will learn:
a. Theoretical: dynamical systems theory, system identification methods, stochastic processes (mainly Markov chains).
b. Experimental: basic cellular and molecular biology techniques, fluorescence microscopy, microfluidics, optogenetics.
The project offers several exciting technical and computational challenges and requires a diverse set of skills that can be
covered either by one or two candidates. Successful candidates should have a background in mathematical/systems biology,
(control) engineering, physics or molecular biology, and ideally have some undergraduate research experience. They should
have good programming skills (e.g. in Matlab, Python or C++) and ideally some knowledge of microscopy image analysis. Some
experience with basic molecular biology techniques for strain construction would also be a plus. Candidates with a theoretical
training are expected to become familiar with the necessary biological/experimental background over time, while candidates with
a biological background should be willing to acquire some mathematical modeling skills. The candidates should have good
command of English (oral and written) and possess excellent communication and collaboration skills.
Conditions of employment
The University of Groningen offers a salary of € 2,174 gross per month in the first year up to a maximum of € 2,779
gross per month in the fourth year. It is a temporary assignment for a period of four years. First, you will get a temporary
position of one year with the perspective of prolongation with another three years. Before the end of the first year, an
evaluation will take place as to the feasibility of successful completion of the PhD thesis within the next three years.
The preferred starting date is earliest December 2016, but the position is remains open until candidate(s) is/are identified.
How to apply
We are looking for excellent and highly motivated candidates. Their applications should contain: (i) a CV, (ii) information
about grades and other measures of success, (iii) two letters of recommendation, (iv) a statement on how the candidate’s prior
experience/expertise could be connected to one of the above mentioned projects.
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