PhD Position in Computational Neuroscience

Radboud University Faculty of Science

PhD Candidate in Computational Neuroscience: Target and Pathway Discovery in Molecular Networks

  • 32 - 40 hours per week
  • Maximum gross monthly salary: € 3,061
  • Faculty of Science
  • Required background: Research University Degree
  • Duration of the contract: 4 or 5 years
  • Application deadline: 31 December 2020

We are looking for

The Department of Neurophysiology, Donders Centre for Neuroscience is looking for a PhD candidate to discover targets and pathways in molecular networks.

You will investigate transcriptomic and proteomic networks in neurons, and how these networks relate to experience-dependent plasticity, i.e. the changes in neuronal and network structure upon sensory input. This includes developing statistical methods for molecular target identification, and comparison of connectivity in molecular networks to connectivity in cellular networks.

In the nervous system, early stages of information processing are performed by primary sensory pathways, where incoming sensory information is encoded topographically to generate neural representations of the sensory world in an activity-dependent manner. These sensory maps are products of anatomically and functionally connected neurons. They are formed by spatiotemporally correlated activation of individual neurons and shaped by sensory and perceptual experience through a process called experience-dependent plasticity. Sensory neuronal plasticity is believed to have a fundamental role in determining where and how information is processed as the aforementioned maps delineate the sensory circuits that represent the environment. Although the plasticity of these maps is critical for the proper development of neural circuits during postnatal brain development, neural plasticity is also needed in adulthood to ensure adaptation of the brain to ever-changing sensory and perceptual environments. However, the neural circuits and molecular mechanisms responsible for map plasticity are still largely unknown. Thanks to the developments in high-throughput mapping of the transcriptome and proteome, we can now have an unprecedented look at the overwhelming majority of the molecular players in play as activity shapes network and animal behaviour. To address this, in you will take advantage of our recent transcriptomic (RNAseq) and proteomic (mass spectroscopy) mapping of the somatosensory cortex in single column and laminae (data already collected) in animals which had all whiskers intact, or in animals that were deprived of somatosensory (whisker) input for 2 weeks. You will develop statistical methods for molecular target identification based on causal inference approaches. You will focus on single-cell transcriptomics from the same region of the brain to map the correlated changes across the transcriptome using information=metric analysis. The outcome is a directed network whose structure can be directly compared to the cellular network connectivity. This comparison of the neighbourhood will help shed light on the common rules of network connectivity across scales. Finally, you will develop methods to visualise these networks as topological networks. The molecular tools required for targeted modulation of the genes of interest will be produced in the Viral Gene Core facility of the Department of Neurophysiology at Radboud University.

Please note that the EU Mobility Rule will be applied: PhD candidates must not have resided or carried out their main activity (work, studies, etc.) in the Netherlands for more than 12 months in the 3 years immediately before the recruitment date. Compulsory national service, short stays such as holidays, and time spent as part of a procedure for obtaining refugee status under the Geneva Convention, are not taken into account.

We ask

  • A (research) MSc degree in a quantitative field (computer science, engineering, physics, mathematics, etc.).
  • Expertise in neuroscience or an interest in acquiring it.
  • Experience with scientific programming or an interest in learning it (Python, Matlab or other).
  • Enthusiasm and the ability to work in a multidisciplinary environment.
  • Excellent communication skills in spoken and written English.

We are

You will be appointed at the Department of Neurophysiology, Donders Centre for Neuroscience and you will be enrolled in the Donders Graduate School. This vibrant and multidisciplinary department studies the organization and function of neural circuits across scales and techniques, from genes and proteins to behavior and from in vitro and in vivo experiments to computational modelling. It is an open and international environment, where young scientists from different backgrounds share a fascination for the interaction between brain structure and function.

You will also be part of the International "SmartNets" consortium in which 13 PhD students from 5 universities work together to understand computation in biological networks. This means that you will have the opportunity to:

  • Follow several international training events and workshops together with other Smartnets PhD candidates.
  • Spend 9 months with Georges Debrégeas at Sorbonne Université, Paris, for functional confirmation of the molecular targets in controlling neuronal excitability in zebrafish brain during sensory navigation. The experiments will create direct collaboration with a SmartNets PhD from this lab, providing molecular insight into neuronal network activity and behaviour.
  • Play an active role in the organisation of the yearly outreach events of the Dutch Brain Olympiad.
  • Note that this will entitle you to mobility allowance and possibly family allowance. Moreover, certain research, training and network costs will be reimbursed.

Radboud University

We want to get the best out of science, others and ourselves. Why? Because this is what the world around us desperately needs. Leading research and education make an indispensable contribution to a healthy, free world with equal opportunities for all. This is what unites the more than 22,000 students and 5,000 employees at Radboud University. And this requires even more talent, collaboration and lifelong learning. You have a part to play!

We offer

  • Employment: 32 - 40 hours per week.
  • The gross starting salary amounts to €2,395 per month, and will increase to €3,061 in the fourth year (p scale).
  • In addition to the salary: an 8% holiday allowance and an 8.3% end-of-year bonus.
  • Duration of the contract: you will be appointed for an initial period of 18 months, after which your performance will be evaluated. If the evaluation is positive, the contract will be extended by 2.5 years (4 year contract) or 3.5 years (5 year contract).
  • Your education task may be up to 10% of your appointment.
  • You will be able to use our Dual Career and Family Care Services. Our Dual Career and Family Care Officer can assist you with family-related support, help your partner or spouse prepare for the local labour market, provide customized support in their search for employment  and help your family settle in Nijmegen.
  • Have a look at our excellent employment conditions. They include a good work-life balance (among other things because of the excellent leave arrangements), opportunities for development and a great pension scheme.

Would you like more information?

For more information about this vacancy, please contact:
Tansu Celikel, Head Department of Neurophysiology and Chair of Donders Institute
Tel.: +31 24 365 2360

Fleur Zeldenrust, Coordinator SmartNets, Head Biophysics of Neural Computation Group
Tel.: +31 24 365 3195

Apply directly

Please address your application to Tansu Celikel and submit it, using the application button, no later than 31 December 2020, 23:59 Amsterdam Time Zone.   

Your application should include the following attachments:

  • Letter of motivation.
  • CV.

We drafted this vacancy to find and hire our new colleague ourselves. Recruitment agencies are kindly requested to refrain from responding.