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Introduction to our PhD Programme

Understanding how neuronal activity supports brain function and redressing aberrant dynamics when the brain goes awry in diseases requires a trans-disciplinary and cross-species approach, integrating experimental and clinical investigations with engineering and computational frameworks. Our PhD programme at the Medical Research Council Brain Network Dynamics Unit (MRC BNDU) trains a future generation of neuroscientists to combine these diverse techniques in innovative research projects serving both foundational, theoretical and translational neuroscience. Ours is a vibrant community of scientists and students drawn from around the world.

PhD students at the MRC BNDU can choose among diverse yet complementary research projects that leverage from a substantial array of research techniques. They benefit from the guidance of two supervisors and the feedback from the outstanding research community, locally in the Unit and in the wider intellectual environment of the University of Oxford.  Students also have opportunities to further their knowledge and skills through seminars, including our Unit “Methods meetings” and practical tutorials.

"My project to advance non-invasive brain modulation is in collaboration with an industrial partner Magstim, who develops and manufactures transcranial magnetic stimulation devices. Working with the neuroscientific, clinical and engineering community in the unit, as well as with Magstim, exposes me to the many aspects of translating a medical device from the benchtop prototype to the clinic."
Karen (current student)
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portrait photo of Karen Wendt

Techniques

Students apply for one or more of the research projects made available each year. Projects involve the intensive use of a focussed set of trans-disciplinary methods but students also become familiar with the full range of approaches taken within the Unit. These include:

  • Behavioural experiment paradigms with rodents and humans 
  • Advanced signals analysis, including statistical analytical techniques, mathematical modelling and machine learning.
  • Cell type-specific monitoring  including  electron microscopy, optogenetics and fast-scan cyclic voltammetry.
  • Computational modelling.
  • System and cell type specific brain stimulation using  closed-loop approaches and magnetic, electrical, pharmacological and optogenetic stimulation.

In addition, to the above we actively develop novel research tools for neuroscience discovery, and  better disease treatments.

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Confocal micrograph of green cells amongst unlabelled cells with white nuclei.

ArchT-GFP–expressing neurons in the pyramidal cell layer of mouse hippocampus. From: Recoding a cocaine-place memory engram to a neutral engram in the hippocampus. Trouche S. et al. Nat Neurosci. 2016 Apr;19(4):564-7.

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Portrait photo of Benoit Duchet
“Synergies between its groups make the Unit a unique environment to get inspired, get feedback on your work, and collaborate. This has been invaluable to grow as a scientist.”

“The Unit has provided three keys ingredients to kickstart my scientific career: a constant source of inspiration, the freedom to explore my ideas, and frequent opportunities for feedback.”
Benoit (currently post-doc with Prof. Bogacz)
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stills from video showing a primary school demonstration of electrodes placed on an arm controlling a robot claw

Ben and Flavie demonstrate how electricity in the muscles of the arm can be detected and used to control a robot claw, during a presentation to primary school children.

Career Development

Career Development is central to the Unit’s ethos.  Every student at the Unit benefits from all the resources the MRC BNDU offers, as well as those offered by our host department, Nuffield Department of Clinical Neurosciences, the Medical Sciences Division, and the student’s own college.  Within the MRC BNDU the Training, Career Development and Capacity Building Strategy Committee meets regularly to oversee training for our students and early career post-docs.  Regular events in the Unit include the biannual science day, which offers a chance for the whole unit to come together and share new and exciting results in a collegiate atmosphere. We run an annual training day which is open to all and focusses on different aspects of career development for academic and non-academic careers. Recent sessions have included developing a patient and public involvement strategy, combining a career with caring responsibilities and a workshop on delivering grant pitches. Previous students at the Unit have all gone on to careers in Academia, Medicine, or Industry.

"I think the interdisciplinarity of the Unit and the very friendly, collaborative nature of the members makes it a great place for studying for a PhD, giving you insights into a range of complimentary topics around your chosen project."

“Previous students who completed their PhD in the Unit have gone on to successful careers in a wide range of job roles. The challenging yet rewarding research in the Unit is a great start to your career and I would definitely recommend working here!”
Luke (current student, Magill Group)
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Portrait photo of Luke

Projects

Supervisors: Prof Huiling Tan and Prof Peter Brown 

Background: Brain-Computer Interface technology (BCI) aims to decode a user’s mental state or movement intent through brain signals, and use this information to operate a computer interface, wheelchair, robotic arm or other device. BCI is not only used to provide an alternative pathway for the brain to interact with the environment, but also provides a potential tool for neurofeedback training, in which patients may learn to modulate their own brain activities through reinforcement learning. In addition, the BCI framework is also used to deliver stimulation to the brain in a closed-loop fashion based on the detection of specific neural signals or specific mental states in order to improve the treatment of neurological disorders such as Parkinson’s disease (PD).  

Project Description: The overall aim of the PhD project is to interface with the brain to modify behaviour and improve therapy.  To achieve this goal, we will investigate the function of frequency-specific neural oscillations in decision-making and motor control in both health and disease through behavioural experiments with electrophysiological recordings and controlled neural stimulation in humans. The project will also involve identifying and extracting features in electrophysiological signals in real-time, as well as the design, implementation and test of BCIs for neurofeedback training and/or for closed-loop neuromodulation to interact with brain activities. 

Training: The project will take place in the Medical Research Council Brain Network Dynamics Unit at the University of Oxford and students will benefit from the both the extensive generic and transdisciplinary skills training available within the Unit. This particular project will also offer the following specific training: 1. Behavioural experiment paradigms with healthy participants and patients with neurological disorders; 2. Advanced signals analysis, including statistical analytical techniques, mathematical modelling and machine learning; 3. Invasive and non-invasive brain stimulation using  closed-loop approaches.  

Key Publications:  

He S, Everest-Phillips C, Clouter A, Brown P and Tan H (2020) Neurofeedback-Linked Suppression of Cortical β Bursts Speeds Up Movement Initiation in Healthy Motor Control: A Double-Blind Sham-Controlled Study. Journal of Neuroscience, 40 (20): 4021-4032 

Little S, Brown P (2020) Debugging Adaptive Deep Brain Stimulation for Parkinson's Disease. Movement Disorder, 35(4):555-561. 

Tan H, Debarros J, He S, Pogosyan A, Aziz TZ, Huang Y, Wang S, Timmermann L, Visser-Vandewalle V, Pedrosa DJ, Green AL, Brown P (2019) Decoding voluntary movements and postural tremor based on thalamic LFPs as a basis for closed-loop stimulation for essential tremor. Brain Stimulation, 12(4):858-867. 

Funding: The successful applicant will be funded by a MRC studentship/considered for a Clarendon fund or other University scholarship. Students with their own independent funding will also be considered.  

Contact: Prof Huiling Tan will be happy to discuss the project and PhD further. Please contact her by email on huiling.tan@ndcn.ox.ac.uk 

Supervisor: David Dupret

Background: Memory is central to adaptation and survival, enabling individuals to predict from past experience what can happen next in an ever-changing environment. The idea that groups of neurons transiently synchronize their spiking activity to organize information-representing cell assemblies is central to the scientific investigation our laboratory carries at the nexus between brain and behaviour.

Project Description: The overall aim of the PhD project is to investigate how neuronal activities distributed across brain regions allow the division of computational labour involved in complex, multimodal memories that hold information spanning the sensory, motor and cognitive domains. To achieve this goal, we will investigate the concerted action of groups of neurons scattered across brain regions as well as frequency-specific network oscillations during memory tasks. The project will also involve identifying electrophysiological signals in real-time to implement closed-loop neuromodulation of brain activities.

Training: The project will take place in the Medical Research Council Brain Network Dynamics Unit at the University of Oxford and students will benefit from the both the extensive generic and transdisciplinary skills training available within the Unit. As a whole, this particular project will expose you to a large array of techniques that are central to the field of Systems Neuroscience. Notably, you will receive advanced training in (1) large-scale electrophysiological recordings of neuronal activity from the rodent brain, (2) optogenetic manipulation of molecularly-defined neuronal populations (with or without closed-loop systems), (3) behavioural assays of learning and memory in rodents, (4) multivariate data analyses (notably using graph-theoretical tools) and programming (Python, R, and Jupyter). We will offer you the possibility to either actively engage with all of these techniques, or concentrate on the analyses of existing electrophysiological datasets that comprise spike trains and local field potentials.

Key Publications:

Barron H.C., Reeve H.M, Koolschijn R.S., Perestenko P.V., Shpektor A., Nili H., R. Rothaermel, Campo-Urriza N., O’Reilly J.X., Bannerman D.M., Behrens T.E.J. and Dupret D. Neuronal computation underlying inferential reasoning in humans and mice. Cell. 2020 Oct 1;183(6):1-16.

Trouche S, Koren V, Doig NM, Ellender TJ, El-Gaby M, Lopes-Dos-Santos V, Reeve HM, Perestenko PV, Garas FN, Magill PJ, Sharott A and Dupret D. A Hippocampus-Accumbens Tripartite Neuronal Motif Guides Appetitive Memory in Space. Cell. 2019 Mar 7;176(6):1393-1406.

Lopes-dos-Santos V, van de Ven GM, Morley A, Trouche S, Campo-Urriza N and Dupret D. Parsing hippocampal theta oscillations by nested spectral components during spatial exploration and memory-guided behavior. Neuron. 2018 Nov 21;100(4):940-952.

van de Ven GM, Trouche S, McNamara CG, Allen K, Dupret D. Hippocampal Offline Reactivation Consolidates Recently Formed Cell Assembly Patterns during Sharp Wave-Ripples. Neuron. 2016 Dec 7;92(5):968-974.

Trouche S, Perestenko PV, van de Ven GM, Bratley CT, McNamara CG, Campo-Urriza N, Black SL, Reijmers LG, Dupret D. Recoding a cocaine-place memory engram to a neutral engram in the hippocampus. Nat Neurosci. 2016 Apr;19(4):564-7.

Funding: The successful applicant will be funded by a MRC studentship/considered for a Clarendon fund or other University scholarship. Students with their own independent funding will also be considered.

Contact: Prof David Dupret will be happy to discuss the project and PhD further. Please contact him by email on david.dupret@bndu.ox.ac.uk

Supervisor: Rafal Bogacz

Background: Neurons releasing dopamine modulate information processing and learning in a brain network playing a key role in selection of movements and more general decision making. Understanding the function of dopamine is important, because the death of dopaminergic neurons in Parkinson’s disease leads to difficulties in movement initiation. A classical reinforcement learning theory (Schultz et al 1997 Science 275, 1593-1599) has provided a beautiful description of dopamine function in learning about rewards, but has not explained why dopamine depletion results in motor impairments. This question was addressed by a recent modelling framework called DopAct (Bogacz 2020 eLife 9, e53262) which has extended the classical theory to also describe dopamine function in planning actions to get the rewards. Although DopAct explains the key data on dopaminergic activity and effects of dopamine depletion, this theory needs to be extended in multiple directions to fully account for experimentally observed patterns of dopamine release and their effects.

Project Description: The goal of the project is to extend the theory of dopamine to describe its effects on the dynamics of various neural populations it modulates, describe the results of dopamine depletion in Parkinson’s disease, and the effects of treatments. The work on the project will involve development and analysis of mathematical models, computer simulations, and comparison with experimental data gathered in MRC BNDU and by other collaborators in Oxford. The applicants need to have strong mathematical skills and background (in calculus, linear algebra and probability theory), and be proficient in computer programming.

Training: The project will take place in the Medical Research Council Brain Network Dynamics Unit at the University of Oxford and students will benefit from the both the extensive generic and transdisciplinary skills training available within the Unit. This particular project will also offer specific training in mathematical modelling, computer simulations, data analysis and machine learning.

Funding: The successful applicant will be funded by a MRC studentship/considered for a Clarendon fund or other University scholarship. MRC funding is available for two studentships working on different aspects of project. Students with their own independent funding will also be considered.

Contact: Prof Rafal Bogacz will be happy to discuss the project and PhD further. Please contact him by email on rafal.bogacz@ndcn.ox.ac.uk

diagram of models of circuits with brain regions and Value, Goal and Habit elements

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A PhD Student Presenting at Unit Science Day
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Portrait photo of Gerd
"The various collaborations and vibrant scientific discussions within the Unit, definitively fostered my critical thinking and allowed me to become a better scientist. Moreover, the Unit gave me a network of great scientists and friends that has lasted far beyond my PhD."
Gerd (Neurologist in training, Bern University Hospital, Switzerland)
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plot of beta frequency brain waves being reduced by adaptive deep brain stimulation

Local field potential signal recorded from a patient with a deep brain stimulation electrode, showing a burst of beta-frequency oscillatory activity (top) and adaptive deep brain stimulation being triggered and reducing the length of another beta burst (bottom).

Applications & Funding

Funding for most PhDs is for three years in the first instance. The BNDU has its own Medical Research Council funded PhD places. As well as being considered for these successful applicants will be considered for University scholarships such as the Clarendon fund. In addition, the Unit sometimes recruits for iCASE studentships in collaboration with industry. Information about University funding is available and an A-Z of Oxford scholarships. Students with their own independent funding will also be considered.

The BNDU is one of the six divisions of the Nuffield Department of Clinical Neurosciences, and as such we benefit from the excellent student services and streamlined application process provided by the Department. The Nuffield Department of Clinical Neurosciences provides general information for prospective students, advice on entry requirements and information of potential costs. There is also specific advice for prospective students from the EU.

Students considering applying for one of the PhD projects available in the BNDU should contact the supervisor named in the project description using the email provided in the project summary. You are encouraged to contact them as soon as possible to find out more about the project and the application process. We look forward to hearing from you.

To be considered for a studentship following contact with the supervisor of your proposed project, please submit an application to the DPhil in the Nuffield Department of Clinical Neurosciences. Applications are made online and full information regarding the online process can be found on the main University Admissions pages. On the application form, in the section headed ‘Departmental Studentship Applications’, you must indicate that you are applying for a studentship and enter the departmental reference code for our studentships.

The code for NDCN applications is 21CLINNEURO01WEB.

In the special instance of an iCASE studentship please contact the primary supervisor directly for advice on the application process.

"The MRC BNDU has many people from several backgrounds working in one place, this allows students to be in touch with people who are working in different fields and exposes them to other methods of research."
Saed (current student)
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portait photo of Saed
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Portrait photo of Anna
"The best experience I recall from my time in the Unit is the overarching sense of community. The Unit helped me grow into an independent scientist while providing close mentoring and excellent training and facilities. In brief, I never felt ‘alone’ during my PhD journey thanks to the great network of support provided by the Unit."
Anna (currently post-doc at EPFL working on Blue Brain project)
"Completing a PhD in the Unit is a wonderful opportunity! The Unit creates a supportive environment to conduct your research: you will be using innovative techniques and work with brilliant colleagues. You will have numerous learning opportunities, like weekly talks and seminars, as well as chances to present your work and get feedback. The Unit is actively involved in outreach activities, which will not only greatly benefit your public speaking and communication skills, but they will also be lot of fun!"
Ioana (current student)
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Portrait photo of Ioana