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.
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.
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.
The Unit has provided three key ingredients to kickstart my scientific career: a constant source of inspiration, the freedom to explore my ideas, and frequent opportunities for feedback.”
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.
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!”
Projects
Project
Brain-inspired machine learning for optimizing deep brain stimulation
This project lies on the interface of machine learning and neuroscience. Each of these areas can benefit from the insight from the other. For example, machine learning can be used for optimizing treatments for neurological disorder, while understanding the brain can help develop new machine learning algorithms. Deep brain stimulation (DBS) is a treatment for several neurological conditions, such as Parkinson’s disease and essential tremor. In these disorders, there are abnormal oscillations in neural activity, and some of them result in the characteristic shaking of hands. DBS desynchronizes these abnormal oscillations. Our group has developed mathematical models of the effects of DBS which suggest how to optimally control DBS to best supress the neural oscillations (Weerasinghe et al. 2019, 2021, PLoS Computational Biology). However, our theory assumes knowledge of certain parameters of the neural system, which need to be estimated. Thus, machine learning may help to find best control policies for DBS. Our group has also investigated the relationship between deep learning algorithms and model of learning in the brain (Whittington & Bogacz, 2019, Trends in Neuroscience). We recently observed that certain biologically inspired models learn more effectively than standard artificial neural networks.
The goal of the project is to develop machine learning methods to find optimal control policy for DBS. The first stage will involve numerical experiments investigating if machine learning algorithms can discover the optimal control policies for DBS in a simulated neural system. Next, it will be tested how these machine learning algorithms perform in experiments with real DBS. The work on the project will involve development and analysis of mathematical models, computer simulations, and comparison with experimental data gathered in 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
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.
This Ph.D. (D.Phil.) studentship is funded by the Medical Research Council (MRC), a part of UKRI. The successful applicant is entitled to receive a tax-free stipend and, as a minimum, tuition fees paid at the Home level, regardless of whether they are Home or International students. Please see further details about MRC/UKRI studentships and guidance regarding Home and International eligibility. International students may be charged international level (‘Overseas’) fees by the University. Overseas fees are typically higher than Home level fees. See further details on fees at the University. Note that this MRC-funded studentship is not able to cover tuition fees above the Home level.
Interested candidates should possess, or expect to receive, a 1st class or upper 2nd class degree (or equivalent) in a related scientific discipline, e.g. computer science, engineering, mathematics, biological or physical sciences. Strong mathematical skills and background (in calculus, linear algebra and probability theory) are essential, as is proficiency in computer programming.
Prof Rafal Bogacz will be happy to discuss the project and PhD further. Please contact him by email on rafal.bogacz@bndu.ox.ac.uk
To be considered for one of these MRC-funded studentships, please submit an application for admission to the D.Phil. in the Nuffield Department of Clinical Neurosciences (course code RD_CU1), following the guidance. According to this guidance, the application should include a brief research proposal, which in this case should describe your ideas on how machine learning could be used to optimize closed-loop deep brain stimulation. On the application form, in the section headed ‘Departmental Studentship Applications’, please indicate that you are applying for a studentship and enter the reference code for a MRC BNDU studentship "2022BNDUDTA".
The closing date for applications is 12.00 midday UK time on Friday 3rd December 2021.
Interviews for short-listed applicants will be held on Friday 7th and Monday 10th January 2022.
Supervisors
Applications are invited from both Home students and International students to join a multidisciplinary team of scientists studying computational models of brain decision networks. An MRC-funded studentship is available from the start of academic year 2022/23, for 3.5 years, and will be primarily supervised by Professor Rafal Bogacz at the MRC BNDU.
Project
Investigating network dynamics of the human hippocampus
A wealth of studies conducted in rodents have established that temporally structured activity in the hippocampus network, analysed with respect to network oscillations and spike time relationships, supports memory-guided behaviour. How such a foundational knowledge discovered in rodents translates to the human hippocampus remains uncertain.
The overall aim of this PhD project is to investigate how hippocampal network activity support memory processes in humans. To achieve this goal, we will investigate patterns of network oscillations and spike time relationships of principal cells and interneurons recorded in the human hippocampus. This project will involve data collection from human participants, and advanced data analyses of network oscillations and spike trains of neuronal ensembles. Comparisons will be performed with respect to network dynamics of the rodent hippocampus, using existing datasets.
The project will take place in the Medical Research Council Brain Network Dynamics Unit at the University of Oxford, and will be conducted in collaboration with Dr. Leila Reddy based at the Brain and Cognition Research Center CERCO, Toulouse, France. The appointed student 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 electrophysiological recordings of neuronal activity and multivariate data analyses (notably using graph-theoretical tools) and programming (Python, R, and Jupyter).
This Ph.D. (D.Phil.) studentship is funded by the Medical Research Council (MRC), a part of UKRI. The successful applicant is entitled to receive a tax-free stipend and, as a minimum, tuition fees paid at the Home level, regardless of whether they are Home or International students. Please see further details about MRC/UKRI studentships and guidance regarding Home and International eligibility. International students may be charged international level (‘Overseas’) fees by the University. Overseas fees are typically higher than Home level fees. See further details on fees at the University. Note that this MRC-funded studentship is not able to cover tuition fees above the Home level.
Interested candidates should possess, or expect to receive, a 1st class or upper 2nd class degree (or equivalent) in a related scientific discipline, e.g. biological or physical sciences, medicine, computer science, engineering, mathematics. Strong experience in programming for the purpose of data-driven science is required. Knowledge of advanced concepts and techniques in Systems Neuroscience is highly desirable.
We strongly encourage candidates to contact the project supervisor before submitting an application. To find out more about these MRC-funded studentships, the research project, and the application process, please contact Professor David Dupret by email on david.dupret@bndu.ox.ac.uk. Professor Dupret is also happy to consider supervising PhD students funded by Departmental scholarships and other doctoral training programmes at Oxford, as well as PhD students with their own independent funding.
To be considered for one of these MRC-funded studentships, please submit an application for admission to the D.Phil. in the Nuffield Department of Clinical Neurosciences (course code RD_CU1), following the guidance. On the application form, in the section headed ‘Departmental Studentship Applications’, please indicate that you are applying for a studentship and enter the reference code for a MRC BNDU studentship "2022BNDUDTA".
The closing date for applications is 12.00 midday UK time on Friday 3rd December 2021.
Interviews for short-listed applicants will be held on Friday 7th and Monday 10th January 2022.
Supervisors
Applications are invited from both Home students and International students to join a multidisciplinary team of scientists studying hippocampal network-level mechanisms supporting memory processing in the mammalian brain. One MRC-funded studentship is available from the start of academic year 2022/23, for 3.5 years, and will be supervised by Professor David Dupret at the MRC BNDU, in collaboration with Dr. Leila Reddy from the CNRS, France.
Project
Brain Computer Interfacing for Closed-loop Neuromodulation
Neural modulation techniques, such as deep brain stimulation (DBS), transcranial magnetic stimulation (TMS) and transcranial electrical stimulation (tES), have the potential to directly influence brain network activities and circuit dynamics. For example, high frequency Deep brain stimulation (DBS) is an effective therapy for movement disorders such as Parkinson’s disease and essential tremor. Repetitive transcranial magnetic stimulation (rTMS) of the left dorsolateral prefrontal cortex (DLPFC) has been approved for major depressive disorder (MDD). However, in currently existing therapy, the stimulation is delivered ‘open-loop’ blinded to the current pathological states or underlying brain activities. Closed-loop neuromodulation using neural activities recorded in real-time as feedback has been shown to improve the efficacy.
The overall aim of the studentship project is to interact with neural dynamics from moment-to-moment as necessary to reverse or ameliorate dysfunctional brain activity. To this end, we must investigate the function of frequency-specific neural oscillations and network connectivity in affective processing 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 designing, implementing and testing different closed-loop neuromodulation strategies to interact with pathological brain activities for better treatment of symptoms.
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 electrophysiological signal processing, data analysis and neuromodulation.
This Ph.D. (D.Phil.) studentship is funded by the Medical Research Council (MRC), a part of UKRI. The successful applicant is entitled to receive a tax-free stipend and, as a minimum, tuition fees paid at the Home level, regardless of whether they are Home or International students. Please see further details about MRC/UKRI studentships and guidance regarding Home and International eligibility. International students may be charged international level (‘Overseas’) fees by the University. Overseas fees are typically higher than Home level fees. See further details on fees at the University. Note that this MRC-funded studentship is not able to cover tuition fees above the Home level.
: Interested candidates should possess, or expect to receive, a 1st class or upper 2nd class degree (or equivalent) in a related scientific discipline, e.g. biological or physical sciences, medicine, computer science, engineering, mathematics. Previous experience in neuroscience research is highly desirable. Students with strong background in engineering science or mathematics and an interest in neuroscience are also welcomed
Associate Professor Huiling Tan will be happy to discuss the project and PhD further. Please contact her by email on huiling.tan@ndcn.ox.ac.uk.
To be considered for one of these MRC-funded studentships, please submit an application for admission to the D.Phil. in the Nuffield Department of Clinical Neurosciences (course code RD_CU1), following the guidance. On the application form, in the section headed ‘Departmental Studentship Applications’, please indicate that you are applying for a studentship and enter the reference code for a MRC BNDU studentship "2022BNDUDTA".
The closing date for applications is 12.00 midday UK time on Friday 3rd December 2021.
Interviews for short-listed applicants will be held on Friday 7th and Monday 10th January 2022.
Supervisors
Applications are invited from both Home students and International students to join a multidisciplinary team of scientists. An MRC-funded studentship is available from the start of academic year 2022/23, for 3.5 years, and will be primarily supervised by Associate Professor Huiling Tan at the MRC BNDU.
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
Applications & Funding
The MRC BNDU has its own MRC-funded Ph.D. (D.Phil.) studentships. Applicants to these MRC-funded studentships can also be considered for University scholarships. The Unit will also consider hosting PhD students funded by Departmental scholarships and other doctoral training programmes at Oxford. 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 MRC 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 about potential costs. There is also specific advice for prospective Home and International students.
Students considering applying for one or more of the PhD studentship projects available in the MRC BNDU should first contact the supervisor(s) named in the project description using the email provided in the project summary. You are encouraged to contact the supervisor(s) 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 MRC-funded studentship following contact with the supervisor(s) of your proposed project, please submit an application following the online guidance for the D.Phil. in Clinical Neurosciences. On the application form, in the section headed ‘Departmental Studentship Applications’, you must indicate that you are applying for a studentship and enter the reference code for a MRC BNDU studentship.
In the special instance of an iCASE studentship, please contact the named supervisor(s) directly for advice on the application process.
Hippocampal theta oscillations (white) with associated faster rhythms (rainbow colours). From: Lopes-Dos-Santos V. et eal. Parsing Hippocampal Theta Oscillations by Nested Spectral Components during Spatial Exploration and Memory-Guided Behavior. 2018. Neuron, 100(4):940–952.