West Wing, Level 6, John Radcliffe Hospital, Oxford, OX3 9DU
Web: www.ndcn.ox.ac.uk | Tel: +44(0)1865 234702 | Email: hr@ndcn.ox.ac.uk
Job description and selection criteria
Job title
Postdoctoral Researcher in Computational Neuroscience
Division
Medical Sciences
Department
Nuffield Department of Clinical Neurosciences, MRC Brain
Network Dynamics Unit
Location
John Radcliffe Hospital, Headington, Oxford, OX3 9DU
Grade and salary
Grade 7: £30,434 -£37,277 per annum
Hours
Full time
Contract type
Fixed-term (3 years with possibility of extension)
Reporting to
Rafal Bogacz (Associate Professor, Senior Research Fellow in
Computational Neuroscience)
Vacancy reference
117683
Additional
information
Introduction
The University
The University of Oxford is a complex and stimulating organisation, which enjoys an
international reputation as a world-class centre of excellence in research and teaching. It
employs over 10,000 staff and has a student population of over 22,000.
Most staff are directly appointed and managed by one of the University’s 130 departments or
other units within a highly devolved operational structure - this includes over 6,500 ‘academicrelated’ staff (postgraduate research, computing, senior library, and administrative staff) and
over 2,700 ‘support’ staff (including clerical, library, technical, and manual staff). There are
also over 1,600 academic staff (professors, readers, lecturers), whose appointments are in
the main overseen by a combination of broader divisional and local faculty board/departmental
structures. Academics are generally all also employed by one of the 38 constituent colleges
of the University as well as by the central University itself.
Our annual income in 2012/13 was £1,086.9m. Oxford is one of Europe's most innovative and
entrepreneurial universities: income from external research contracts exceeds £436.8m p.a.,
and more than 80 spin-off companies have been created.
For more information please visit www.ox.ac.uk/staff/about_the_university.html
Medical Sciences Division
The Medical Sciences Division is an internationally recognized centre of excellence for
biomedical and clinical research and teaching, and the largest academic division in the
University of Oxford.
World-leading programmes, housed in state-of-the-art facilities, cover the full range of
scientific endeavour from the molecule to the population. With our NHS partners we also
foster the highest possible standards in patient care.
For more information please visit: www.medsci.ox.ac.uk
The Nuffield Department of Clinical Neurosciences
The Nuffield Department of Clinical Neurosciences (NDCN), led by Prof Christopher Kennard,
was created in November 2010 by a federation of the Nuffield Department of Anaesthetics
(NDA), the Department of Clinical Neurology (DCN) and the Nuffield Laboratory of
Ophthalmology (NLO). The Department has over 320 staff and 100 postgraduate students.
NDCN has an established research and teaching portfolio with a national and international
reputation for excellence. NDCN is based in high quality research and clinical facilities in the
West Wing of the John Radcliffe Hospital, alongside the Department's world-class Oxford
Centre for Functional MRI of the Brain (FMRIB), the Wetherall Institute of Molecular Medicine
(which houses 3 of our research groups) and provides the ideal facilities to translate research
from bench to bedside. In keeping with the award of NIHR Comprehensive Biomedical
Research Centre status, to a partnership between Oxford University and the Oxford Radcliffe
Hospitals NHS Trust, we have developed a highly integrated and interdisciplinary environment
in which research, teaching, clinical training and clinical care interact. This enables us to
establish new approaches to the understanding, diagnosis and treatment of brain
diseases. To this end the Department fosters collaborations worldwide and warmly welcomes
visiting scientists, clinical fellows and students.
For more information visit: www.ndcn.ox.ac.uk
Nuffield Division of Anaesthesia
NDA is led by Professor Irene Tracey (see also FMRIB). The NDA is committed to the development
and maintenance of internationally competitive research programmes in pain and
consciousness; respiration and hypoxia; adult and neurointensive care; simulation and human
factors training.
For more information visit www.nda.ox.ac.uk
Division of Clinical Neurology
DCN is led by Professor Christopher Kennard. DCN is committed to the development of
research programs that improve understanding of the nervous system in health and disease.
For more information visit www.dcn.ox.ac.uk
Centre for Functional Magnetic resonance Imaging of the Brain
FMRIB is led by Professor Irene Tracey (see also NDA). FMRIB is an internally recognised human
neuroimaging centre housing both 3T and 7T scanners. The Centre has strong programmes
of research in MR physics, image analysis and the applications of neuroscience in health and
disease.
For more information visit www.fmrib.ox.ac.uk
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Nuffield Laboratory of Ophthalmology
NLO is led by Professor Russell Foster, who leads the Sleep & Circadian Neuroscience
Institute. NLO pursues scientific and clinical research into a range of areas related to vision,
the eye and circadian neuroscience.
Job description
Research topic
Using computational techniques for predicting the effects
of deep brain stimulations on neural activity
Principal
Investigator /
supervisor
Rafal Bogacz
Funding partner
Medical Research Council
Recent publications
Technical skills
See http://www.clneuro.ox.ac.uk/team/principalinvestigators/rafal-bogacz
Machine Learning or Statistics (essential), Dynamical Systems
Theory (desired)
The MRC Brain Network Dynamics Unit at the University of Oxford (BNDU)
In 1984, the Medical Research Council established the Anatomical Neuropharmacology Unit
(ANU) attached to the University Department of Pharmacology at Oxford. The MRC ANU
transferred to the University on 1 July 2013. For more information please visit:
mrcanu.pharm.ox.ac.uk. The MRC ANU will close on 1 April 2015 when a new unit, the MRC
Brain Network Dynamics Unit at the University of Oxford (BNDU), will open. The aim of the
new unit is to build on the success of the MRC ANU and develop novel therapies by exploiting
the moment-to-moment neural dynamics that are key to brain function and dysfunction. The
BNDU will realise this by defining aberrant neural dynamics in neurological and psychiatric
disorders and developing recurrent Brain Computer Interfaces that respond to circuit dynamics
and control brain stimulation, and thereby abnormal neural activity, with fine spatio-temporal
precision. The BNDU will be directed by Professor Peter Brown and open with the following
research programmes:
 Dr Rafal Bogacz: Using computer simulations for predicting interventions restoring
healthy patterns of neural activity
 Prof Peter Brown and Dr Andrew Sharott: Temporally patterned closed-loop stimulation
for therapy of brain disorders
 Dr David Dupret: Dynamics of cell assemblies underlying adaptive and mal-adaptive
memories
 Prof Peter J. Magill: Accessing and actuating specified neural circuits underlying motor
function and dysfunction
 Prof Peter Somogyi: Synaptic circuit mechanisms of rhythmic slow oscillatory dynamics
in the rodent and human cerebral cortex
For more information please visit: mrcbndu.ox.ac.uk (available after 1 April 2015
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Overview of the role
This Postdoctoral Researcher will develop computational methods for predicting the effects of
deep brain stimulation on neural activity as part of a multidisciplinary scientific programme that
is designed to develop closed-loop deep brain stimulation for the treatment of neurological
and neuropsychiatric disorders. This work will be done as part of a 5 year MRC programme
entitled “Using computer simulations for predicting interventions restoring healthy patterns of
neural activity” led by Dr. Rafal Bogacz in close collaboration with experimental neuroscientists
in the programme jointly led by Prof. Peter Brown and Dr Andrew Sharott. Candidates should
have a promising track record in original research in their particular field. Candidates are
expected to have advanced technical expertise in data analysis and general expertise in
machine learning and dynamical systems theory. They also need to be highly proficient in
programming. They should provide evidence of designing and completing high quality
research as part of a cohesive programme.
The post holder will work on development of a computational model, which can accurately
predict responses to electrical deep brain stimulation (DBS), and can be used to recommend
their optimal settings. The DBS is a treatment routinely used for various neurological disorders
such Parkinson’s disease. It is thought to work by desynchronizing pathological oscillations in
neural activity arising in Parkinson’s disease, but the details of the mechanism of its action are
still a matter of debate.
The work of the post-holder will focus on recently developed closed-loop DBS systems which
monitor neural activity and can vary timing, frequency and amplitude of stimulation depending
on the ongoing pattern of neural activity. Such systems offer a potential to desynchronize
neural activity to a greater extent with less power than traditional DBS, but their therapeutic
effects critically depend on how and when (in relation to ongoing brain activity) the stimulation
is delivered. Since the space of possible settings of closed-loop DBS is much larger, and
testing all of them experimentally would be intractable, suggesting the best candidate closedloop DBS protocols on the basis of simulations is particularly useful.
The proposed work will be performed in close collaboration with experimental neuroscientists
in the programme led by Dr Sharott and Prof Brown. The data gathered in the MRC Unit will
be used to constrain the models (by the post-holder), the closed-loop DBS settings predicted
by the model will be tested experimentally (by other researchers), and the results of these
tests will be used to improve the simulation methodology for the next iteration (by the postholder).
In the proposed work, the predictive power of the model will be maximized by choosing the
optimal level of model complexity. Currently in computational neuroscience there exist
different frameworks for simulation of neural circuits that differ in the level of biological detail
they capture. Since with current experimental techniques it is not possible to fully characterize
all parameters of all neurons in a circuit, the more biological detail the model attempts to
capture, the more free parameters it has that have to be estimated from experimental data. It
is a well-known statistical principle, that if the number of the model’s parameters is increased
too much, the model can over-fit the data and lose predictive ability. In our study we will choose
the model complexity pragmatically by training models of different levels of complexity on
subsets of experimental data (describing the responses to different protocols of stimulation)
and assessing their ability to predict the remaining data. The models that the post-holder will
develop may range from statistical model based on machine learning, through abstract
phenomenological models describing the dynamics of neural activity to more detailed models
of underlying neural circuits.
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The post holder is also expected to contribute to the intellectual environment in the MRC Unit
and in the theoretical neuroscience community in Oxford, by actively participating in seminars
and meetings. The post holder is also expected to provide guidance to less experienced
members of the research group, including PhD and project students.
Responsibilities/duties

Analyse data recorded from brains of human patients and rodents with closed-loop DBS
systems to discover new patterns and relationships present in the data.

Design and implement computational models that are able to predict the responses of
the brain to stimulation.

Design new protocols of closed-loop DBS on the basis of the above models, and update
the models according to the obtained data.

Effectively collaborate and communicate with other members of the MRC unit involved
in development of closed-loop DBS systems.

Ensure good level of productivity by managing own workload and delivering relevant
scientific results.

Contribute ideas for new research projects. Develop ideas for generating research
income, and present detailed research proposals to senior researchers.

Communicate the results in the form of original research papers for publication in
international peer-reviewed journals, as well as in the form of presentations at scientific
meetings and lectures/seminars within Oxford and at other institutions.

Undertake the training and supervision of students, other host Group members, and
visiting scientists in his/her areas of expertise when appropriate.

Assist supervisor in carrying out host Group’s public engagement and communication
activities.
Selection criteria
Essential

Education, qualifications and training: PhD or equivalent qualification in a relevant area
(e.g. computer science, neuroscience, engineering, mathematics, physics).

Previous work experience: Expertise in data analysis using machine learning or
sophisticated statistical methods.

Knowledge: Proficiency in programming.

Research profile: Demonstrable record of originality, creativity and productivity in
research, including first-author publications.

Research delivery: Evidence of executing a focused and cohesive programme of
research.
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
Personal skills/qualities: The post holder should be capable of independent decision
making and collaboration with research colleagues.

Communication skills: the ability to write for publication, present research proposals and
results, and represent the research group at meetings.
Desirable

Experience in modelling and analysing dynamical systems.

Experience in computational neuroscience.
Working at NDCN
NDCN actively promotes a healthy work life balance amongst employees through a number
of family friendly policies. See http://www.admin.ox.ac.uk/personnel/staffinfo/benefits/ for
further information.
Working at the University of Oxford
For further information about working at Oxford, please see: (relevant link to be inserted here,
please select from one of the three below):
http://www.ox.ac.uk/about_the_university/jobs/professionalandmanagement/
How to apply
If you consider that you meet the selection criteria, click on the Apply Now button on the ‘Job
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