Summary

This project spans 3 different units of assessment at UU (Biomedical Sciences, Computing and Psychology) and involves an industrial partner (GMI, Dublin) who will provide on-site internships for the PhD researcher.

Background:

Depression is a complex heterogeneous disorder. In severe depressive episodes, patients experience feelings of hopelessness/worthlessness, and suicide is a prominent risk. As the leading cause of global disability[1], 300 million people are affected by depression and public health figures indicate depression accounts for 76.4 million years lost to disability; more than any other condition[2]. NI has one of the highest rates of depression in Europe with a lifetime prevalence rate of 16.3%[3] and continues to have the highest rate of suicide of any UK country, at 16.5/100,000 (NISRA, reported by BBC News). NI has a 20-25% higher prevalence rate of mental health problems than the rest of the UK, with associated costs of £3.5 billion. The cost of depression to the UK economy is £70-£100 billion/year. In the UK, depression is predominantly diagnosed by general practitioners in primary care, but diagnosis and treatment selection is largely subjective, and reliant on patient self-report and clinical judgment and experience. Recent advancements have prompted the investigation of patients clinical and physiological profiles to determine biological features (biomarkers) that can be used to identify mental health disorders such as depression. However, there is a huge need to further investigate various biomarkers and intelligently combine these to develop a robust clinical diagnosis tool, which would allow clinicians to effectively diagnose and stratify patients with depression, and ultimately determine the most stratified/personalised treatment.

Dataset:

NICSM have recently procured access to the UK Biobank dataset, including imaging, genomic, biochemical, diagnosis, medication/treatment, demographic/local-environment data of 500,000 participants. Approximately 20,000 of these participants are diagnosed with depression according to International Classification of Diseases Tenth Revision (ICD10).

Method:

This project will investigate the use of medical imaging, specifically, structural Magnetic Resonance Imaging (MRI), to identify neuro-biomarkers (neuromarkers) within the brain that can be used, in combination with existing genetic biomarker approaches (e.g. polygenic risk scoring), to classify major depressive disorder within a patient into specific endotypes for stratified/personalised diagnosis and treatment. A deep-learning model, specifically a convolutional neural network (CNN), will be developed to extract key features from the MRI data, which can be used to identify and classify neuromarkers for depression. Using a cognitive analytic approach, supervised machine learning methodology will be used to analyse correlations between these neuromarkers, genetic biomarkers and phenotypic information to develop a robust diagnosis system to clinically identify endotypes of depression.

Project tasks to be performed by the PhD student:

1. Extract depression cohort from UK Biobank dataset using ICD10 and validated clinical questionnaires and associated genetic and medical imaging data;

2. Perform image data processing (dimensionality reduction, structural analysis, etc.) to determine imaging signatures (neuromarkers) predictive of depression;

3. Using the combination of genetic biomarkers, phenotypic information and acquired neuromarkers, perform big data cognitive analytics to clinically identify endotypes of depression.

References:

1. World Health Organization. (2018). Depression. [online] Available at: http://www.who.int/mediacentre/factsheets/fs369/en/.

2. Global Burden of Disease Study 2013 Collaborators. (2015). Global, regional, and national incidence, prevalence, and years lived with disability for 301 acute and chronic diseases and injuries in 188 countries, 1990-2013: a systematic analysis for the Global Burden of Disease Study 2013. Lancet (London, England), 386 (9995), 743-800.

3. Bunting, BP, Murphy, SD, O'Neill, SM & Ferry, FR. (2012). 'Lifetime prevalence of mental health disorders and delay in treatment following initial onset: evidence from the Northern Ireland Study of Health and Stress', Psychol Med, vol. 42, no. 8, pp.1727-39.

Other Project Specific Requirements:

Degree/MSc in Stratified Medicine, Bioinformatics, Biomedical Sciences, Computer Science, Computer Engineering, or another relevant field. Experience in tools/languages such as MATLAB, R, Python, Linux, or C\C++. Desirable - understanding/experience in machine learning, image processing.

Researcher will be based at C-TRIC (Altnagelvin Hospital site).

Prospective candidate:

The project will be entirely computational. Thus, we are seeking a student having a strong interest in computational approaches evidenced by good programming skills (preferable in Linux, MATLAB, C/C++, Python or R) and knowledge in biomedical/biological sciences, computational biology and statistics. However, students from more biology oriented background but strong interest to learn bioinformatics and programming are also encouraged to apply. Appropriate training will be provided during the course of PhD study. For any informal enquiry and/or to discuss more about the project, please contact the lead supervisor or any member of the supervisory team. Contact details of the supervisory team are mentioned on the right hand side of this webpage.


Essential criteria

  • To hold, or expect to achieve by 15 August, an Upper Second Class Honours (2:1) Degree or equivalent from a UK institution (or overseas award deemed to be equivalent via UK NARIC) in a related or cognate field.
  • Sound understanding of subject area as evidenced by a comprehensive research proposal

Desirable Criteria

If the University receives a large number of applicants for the project, the following desirable criteria may be applied to shortlist applicants for interview.

  • Completion of Masters at a level equivalent to commendation or distinction at Ulster
  • Experience using research methods or other approaches relevant to the subject domain
  • Work experience relevant to the proposed project
  • Publications - peer-reviewed
  • Publications record appropriate to career stage
  • Experience of presentation of research findings
  • A comprehensive and articulate personal statement
  • Use of personal initiative as evidenced by record of work above that normally expected at career stage.
  • Relevant professional qualification and/or a Degree in a Health or Health related area

    The University offers the following awards to support PhD study and applications are invited from UK, EU and overseas for the following levels of support:

    Department for the Economy (DFE)

    The scholarship will cover tuition fees at the Home rate and a maintenance allowance of £15,285 per annum for three years. EU applicants will only be eligible for the fee’s component of the studentship (no maintenance award is provided). For Non-EU nationals the candidate must be "settled" in the UK. This scholarship also comes with £900 per annum for three years as a research training support grant (RTSG) allocation to help support the PhD researcher.

    Due consideration should be given to financing your studies; for further information on cost of living etc. please refer to: www.ulster.ac.uk/doctoralcollege/postgraduate-research/fees-and-funding/financing-your-studies



The Doctoral College at Ulster University


Reviews

Profile picture of Kieran O'Donnell

My experience has been great and the people that I have worked with have been amazing

Kieran O'Donnell - 3D printing of biological cells for tissue engineering applications

Watch Video  

Profile picture of Kamin Hau

Kamin Hau - PhD in Biomedical Sciences


Profile picture of Michelle Clements Clements

Completing the MRes provided me with a lot of different skills, particularly in research methods and lab skills.

Michelle Clements Clements - MRes - Life and Health Sciences

Watch Video  

Profile picture of Sarah Craig

I completed my undergraduate studies at Ulster University, where I graduated in 2017 with first class honours in Biomedical Science with a Diploma in Professional Practice . I joined the Diabetes Research group as a PhD researcher in September 2017 and completed my PhD studies in June 2020.I am proud to say I not only completed my PhD studies within 3 years, but also became the World Champion (with a perfect score!) in Irish Dance during my PhD studies. My favourite memory was the opportunity to present my PhD work at the EASD conference in 2019. If I could speak to myself at the start of my PhD, the best piece of advice I would give myself would be to enjoy every single minute as the time flies in. I really would do another PhD!

Sarah Craig - PhD in Biomedical Sciences


Profile picture of Natalie Klempel

I completed my undergraduate studies in America at Texas Woman’s University where I majored in Kinesiology. I then moved to Scotland to successfully complete my Masters with Merit in Human Anatomy at the University of Dundee.My proudest moment was when I passed my viva! My favourite memory was …the dissections. I’ll never forget the friends I made and the good times we had together. I couldn’t have got through this without the support of my family, friends, lab colleagues, supervisors, and my boyfriend. If I could speak to myself at the start of my PhD, the best piece of advice I would give myself would be to write up after every experiment, keep a lot of back up copies of the work, and to enjoy the experience.

Natalie Klempel - PhD in Biomedical Sciences


Profile picture of William Crowe

Throughout my PhD I’ve been provided with continuous support and guidance by my supervisors and the staff at the University.I’ve also received many opportunities to further enhance my professional development in the form of teaching experience and presenting my work at conferences which will aid in my pursuit of a career in academia or industry.

William Crowe


Profile picture of Poonam Singh Nigam

I joined Ulster university in Jan 1990 after completing Postdoctoral research in Germany (1986-88) and PhD in India (1985). DSc degree in Applied Microbial-Biotechnology has been awarded after the evaluation of my thesis based on Research, Publication & related activities, completed as a research-active academic member of staff (1990-2019). DSc thesis summarised my scientific outputs and contributions (183 research papers, 3 biotechnology reference-books, 43 research-informed book-chapters, 26 research-informed review-articles, 90 conference-abstracts,1 European Patent and 2 Technology-transfers; Supervision of National & International researchers-18 Postdoctoral/Exchange and 12 PhD; and affiliations as Examiner of 58 PhD researchers globally, and Fellow & Member of nine scientific & academic societies.My message to all researchers is that "Chase your Aspirations and Never Give up". I couldn’t have got through my long academic & Professional journey without

Poonam Singh Nigam - DSc in Biomedical Sciences


Profile picture of Karl Smith

I started my PhD after I completed my undergraduate in Biology at Ulster University in 2016, with a dissertation project that focused on genetic variations in bacterial species. I continued using some of these techniques in my doctoral research, which primarily involved the investigation and development of mass spectrometry imaging in vitamin D treated prostate cancer, looking at the metabolic and genetic variations upon treatment. I worked with international collaborators at the University of Edinburgh and Maastricht University, where I got to learn and develop mass spectrometry techniques that have not previously been carried out in Northern Ireland. I now work as a postdoctoral researcher at the National High Magnetic Field Laboratory at Florida State University in Tallahassee, Florida, where I am helping to develop and implement a mass spectrometry imaging facility for users across the world with the super powerful 21T FT-ICR mass spectrometer.A PhD is a demanding process but when

Karl Smith - PhD in Biomedical Sciences


Profile picture of Ryan Kelsey

I graduated Ulster University in 2016 with a degree in Biomedical Science with DPP (Pathology). I was then offered a PhD studentship with Dr Catriona Kelly and Professor Neville McClenaghan at CTRIC which I started in September 2016. My PhD explored the pathophysiology of Cystic Fibrosis-Related Diabetes, the most common co-morbidity associated with Cystic Fibrosis.My proudest moment was undoubtedly passing my Viva (via Skype!), but I was also proud to be given the opportunity to present my work at the UK Cystic Fibrosis Trust Conference in 2018. Through this conference, I was able to meet with people with CF and the challenges they face which was important reminder that the research I was doing mattered. I couldn't have got through this without the unwavering support of my family, who were always there for me in the good times and the bad. I am also extremely grateful for the support and mentorship of my supervisors Dr Catriona Kelly, Professor Neville McClenaghan and Dr Dawood Khan

Ryan Kelsey - PhD in Biomedical Sciences


Profile picture of Ahmed Abuelhana

My proudest moment was when I knew the possibility of the full transfer of my PhD project to Ulster University, the University which I loved and started my first steps towards my PhD in, and also being a PhD graduate from one of the highly reputable universities such as Ulster is a big thing which I should always be proud of. I think there is no that word that can ever express my deepest thanks and sincere appreciation to my supervisor Professor Kathryn Burnett for her ideal supervision, valuable guidance, encouragement, generous help and ultimate support throughout my PhD project. I have been really lucky to have her as a supervisor. Also my deepest gratitude to Mr Linden Ashfield, Principal Clinical Pharmacist, Antrim Area Hospital (NHSCT) for his help and endless support throughout the whole research project. Also, I could not have got through this without the support of my beloved family (my father ”Sayed”, my mother ”Gamila”, my wife “Nermeen”

Ahmed Abuelhana - PhD in Biomedical Sciences


Profile picture of Ryan Lafferty

I graduated from Queen's University Belfast with a Master's in pharmacy in 2014 and subsequently began working as a community pharmacist in the Greater Belfast area. My career began to take an unusual turn when I got involved with a small startup company who developed a novel blood glucose monitor for diabetic patients. From here, my interest in diabetes was piqued and I applied for a PhD project (somewhat optimistically!) in the Diabetes Research Group at Ulster. Nearly four years later, I'm still there working as a postdoctoral researcher. Not bad considering I never thought I had a chance of getting a PhD spot!My time within the DRG has been, and still is, fantastic. I've made life-long friends (and surprisingly few enemies!) who have been patient, helpful and a joy to collaborate with. I couldn't have got through it without them (you know who you are). Likewise, the guidance from my supervisors, Prof. Peter Flatt and Dr. Nigel Irwin, has been invaluable. I'm probably most proud of

Ryan Lafferty - PhD in Biomedical Sciences