PhD Study : DeepMeta: Deep multiplexed metagenomics approach to biomarkers discovery and explanation of Covid-19 severity

Summary

COVID-19 is the disease responsible for the biggest pandemic crisis since the Spanish flu. Several studies have been conducted and linked COVID-19 severity to the patient’s microbiomes from different body parts. However, the role of such microorganisms in the pathogenesis of Covid infection and the long-Covid syndrome is yet to be understood. Based on the ongoing collaboration, this proposal aims to develop a deep learning-based multiplexed metagenomics approach for the identification of key network biomarkers associated with Covid-19 severity based on human oral microbiomes.

Methodology:

The project aims to achieve the following three objectives via a deep multiplexed metagenomics approach:

1. Inference of microbial co-occurrence networks associated with COVID severity:This will be achieved based on our previous research, in which a framework was introduced to mitigate the composition effect in the inference of significant associations between microbiome. A deep learning-based multiplex network model then will be developed for integrative analysis of co-occurrence to bridge together different co-presence and mutual-exclusion relations and to facilitate the crosstalk and interactions between co-occurrence networks.

2. Dynamical network analysis for identifying key network biomarkers linking to COVID-19 progression: This will be fulfilled based on the concept of dynamic network biomarkers which has been proposed to detect early-warning signals during the disease progression at the molecular network level. Output from Objective 1 will be incorporated to develop a new framework, DeepMeta, to identify the critical stage of phenotypic changes, i.e. from normal to long Covid, during which dramatic changes in the abundance of microbiome components led to differentiation of the phenotypes.

3. Biomarker explanation and evaluation: Biomarker data will be used for meta comparisons to evaluate the proposed DeepMeta framework. The proposed methods and tools will be evaluated using the nasopharynx microbial community of 72 patients that developed different severity levels of COVID-19 released by our collaborators at the first instance.

Essential criteria

Applicants should hold, or expect to obtain, a First or Upper Second Class Honours Degree in a subject relevant to the proposed area of study.

We may also consider applications from those who hold equivalent qualifications, for example, a Lower Second Class Honours Degree plus a Master’s Degree with Distinction.

In exceptional circumstances, the University may consider a portfolio of evidence from applicants who have appropriate professional experience which is equivalent to the learning outcomes of an Honours degree in lieu of academic qualifications.

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.

• Masters at 75%
• Sound understanding of subject area as evidenced by a comprehensive research proposal
• Publications record appropriate to career stage

Funding and eligibility

The University offers the following levels of support:

Vice Chancellors Research Studentship (VCRS)

The following scholarship options are available to applicants worldwide:

• Full Award: (full-time tuition fees + £19,000 (tbc))
• Part Award: (full-time tuition fees + £9,500)
• Fees Only Award: (full-time tuition fees)

These scholarships will cover full-time PhD tuition fees for three years (subject to satisfactory academic performance) and will provide a £900 per annum research training support grant (RTSG) to help support the PhD researcher.

Applicants who already hold a doctoral degree or who have been registered on a programme of research leading to the award of a doctoral degree on a full-time basis for more than one year (or part-time equivalent) are NOT eligible to apply for an award.

Please note: you will automatically be entered into the competition for the Full Award, unless you state otherwise in your application.

Department for the Economy (DFE)

The scholarship will cover tuition fees at the Home rate and a maintenance allowance of £19,000 (tbc) per annum for three years (subject to satisfactory academic performance).

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.

• Candidates with pre-settled or settled status under the EU Settlement Scheme, who also satisfy a three year residency requirement in the UK prior to the start of the course for which a Studentship is held MAY receive a Studentship covering fees and maintenance.
• Republic of Ireland (ROI) nationals who satisfy three years’ residency in the UK prior to the start of the course MAY receive a Studentship covering fees and maintenance (ROI nationals don’t need to have pre-settled or settled status under the EU Settlement Scheme to qualify).
• Other non-ROI EU applicants are ‘International’ are not eligible for this source of funding.
• Applicants who already hold a doctoral degree or who have been registered on a programme of research leading to the award of a doctoral degree on a full-time basis for more than one year (or part-time equivalent) are NOT eligible to apply for an award.

Due consideration should be given to financing your studies. Further information on cost of living