Development of an immunoinformatics and artificial intelligence based computational platform for vaccine discovery and design

Summary

Advanced next generation sequencing and metagenomics analysis with diverse bioinformatics pipeline have revolutionised the discovery of novel viruses. In recent years we have seen outbreak of Zika, Ebola, Mpox, etc, in different parts of the world, and the worse of them all was SARS-CoV-2 which caused global pandemic. The unprecedented scale and rapidity of spread of recent emerging infectious diseases pose new challenges for vaccine development¹. The conventional ways of developing vaccine, which involves attenuated or protein-based approaches might take up 10-15 years of development; however, recent advancement in mRNA technology has reduced the timeline substantially. The COVID-19 pandemic has demonstrated the transformative impact of vaccines in saving lives and mitigating public health crises. It has also highlighted the critical need for future investments to ensure the rapid and equitable distribution of vaccines globally. The "100 Days Mission" seeks to address this by aiming to develop and deploy a new vaccine against any emerging pathogen with pandemic potential within 100 days of identifying the threat^2,3. Development of artificial intelligence based bioinformatics tools has made it possible to define vaccine candidates by in silico predictions⁴. Shukla Lab at the Personalised Medicine Centre, School of Medicine, Ulster University, has designed peptide-based vaccine candidates for SARS-CoV-2⁵ and filed patent (pending) in US and Europe⁶. The lab has secured funding from Innovate UK’s ICURe Explore followed by ICURe Exploit programmes to work towards commercialisation of these candidates. The lab is currently working on multiple viruses from the WHO’s prioritised list of pathogens which pose the greatest risk due to their epidemic potential⁷. This includes, COVID-19, Ebola virus, Lassa fever and Disease X. This PhD project aims to develop an immunoinformatics and artificial intelligence based computational platform which can speed up the vaccine discovery and design process to meet the threat of any upcoming viruses.

Important Information: Applications for more than one PhD studentship are welcome, however if you apply for more than one PhD project within Medicine, your first application on the system will be deemed your first-choice preference and further applications will be ordered based on the sequential time of submission. If you are successfully shortlisted, you will be interviewed only on your first-choice application and ranked accordingly. Those ranked highest will be offered a PhD studentship. In the situation where you are ranked highly and your first-choice project is already allocated to someone who was ranked higher than you, you may be offered your 2nd or 3rd choice project depending on the availability of this project.

Specific skills requirements of the applicant:  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/Shell, Python and R) and knowledge in immunology, bioinformatics 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. This PhD project will provide opportunity to a PhD researcher to develop computational skills in immunoinformatics, artificial intelligence and vaccine designing. For any informal enquiry and/or to discuss more about the project, please contact the chair of the supervisory team: Dr Priyank Shukla (p.shukla@ulster.ac.uk).

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.

• Experience using research methods or other approaches relevant to the subject domain
• Sound understanding of subject area as evidenced by a comprehensive research proposal
• A comprehensive and articulate personal statement
• Research proposal of 1500 words detailing aims, objectives, milestones and methodology of the project

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.

• First Class Honours (1st) Degree
• Masters at 70%
• Research project completion within taught Masters degree or MRES
• Experience using research methods or other approaches relevant to the subject domain
• Publications record appropriate to career stage
• Experience of presentation of research findings

Equal Opportunities

The University is an equal opportunities employer and welcomes applicants from all sections of the community, particularly from those with disabilities.

Appointment will be made on merit.

Funding and eligibility

This project is funded by:

• Department for the Economy (DfE)

These scholarships will cover tuition fees and provide a maintenance allowance of £19,237 (tbc) per annum for three years (subject to satisfactory academic performance).  A Research Training Support Grant (RTSG) of £900 per annum is also available.

To be eligible for these scholarships, applicants must meet the following criteria:

• Be a UK National, or

• Have settled status, or

• Have pre-settled status, or

• Have indefinite leave to remain or enter, or

• be an Irish National

Applicants should also meet the residency criteria which requires that they have lived in the EEA, Switzerland, the UK or Gibraltar for at least the three years preceding the start date of the research degree programme.

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.