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Novel Bioinformatics and Artificial Intelligence approaches for microbiome analysis (Ref: ET20/HLS/APP/BASHTON)

  • Full or part time
  • Application Deadline
    Friday, May 08, 2020
  • Funded PhD Project (European/UK Students Only)
    Funded PhD Project (European/UK Students Only)

Project Description

The microbiome, the collective genomic entity of all microbiota - bacteria, archaea, fungi, protozoa, and viruses of an environment holds an immense amount of information, a considerable amount of improvement with respect to data analysis and real-time interpretation is still needed to bring research out of the lab and into everyday usage in our home environment and health system. Collectively the microbiota, which we initially acquire at birth, have a huge lifelong impact on health defining our gut ecosystem, and impact on complex health problems such as: mental-health, cancer, neurodegenerative and autoimmune diseases. Humans encounter and pass on microbiota from one and other and their environment, including the built environment of constructed buildings. Optimal and timely analysis and information extraction from the microbiome is a key hurdle in leveraging it to effetely improve human and environmental health.

This project will focus on developing novel bioinformatics approaches for real-time and in-depth functional analysis of the microbiome from meta- genomics/transcriptomics data, including long read sequencing (ONT, PacBio), and translating these into informing our relationships with our built environment for improved health and environmental sustainability. The aim of the project is to utilise cutting edge Artificial Intelligence and Machine/Deep Learning techniques (such as Sonnet/TensorFlow) to enable faster and deeper analysis of data rich microbiomes. The PhD will be a dry computer-based project utilising high-performance and cloud computing environments and would ideally suit someone with a Bioinformatics, Computer Science, Data Science, Mathematical/Statistical, or Molecular Biology (with Bioinformatics knowledge), or similar background, who has an interest in molecular biology and the microbiome. Knowledge of programming and scripting languages (Such as R, Bash, and Python) is also desirable.

This project will take place within the world’s first Hub for Biotechnology in the Built Environment (HBBE, This is a £8M initiative between Northumbria and Newcastle Universities funded by Research England. The Hub will develop biotechnologies to create a new generation of buildings which are responsive to their environment, grown using engineered living materials, metabolise their own waste, and modulate their microbiome to benefit human health. The Hub is a strategic expansion that will soon including 13 new academic staff, including Biologists, Architectural Designers and Engineers, supported by 5 PDRAs, 14 PhD students and 3 support staff. This will include 3 new research facilities that will integrate our research: the Micro Bio-Design Lab (Northumbria), the Macro Bio-Design Lab (Newcastle) and a unique Experimental ‘Living’ House, ‘The OME’.

Eligibility and How to Apply:
Please note eligibility requirement:
• Academic excellence of the proposed student i.e. 2:1 (or equivalent GPA from non-UK universities [preference for 1st class honours]); or a Masters (preference for Merit or above); or APEL evidence of substantial practitioner achievement.
• Appropriate IELTS score, if required.

For further details of how to apply, entry requirements and the application form, see

Please note: Applications should include a covering letter that includes a short summary (500 words max.) of a relevant piece of research that you have previously completed and the reasons you consider yourself suited to the project. Applications that do not include the advert reference (e.g. ET20/…) will not be considered.

Deadline for applications: 8th May 2020
Start Date: 1st Aug 2020

Northumbria University takes pride in, and values, the quality and diversity of our staff. We welcome applications from all members of the community. The University holds an Athena SWAN Bronze award in recognition of our commitment to improving employment practices for the advancement of gender equality.

For informal enquiries please contact Dr Matthew Bashton ()

Funding Notes

The studentship is available to Home and EU students with a full stipend, paid for three years at RCUK rates (for 2020/21, this is £15,285 pa) and full Home/ EU Fees.


Schwalbe, E.C. et al., 2017. Minimal methylation classifier (MIMIC): A novel method for derivation and rapid diagnostic detection of disease-associated DNA methylation signatures. Scientific Reports, 7(1), pp.13421–8.

Maclean, D. et al., 2013. Crowdsourcing genomic analyses of ash and ash dieback - power to the people. GigaScience, 2(1), p.2.

Bashton, M., Nobeli, I. & Thornton, J.M., 2007. PROCOGNATE: a cognate ligand domain mapping for enzymes. Nucleic Acids Research, 36(Database), pp.D618–D622.

Bashton, M. & Chothia, C., 2007. The generation of new protein functions by the combination of domains. Structure, 15(1), pp.85–99.

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