PhD Studentship: Genomic prediction of antimicrobial resistance spread

This position is now closed
An opportunity has arisen for a D.Phil. (Ph.D.) place on the BBSRC-funded Oxford Interdisciplinary Bioscience Doctoral Training Partnership in the area of Artificial Intelligence, specifically Predicting the spread of antimicrobial resistance from genomics using machine learning.

If successful in a competitive application process, the candidate will join a cohort of students enrolled in the DTP’s one-year interdisciplinary training programme, before commencing the research project and joining my research group at the Big Data Institute.

This project addresses the BBSRC priority area “Combatting antimicrobial resistance” by using ML to predict the spread of antimicrobial resistance in human, animal and environmental bacteria exemplified by Escherichia coli. Understanding how quickly antimicrobial resistance (AMR) will spread helps plan effective prevention, improved biosecurity, and strategic investment into new measures. We will develop ML tools for large genomic datasets to predict the future spread of AMR in humans, animals and the environment. The project will create new methods based on award-winning probabilistic ML tools pioneered in my group (BASTA, SCOTTI) by training models using genomic and epidemiological data informative about past spread of AMR. We will apply the tools collaboratively to genomic studies of E. coli in Kenya, the UK and across Europe from humans, animals and the environment, Enterobacteriaceae in North-West England, and Campylobacter in Wales. Genomics has proven effective for asking “what went wrong” in the context of outbreak investigation and AMR spread; here we will address the greater challenge of repurposing such information using ML for forward prediction of future spread of AMR. Scrutiny will be intense because future predictions can and will be tested, raising the bar for the biological realism required while producing computationally efficient tools.

Attributes of suitable applicants: Understanding of genomics. Interest in infectious disease. Some numeracy, e.g. mathematics A-level, desirable. Experience of coding would help.

Funding notes: BBSRC eligibility criteria for studentship funding applies (https://www.ukri.org/files/legacy/news/training-grants-january-2018-pdf/). Successful students will receive a stipend of no less than the standard RCUK stipend rate, currently set at £14,777 per year.

How to apply: send me a CV and brief covering letter/email (no more than 1 page) explaining why you are interested and suitable by the Wednesday 11 July initial deadline. I will invite the best applicant/s to submit with me a formal application in time for the Friday 13 July second-stage deadline.

Royal Society Summer Science Exhibition Stall July 2-8

Next week researchers from the Modernising Medical Microbiology consortium, collaborating groups and I will exhibit the Resistance is Futile stall at the Royal Society Summer Science Exhibition. The exhibition is a free event in central London open to all visitors. Our stall is an opportunity to tell visitors about our research, and how advances in genetics are influencing day-to-day life. On show at the Resistance is Futile stall:

Oxford Nanopore Technology Demos

DNA sequencing in the NHS is shortening the time to diagnose antibiotic resistance in serious infections

Evolution Dance Mat

Resistance mutants arise spontaneously through chance copying errors during DNA replication

Antibiotic Resistance Coconut Shy

Antibiotic use gives resistance mutants a strong advantage so they rapidly increase in frequency.

The exhibition runs from Monday 2 July - Sunday 8 July at Carlton House Terrace, London, SW1Y 5AG. For more information about our stall click here and for general visitor information about the exhibition click here. Please spread the word!

During the exhibition we will be tweeting from @ResistanceIF

Our stall is generously supported by Oxford Nanopore Technology, the Nuffield Department of Medicine, and through public engagement research funding awarded to our research groups by the Wellcome Trust, the Royal Society, the National Institute for Health Research, the Oxford Biomedical Research Centre, the Natural Environment Research Council, the Medical Research Council, the Newton Fund and the Bill & Melinda Gates Foundation.