Research Assistant/Associate in Genomics of Infectious Disease

Job description
Job summary

We are seeking a Research Associate to work on antimicrobial resistance and genomic epidemiology of the major mould pathogen Aspergillus fumigatus. The post will be based in the MRC Centre for Global Infectious Disease Analysis (GIDA) within the School of Public Health at Imperial College London. The position is funded by a NERC Highlight 4-year Award, led by Prof Matthew Fisher, and will investigate the eco-evolutionary drivers of drug-resistant Aspergillus fumigatus . The overarching aim of the project is to use a landscape-scale systems analysis that links the usage of fungicides in the environment to ecological settings where selection for antifungal resistance occurs.

Your main research directions are to:

Develop a population genomic framework to track and trace the flow of antifungal resistant genotypes using a landscape genetic framework.

Understand the dispersal kernel of antifungal resistant bioaerosols across spatial scales in order to provide a better understanding of sources and resulting human exposures.

Develop metagenomic approaches to identify patterns of co-occurrence between fungicides, microbial community diversity / ecosystem functioning and the prevalence of antifungal resistance to provide better understanding of the occurrence of antifungal resistance hotspots.

To develop methods to integrate genomic date with other types of data – spatial, land-use, chemistry, biodiversity (microbiomes)

By dissecting the extended consequence of fungicide use as these chemicals drive the evolution of fungal antimicrobial resistance, the project will address this problem within its greater ‘One Health’ context. Our approach will develop the knowledge base that is needed for policy makers to understand the current risk as well as to mitigate the selection-pressure driving future emergence of fungal antimicrobial resistance in the environment.

Duties and responsibilities

You will use your skills as a bioinformatician to innovate approaches that use modern genomic toolkits to track the spread of antifungal resistant A. fumigatus in the UK environment. Key duties will be to:

• Use Phylogenetic Generalised Linear Mixed Models (PGLMM ) and allied approaches to integrate evolutionary and microbial community diversity across the fungicide exposome that we measure.
• You will also work within the wider team to develop methods to shotgun-sequence air (AirSeq) in order to better understand the dispersal kernel of antifungal resistant bioaerosols in order to assess exposure risk from environmental hotspots.
• The position will be a key role within the project, coordinating research across our partners at the UK Centre for Ecology and Hydrology CEH, NIAB and the Open University.

Essential requirements

We are looking for a skilled bioinformatician / genomicist to undertake population genomic analysis of fungal (eukaryote) genomes.

• You will hold a PhD in genomics / bioinformatics or a closely related discipline, or equivalent research, industrial or commercial experience.*
• You should be able to creatively code in a suitable bioinformatic scripting language (e.g.t, Python, C++ etc.) and to be familiar with R and GitHub.
• You should be comfortable working within a large team that spans several institutions, and to have the appropriate communication skills.
• We ideally require strong biological knowledge in ecology, evolution and microbiome analysis. A driving licence is not a prerequisite but would be an advantage as there is a strong fieldwork component to the project.

*Candidates who have not yet been officially awarded their PhD will be appointed as Research Assistant.

Further information

Should you require any further details on the role please contact: Matthew Fisher ([email protected] )

Candidates who have not yet been officially awarded their PhD will be appointed as a Research Assistant within the salary range £38,194 – £41,388 per annum.

The College is currently trialling a Work Location Framework until early 2023.  Hybrid working may be considered for this role and the role holder may be expected to work 60% or more of their time onsite, with 40% the minimum time spent onsite.  The opportunity for hybrid working will be discussed at interview.

The College is a proud signatory to the San-Francisco Declaration on Research Assessment (DORA),which means that in hiring and promotion decisions, we evaluate applicants on the quality of their work, not the journal impact factor where it is published. For more information, see https://www.imperial.ac.uk/research-and-innovation/about-imperial-research/research-evaluation/

The College believes that the use of animals in research is vital to improve human and animal health and welfare. Animals may only be used in research programmes where their use is shown to be necessary for developing new treatments and making medical advances. Imperial is committed to ensuring that, in cases where this research is deemed essential, all animals in the College’s care are treated with full respect, and that all staff involved with this work show due consideration at every level.

http://www.imperial.ac.uk/research-and-innovation/about-imperial-research/research-integrity/animal-research / 

Imperial College is committed to equality of opportunity, to eliminating discrimination and to creating an inclusive working environment. We are an Athena SWAN Silver award winner, a Stonewall Diversity Champion, a Disability Confident Employer and work in partnership with GIRES to promote respect for trans people.

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