JOB SUMMARY

This post will focus on helping shape and deliver the objectives of the Genomics Health Protection Research Unit (HPRU) as set out in its yearly Forward Business Plan.
This bioinformatics role within the genomics HPRU will work with partners at UKHSA to develop methods which allow complex whole genome sequence data to be used as an input into AI and deep learning methodologies. In the first instance the theme will focus on Tuberculosis mycobacterium antimicrobial resistance, but there will be opportunities to expand approaches to other human pathogens. This role will also provide bioinformatics support for other whole genome sequencing analysis projects within themes 2 and 3, these are likely to include phylogenetic, AMR and SNP analysis of both viral and bacterial pathogens. A key aim of the genomics HPRU is the translation of methodology into UKHSA routine sequencing activity, therefore this post holder will also work with the Bioinformatics division to ensure that methodologies and tools are compatible with deployment as part of routine WGS processing.

JOB DESCRIPTION

The postholder will develop bioinformatics and public health informatics for the Genomics HPRU:

• Provide bioinformatics expertise and insight into projects and proposals put forward as part of the Genomics HPRU
• Design and validate bioinformatics tools, pipelines, and methods suitable for analysis and comparison of the genome sequences generated at UKHSA and elsewhere.
• Compile, in appropriate databases and formats, complex data arising from whole-genome sequencing (WGS) from a range of pathogens.
• Undertake analysis on data arising from WGS, in particular for the validation of proposed methods and techniques.

To support delivery of the objectives of the Genomics Health Protection Research Unit (HPRU) as set out in its yearly Forward Business Plan, including:

• Liaise with the HPRU directors and other scientists involved in order to develop and deliver the main goals of the yearly Forward Business Plan and provide expert support and leadership.
• Assist with developing and updating the yearly Forward Business Plan
• Work with other bioinformaticians and academics in the Genomics HPRU and at UKHSA on designing, implementing, and validating efficient bioinformatics pipelines suitable for analysis and comparative genomics of relevant pathogen sequences.
• Undertake SNP, recombination and phylogenetic analyses, and analysis of data arising from WGS, including temporal and geographic cluster analysis, characterisation of clones, correlation of genotypic vs. phenotypic characteristics, and others, as needed, in order to validate proposed methods and to generate databases that can be used as unit test data for such methods.
• Assist with the deployment of technologies for the analysis and comparative analysis of high-throughput WGS in all sections of UKHSA, as required including graphical user interfaces and data collection tools to help epidemiologists.
• Provide mentoring, technical tutoring and strategic advice to other HPRU members.
• Supervise and train junior and visiting Bioinformaticians in the use of appropriate bioinformatics applications, tools and safe coding practices and work in collaboration with others in UKHSA and externally as required.
• Prepare and present reports, posters and publications arising from the work. There may be opportunities to present at international meetings.
• Participate and contribute to UKHSA meetings and the development and implementation of a bioinformatics strategy.

NATIONALITY REQUIREMENTS

This job is broadly open to the following groups:

• UK nationals
• nationals of the Republic of Ireland
• nationals of Commonwealth countries who have the right to work in the UK
• nationals of the EU, Switzerland, Norway, Iceland or Liechtenstein and family members of those nationalities with settled or pre-settled status under the European Union Settlement Scheme (EUSS)
• nationals of the EU, Switzerland, Norway, Iceland or Liechtenstein and family members of those nationalities who have made a valid application for settled or pre-settled status under the European Union Settlement Scheme (EUSS)
• individuals with limited leave to remain or indefinite leave to remain who were eligible to apply for EUSS on or before 31 December 2020
• Turkish nationals, and certain family members of Turkish nationals, who have accrued the right to work in the Civil Service

Further information on nationality requirements

ESSENTIAL ROLE CRITERIA:

• Higher degree (i.e., PhD or above, or several years’ experience in a similar position) in Bioinformatics or a related quantitative discipline
• Application and adaptation of bioinformatics tools to analyse biological data using the UNIX command line.
• Experience in the analysis of large molecular datasets (incl. high throughput sequencing data).
• In-depth understanding of the principles of DNA sequence analysis and phylogenetics.
• Substantial record of peer-reviewed publications and involvement in securing research proposal funding
• Fluent at programming / script writing (eg. Python, bash, R, C, C++, functional languages)

DESIRABLE ROLE CRITERIA:

• Knowledge of Molecular microbiology and Molecular epidemiology
• Demonstrated experience of co-ordinating projects in complex and challenging environments
• Understanding of the public sector
• Understanding of the relevance of microbiology, epidemiology, bioinformatics and genomics on public health issues
• Knowledge of pathogens relevant to the Genomics HPRU and their impact on public health
• Experience of managing collaborative research projects
• Database management