• Anywhere

Job summary

Job title � Bioinformatician

Profession � Gastrointestinal Infections and Food Safety (One Health)

Directorate – Clinical & Public Health�

Full Time equivalent – 37.5 hours

No of Roles � 1

Contract Type � Fixed Term Contract till 31st March 2025

Location � Colindale, London, NW9 5EQ

UKHSA offers hybrid working or home working for its employees � this means that whilst the role will be based in one of our UKHSA offices, there will be opportunities for an element of working from home. The balance between home and workplace working is to be agreed with the line manager, determined primarily by business need and in line with departmental policy. Some business travel will be required to other UKHSA offices.�Please be aware that this role can only be worked from within the UK and not overseas. Relocation expenses are not available

Working Pattern � Full Time /Flexible Working / Hybrid Working

Grade & Salary � Grade 7. Inner London – �53,396 – �62,286 per annum.�

New entrants to the Civil Service are expected to start on the minimum of the pay band.

The internal roles rules apply to existing Civil Servants, i.e. level transfers move on current salary or the pay range minimum, transfers on promotion move to new pay range minimum or receive 10% increase. Either case is determined by whichever is the highest.

This role is to be appointed under Civil Service Terms & Conditions. Full details on the T&C�s are found .

Closing Date � 28/05/2023 23:55pm. Unfortunately, late applications will not be considered

Interview Date � June 2023. Please note, these dates are subject to change.


At the United Kingdom Health Security Agency (UKHSA) our mission is to provide health security for the nation by protecting from infectious disease and external hazards.� We are a trusted source of advice to government and to the public, focusing on reducing inequalities in the way different communities experience and are impacted by infectious disease, environmental hazards, and other threats to health.

Our mission is challenging, innovative and in the spotlight. We will work to ensure our people have the diverse skills, experiences and backgrounds we need to thrive, that our employees are representative of the communities we serve and feel valued and enabled to play their part in delivering our work.

Creating our working culture is an ongoing process which we are developing by listening and learning together, hearing and acting upon diverse voices and opinions to develop a common sense of identity and effective ways of working.

Gastrointestinal Infections and Food Safety (One Health) Division

The Gastrointestinal Infections and Food safety (One Health) Division is located within UKHSA�s Clinical and Public health Directorate at Colindale. The Division remit includes providing specialist epidemiology and surveillance for Gastrointestinal Infections (GI), coordinating the investigation of national outbreaks, advising government on the risks posed by various gastrointestinal pathogens and responding to national and international health concerns.�

The Division manages the above functions across a broad range of pathogens including enteric and food borne bacteria, viruses and parasites. It plays an important role in Food safety and One Health and in using advanced techniques such as whole genome sequencing to track national and international outbreaks and antimicrobial resistance in foodborne bacteria.

The post is funded by the National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Genomics and Enabling Data (GED).� It brings together leading researchers from the Universities of Warwick, Cambridge and the Wellcome Trust Sanger Institute with UKHSA working in partnership to exploit synergy, world-class facilities, and breadth and depth in relevant research between these institutions.

The mission of the HPRU in Genomics and Enabling Data is to provide the methodological backbone required to improve national public health using new rich data sources. In particular, recent and ongoing developments in whole-genome sequencing technologies have a widely acknowledged great potential to help us improve public health, but this potential is currently incompletely realised due to a lack of sound and scalable methodology to interpret the data in the correct epidemiological context.

Job Overview

This post will focus on helping shape and deliver the objectives of the HPRU GED as set out in its yearly Forward Business Plan, and especially those of its Research Theme 3, Interface and Implementation.

Although public repositories are available to store genome sequences, they offer little capacity for linkage of enabling metadata. In addition, many genomic analysis and visualisation tools require bioinformatic expertise that can create a barrier to those responsible for managing public health incidents informed by genomic data. The Interface and Implementation Theme will optimise the methodologies for genomics integration into surveillance, including sample metadata collection, genome analysis and visualisation of complex merged genomic and epidemiological data, such as location, time of sampling and non-identifying information about patients. We aim to enhance the interfaces to data collection tools, the databases themselves and the combined genomic and epidemiological datasets in such a way that data flow and interpretation is as frictionless as possible across the whole range of UKHSA activities.

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

  • Provide strategic direction and goals within the remit of HPRU GED, especially Research Theme 3.
  • 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.
  • Prepare and present at national and international meetings reports, posters and publications arising from data.
  • Job description

    To support delivery of the objectives of the HPRU GED as set out in its yearly Forward Business Plan, and especially those of its Research Theme 3, Interface and Implementation, including:

  • Liaise with the HPRU GED directors and other scientists involved (especially the Research Theme 3 leads) in order to understand the main goals of the yearly Forward Business Plan and provide expert support and leadership.
  • Assist with setting out the yearly Forward Business Plan and implement it as needed.
  • Work with other bioinformaticians and academics in the HPRU GED 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 by HPRU GED and especially Research Theme 3, including graphical user interfaces and data collection tools to help epidemiologists.
  • Provide mentoring, technical tutoring and strategic advice to other HPRU GED 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 reports, posters and publications arising from the work.
  • Participate and contribute to UKHSA meetings and the development and implementation of a bioinformatics strategy.

    The above is only an outline of the tasks, responsibilities and outcomes required of the role.

  • You will carry out any other duties as may reasonably be required by your line manager.
  • The job description and person specification may be reviewed on an ongoing basis in accordance with the changing needs of the division and UKHSA.
  • It should be noted that some of the data is of a confidential nature and must not be communicated to other persons except where required for authorised purposes.

  • Identify, discuss and action own professional performance and training / development needs with your line manager through appraisal / individual development plan. Attending internal / external training events
  • Participate in all mandatory training as required.

    The post holder will develop working relationships and communicate regularly with a wide range of individuals, clinical and non-clinical, internal and external to UKHSA. This will include;


  • HPRU GED Directors
  • HPRU GED Theme Leads
  • Staff in Gastrointestinal Infections and Food Safety (One Health) Division.
  • Bioinformatics and Laboratory staff in Colindale and UK Health Security Agency
  • HPRU GED staff in Warwick and elsewhere, as needed.
  • Bioinformaticians in the Unit, core bioinformaticians and the IT department in the deployment of pipelines and tools.
  • Staff with pathogen specific expertise within UKHSA.
  • External

  • Collaborators from devolved administrations including but not limited to Animal Plant Health Agency, Public Health Wales, Public Health Scotland
  • Collaborators on projects at other Institutes and academic centres including ECDC and EFSA.
  • Collaborators and other groups working on genomics of bacterial pathogens.
  • We pride ourselves as being an employer of choice, where Everyone Matters promoting equality of opportunity to actively encourage applications from everyone, including groups currently underrepresented in our workforce.

    UKHSA ethos is to be an inclusive organisation for all our staff and stakeholders. To create, nurture and sustain an inclusive culture, where differences drive innovative solutions to meet the needs of our workforce and wider communities. We do this through celebrating and protecting differences by removing barriers and promoting equity and equality of opportunity for all.

    Person specification

    Essential Criteria:

  • Higher degree (i.e., PhD or above) in Bioinformatics or a related quantitative discipline
  • Evidence of continuous professional and academic development
  • 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
  • Multitasking; time management skills; able to work to deadlines and achieve milestones
  • Substantial experience at a senior level including team leadership and management
  • 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)
  • Able to make decisions autonomously, when required, on difficult issue, working to tight and often changing timescales
  • Evidence of clear and concise scientific writing and high-level oral presentation skills at national and international level. Able to convey instructions, ideas and opinions clearly
  • Ability to analyse, interpret and summarise complex data and prepare reports
  • Ability to provide future direction and strategy
  • Ability to plan and manage several high-profile projects simultaneously and conduct multidisciplinary scientific activity
  • Ability to analyse complex facts and situations and demonstrate good judgment and decision-making skills and develop a range of options of solutions
  • Ability to take decisions on difficult and contentious issues where there may be a number of courses of action
  • Self-motivated and able to motivate others and an effective facilitator of team working
  • Ability to work under pressure and to deadlines
  • The promotion of equality of opportunity and good working relations (providing practical leadership).
  • Desirable 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 HPRU GED and their impact on public health
  • Experience of managing collaborative research projects
  • Database management
  • Benefits

  • Learning and development tailored to your role
  • An environment with flexible working options
  • A culture encouraging inclusion and diversity
  • A with an average employer contribution of 27%