Bioinformatician

The United Kingdom Health Security Agency (UKHSA) is a system leader for health security; taking action internationally to strengthen global health security, providing trusted advice to government and the public and reducing inequalities in the way different communities experience and are impacted by infectious disease, environmental hazards, and other threats to health.

UKHSA's remit, as an agency with a global-to-local reach, is to protect the health of the nation from infectious diseases and other external threats to health. As the nation's expert national health security agency UKHSA will:

• Prevent: anticipate threats to health and help build the nation's readiness, defences and health security
• Detect: use cutting edge environmental and biological surveillance to proactively detect and monitor infectious diseases and threats to health
• Analyse: use world-class science and data analytics to assess and continually monitor threats to health, identifying how best to control and mitigate the risks
• Respond: take rapid, collaborative and effective actions nationally and locally to mitigate threats to health when they materialise
• Lead: lead strong and sustainable global, national, regional and local partnerships designed to save lives, protect the nation from public health threats and reduce inequalities.

Job overview

This post is based within the Sexually Transmitted Infections Reference Laboratory at Colindale, part of the Bacteriology Reference Department within UKHSA's Science Group. STIRL provides national reference and surveillance services for bacterial sexually transmitted infections (STIs), supporting diagnostic laboratories, clinicians, and public health teams. STIRL includes microbiologists, healthcare scientists, and bioinformaticians working collaboratively to deliver world-class reference testing, surveillance, and outbreak support.

STIRL provides specialised testing to detect, investigate, and characterise clinically important STIs and monitor antimicrobial resistance. Using established and innovative phenotypic and genotypic assays, STIRL assesses the susceptibility of STIs to treatments, supporting case management and national surveillance. It plays a key role in defining and investigating outbreaks, identifying diagnostic escape mutants, and providing guidance on STIs.

The Bioinformatician will play a pivotal role in developing and implementing the bioinformatics and public health informatics strategy for STIRL. They will design and build analytical pipelines for genomic data from surveillance programmes, reference investigations, and research studies. The post holder will lead genomic analyses of N. gonorrhoeae, C. trachomatis, and M. genitalium, support national surveillance programmes, and contribute to publications, reports, and outbreak investigations.

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Bioinformatics

• Lead the analysis and interpretation of bacterial genomic sequences within the remit of the Unit
• Conduct whole and partial genome analyses to address evolutionary, epidemiological, and antimicrobial resistance questions.
• Monitor developments in bioinformatics and assess their application to the Unit and the wider GRASP and MARS programmes
• Provide expert technical advice on bioinformatics approaches and scientific solutions
• Ensure the secure handling, storage, and retrieval of sensitive data
• Troubleshoot and resolve issues with bioinformatics software and pipelines

Information Technology

• Work with the Lead Bioinformatician, Unit Head, Technical Manager, and Quality teams to ensure the accuracy of laboratory information systems, contributing to data quality audits
• Maintain up-to-date knowledge of IT and informatics developments relevant to UKHSA operations

Professional Development and Collaboration

• Identify and pursue professional development needs through the appraisal process and attend all mandatory training
• Collaborate closely with the Bioinformatics Unit, Reference Services, and the Central Sequencing Unit
• Liaise with UKHSA ICT and relevant internal and external stakeholders, including NHS, academic, and commercial partners
• Undertake other reasonable duties aligned with the evolving needs of the organisation

Please be aware this list is not exhaustive.

Working for our organisation

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.  

Please visit our careers site for more information

Detailed job description and main responsibilities

The Bioinformatician will play a key role within the Sexually Transmitted Infections Reference Laboratory (STIRL), the national reference centre for bacterial STIs. The post holder will support surveillance, outbreak investigation, and research through the analysis, interpretation, and management of genomic data.

They will design, develop, and maintain bioinformatics pipelines for bacterial genome analysis, enabling detection and monitoring of antimicrobial resistance. The role involves close collaboration with scientific colleagues across UKHSA to deliver high-quality, reproducible outputs informing national surveillance programmes, including GRASP and MARS.

The Bioinformatician will also contribute to the development of analytical approaches, advise scientific staff, and support publications, technical reports, and presentations. Collaboration with the UKHSA Bioinformatics Unit, Reference Services, and Central Sequencing Unit is essential to ensure delivery aligns with national quality and accreditation standards.

Bioinformatics

• Conduct whole and partial genome analyses to investigate evolution, epidemiology, and antimicrobial resistance
• Evaluate and apply bioinformatics tools and methodologies to strengthen laboratory outputs and surveillance
• Provide specialist guidance on analytical approaches, visualisation, and bioinformatics practice to colleagues and collaborators
• Ensure secure handling, storage, and retrieval of genomic data in line with UKHSA governance
• Develop, maintain, and troubleshoot pipelines, workflows, and computational tools for operational and research needs
• Work with senior scientists, management, and quality teams to maintain data integrity and accuracy
• Support data quality audits and contribute to laboratory information system improvements
• Maintain awareness of relevant IT and informatics developments
• Assist with documentation and validation of software linked to UKAS accreditation

Professional Development

• Support genomic analysis pipelines for N. gonorrhoeae, C. trachomatis, M. genitalium, and other bacterial STIs
• Generate analyses and reporting to support surveillance and outbreak response
• Contribute to reports, publications, and national surveillance outputs
• Work collaboratively with UKHSA units, NHS partners, and academic institutions to enhance surveillance and data interpretation
• Provide supervision, training, and mentoring for staff, students, and visitors where delegated
• Identify and pursue learning needs through appraisal and development review
• Maintain competencies and complete mandatory UKHSA training, including governance, safety, and compliance
• Represent the Unit at meetings, conferences, and seminars as required
• Undertake duties consistent with the nature and grade of the role as requested by senior management
• Promote and uphold UKHSA values including excellence, integrity, and inclusivity

Essential role criteria (including qualifications, licenses and registrations):

• A higher degree (MSc or equivalent experience) in Bioinformatics, Computer Science, or a related subject
• Experience in interpreting bacterial sequences, genotyping, and phylogenetic analysis
• Proven experience in analysing Illumina datasets and proficiency with standard bioinformatics and statistical tools for sequence assembly, alignment, and interpretation
• Demonstrated expertise in large-scale analyses of molecular sequence data and programming/scripting languages such as Python, Perl, or C
• Proven ability to analyse, summarise, and interpret complex epidemiological and genomic data
• Experience of coordinating projects in complex or multi-stakeholder scientific environments
• Excellent communication skills, with the ability to produce scientific reports, correspondence, and presentations for diverse audiences

Desirable role criteria:

• Knowledge and experience of using high-performance computing (HPC) clusters and version control systems (e.g. Git)
• Experience of software containerization (e.g. singularity) and use of workflow managers (e.g. Nextflow) for pipeline development
• Understanding of database design, architecture, and implementation on a range of platforms
• Experience of authoring or contributing to peer-reviewed publications within the field of bacterial genomics or STIs

Selection Process Details

Stage 1: Application & Sift  

This vacancy is using Competency.

At sift stage you will be assessed against the 7 Essential Criteria listed in the job advert.

You will be required to complete an:

•    Application form ('Employer/ Activity history' section on the application) 

• word supporting statement.

Healthjobs UK has a word limit of 1500, but your supporting statement must be no more than 700 word-count. This should outline how your skills, experience, and knowledge, provide evidence of your suitability for the role.

Please note you will not be able to upload your CV. You must complete the application form in as much detail as possible. Please do not email us your CV. 

The application form and supporting statement will be marked together.

Longlisting

In the event of a large number of applications we may longlist into 3 piles of:

• Meets all essential criteria 
• Meets some essential criteria  
• Meets no essential criteria  

We will take piles "Meets all essential criteria" through to shortlisting.

Shortlisting

In the event of a large amount of applications, we will sift on:

• Experience in interpreting bacterial sequences, genotyping, and phylogenetic analysis
• Proven experience in analysing Illumina datasets and proficiency with standard bioinformatics and statistical tools for sequence assembly, alignment, and interpretation
• Demonstrated expertise in large-scale analyses of molecular sequence data and programming/scripting languages such as Python, Perl, or C

Please note feedback will not be provided at this stage.

Interview stage (competency based):

You will be invited to a face to face interview. In exceptional circumstances, we may be able to offer a remote interview.

This vacancy is being assessed using Competency framework. During the interview we will assess against the below:

• Knowledge
• Experience
• Skills and Abilities 

You will be asked to prepare and present a 5-10 minute presentation at the start of your interview. 

Please prepare a ten-minute presentation describing a bioinformatics project you have been involved in. The presentation should include the biological question, your analytical approach, and some Python source code that you contributed to the project (at least one slide). We suggest you select a representative sample of code (e.g. a function, class, or module rather than a complete pipeline or analysis). The objective is for us to gain insights into your coding style and practices and to assess your ability to communicate.

After your presentation, we will ask questions about the information you have shared with us. The interview will then continue with questions covering the competencies specified in the advert. Finally, there will be time for you to ask us some questions about the role and organisation.

Once this job has closed, the job advert will no longer be available. You may want to save a copy for your records.

Additional Information

Location 

This role is being offered as hybrid working based at our Scientific Campus in Colindale, London. We offer great flexible working opportunities at UKHSA and operate using a hybrid working model where business needs allow. This provides us with greater flexibility about how and where we work, to get the best from our workforce. As a hybrid worker, you will be expected to spend a minimum of 60% of your contractual working hours (approximately 3 days a week pro rata, (averaged over a month). If based at one of our scientific campuses, you will be required to have a minimum of a Counter Terrorism Check security vetting check as a minimum. For meaningful National Security Vetting checks to be carried out individuals need to have lived in the UK for a sufficient period of time.

Security Clearance Level Requirement  

Successful candidates must pass a disclosure and barring security check.   

You should normally have been resident in the United Kingdom for the last 3 years as the role requires Counter Terrorism Check (CTC) clearance. In exceptional circumstances UK residency less than the outlined periods may not necessarily bar you from gaining national security vetting and applicants should contact the Vacancy Holder/Recruiting Manager listed in the advert for 
further advice.   

Eligibility Criteria

External: Open to all external applicants (anyone) from outside the Civil Service (including internal applicants).   

Salary Information

If you are successful at interview, and are moving from another government department, NHS, or Local Authority, the relevant starting salary principles for level transfers or promotions will apply. Otherwise, roles are offered at the pay scale minimum for the grade, but in exceptional circumstances there may be flexibility if you are able to demonstrate you are already in receipt of an existing, higher salary. Pay increases are through the relevant annual pay award for the role and terms. 

IMPORTANT - PLEASE READ 

Artificial Intelligence (AI)

Artificial Intelligence can be a useful tool to support your application, however, all examples and statements provided must be truthful, factually accurate and taken directly from your own experience. Where plagiarism has been identified (presenting the ideas and experiences of others, or generated by artificial intelligence, as your own) applications may be withdrawn and internal candidates may be subject to disciplinary action. Please see our candidate guidance for more information on appropriate and inappropriate use. 

Link below:

Artificial intelligence and recruitment | Civil Service Careers

This is a Non-Reserved post under the Civil Service Nationality Rules. To be eligible for employment in the UK Civil Service applicants must meet the Civil Service Nationality Rules (CSNRs) which operate independently of and additionally to the Immigration Rules. Applicants must also meet necessary security and vetting requirements, along with any other relevant pre-employment checks. 

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) (opens in a new window)
• 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

For more information on job nationality requirements and the right to work in the UK, see the Civil Service Nationality rules (opens in a new window) and the UK Visas and Immigration rules (opens in a new window)

For posts on UKHSA Civil Service terms and conditions, new entrants to the Civil Service are expected to start on the minimum of the pay band. For existing Civil Servants and roles advertised across government, the rules of transfer apply, i.e., level transfers move on current salary or the pay range minimum, transfers on promotion move to new pay range minimum or receive a 10% increase. Either case is determined by whichever is the highest.  

The Civil Service pay structure and progression is different from NHS Agenda for Change (AfC), most local authority pay grades and other systems that have annual pay increments. For further details, please refer to the Information Sheet- Starting Salaries & Benefits attachment. 

For AfC or Medical/Dental posts, you must have the correct professional registration to be appointed. The pay will follow the AfC or Medical & Dental terms & conditions. You may be asked to provide evidence of previous service whilst we are conducting pre-employment checks to determine your starting salary. 

For Temporary Appointments, if you are not currently a civil servant, you will take up the post on a Fixed Term appointment.  You may be able to take this role up as a Secondment.  If you are an existing Civil Servant, based outside of the UKHSA, you will take up the post as a loan which you will need your department to agree. You cannot take the post up as a fixed term. If you are an existing UKHSA member of staff, you will take up the post as either a level transfer or a temporary promotion as per the UKHSA's Pay policy.  

Given the nature of the work of the UKHSA, as a Category 1 responder under the Civil Contingencies Act, you may be required in an emergency, if deemed a necessity, to redeploy to another role at short notice. You may also be required to work at any other location, within reasonable travelling distance of your permanent home address, in line with the provisions set out in your contract of employment. 

Late Applications will unfortunately not be considered. 

Working for the Civil Service

The Civil Service Code (opens in a new window) sets out the standards of behaviour expected of civil servants.

We recruit by merit on the basis of fair and open competition, as outlined in the Civil Service Commission's recruitment principles (opens in a new window).

The Civil Service embraces diversity and promotes equality of opportunity. The law requires that selection for appointment to the Civil Service is on merit on the basis of fair and open competition, as outlined in the Civil Service Commission's Recruitment Principles.

If you feel your application has not been treated in accordance with the Recruitment Principles, and you wish to make a complaint, in the first instance, you should contact UKHSA Public Accountability Unit via  email:  [email protected] If you are not satisfied with the response you receive from the Department, you can contact the Civil Service Commission: Visit the Civil Service Commission website here. 

Reserve List - If more than the required number of suitable candidates pass the interview criteria, you may be kept on a reserve list for 12 months subject to your agreement. You may be contacted, in merit-order, if similar roles with closely matching essential criteria become available and the department choose to appoint from a reserve list. 

The panel will assess if candidates meet the requirement of the role first, using a specific benchmark system. If you are interviewed for the post and do not meet the required threshold for the specified grade, your application may be assessed against a similar, lower grade role and you may be offered the post should one be available. 

Interview expenses will not be reimbursed. 

UKHSA is required to check employment and/or education history covering three consecutive years. Please ensure you give details of at least two different referees, even if you were employed in one company for three years or more. 
 
If you are offered a job, information will also be transferred into the national NHS Electronic Staff Records system. Please note, all communication regarding your application will be made via email, please ensure you check your junk/spam folders as emails are sometimes filtered there. 

Any move to UKHSA from another employer will mean you can no longer access childcare vouchers. This includes moves between government departments. You may however be eligible for other government schemes, including Tax-Free Childcare. Determine your eligibility at . 

 Benefits of working at UKHSA include: 

• Generous annual leave: 
  -26 days for the first 5 years of continuous service 
  -28 days after 5 years of continuous service 
  -32 days after 10 years of continuous service 
  -Plus public holidays and one privilege day for the King's birthday 
• Access to a generous Defined Benefit pension scheme with employer contributions. 
• Access to a cycle-to-work salary sacrifice scheme, season ticket advances and payroll giving.
• Access to a retail discounts and cashback site.
• We also promote flexible working patterns (part-time, job-share, condensed hours). UKHSA views flexible working as essential in enabling us to recruit and retain talented people, ensuring that they are able to enjoy a long-lasting career with us. All employees have the right to apply for flexible working and there are a range of options available including working from home, compressed hours and job sharing.
• We also offer a generous maternity/ paternity and adoption leave package. 

Hybrid Working

UKHSA operates a hybrid working model where business needs allow.  This provides us with greater flexibility about how and where we work, to get the best from our workforce.  

As a hybrid worker, you will usually spend a minimum of 60% of your contracted hours (averaged over a month) working at one of UKHSA's locations (approximately 3 days a week pro rata) and the rest of your time working from home. 

Disability Confident Scheme

The Civil Service embraces diversity and promotes equal opportunities. As such, we run a Disability Confident Scheme for candidates with disabilities who meet the minimum selection criteria at sift to ensure these candidates are invited to interview.   If you wish to be included in this scheme please tick the box on your application form.  

Reasonable Adjustments

The Civil Service is committed to making sure that our selection methods are fair to everyone.

To help you during the recruitment process, we will take into account any reasonable adjustments that could help you.

An adjustment is a change to the recruitment process or an adjustment at work. 

This is separate to the Disability Confident Scheme. 

If you need an adjustment to be made at any point during the recruitment process you should: 

Contact the recruitment team in confidence as soon as possible to discuss your needs. 

You can find out more information about reasonable adjustments across the Civil Service here:

International Police Check

If you have spent more than 6 months abroad over the last 3 years you may need an International Police Check.  This would not necessarily have to be in a single block, and could be time accrued over that period. 

Internal Fraud check 

If successful for this role as one aspect of pre-employment screening, applicant's personal details – name, national insurance number and date of birth - will be checked against the Cabinet Office Internal Fraud Hub and anyone included on the database will be refused employment unless they can show exceptional circumstances. Currently this is only for External candidates to the Civil Service.

Security Vetting

Please check the Security Clearance needed for the role and follow the link for more information:

Future location 

UKHSA is investing in a new state-of-the-art National Biosecurity Centre in Harlow, Essex, which will eventually bring together teams currently based at Canary Wharf, Colindale and Porton Down. For more details, please see: Huge biosecurity centre investment to boost pandemic protection - GOV.UK.

The new facilities will start becoming operational in the mid-2030s, with full completion by 2038. Staff will move in phases as facilities become available. If you're appointed to a role currently based at Canary Wharf, Colindale or Porton Down, please note that we'll continue investing in these sites for the next decade. As we get closer to the transition, we'll provide full information about relocation support available to staff.

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