Salmonella Genomics Team Lead

**Details**:
**Reference number**:

- 336532**Salary**:

- £42,577 - £47,039-
- A Civil Service Pension with an average employer contribution of 27%**Job grade**:

- Senior Executive Officer- Senior Scientific Officer**Contract type**:

- Permanent**Business area**:

- APHA - Science**Type of role**:

- Science**Working pattern**:

- Flexible working, Full-time, Job share, Part-time**Number of jobs available**:

- 1Contents

Location

About the job

**Benefits**:
Things you need to know

Location
- New Haw, South East England, KT15 3NBAbout the job

**Job summary**:
Are you someone who can lead and manage change in a challenging and dynamic environment? Do you want a role safeguarding standards of animal and plant health and welfare? Then we would be interested in hearing from you.

You will be responsible for working independently to provide scientific and management leadership of the Salmonella Genomics Team within the Department of Bacteriology. The team collaborate with other teams across the Agency to deliver work commissioned under research projects and surveillance contracts involving the investigation of Salmonella of significance to food safety and public health. In particular, the Team Lead will provide critical support and guidance for outbreak investigations and delivery of Salmonella ‘serotyping’ using whole genome sequencing (WGS), with overall responsibility for a bioinformatics pipeline developed for this purpose.

**Job description**:
**You will**:

- Provide scientific and managerial leadership for the Salmonella Genomics Team
- Overall responsibility for the UKAS accredited Salmonella pipeline developed for automated, in silico serotyping of Salmonella spp using WGS generated data, meeting performance standards for operational delivery, maintenance and troubleshooting, as well as data archiving and quality assurance requirements
- Be a test consultant for Salmonella WGS based diagnostics
- Horizon scan for continuous improvement of bioinformatics analysis of large genomic datasets including the UKAS accredited bioinformatic pipeline for typing Salmonella
- Provide leadership in the enhancement of the developed Machine Learning (ML) models for source attribution of Salmonella
- Work with internal and external partners to ensure that the best and most robust bioinformatic methods are utilized, keeping abreast of all relevant developments, ensuring all new/novel tools selected for analysis are the most appropriate ones which are validated in a rigorous manner
- Provide oversight and guidance in development of searchable databases integrating NGS data with metadata from surveillance and research to enhance usability, interpretation, and generation of automated reports
- Be responsible for writing and delivering cutting-edge high impact manuscripts, reports and presentations to stakeholders at all levels
- Manage competing priorities, organising workload and requests from internal and external stakeholders at all levels
- Work to ensure that the team is appropriately resourced and equipped
- Provide leadership on the management, deployment, and storage of data, especially within the cloud - considering costs, accessibility, and legislative implications
- Work with internal teams across the Bacterial Characterisation Workgroup, Department of Bacteriology and Department of Epidemiological Sciences, as well as external collaborators, to integrate data analysis and data visualisation platforms from across the Department and other institutions into the work stream
- Manage good working relationship with UKHSA in relation to Salmonella
- Provide direct and functional management of scientists / bioinformaticians within the Team, with responsibility for performance monitoring, mentoring and development

**Person specification**:
**You will need experience and skills in the following**:

- Management, providing oversight and direction of two HSOs and a SO within the Team
- Design, delivery and reporting of Defra funded research work in a timely fashion
- Running and maintenance of Salmonella serotyping bioinformatics pipeline
- Working across Bacteriology, in particular the Bacterial Characterisation and Field Epidemiology Workgroups, and with Epidemiological Sciences to deliver BAU activities and rapid response to Salmonella
- Scientific knowledge and experience in food borne pathogens
- Good organisation skills and the ability to work on multiple projects and prioritise workloads
- Experience of taking a leading role on projects undertaken as part of a development team
- Ability to motivate and direct staff with differing skills and needs in science and bioinformatics to increase proficiency
- Demonstrated expertise in the management and analysis of large datasets
- Experience of writing manuscripts for publication, with a good publication record
- Proven understanding and experience in high-throughput data analysis and data processing in the field of genomics
- Experience in programming in hig