Job Description

Your role 

We are seeking a highly motivated Bioinformatician to strengthen our submission and analysis pipelines for functional genomics data, with a strong focus on new technologies such as spatial transcriptomics and AI-ready data formats.

You will

• Develop and maintain submission and brokering pipelines, including new functionality for spatial transcriptomics and emerging functional genomics technologies.
• Design and implement validation tools for both metadata and file formats of existing and emerging functional genomics assays, contributing to community standards and FAIR data practices.
• Support and enhance internal brokering services for functional genomics submissions, ensuring they remain sustainable and adaptable.
• Develop, maintain, and optimise automated processing pipelines (HPC and Cloud) for harmonisation of functional genomics datasets (bulk RNA-seq, scRNA-seq, spatial assays).
• Contribute to downstream integration into Expression Atlas and related resources, with scope to explore new visualisation or analysis approaches.
• Update data models and outputs to ensure they are AI-ready, interoperable, and reusable.
• Apply modern software engineering best practices, including version control, testing, CI/CD, reproducibility, and containerisation.
• Ensure pipelines and services run reliably in production, with a strong focus on usability and reproducibility for end-users.
• Engage actively with the user community through helpdesk support, training events, and presentations, ensuring that tools and services meet their needs.
• Collaborate with curators, developers, and external partners, engage with the user community, and represent the team at international meetings.

You have 

• MSc or PhD in Bioinformatics, Computer Science, or a related field (or equivalent experience)
• Proven experience developing and optimising bioinformatics pipelines
• Strong experience working in Unix/Linux environments on HPC and/or Cloud platforms with demanding use cases.
• Strong programming skills in at least two of Python, R, Bash, or Perl.
• Proven experience with workflow management systems (e.g. Nextflow or Snakemake).
• Proficiency in Git/GitHub and robust testing strategies
• Experience with dependency management (containers, Conda).
• Working knowledge of relational databases (SQL and NoSQL) and REST APIs.
• Familiarity with functional genomics data types (bulk RNA-seq, single-cell RNA-seq; spatial an advantage).
• Excellent communication skills, attention to detail, and ability to deliver high-quality work to deadlines.

You may also have

• Experience with data brokering and curation, metadata standards, or ontologies.
• Interest in functional genomics data visualisation or data science.
• Knowledge of DevOps practices, Kubernetes, CI/CD, or software packaging.
• Interest in data visualisation or AI/ML methods for bioinformatics.
• DevOps experience is a plus

Apply now! Benefits and Contract Information

• Financial incentives: depending on circumstances, monthly family/marriage allowance of £278 monthly child allowance of £336 per child. Non resident allowance up to £569 per month. Annual salary review, pension scheme, death benefit, long-term care, accident-at-work and unemployment insurances
• Hybrid working arrangements
• Private medical insurance for you and your immediate family (including all prescriptions and generous dental & optical cover)
• Generous time off: 30 days annual leave per year, in addition to eight bank holidays
• Relocation package including installation grant (as applicable)
• Campus life: Free shuttle bus to and from work, on-site library, subsidised on-site gym and cafeteria, casual dress code, extensive sports and social club activities (on campus and remotely)
• Family benefits: On-site nursery, child sick leave, generous parental leave, holiday clubs on campus and monthly family and child allowances
• Contract duration: This position is a 12 month fixed-term contract – Project limited (with potential for renewal depending on funding).
• Salary: Monthly salary starting at £3,303 after tax but excl. pension & insurances) + benefits (Total package will be dependent on family circumstances) 
• International applicants: We recruit internationally and successful candidates are offered visa exemptions. Read more on our page for international applicants.
• Diversity and inclusion: At EMBL-EBI, we strongly believe that inclusive and diverse teams benefit from higher levels of innovation and creative thought. We encourage applications from women, LGBTQ+ and individuals from all nationalities.
• Job location: This role is based in Hinxton, near Cambridge, UK. You will be required to relocate if you are based overseas and you will receive a generous relocation package to support you.

How to Apply

Job Categories: Equal Opportunities. Job Types: Full-Time. Salaries: 40,000 - 60,000.

Apply for this Job