Bioinformatician - Functional Genomics Submissions and Pipelines at Embl

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

Contract length:

12 month fixed-term contract - Project limited (with potential for renewal depending on funding).

Salary:

Grade 5 or 6 - monthly salary starting at £3,303.40 per month after tax but excluding pension and insurance contributions. Plus generous benefits.

Why join us

Do something meaningful
At EMBL-EBI you can apply your talent and passion to accelerate science and tackle some of humankind's greatest challenges. EMBL-EBI, part of the European Molecular Biology Laboratory, is a worldwide leader in the storage, analysis and dissemination of large biological datasets. We provide the global research community with access to publicly available databases and tools which are crucial for the advancement of healthcare, food security, and biodiversity.
 

Join a culture of innovation
We are located on the Wellcome Genome Campus, alongside other prominent research and biotech organisations, and surrounded by beautiful Cambridgeshire countryside. This is a highly collaborative and inclusive community where our employees enjoy a relaxed atmosphere. We are committed to ensuring our employees feel valued, supported and empowered to reach their professional potential.  Watch this video to see how EMBL-EBI makes an impact.

Enjoy lots of benefits:

• Financial incentives: Monthly family, child and non-resident allowances, annual salary review, pension scheme, death benefit, long-term care, accident-at-work and unemployment insurances

• Flexible working arrangements - including hybrid working patterns 

• 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 public holidays

• Relocation package including installation grant (if required)

• 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, 10 days of child sick leave, generous parental leave, holiday clubs on campus and monthly family and child allowances

• Benefits for non-UK residents: Visa exemption, education grant for private schooling, financial support to travel back to your home country every second year and a monthly non-resident allowance.

For detailed information please visit our employee benefits page here. 

What else you need to know

• International applicants: We recruit internationally and successful candidates are offered visa exemptions. Please take a look at our International Applicants page for further information.  

• EMBL is a signatory of DORA. Find out how we apply DORA principles to our recruitment and performance assessment processes here.

• Diversity and inclusion: At EMBL, we strongly believe that inclusive and diverse teams benefit from higher levels of innovation and creative thought. We encourage applications from women, LGBTQ+ & individuals from all nationalities. 

• How to apply: To apply please submit a cover letter and a CV through our online system. Applications will close at 23:59 CET on the date shown below. We aim to provide a response within two weeks after the closing date.

Closing Date