Ensembl Microbes Bioinformatician

EMBL EBI; Saffron Walden; Hybrid; GBP 35,000 - 42,000; Full time

Benefits offered by this job

Hybrid working

Private medical insurance

30 days annual leave

Relocation package

Family benefits

Non-UK resident allowances

Job summary

EMBL-EBI’s Ensembl Microbes team develops and maintains genome resources for microbial research communities. The role supports Ensembl microbes across bacteria, archaea, fungi and protists, collaborating with bioinformaticians, software engineers and project leads to expand pangenome representations and improve annotations.

The post reports to the Microbial Genomes Project Lead and offers hybrid working with two on-site days per week on the Wellcome Genome Campus in Cambridgeshire.

Qualifications

• PhD or Master with equivalent experience in a relevant field.
• Knowledge of prokaryotic and/or microbial biology.
• Strong Python skills with production-quality code.
• Experience building computational pipelines with Nextflow or Snakemake.
• Experience with relational databases (MySQL, PostgreSQL), UNIX/Linux, and HPC/cloud environments.
• Experience applying genome analysis/annotation tools and formats (FASTA, GFF3).
• Experience with software development practices: Git, testing, code reviews.
• Proficiency in English, written and spoken.
• Ability to work independently and in a team.

Responsibilities

• Maintain microbial genomes in Ensembl, load annotations, and diagnose issues.
• Coordinate releases in a release-based environment with subteams.
• Assess genome annotation tools for microbial taxa to enhance annotations.
• Develop functional annotation pipelines and microbial pangenome representations.
• Design, build and test technical solutions to improve efficiency.
• Create and maintain up-to-date documentation.
• Contribute to code reviews and team meetings.
• Collaborate with EMBL-EBI groups, data generators and user communities.

Skills

Python

Nextflow

Snakemake

Relational databases

UNIX/Linux

HPC/Cloud

Genome annotation tools

Git

AI-assisted coding tools

English communication

Education

PhD in bioinformatics/biology/computer science

Master's + relevant experience

Tools

MySQL

PostgreSQL

Git

Nextflow

Snakemake

Apache Parquet

Job description

We are seeking a skilled bioinformatician who is enthusiastic about developing and maintaining high-quality genome resources for microbial research communities to join the Ensembl Microbes team. As part of the Ensembl project, Ensembl Microbes provides access to bacterial, archaeal, fungal and protist genomes and their annotations to research communities worldwide. We work to expand the representation of microbial genomes, evaluate and develop approaches for representing pangenomes, and broaden the range of annotations provided by Ensembl. We collaborate closely with bioinformaticians, software engineers and project leaders across Ensembl to develop new features, manage data flows and ensure reliable data delivery. Ensembl Microbes is also part of EMBL-EBI's Microbial Informatics team, which develops the MGnify resource and AMR portal, providing opportunities for collaboration on shared datasets and methods. We are also active partners in international collaborations to support the annotation and dissemination of microbial genomes. The Microbial Informatics team is led by Rob Finn, who also oversees the Ensembl resource. You will report directly to Tatiana Gurbich, the Microbial Genomes Project Lead.

Main Duties and Responsibilities

• Maintain the microbial genomes in Ensembl, including identifying and loading new genome annotations, ensuring data is presented correctly, and diagnosing and resolving issues promptly
• Coordinate releases within a release-based environment, working closely with other Ensembl subteams
• Identify and assess new genome annotation tools, especially those that are specific to microbial taxa, to provide specific annotations that go beyond the default annotations provided by Ensembl
• Contribute to the development of our functional annotation pipelines and help shape representation of microbial functional annotations in Ensembl
• Contribute to the development of approaches for representing microbial pangenomes in Ensembl
• Design, build and test technical solutions to make processes more efficient
• Create and maintain clear, up to date documentation
• Contribute to code reviews and team meetings
• Interact with other groups at EMBL-EBI and external collaborators, data generators and user communities, representing the team's work

Essential Qualifications

• A PhD in bioinformatics, biology, computer science or a related field, or a Master's degree in a relevant field combined with equivalent professional experience
• Knowledge of prokaryotic and/or microbial eukaryotic biology
• Strong Python skills, with demonstrable ability to write, understand and independently review production-quality code
• Experience building computational pipelines with Nextflow, Snakemake or similar
• Experience with relational databases (e.g. MySQL, PostgreSQL), UNIX/Linux, and HPC or cloud environments
• Experience applying genome analysis/annotation tools and working with common bioinformatics formats (e.g. FASTA, GFF3)
• Experience with software development best practices, including version control (e.g. Git), testing and code review
• Familiarity with AI-assisted coding tools, and an understanding of how to critically evaluate, validate, and improve their outputs
• Excellent interpersonal and communication skills, with the ability to communicate effectively in English, both verbally and in writing
• Strong attention to detail and commitment to producing accurate, reproducible work
• Ability to work independently and collaboratively as part of a team, prioritise tasks, and take ownership of projects from development through to delivery

Desirable Qualifications

• Hands-on experience with the Ensembl platform or other genome browser
• Experience working in a multi-person team delivering production services
• Experience with large-scale biological datasets
• Experience working with the Apache Parquet file format
• Experience implementing AI/ML approaches for quality control and/or genome annotation

Behaviours we value in our team

You bring curiosity, enthusiasm and a focus on impact to your work. You enjoy turning ideas into well-executed solutions, are able to manage multiple priorities, and collaborate effectively with colleagues across multidisciplinary and international teams.

Diversity and inclusion

At EMBL, we believe that diverse teams drive innovation and scientific excellence. We encourage applications from candidates of all genders, identities, nationalities and/or any other diverse backgrounds.

Contract length: 3 years

Salary and Benefits

Salary: Grade 5, monthly salary from £3,452.05 after tax, plus generous benefits and financial allowances based on individual circumstances. Excluding 12.99% personal pension and insurance contributions.

Hybrid Working: At EMBL-EBI we are pleased to offer hybrid working options for all our employees. A dedicated desk will be available everyday, our team works a minimum of two days on site (Tuesday and Thursday).

Interviews: We anticipate that panel interviews for this post will take place on November 27th, 2026 remotely.

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 (conditions apply)
• 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.