Ensembl Microbes Bioinformatician

1000 European Molecular Biology Laboratory; Hinxton; Hybrid; GBP 56,000 - 78,000; Full time

Benefits offered by this job

Hybrid working

30 days leave per year

Private medical insurance

Relocation assistance

On-site shuttle / campus facilities

Job summary

EMBL-EBI’s Ensembl Microbes team seeks a skilled bioinformatician to maintain and expand microbial genome resources. You will work on annotations, pangenome representations and functional pipelines, collaborating with diverse teams across EMBL-EBI.

The role reports to the Microbial Genomes Project Lead and involves building scalable workflows, validating outputs, and delivering high-quality data to researchers worldwide. Hybrid working with on-site days is available.

Qualifications

• PhD in bioinformatics, biology, computer science or related field, or Master’s with equivalent experience.
• Knowledge of prokaryotic and/or microbial biology.
• Strong Python skills and production-quality code.
• Experience building computational pipelines (Nextflow/Snakemake) and working with bioinformatics data formats.

Responsibilities

• Maintain microbial genomes in Ensembl, loading new annotations and diagnosing issues.
• Coordinate releases in a release-based environment with subteams.
• Assess new genome annotation tools for microbial taxa.
• Develop functional annotation pipelines and pangenome representations.
• Create and maintain documentation and contribute to code reviews.

Skills

Python

Nextflow

Snakemake

relational databases

UNIX/Linux

HPC / Cloud

Bioinformatics formats (FASTA, GFF3)

Git

AI-assisted coding tools

English communication

Education

PhD in bioinformatics / biology / CS or related (or MSc with equivalent experience)

Tools

Nextflow

Snakemake

Git

MySQL

PostgreSQL

Linux HPC

Job description

Role Summary / Context

About the Team 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

Person Specification

Essential

• 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

• 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.

Contract length

3 years

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.

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.

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 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.