Bioinformatician

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

Benefits offered by this job

Hybrid working

Pension scheme

Private medical insurance

30 days annual leave

Relocation support

On-site campus facilities

Job summary

EMBL-EBI in the United Kingdom is seeking a senior bioinformatician to maintain microbial genomes within Ensembl, load new annotations, and diagnose issues promptly. You will coordinate releases and assess new microbial annotation tools, contributing to functional pipelines and pangenome representations.

You will design efficient solutions, document clearly, review code, and collaborate with internal teams and external partners to advance microbial genomics work.

Qualifications

• PhD in bioinformatics or related field or Master’s with equivalent experience.
• Strong programming and pipeline development experience in bioinformatics.

Responsibilities

• Maintain the microbial genomes in Ensembl, including identifying and loading new genome annotations and diagnosing issues.
• Coordinate releases within a release-based environment with Ensembl subteams.
• Identify and assess genome annotation tools for microbial taxa-specific annotations.
• Contribute to development of functional annotation pipelines and microbial pangenome representation.
• Design, build and test technical solutions to improve efficiency of processes.
• Create and maintain up-to-date documentation.
• Contribute to code reviews and team meetings.
• Interact with EMBL-EBI groups and external collaborators.

Skills

Python

Nextflow

Snakemake

Git

MySQL

PostgreSQL

UNIX/Linux

Cloud computing

English communication

Education

PhD in bioinformatics or related field

Master's degree + equivalent experience

Tools

Parquet format

Ensembl platform experience

FASTA/GFF3 formats

Job description

Application instructions

• Please submit an up- to-date CV and a supporting cover letterdescribing specific examples of your experience analysing microbial data and developing computational pipelines using Nextflow, Snakemake or similar workflow management systems. Applications without a cover letter will not be considered.

In this role you will:

• 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

• 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.

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.

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).

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.

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.