Job Description
The European Bioinformatics Institute (EMBL-EBI), Hinxton near Cambridge, UK, is recruiting an Ensembl Microbes Bioinformatician to develop and maintain high-quality genome resources for microbial research communities.
As part of the Ensembl project, Ensembl Microbes provides access to bacterial, archaeal, fungal and protist genomes and their annotations. The team expands the representation of microbial genomes, develops approaches for representing pangenomes and broadens the annotations Ensembl provides. Ensembl Microbes is part of EMBL-EBI’s Microbial Informatics team (led by Rob Finn), which also develops the MGnify resource and AMR portal. The post reports to Tatiana Gurbich, Microbial Genomes Project Lead.
Position Details
- Post: Ensembl Microbes Bioinformatician
- Reference no.: JR4343
- Contract: 3 years, full time
- Salary: Grade 5; monthly salary from £3,452.05 after tax, plus benefits and allowances based on individual circumstances (excluding 12.99% personal pension and insurance contributions)
- Location: Hinxton, Cambridgeshire, UK (Wellcome Genome Campus)
- Working pattern: Hybrid; minimum two days on site (Tuesday and Thursday)
- Interviews: Remote panel interviews expected on 27 November 2026
- Last date: 10 November 2026 (23:59 CET)
Responsibilities
- Maintain the microbial genomes in Ensembl: identify and load new genome annotations, check data presentation, and diagnose and resolve issues
- Coordinate releases in a release-based environment with other Ensembl subteams
- Identify and assess new genome annotation tools, especially those specific to microbial taxa
- Contribute to functional annotation pipelines and to approaches for representing microbial pangenomes
- Design, build and test technical solutions to make processes more efficient
- Maintain clear documentation and contribute to code reviews and team meetings
- Represent the team’s work to other EMBL-EBI groups, external collaborators, data generators and user communities
Essential Qualification
- PhD in bioinformatics, biology, computer science or a related field, or a Master’s degree in a relevant field with equivalent professional experience
- Knowledge of prokaryotic and/or microbial eukaryotic biology
- Strong Python skills; able to write, understand and independently review production-quality code
- Experience building pipelines with Nextflow, Snakemake or similar
- Experience with relational databases (e.g. MySQL, PostgreSQL), UNIX/Linux, and HPC or cloud environments
- Experience with genome analysis/annotation tools and common formats (e.g. FASTA, GFF3)
- Software development best practices: version control (e.g. Git), testing and code review
- Familiarity with AI-assisted coding tools and the ability to critically evaluate and validate their outputs
- Excellent communication skills in English; strong attention to detail; able to work independently and in a team
Desirable
- Hands-on experience with the Ensembl platform or another genome browser
- Experience in a multi-person team delivering production services
- Experience with large-scale biological datasets and the Apache Parquet format
- Experience applying AI/ML approaches to quality control and/or genome annotation
