Ensembl Microbes Bioinformatician – EMBL-EBI, Hinxton

Job Description

EMBL-EBI is seeking a skilled bioinformatician 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. The team expands the representation of microbial genomes, evaluates and develops approaches for representing pangenomes, and broadens the range of annotations in Ensembl, working closely with bioinformaticians, software engineers and project leaders across Ensembl. Ensembl Microbes is also part of EMBL-EBI's Microbial Informatics team (MGnify resource and AMR portal), led by Rob Finn. The post reports to Tatiana Gurbich, Microbial Genomes Project Lead.

Key Responsibilities

• Maintain the microbial genomes in Ensembl: identify and load new genome annotations, ensure correct presentation, diagnose and resolve issues
• Coordinate releases within a release-based environment with other Ensembl subteams
• Identify and assess new genome annotation tools, especially taxon-specific ones
• Contribute to functional annotation pipelines and representation of microbial functional annotations
• Contribute to 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 EMBL-EBI groups, external collaborators, data generators and user communities

Qualifications

• PhD in bioinformatics, biology, computer science or a related field, or a relevant Master's plus equivalent professional experience
• Knowledge of prokaryotic and/or microbial eukaryotic biology
• Excellent communication skills in English

Experience

Experience building computational pipelines (Nextflow, Snakemake or similar), working with relational databases, UNIX/Linux and HPC/cloud, and applying genome analysis/annotation tools to common formats (FASTA, GFF3). Desirable: Ensembl or other genome browser experience, production-service teamwork, large-scale datasets, Apache Parquet, AI/ML for QC or genome annotation.

Skills Required

• Strong Python (production-quality code and review)
• Nextflow / Snakemake pipelines
• MySQL / PostgreSQL, UNIX/Linux, HPC or cloud
• Git, testing and code review
• Critical use of AI-assisted coding tools
• Attention to detail and reproducible work

Additional Information

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