Ensembl Microbes Bioinformatician

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.

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

• 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

• 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

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…