Ensembl Microbes Bioinformatician

EMBL-EBI - European Bioinformatics Institute; Hinxton; On-site; GBP 35,000 - 42,000; Full time

Job summary

EMBL-EBI - European Bioinformatics Institute in Hinxton, United Kingdom is seeking a Bioinformatician to maintain Ensembl Microbes genomes, load new annotations, and ensure data accuracy. You will coordinate releases within a release-based environment and collaborate with Ensembl subteams and external partners.

The role requires strong Python, experience with workflows such as Nextflow or Snakemake, and familiarity with MySQL/PostgreSQL, UNIX/Linux, and HPC.

Qualifications

• PhD in bioinformatics, biology, computer science or related field, or MSc with equivalent professional experience.
• Knowledge of prokaryotic and/or microbial eukaryotic biology.
• Strong Python skills and production-quality code writing/understanding.
• 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 FASTA, GFF3 formats.
• Experience with software development best practices, including version control (Git), testing and code review.
• Familiarity with AI-assisted coding tools and evaluation of outputs.
• Excellent English communication skills, both written and spoken.
• Strong attention to detail and reproducible work.
• Ability to work independently and in a team.

Responsibilities

• Maintain the microbial genomes in Ensembl, including loading new genome annotations and ensuring data accuracy.
• Coordinate releases within a release-based environment with Ensembl subteams.
• Identify and assess genome annotation tools for microbial taxa beyond default annotations.
• Contribute to development of functional annotation pipelines and representation of microbial functions in Ensembl.
• Contribute to approaches for representing microbial pangenomes in Ensembl.
• Design, build and test technical solutions to improve processes.
• Create and maintain up-to-date documentation.
• Participate in code reviews and team meetings.
• Collaborate with EMBL-EBI groups and external collaborators, data generators and user communities.

Skills

Python

Nextflow

Snakemake

MySQL/PostgreSQL

UNIX/Linux

HPC/Cloud

FASTA/GFF3

Git

AI-assisted coding tools

English communication

Attention to detail

Independent & team work

Education

PhD in bioinformatics, biology, computer science or related field; or MSc with equivalent experience

Tools

Git

Job description

Ensembl Microbes Bioinformatician

EMBL-EBI - European Bioinformatics Institute

Hinxton, United Kingdom

From GBP 3,452.05 per month

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