Bioinformatician

Join us as a Bioinformatician at the European Bioinformatics Institute (EMBL‑EBI – HAVANA team).

About the Team

Part of Ensembl, a world‑leading provider of genomics data resources and bioinformatics software tools, the HAVANA team produces reference‑quality gene annotation for the human and mouse genomes. As part of the GENCODE project we leverage cutting‑edge technologies and develop novel approaches to ensure GENCODE provides foundational reference genome annotation for human and mouse. GENCODE is a Global Core Biodata Resource with users ranging from international consortia to individual researchers. Our role in the Primary Annotated Resources to Advance Discovery In Genomic Medicine (PARADIGM) consortium is to optimise gene annotation to support genomic medicine, for example through collaboration with NCBI RefSeq to produce the Matched Annotation from NCBI and EMBL‑EBI (MANE) transcript set.
Our team comprises genomic data analysts and bioinformatics developers who incorporate scientific knowledge and data into gene annotation. Hands‑on annotation of genes and transcripts by expert scientists informs the development of manually supervised automated pipelines that support scalable, human‑expert quality annotation.

Duties & Responsibilities

• Develop and deploy annotation systems to produce and validate reference‑quality gene annotations.
• Work alongside genomic data analysts to produce and improve reference‑quality, evidence‑based annotation of protein‑coding genes, non‑coding RNA genes, and others.
• Integrate cutting‑edge primary data to create and validate gene structure and function annotation.
• Develop pipelines to extend GENCODE annotation from a single reference genome to the human and mouse pan‑genomes.
• Develop pipelines to generate training sets for machine‑learning initiatives.
• Maintain a version‑controlled code base.
• Query databases and help maintain/expand associated schemas.
• Operate in a release‑based environment and coordinate with other teams.
• Collaborate with international partners on genome projects.
• Participate in training users in our annotation methods and workflows.

Qualifications & Requirements

Applicants should hold an MSc, PhD, or equivalent experience in Computer Science, Bioinformatics, Genetics, or a related field.

• Strong programming skills: writing, understanding, and maintaining complex code.
• Domain experience in genome annotation.
• Knowledge of DNA/RNA sequencing and sequence alignment methods.
• Experience with relational databases.
• Understanding of scaling and optimisation.
• Basic machine‑learning concepts.

Behaviours We Look For

• Strong communication and interpersonal skills.
• Ability to manage own time and balance multiple tasks.
• Excellent attention to detail and problem‑solving skills.
• Ability to work effectively in a team.
• Willingness to learn, develop, and adapt in a fast‑moving research environment.
• Confidence communicating both biological and computational concepts, orally and in writing.

Desirable

• Experience processing large biological data sets in a production environment, including compute clusters, pipeline workflows, software design, and automation.
• Evidence of contributing to a large, shared codebase; experience with Riboseq data is highly desirable.

Benefits & Working Conditions

• Hybrid working: three days on site, two days from home.
• Contract length: 3 years (grant‑based).
• Salary: Grade 5, £3,303 per month after tax (pension and insurance contributions excluded).
• 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 patterns.
• Private medical insurance for you and immediate family.
• Generous time off: 30 days annual leave plus public holidays.
• Relocation package incl. installation grant.
• Campus life: free shuttle bus, on‑site library, subsidised gym and cafeteria, casual dress code, extensive sports and social club activities.
• Family benefits: on‑site nursery, child sick leave, parental leave, holiday clubs, monthly allowances.
• Non‑UK resident benefits: visa exemption, education grant for private schooling, monthly non‑resident allowance, travel support every second year.

Application Process

Submit a personalised cover letter and CV online. Incomplete applications will not be considered. We aim to respond within two weeks after the closing date.

Closing date: 10/01/2026.

Diversity & Inclusion

EMBL‑EBI is a signatory of DORA and encourages applications from candidates of all genders, identities, nationalities, and backgrounds.