Ensembl Genebuild Project Leader

Ensembl is seeking a talented and motivated Project Leader to manage our activities in annotating thousands of genomes across the eukaryotic tree of life. Ensembl is one of the world's leading large-scale genomics resources. The Ensembl Genebuild team develops high-performance, large-scale annotation pipelines to define gene structures and other genomic features across the eukaryotic tree of life. Our team is at the cutting edge of gene annotation, contributing to major genome sequencing initiatives, including:

• European Reference Genome Atlas under the Biodiversity Genomics Europe (ERGA-BGE)
• Human Pangenome Reference Consortium (HPRC)
• Farmed Animal Resources (EuroFAANG)
• Ancient Environmental Genomics Initiative for Sustainability (AEGIS)

As Project Leader, you will lead the Genebuild team in developing accurate and scalable pipelines for annotating eukaryotic genomes with transcript structures and other genic features. Your responsibilities will include:

• Pipeline and workflow development for large-scale genome annotation
• Software development and automation
• Integration of machine learning and big data approaches
• Community engagement to support large collaborative projects
• Strategic development of the next generation of Ensembl’s world-class data services

As part of this role, you will also join the Ensembl management team, working closely with leadership to shape the future of genome annotation.

We Are Looking For An Individual With:

• Strong expertise in genome annotation, bioinformatics, or computational biology
• Experience in pipeline development, high-performance computing, or machine learning
• Leadership experience in managing projects, teams, or large-scale collaborations
• Excellent communication and stakeholder engagement skills

Ensembl Genebuild is part of the Eukaryotic Annotation Team, led by Fergal Martin. This team operates within a broader cluster of Ensembl resources, overseen by Rob Finn. You will report directly to Leanne Haggerty, Coordinator for Eukaryotic Annotation Data Flow.

As Project Leader, you will be responsible for the operational leadership of high-throughput gene annotation activities within Ensembl. Under the supervision of the Coordinator for Eukaryotic Annotation Data Flow, you will drive the expansion of Ensembl’s gene annotation resources to thousands of genomes, focusing on the development of modernised pipelines for eukaryotic gene annotation using state-of-the-art methods.

Your Key Responsibilities Will Include:

• Team Leadership: Manage and mentor a team of 6–7 bioinformaticians and developers.
• Pipeline & Production Management: Oversee the team’s development and production workflows for Ensembl releases.
• Community & Cross-Team Collaboration: Work with scientific communities and other Ensembl teams to develop APIs and effective data displays for gene annotation data.
• Scientific Communication: Write reports and publications on Ensembl gene annotation resources.
• Research & Innovation: Stay up to date with the latest research, primary data sources, gene-finding tools, and methodologies in genome annotation.

You have:

• A PhD or equivalent in Molecular Biology, Bioinformatics, or a related field, with demonstrated experience in gene annotation. Applicants with an MSc and significant relevant experience will also be considered.
• Broad knowledge of gene annotation concepts and methods.
• Experience with relational databases for handling biological data.
• Familiarity with sequence alignment algorithms.
• Experience in designing and deploying complex analysis pipelines on HPC clusters.
• Proficiency in at least one programming language (e.g., Python).
• Strong verbal and written communication skills, with the ability to lead cross-disciplinary teams of biologists and computational scientists.
• Excellent organisational skills, ensuring deadlines, reports, and procedures are met across the Ensembl project.

You may also have:

• Formal project management principles and techniques.
• Working within a release cycle for software or data.
• Hands-on experience with the Ensembl platform.
• Expertise specifically in Perl and MySQL.
• Previous involvement in large-scale collaborative genomics projects.

Contract Length: 3 years (grant based contract)

Salary: Monthly salary starting at £4,111 after tax but excluding pension and insurance contributions. Plus generous benefits.

Why join us:

At EMBL-EBI you can apply your talent and passion to accelerate science and tackle some of humankind's greatest challenges. EMBL-EBI, part of the European Molecular Biology Laboratory, is a worldwide leader in the storage, analysis and dissemination of large biological datasets. We provide the global research community with access to publicly available databases and tools which are crucial for the advancement of healthcare, food security, and biodiversity.

We are located on the Wellcome Genome Campus, alongside other prominent research and biotech organisations, and surrounded by beautiful Cambridgeshire countryside. This is a highly collaborative and inclusive community where our employees enjoy a relaxed atmosphere. We are committed to ensuring our employees feel valued, supported and empowered to reach their professional potential.

Enjoy Lots Of Benefits:

• 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 working patterns
• Private medical insurance for you and your immediate family (including all prescriptions and generous dental & optical cover)
• Generous time off: 30 days annual leave per year, in addition public holidays
• Relocation package including installation grant (if required)
• Campus life: Free shuttle bus to and from work, on-site library, subsidised on-site gym and cafeteria, casual dress code, extensive sports and social club activities (on campus and remotely)
• Family benefits: On-site nursery, 10 days of child sick leave, generous parental leave, holiday clubs on campus and monthly family and child allowances
• Benefits for non-UK residents: Visa exemption, education grant for private schooling, financial support to travel back to your home country every second year and a monthly non-resident allowance.

What else you need to know:

International applicants: We recruit internationally and successful candidates are offered visa exemptions. EMBL is a signatory of DORA. Diversity and inclusion: At EMBL, we strongly believe that inclusive and diverse teams benefit from higher levels of innovation and creative thought. We encourage applications from women, LGBTQ+ & individuals from all nationalities.

How to apply: To apply please submit a cover letter and a CV through our online system. Applications will close at 23:59 CET on the date shown below. We aim to provide a response within two weeks after the closing date.

Closing Date: 30/06/2025