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Ensembl are seeking a talented and motivated Project Leader to manage our activities in annotating thousands of genomes across the eukaryotic tree of life.
Ensembl (http://www.ensembl.org/) is one of the world’s leading large-scale genomics resources. We are the cutting edge of gene annotation, working as part of large genome sequencing projects such as the Darwin Tree of Life (DToL) project and the Vertebrate Genomes Project (VGP) to annotate hundreds (and ultimately many thousands) of genomes.
You will lead the Genebuild team, who are responsible for developing accurate and scalable pipelines and workflows for annotating eukaryotic genomes with transcript structures and other genic features. The team’s activities and expertise span software development, machine learning, large-scale compute, big data, pipeline workflows, automation and community engagement. You will work to deliver annotation for a variety of communities and collaborators, including large consortium projects such DToL and the VGP. You will also join the Ensembl management team, and will work closely with them to develop the next generation of Ensembl’s world-leading data and services.
Ensembl Genebuild is part of the Eukaryotic Annotation Team (led by Kevin Howe), which itself is part of a wider cluster of resources that includes Ensembl (led by Paul Flicek). You will report directly to the Coordinator for Vertebrate Annotation (Fergal Martin). EMBL–EBI is part of the European Molecular Biology Laboratory (EMBL) and is Europe’s leading provider of information services to biological researchers in academia and industry.
Your role
You will be responsible for operational leadership of high-throughput gene annotation activities in Ensembl. Under the immediate supervision of the Coordinator for Vertebrate Annotation, you will lead the expansion of Ensembl’s gene annotation resources to many thousands of genomes, with focus on the development of scalable pipelines for eukaryotic gene annotation. You will also:
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- Manage and mentor a team 7-9 bioinformaticians/developers
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- Manage the team’s development and production work for Ensembl releases
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- Engage with communities and other Ensembl teams to develop effective displays and APIs for gene annotation data
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- Write reports and papers describing Ensembl gene annotation resources
- Keep up-to-date with current research in related primary data, gene finding tools and methods
You have
You will ideally hold a PhD or equivalent in Molecular Biology, Bioinformatics or related field with demonstrated experience in gene annotation. Applicants with a MSc and appropriate experience will also be considered. You will additionally have:
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- Broad knowledge of gene annotation concepts and methods
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- Experience with using relational databases for biological data
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- Knowledge of multiple sequence alignment algorithms
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- Experience with designing and deploying complex analysis pipelines on an HPC cluster
- Proficiency in at least one programming language (e.g. Perl or Python)
You will have excellent verbal and written communication skills to lead within a project where biologists and computer scientists work closely together. You will also be highly organized in order to meet the regular deadlines, reports and procedures across the wider Ensembl project.
You might also have
The ideal candidate might also have the following:
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- Experience with formal project management principles and techniques
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- Experience of working with a release cycle
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- Experience of working with the Ensembl platform
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- Expertise specifically in Perl and MySQL
- Experience with working in large collaborative genomics projects
Why join us
At EMBL–EBI, we help scientists realise the potential of ‘big data’ in biology by enabling them to exploit complex information to make discoveries that benefit mankind.
Working for EMBL–EBI gives you an opportunity to apply your skills and energy for the greater good.
As part of the European Molecular Biology Laboratory (EMBL), we are a non-profit, intergovernmental organisation funded by 27 member states and two associate member states.
We are located on the Wellcome Genome Campus near Cambridge in the UK, and our 850 staff are engineers, technicians, scientists and other professionals from all over the world.
EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation. The remuneration package comprises a competitive salary, a comprehensive pension scheme and health insurance, educational and other family related benefits where applicable, as well as financial support for relocation and installation. For more information about pay and benefits click here
We have an informal culture, international working environment and excellent professional development opportunities but one of the really amazing things about us is the concentration of technical and scientific expertise – something you probably won’t find anywhere else.
If you’ve ever visited the campus you’ll have experienced first-hand our friendly, collegial and supportive atmosphere, set in the beautiful Cambridgeshire countryside. Our staff also enjoy excellent sports facilities including a gym, a free shuttle bus, an on-site nursery, cafés and restaurant and a library.
What else you need to know
To view a copy of the full job description please click here
To apply please submit a covering letter and CV through our online system. Applications are welcome from all nationalities and this will continue after Brexit. For more information please see our website. Visa information will be discussed in more depth with applicants selected for interview.
3 year staff member contract renewable up to 9 years of service
EMBL–EBI is committed to achieving gender balance and strongly encourages applications from women, who are currently under-represented at all levels.
Appointment will be based on merit alone.
Applications will close at 23:00 GMT on the date listed above.
