Bioinformatician/Senior Bioinformatician


Key information

  • Location: EMBL-EBI Hinxton
  • Staff category: Staff Member - Science, research and training
  • Contract duration: 3 years
  • Grading: 5 or 6 (monthly salary starting at £2,676.73 after tax)
  • Closing date: 22 July 2020
  • Reference number: EBI01652

Continue reading for more information about this position, or apply now.




About this position

We are looking for a highly motivated Bioinformatician/Senior Bioinformatician to contribute to the development of the analysis pipelines behind EMBL-EBI’s Expression Atlas and particularly the Single Cell Expression Atlas, an added-value database providing information about gene expression in single cells across different cell types, tissues and conditions, across all species. A significant part of your work will involve working on the pipelines that will process data from projects such as the Human Cell Atlas (HCA), Fly Cell Atlas.

You will develop, maintain and deploy robust analysis pipelines for single cell RNA-seq. You will participate in collaborative projects aiming to add value to large cell atlas datasets by implementing cell type annotation and cell type deconvolution strategies with our partners in Open Targets.

Open Targets is a pioneering public-private partnership between EMBL-EBI (European Bioinformatics Institute), GlaxoSmithKline (GSK), the Wellcome Sanger Institute (Sanger), Bristol Myers Squibb (BMS), Sanofi and Takeda, located on the Wellcome Genome Campus in Hinxton, near Cambridge, UK. Open Targets brings together expertise from six complementary institutions to generate evidence on the biological validity of therapeutic targets and provide an initial assessment of the likely effectiveness of pharmacological intervention on these targets, using genome-scale experiments and analysis. Open Targets aims to provide an R&D framework that applies to all aspects of human disease, to improve the success rate for discovering new medicines and share its data openly in the interests of accelerating drug discovery.

In addition, you will also be contributing to the maintenance and running of our bulk RNA-Seq pipelines for our existing service Expression Atlas. You will work at EMBL-EBI located on the Wellcome Genome Campus, near Cambridge, in the UK.

Your role

Your role will include the following tasks:

  • Working with the Expression Atlas team to deliver a data production analysis pipelines for single cell RNA-seq data, specifically for cell type annotation.
  • Working on projects that will design cell type deconvolution strategies to assign pathogenic cell types to different disease phenotypes.
  • Proposing and implementing new features for the Single Cell Portal and Expression Atlas in general.
  • Collaborating with other teams EMBL-EBI, the Wellcome Trust Sanger Institute working on single cell transcriptomics
  • Keeping up to date with modern software engineering best practice and new technologies.
  • Representing the team and the institute at Open Targets/HCA project meetings and international scientific conferences.

You have

You should hold a PhD or higher degree in bioinformatics or computer science. Research experience in genomics would be highly desirable and experience working on single cell transcriptomics analysis is highly advantageous.  You should have experience working in a Unix-based environment, good programming skills, excellent Unix shell scripting skills, along with good knowledge of R (including Bioconductor). 

The ability to work within a team is critical to this position. Excellent communication skills and an ability to work to tight deadlines are essential. You will be required to communicate technical documents, to contribute to development team meetings, as well as provide user orientated communication with external and internal users of the systems.

You might also have

Previous experience in working in a continuous deployment environment with source control and management of releases and in gene expression data analysis is highly desirable. You may also have experience working with pipeline deployments on different clouds.

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 BST on the date listed above.


Join EMBL and you’ll join a community of world-class researchers and skilled professionals working together to uncover the secrets of life.

We offer attractive conditions and benefits to attract and retain the brightest talent. Learn more.

One laboratory. Six locations. Global reach.

The European Molecular Biology Laboratory is a single organisation spread across six European locations. Each of our sites hosts its own research units, services and facilities.

EMBL is Europe’s leading life sciences laboratory.

EMBL seeks to better understand the molecular basis of life. In the process, we’re changing European science.