HCA Bioinformatician
Location:EMBL-EBI Hinxton near Cambridge, UK
Staff Category:Staff member
Contract Duration:3 years
Grading:5 or 6 (monthly salary starting at £2,552 or £2,855 after tax). For more information about pay and benefits click here
Closing Date:8th October 2017
Reference Number:EBI_01042

Job Description

We are looking for a highly motivated Bioinformatician/Senior Bioinformatician to contribute to the development of the analysis pipelines behind EMBL-EBI’s Single Cell RNA-Seq portal, a new added-value database providing information about gene expression in single cells across different cell types, tissues and conditions. A significant part of your work will involve working on the pipelines that will process data from the Human Cell Atlas (HCA) project for visualising through the portal.

The HCA project aims to build comprehensive reference maps of all human cells. These maps will provide a basis for both understanding human health and the molecular basis of disease. For more information about the HCA project click here.

You will develop, maintain and deploy robust analysis pipelines for single cell RNA-seq. 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 will include the following tasks:

  • Working with the Expression Atlas team to deliver a data production analysis pipelines for single cell RNA-seq data
  • Investigate different SOPs for processing single cell RNA-seq data from different experimental protocols
  • Proposing and implementing new features for the Single Cell Portal and Expression Atlas in general
  • Collaborating with experimental teams at 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 HCA project meetings and international scientific conferences.

Qualifications and Experience

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). 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.

Do you love developing code as part of a team? 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


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.

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.

Application Instructions

To apply please submit a covering letter and CV, with two referees, through our online system.

Additional Information

Applications are welcome from all nationalities - visa information will be discussed in more depth with applicants selected for interview.

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.

This position is limited to the project duration specified.

Applications will close at 23:00 BST on the date listed above.