Job Location
EMBL-EBI Wellcome Genome Campus
CB10 1SD
United Kingdom

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.

Job Description

We are looking for a highly motivated bioinformatician to help build the pipelines and associated analysis tools for the single cell data analysis of the Single Cell Portal of Expression Atlas. You will be largely involved in the data production for a visualisation portal of the Human Cell Atlas project (HCA). You will work at EMBL-EBI located on the Wellcome Genome Campus, near Cambridge, in the UK.

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.

The pipelines we are building will access and process data through a cloud infrastructure and prepare the appropriate formats for the different visualisations and bulk downloads that will be made available through our web-interface. As part of this team you will have great opportunities to engage with the data generators, project users and our collaborators from the University of California, Santa Cruz (UCSC), the Broad Institute and the funders the Chan Zuckerberg Initiative (CZI) to build the DCP. 

Your role will include the following tasks:

  • Working with Expression Atlas team to deliver a data production pipeline for single cell RNA-seq data
  • Investigate different SOPs for processing scRNA-seq data from different experimental protocols
  • Investigate visualisation tools for single cell data sets
  • Proposing and implementing new features for the Single Cell Portal and Expression Atlas in general
  • Collaborate with experimental teams at the Wellcome Trust Sanger Institute working on single cell transcriptomics
  • Keep 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.


You should hold an MSc or higher degree in bioinformatics or computer science. Research experience in genomics and bioinformatics would be highly desirable and experience working on single cell transcriptomics analysis is highly advantageous. Experience delivering production quality software on a regular release cycle to meet project needs is 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. Experience in working independently but also working within a small development team will be considered an advantage.

You should have a minimum of three years' experience in Bioinformatics, as well as experience working in a Unix-based environment in a high-performance computing cluster environment. Excellent shell scripting skills, along with good knowledge of R (including Bioconductor) and gene expression data analysis. Previous experience in working in a continuous deployment environment with source control and management of releases would be valuable.

How to Apply

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

About Our Organization

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 22 member states and two associate member states and proud to be an equal-opportunity employer. We are located on the Wellcome Genome Campus near Cambridge in the UK, and our 600 staff are engineers, technicians, scientists and other professionals from all over the world.

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