European Molecular Biology Laboratory (EMBL) - EBI

Hinxton, Cambridge, East of England, United Kingdom

About the team/job

We are looking to appoint a highly motivated bioinformatician to manage the submission and distribution of data generated as part of the international Human Cell Atlas project.

Recent advances in the area of single cell genomics have facilitated the possibility of generating a Human Cell Atlas, where cutting-edge molecular biology techniques can be used to refine our understanding of cell types within the human body, thereby building a platform for future transformative research in understanding tissue homeostasis and, ultimately, disease1-3.

The Marioni group is a world leader in computational biology, with a particular focus on developing methods for data generated using single cell genomics technologies4-8.

The HCA DCP team at EMBL-EBI is leading efforts to build the ingestion service enabling submission of data to the DCP and validating these datasets meet HCA standards. This team also works with biologists and bioinformaticians to under the different HCA data types.

1. Young et al., Science, 2018.
2. Hagai et al., Nature (in press)
3. Gomes et al., BiorXiv,
4. Haghverdi et al., Nature Biotechnology, 2018
5. Lun et al., Nature Methods, 2017
6. Vallejos et al., Nature Methods, 2017
7. Achim et al., Nature Biotechnology, 2015
8. Buettner et al., Nature Biotechnology, 2015


Your role

You will be a key link between data generators, based primarily within the UK, the Human Cell Atlas Data Coordination Platform (DCP), and downstream visualisation and analysis portals such as the Single Cell Expression Atlas Single Cell Expression Atlas . You will interact closely with all three of these groups to facilitate smooth upload, processing and dissemination of the data generated as part of this project.

You will be based within the HCA DCP team at Hinxton led by Laura Clarke and work closely with the EMBL-EBI based groups of John Marioni, Irene Papatheodorou and will collaborate with the group of Sarah Teichmann at the Wellcome Sanger Institute.

Your role will include the following tasks:

  • Designing and extending services to ensure the HCA is collecting high quality metadata to support and enable discovery and integration operations on its data
  • Supporting the data flow into the HCA and EMBL-EBI archives from project contributors
  • Collaborating with expert biologists and external collaborators to define and extend the minimum standards for the various HCA data types
  • Working with biologists and other collaborators to define requirements for HCA services
  • Running training courses on how to submit data to the HCA project
  • Working with other teams across EMBL-EBI to deliver our components of the HCA Data Coordination Platform
  • Representing the team and the institute at HCA project meetings and international scientific conferences.

You have

You should hold an MSc, PhD, or have equivalent experience in Bioinformatics, Genetics, Computer Science, or related fields including evidence of your ability to operate, understand, and maintain complex data flows and pipelines.

You should have experience in programming and in running and developing software in a primarily Unix-based environment. You should be familiar with development tools such as Git. Knowledge of python/perl, javascript, and JSON/YAML are preferred. Experience in operating computationally efficient solutions for running complex data flows and familiarity with both relational databases and document stores would be an advantage.

Do you love working in a team to support users to provide high quality, well described data? As a member of this team you will need to interact with users of the system, training them and providing ongoing support while they use the HCA ingestion service. You will also gather requirements from these users to inform new features in the system and help us improve the service we offer. Experience supporting data flow in large scientific collaborations will be considered an advantage.

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 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.

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. For more information about pay and benefits click here

What else do I need to know

This position is grant limited up to the project duration 31/06/2021.

The Wellcome Strategic Support Science (WSSS) award aims to demonstrate the utility of a human cell atlas as a healthy reference and will focus on selected tissues, primarily of barrier and immune function. These will be profiled in adults as well as during human development, and in inflammatory disorders. A large team of scientists will be generating single cell as well as spatially resolved gene expression data. A key aspect of this grant is the integration of these two lines of work.

The work proposed will create an unprecedented amount of high-quality, openly accessible data for deposition into the HCA Data Coordination Platform

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.

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

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.

Please apply via recruiter’s website.

Quote Reference: EMBL-embl-EBI01292