About the team/job
We are looking to appoint a highly motivated Senior Bioinformatician to develop processing pipelines and drive the development of visualisation tools for spatially-resolved single-cell genomics data.
Recent advances in the area of single cell genomics have facilitated the possibility of generating a
Human Cell Atlas(HCA), 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. Irene Papatheodorou’s team analyses expression data sets at tissue or single cell level and develops Expression Atlas, a resource that provides information about the expression of genes and proteins in different cells, tissues, developmental stages and conditions.
1. Young et al., Science, 2018.
2. Hagai et al., Nature (in press)
3. Gomes et al., BiorXiv, www.biorxiv.org/content/early/2017/11/22/217489
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
You will generate production-quality processing pipelines for single cell, spatial transcriptomics data and meta-data. Additionally, you will work together with software engineers to develop a user interface that will visualise the data where a cell’s location within a tissue as well as its molecular profile will be available. The interface will open the possibility of overlaying a cell’s molecular signature with its location in a tissue and will be made available through the single cell component of Expression Atlas the
Single Cell Expression Atlas in the first instance. The Single Cell Expression Atlas is EMBL-EBI’s portal for the Human Cell Atlas It will provide a robust infrastructure for visualising and analysing cells within a 3D environment and will be critical to the success of the Human Cell Atlas.
You will be based with the groups of John Marioni and Irene Papatheodorou at the EMBL-EBI and collaborate closely with the group of Sarah Teichmann at the Wellcome Sanger Institute.
The successful candidate will:
- Design and implement processing pipelines for spatial transcriptomics data and meta-data
- Gather requirements from researchers working in the field of spatial transcriptomics to inform processing pipelines and visualisation tool development
- Collaborating with other members of the team, web developers, bioinformaticians and curators to develop a complete data flow from raw data and meta-data to visualisation.
- Collaborating with other EMBL-EBI resources, especially the HCA’s Data Ingest team
- Collaborating with external partners, especially within the HCA
- Contributing to publications describing data sets and processes.
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 spatial transcriptomics analysis is highly advantageous. You should have experience working in a Unix-based environment, good programming skills, excellent Unix shell scripting skills.
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. Experience working in large scientific projects would be 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.