Postdoctoral Fellow- Large-scale Spatial Transcriptomics

Postdoctoral Fellow- Large-scale Spatial Transcriptomics

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 postdoctoral fellow to work in the area of spatial transcriptomics and high-throughput imaging. The position will be based in the laboratory of John Marioni at the EMBL-EBI and will work closely with the groups of Leopold Parts and Omer Bayraktar at the Wellcome Sanger Institute. The methods developed will be applied to data generated as part of the international Human Cell Atlas project.

To date, single cell genomics, specifically single-cell RNA-sequencing, has revolutionised our ability to understand cell type heterogeneity in contexts ranging from the mouse embryo1,2 to terminally differentiated human cell types. However, most existing protocols require cells to be dissociated, meaning that the spatial location of a cell within its tissue of origin is lost and, consequently hindering a deep understanding of tissue organisation and cell type heterogeneity.

Recent technological advances have overcome this problem, meaning that a cell’s transcriptome can be assayed within a spatial context via tissue imaging. However, computational methods for analysing such data are in their infancy with, for example, substantial challenges remaining in image segmentation and cell identification as well as downstream steps such as data normalisation and identification of spatial patterns of heterogeneity using statistically robust approaches.

The Marioni group is a world leader in computational biology, with a particular focus on developing methods for data generated using single cell genomics technologies 3-7 Leo Parts is a group leader in computational biology at the Wellcome Sanger Institute, with a strength in machine learning methods8, including applications to imaging data9. Omer Bayraktar is a new group leader at Sanger institute with experience in large-scale tissue histology and imaging.

1. Scialdone et al., Nature, 2016
2. Ibarra-Soria et al., Nature Cell Biology, 2018
3. Haghverdi et al., Nature Biotechnology, 2018
4. Lun et al., Nature Methods, 2017
5. Vallejos et al., Nature Methods, 2017
6. Achim et al., Nature Biotechnology, 2015
7. Buettner et al., Nature Biotechnology, 2015
8. Angermueller et al., Molecular Systems Biology, 2016
9. Parnamaa and Parts, G3, 2017


You have

The successful candidate will have a strong background in computational biology, with a PhD in a relevant discipline. They will be experienced in image data analysis. They will also have excellent communication skills and a genuine interest in applying computational methods to biological questions.


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.


What else do I need to know

This position will be for the duration of the grant until 30.06.2021.

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-EBI01289

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