Senior Bioinformatician in Image-based Spatial Transcriptomics

The Opportunity:

We are seeking a Senior Bioinformatician to join the High Throughput Spatial Genomics (HTSG) team to contribute 2D/3D image analysis to exciting spatial transcriptomics projects of human tissues. You will be embedded in the Bayraktar Research Group and the Cellular Genetics Informatics Teams.

Our Mission:

The HTSG Team applies newly developed spatial transcriptomics technologies to analyse the transcriptome and other genomic information of cells in their native tissue environment. As part of the Human Cell Atlas and other projects, we aim to generate 3D cellular maps of diverse human organs to serve as a foundation to understand tissue organisation, cell-cell communication and pathology. The Cellular Genetics Informatics team provides comprehensive support to our Faculty research teams, including but not limited to; creating and scaling bioinformatics analysis pipelines and software, performing bioinformatics analysis on datasets in collaboration with Faculty teams and contributing to publications accordingly.

​​Our Team and Technological Platforms:

Our multi-disciplinary teams consist of experimental and computational scientists with diverse backgrounds in biology, physics, microscopy and software development. We extensively use spatial RNA-Sequencing (e.g. Visium Spatial Transcriptomics), high-multiplexed cyclic RNA imaging (e.g. In Situ Sequencing) and high-throughput confocal microscopy. Our computational pipelines enable diverse bioimage and spatial transcriptomic data analysis, including cell segmentation and single cell & spatial data integration. Our IT platforms support these activities by providing petabyte-scale image data storage, OMERO-based image visualisation and dissemination, nextflow/jupyter based pipelines and high-performance GPUs.

About the Role/You:

You will participate in exciting projects to map human tissue cell types with spatial transcriptomics. You will work with highly-multiplexed RNA imaging datasets of human tissues to quantify cellular and tissue level features. You will apply low-level (e.g. stitching, registration, barcode decoding) and high-level (e.g. cell/tissue segmentation, morphological quantification, spatial neighbourhood mapping) bioimage analysis to quantify human tissue architecture. You will work with diverse image datasets and improve/develop large-scale analysis pipelines on our HPC environment. You will work closely with HTSG and informatics team members to deliver results and are expected to contribute to publications.

We aim to attract, recruit, retain and develop talent from the widest possible talent pool, thereby gaining insight and access to different markets to generate a greater impact on the world. We have a supportive culture with the following staff networks, LGBTQ+, Parents and Carers and Race Equity to bring people together to share experiences, offer specific support and development opportunities and raise awareness. The networks are also a place for allies to provide support to others.

Relevant publications of the team:

Cell2location maps fine-grained cell types in spatial transcriptomic data . Kleshchevnikov V,  Shmatko A….Stegle O,  Bayraktar OA.

Nature Biotechnology 2022 40, 661–671.

https://www.nature.com/articles/s41587-021-01139-4

PoSTcode: Probabilistic image-based spatial transcriptomics decoder . Gataric M, Park J…Bayraktar OA*, Gerstrung M*.

bioRxiv 2021

https://doi.org/10.1101/2021.10.12.464086

Transcriptome-wide spatial RNA profiling maps the cellular architecture of the developing human neocortex. Roberts K, Aivazidis A, Kleshchevnikov V, Li T, Fropf R, Rhodes M, Beechem J, Hemberg M, Bayraktar OA.

bioRxiv 2021

https://doi.org/10.1101/2021.03.20.436265

Please apply with your CV and a Cover letter outlining how you meet the criteria set out above and in the job description.

Applications will be considered on an ongoing basis and the role will close when a successful appointment has been made.

The Wellcome Sanger Institute is a world leading genomics research centre. Our findings are used to improve health and to understand life on Earth.

There’s an attractive benefits package on offer at the Wellcome Genome Campus. We appreciate the importance of achieving work-life balance and support this with a number of family and carer-friendly policies. Plus a flexible working policy for those who may wish to amend their working pattern or arrangement.
As well as the usual benefits you would expect, we go much further:

Being part of the Wellcome Genome Campus you will be part of the beautiful working environment with an impressive range of benefits, services and facilities also including:

In 2020 we were awarded an Athena SWAN Silver Award. We will consider all individuals without discrimination and are committed to creating an inclusive environment for all employees, where everyone can thrive.