Bioinformatician/Senior Bioinformatician

We are looking for a highly motivated Bioinformatician/Senior Bioinformatician to contribute to the development of the analysis pipelines behind EMBL-EBI’s Expression Atlas and particularly the Single Cell Expression Atlas, an added-value database providing information about gene expression in single cells across different cell types, tissues and conditions, across all species. A significant part of your work will involve working on the pipelines that will process data from projects such as the Human Cell Atlas (HCA), Fly Cell Atlas.

You will develop, maintain and deploy robust analysis pipelines for single cell RNA-seq. You will participate in collaborative projects aiming to add value to large cell atlas datasets by implementing cell type annotation and cell type deconvolution strategies with our partners in Open Targets.

Open Targets is a pioneering public-private partnership between EMBL-EBI (European Bioinformatics Institute), GlaxoSmithKline (GSK), the Wellcome Sanger Institute (Sanger), Bristol Myers Squibb (BMS), Sanofi and Takeda, located on the Wellcome Genome Campus in Hinxton, near Cambridge, UK. Open Targets brings together expertise from six complementary institutions to generate evidence on the biological validity of therapeutic targets and provide an initial assessment of the likely effectiveness of pharmacological intervention on these targets, using genome-scale experiments and analysis. Open Targets aims to provide an R&D framework that applies to all aspects of human disease, to improve the success rate for discovering new medicines and share its data openly in the interests of accelerating drug discovery.

In addition, you will also be contributing to the maintenance and running of our bulk RNA-Seq pipelines for our existing service Expression Atlas. You will work at EMBL-EBI located on the Wellcome Genome Campus, near Cambridge, in the UK.

Your role will include the following tasks:
Working with the Expression Atlas team to deliver a data production analysis pipelines for single cell RNA-seq data, specifically for cell type annotation.
Working on projects that will design cell type deconvolution strategies to assign pathogenic cell types to different disease phenotypes.
Proposing and implementing new features for the Single Cell Portal and Expression Atlas in general.
Collaborating with other teams EMBL-EBI, the Wellcome Trust Sanger Institute working on single cell transcriptomics
Keeping up to date with modern software engineering best practice and new technologies.
Representing the team and the institute at Open Targets/HCA project meetings and international scientific conferences.
You have
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 single cell transcriptomics analysis is highly advantageous. You should have experience working in a Unix-based environment, good programming skills, excellent Unix shell scripting skills, along with good knowledge of R (including Bioconductor).

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.

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. You may also have experience working with pipeline deployments on different clouds.