Job:Ensembl Regulation Developer
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4.2 years ago
Emily 23k

Location: EMBL-EBI, Hinxton near Cambridge, UK
Staff Category: Staff Member
Contract Duration: 3 years
Grading: 5-6 (monthly salary starting at £2,631.99 - £2,944.48 after tax)
Closing Date: 13 August 2019
Reference Number: EBI01473

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The Ensembl Regulation team seeks an enthusiastic bioinformatician to join the team and contribute to the annotation of regulatory elements across the genome and across cell types.

Ensembl ( is one of the most successful large-scale bioinformatics projects and one of the leading projects for genome annotation. We import massive amounts of data from various archives (genome sequences, variation archives, etc) and use them to create syntheses (gene annotation, whole-genome alignments, gene trees, regulatory elements, etc). Our services are freely open to all scientists around the world, and serve a range of uses, from basic science to biomedical research.

Ensembl Regulation is specialised in epigenomic and cis-regulatory datasets, which are used to define the Ensembl Regulatory Build. This annotation highlights the regulatory regions of the genome that control when genes are expressed and in which tissues. These elements have been shown to play a significant role in explaining the mechanisms underlying evolution as well as disease.

Your role

You will work alongside the existing developers and:

  • Incorporate more public datasets into our existing database, thus extending our coverage of cell types, tissues and species,
  • Implement new bioinformatic pipelines to process different assay types (e.g. DNA methylation data, Hi-C, single-cell ATAC-Seq…),
  • Perform various downstream analyses (e.g. differential analysis of epigenetic signatures),
  • Support international and regional consortia (e.g. IHEC, FAANG) by processing their data and providing expertise,
  • Help out users of the Ensembl website and APIs and develop new features or tools to make their research more efficient,
  • Extend the current MySQL database schemas and the Perl API to handle new data types/results.

You have

Ideally, you should hold an MSc or PhD, or have an equivalent qualification/professional experience, in:

  • Molecular biology
  • Bioinformatics
  • Computer science
  • Statistics
  • Any related field
  • Experience in epigenomics or biostatistics would be a plus

You must have experience developing scientific software and analysing the results of large-scale experimental datasets. Experience in team software development and/or working in large scientific consortia, especially in the field of genomics, would be strongly preferred.

You should be team oriented, ready to contribute to Ensembl's 50+ development team, and will be expected to work in step with the procedures and time constraints of the entire project. You must also be capable of autonomously leading your work in a thorough, timely and detail-oriented fashion, as you will have to keep track of many parallel tasks. Communication and presentation skills will be highly valued.

You should be comfortable with the Unix shell and have demonstrable experience using scripting languages (e.g. Python or Perl), Git and SQL. Your job will include programming in object-oriented Perl, although knowledge of technologies like Kubernetes and Apache Spark will open up further opportunities. Experience with high-throughput computing, MySQL, the Ensembl codebase, the eHive pipeline system or C programming would be a plus

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 over 27 member states and two associate member states.

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. For more information about pay and benefits click here.

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 you need to know

To view a copy of the full job description please click here.

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

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 GMT on the date listed above.

Apply now

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