Postdoctoral Fellow - Comparative Genomics
Location: EMBL-EBI, Hinxton near Cambridge, UK
Staff Category: Postdoctoral Fellow
Contract Duration: 2 years
Grading: Postdoctoral Fellow - Year 1 Stipend
Closing Date: 30 June 2019
Reference Number: EBI01445
Over the last 10 years, the Mouse Genomes Project has sequenced the most highly used laboratory mouse strains to discover and interpret genetic variation and its effect on phenotypes. This has resulted in the most comprehensive genome-wide maps of genetic and transcriptional variation in mouse (SNPs, indels, structural variation, RNA-editing, and gene expression) [1,2,3]. In 2018, we produced the first draft chromosome scale assembled genome sequences and strain specific gene annotation [4]. This enabled us to discover thousands of novel haplotypes across the Mus lineage, not detectable by reference genome based approaches, identifying enrichment for recent transposable elements that drive recombination in these regions and enrichment for genes involved in immunity, pathogen defence, and sensory functions. In the next phase of the project, we will using third generation sequencing technologies to build reference quality genome sequences that will enable us to expand our understanding of the haplotypic variation through improved sequence assemblies and further understand their association with medically relevant phenotypes by incorporating evidence from sources such as QTL/eQTL mapping studies, pathway analysis, and protein interactions.

[1] Keane et al. (2011) Mouse genomic variation and its effect on phenotypes and gene regulation, Nature, 477:289-294.

[2] Danecek et al. (2012) High levels of RNA-editing site conservation amongst 15 laboratory mouse strains, Genome Biology, 13:r26.

[3] Nellaker et al. (2012) The genomic landscape shaped by selection on transposable elements across 18 mouse strains, Genome Biology, 13:r45.

[4] Lilue et al. (2018) Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci, Nature Genetics, 50(11):1574.

Your role

We are seeking an outstanding postdoctoral researcher to contribute to the comparative analysis and interpretation of the whole-genome and transcript sequencing data from a variety of third generation sequencing technologies. You will engage in both internal and external (national and international) collaborations and will have the opportunity to gain expertise in genome sequencing technologies and comparative genomics. The successful candidate will be encouraged to seek and pursue new collaborations. Opportunities to supervise and mentor junior researchers are likely to arise during the appointment.

You have

Essential skills and experience include:
  • PhD in either Computer Science, Computational Biology, or Bioinformatics
  • Demonstrable record in carrying out bioinformatics analysis
  • Highly developed unix command line skills
  • Proficiency in at least one modern computer programming language
  • Second or third generation sequencing
  • Ability to plan and work independently
  • Excellent communication skills (written and verbal)

You might also have

You might also have experience in:
  • Developing and running complex workflows on large scale compute clusters
  • Comparative genomics
  • Genetic association studies
  • Gene pathway and protein interaction analysis
  • Genome assembly or annotation

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. 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.

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

Informal enquiries can be directed to Prof. Thomas Keane (tk2@ebi.ac.uk).

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 BST on the date listed above.