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Postdoctoral Fellow: Mouse Genomes Project

EMBL-EBI
Hinxton, Cambridgeshire, England, UK
Jobs in UKJobs in EnglandFull-time

Staff category
Postdoctoral Fellow

Contract duration
3 years

Grading
Year 1 stipend (£2,630.10 monthly)

Reference number
EBI_01171

Job description
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 all forms of genetic and transcriptional variation in mouse (SNPs, indels, structural variation, RNA-editing, and gene expression) [1,2,3]. Recently, 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 based approaches, showing that most variable regions are enriched for genes involved in immunity and defence. 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 examine the underlying mechanisms of formation of these regions, expand our understanding of the haplotypic variation and its association with medically relevant phenotypes by incorporating evidence from sources such as QTL/eQTL mapping studies, pathway analysis, and protein interactions.

The Mouse Genomes Project has become an essential resource for the wider mouse genetics community. We are seeking an outstanding postdoctoral researcher to contribute to the generation, comparative analysis, and interpretation of the genome and transcript sequencing data. 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 mentor junior staff are likely to arise during the appointment.

The EBI is part of the European Molecular Biology Laboratory (EMBL) and it is a world-leading bioinformatics centre providing biological data to the scientific community with expertise in data storage, analysis and representation. EMBL-EBI provides freely available data from life science experiments, performs basic research in computational biology and offers an extensive user training programme, supporting researchers in academic and industry.

[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. (2017) Multiple mouse reference genomes define strain specific haplotypes and novel functional loci, BiorXiv, doi:https://doi.org/10.1101/235838

Qualifications and experience
Essential skills and experience include:

– PhD in either Computer Science or Bioinformatics
– Demonstrable record in bioinformatics
– Highly developed unix command line skills
– Proficiency in at least one modern computer programming language
– Ability to plan and work independently
– Excellent communication skills (written and verbal)

Experience or knowledge of the following are desirable:

– Developing and running complex workflows on large scale compute clusters
– Comparative genomics
– Genetic association studies
– Second or third generation sequencing technologies
– Genome assembly or annotation

Benefits
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.

How to apply
To apply please submit a covering letter and CV, with two referees, through our online system.

Please apply online via www.embl.org/jobs.

Closing date: 6 May 2018

Applications are welcome from all nationalities – 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.

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