Postdoctoral Fellow - Mouse Genomes Project

European Molecular Biology Laboratory (EMBL)

Contract Duration: 3 Years
Salary: Year 1 stipend (£2,630.10 monthly)

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
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South East England