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Opportunity: Research Associate in Bioinformatics @ University of Oxford -- Oxford, UK
Submitted by NDORMS, University of Oxford; posted on Thursday, February 08, 2018
SUMMARY
We have an exciting opportunity for a talented bioinformatician to join a team led by Dr Stephen Sansom at the Kennedy Institute of Rheumatology (KIR).
In this role, you will work in the computational genomics group to develop and run bioinformatics pipelines for the analysis of next-generation sequencing (NGS) data. Taking advantage of our state-of-the-art high-performance compute (HPC) facility you will collaborate closely with wet-lab scientists to analyse diverse types of data including those from RNA-seq, single-cell RNA-seq, ATAC/ChIP-seq, micobiome and CyTOF experiments. At the KIR – which is a world-class academic research Institute – researchers are now using such techniques to advance understanding and treatment of diseases such as rheumatoid arthritis, cancer and inflammatory bowel disease.
You will hold a degree of direct relevance to bioinformatics data analysis (or equivalent experience). Strong programming skills and experience with analysis of next-generation sequencing data essential for this post. A PhD in bioinformatics or computational biology, record with collaborative scientific research and of Immunology would be desirable.
Informal enquires to Dr Stephen Sansom are welcomed (stephen.sansom[at]kennedy.ox.ac.uk).
BACKGROUND
Research context:
The Kennedy Institute of Rheumatology (KIR) is a world-class academic research Institute at the University of Oxford. It has a mission to advance understanding and treatment of inflammatory diseases such as Rheumatoid Arthritis and Inflammatory Bowel Disease. In the course of their investigations, scientists at the KIR are increasingly using high-throughput genome-scale approaches for which bioinformatics analysis is essential. Such techniques include next-generation sequencing (NGS) based methods such as RNA-seq, single-cell RNA-seq, ATAC/ChIP-seq and microbiome analysis, as well as mass cytometry (CyTOF). The KIR has two computational research groups and has recently invested in a state-of-the-art high-performance compute (HPC) facility.
RESPONSIBILITIES
Role overview:
In this role, you will join our Computational Genomics research group to help develop and run bioinformatics analysis pipelines. You will work closely with students and post-docs from the KIRs' wet-lab research teams, taking responsibility for the routine analysis of next-generation-sequencing and CyTOF datasets. You will have the opportunity to develop and gain skills with a diverse range of bioinformatics techniques, to acquire knowledge of immunological research and to contribute (as a named author) to peer-reviewed research publications. Applicants at all career stages are encouraged to apply.
Key responsibilities:
- To develop, maintain and document bioinformatics pipelines in consultation with other members of the Computational Genomics research group
- To use bioinformatics pipelines to perform analysis of genomic data generated by researchers within the KIR
- To prepare project-specific data-analysis reports from pipeline results, and to present and discuss these with individual KIR scientists and research groups
- To advise and assist other research staff with the design and bioinformatics analysis of genomic experiments as appropriate
- To contribute to manuscripts, presentations and other means of disseminating results
- To attend scientific seminars, meetings and training as appropriate
- To help evaluate new methods of relevance to KIR researchers
- To support and participate in the activities of the Computational Genomics team
- To keep accurate, up-date and accessible records of project work and pipeline development
Relationships:
- You will be a member of the Computational Genomics team led by Dr Stephen Sansom at the KIR.
- You will be supported in your role by the KIR HPC Systems Administrator and Research Informatics team.
- You will also provide regular (i.e. monthly to quarterly) updates to the KIR Computational Genomics Strategy Group and this group will also contribute to setting priorities.
REQUIREMENTS
- A degree of direct relevance to bioinformatics data analysis (or equivalent experience)
- Experience with the analysis of next-generation sequencing data
- Demonstrated proficiency with scripting languages (including Python) and familiarity with a lower-level language such as Lisp, C or Java
- Software development experience including expertise with version-control systems
- Statistical expertise and experience with R or Matlab
- Expert knowledge of Bash, Linux and High-performance computing
- Excellent interpersonal skills, able to work independently and collaboratively
- Excellent communication skills, both oral and written
- Good working knowledge of office software
- Excellent organisational skills – managing both time and records effectively
- Able to use own initiative to solve problems
PREFERENCES
- A PhD in bioinformatics or computational biology
- Successful track record with collaborative scientific research
- Academic training or research experience in the field of Immunology
- Experience with the use of SQL databases
- Experience with the teaching of bioinformatics skills to others
- Experience with automated report generation (e.g. via Latex, Sphinx or Rmd)
- Experience with the development of pipelines for genomic data analysis
- Good project management skills and a track record in meeting deadlines
TERMS
This is a full-time fixed-term appointment for 3 years.
LOCALE
Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Kennedy Institute of Rheumatology, Old Road Campus, Oxford
COMPENSATION
Grade 7: £31,604 - £38,883 p.a.
A lower grade offer may be made (Grade 6: £28,098 - £33,518 p.a.) with commensurate reduction in responsibilities (and amendment in job title to Research Assistant in Bioinformatics) if a suitable candidate cannot be found to fill the Grade 7 position.
DEADLINE
The closing date for applications is 12.00 noon on Monday 5 March 2018.
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