School of Medicine (Division of Cancer)

& School of Life Sciences (Division of Computational Biology)

Postdoctoral Research Assistant - Bioinformatics

1.0 FTE

Grade 8 - up to point 38

Salary Scale £38,896 - £40,082

Fixed Term 36 months

Please note: Applicants whose experience level is below grade 8 are welcome to apply; salary will be paid in accordance with qualifications, training & experience

For informal enquires please contact:

Prof Sara Brown
Professor of Molecular & Genetic Dermatology, Wellcome Trust Senior Research Fellow in Clinical Science & Honorary Consultant Dermatologist
Skin Research Group, School of Medicine,
University of Dundee, James Arrott Drive,
Ninewells Hospital and Medical School, Dundee DD1 9SY Scotland, UK
Tel: +44 1382 383210
email: s.j.brown@dundee.ac.uk http://medicine.dundee.ac.uk/staff-member/professor-sara-brown

Prof Geoff Barton
Professor of Bioinformatics and Head of Division of Computational Biology
School of Life Sciences,
University of Dundee,
Scotland, UK
Tel: +44 1382 385860
email: g.j.barton@dundee.ac.uk http://www.compbio.dundee.ac.uk

Further Particulars

Job Title and Reporting

Postdoctoral Research Assistant (1.0 FTE) - Bioinformatics

Grade of Post/Salary: Grade 8 / £38,896 - £40,082

Day to Day Reporting to: Geoff Barton & Sara Brown

Reporting Line Manager: Sara Brown

Staff Supervision: PhD student(s) and undergraduate project students, if appropriate

Duration of employment: 36 months (dependent on a 12-month probationary period)

Role and Purpose

Investigating molecular mechanisms in atopic eczema

Atopic eczema is an itchy inflammatory skin disease which affects up to 25% of school aged children in the UK and up to 10% of adults, causing significant morbidity. The causes of eczema and its recent increase in prevalence remain poorly understood and treatment options are limited.

This is an exciting opportunity for a skilled bioinformatician/computational biologist or scientist with strong data analysis skills to play a significant part in a £1.8 million Wellcome Trust-funded project that will combine cutting-edge technology in molecular genetics and cell biology with bioinformatic analysis to answer fundamental questions about the mechanisms leading to skin inflammation and eczema.

The project builds on an established collaboration between the bioinformatics research group led by Prof Geoff Barton (School of Life Sciences) and the molecular genetics group led by Prof Sara Brown (School of Medicine).

The successful applicant will:

1. Interrogate an ultra deep sequencing datasets and develop analytical techniques to investigate evidence of copy number variation within genes of the epidermal differentiation complex
2. Analyse RNA-seq and proteomic data arising from organotypic skin culture models to test eczema candidate gene.

Findings will influence the design and interpretation of future molecular studies.

The successful applicant will have the opportunity to work within the environment of a strong bioinformatics research group (Barton) as well as having close interactions with an RA and PDRA in a wet-lab focussed on clinical translational research (Brown).

We seek a highly motivated individual with strong computational skills and excellent communication skills, who is able to adapt, develop and acquire new computational and data analysis skills as required.

Location & Environment

The post holder will have dedicated workspace both at the School of Medicine, Clinical Research Centre on the Ninewells Campus and the School of Life Sciences, University of Dundee, Dow Street, Dundee.

Prof Geoff Barton: http://www.compbio.dundee.ac.uk/

The Barton Bioinformatics Group provides an excellent environment for bioinformatics research that includes dedicated high-performance computing facilities and support staff. The group has extensive expertise in NGS sequence analysis and is located in the Discovery Centre which provides purpose-built space for computational biology research in an interdisciplinary environment.

Prof Sara Brown: http://medicine.dundee.ac.uk/staff-member/professor-sara-brown

Sara Brown, Professor of Molecular and Genetic Dermatology, is an honorary consultant dermatologist within the NHS and a Wellcome Trust Senior Fellow in Clinical Research. She leads a dedicated laboratory group focussed on the investigation of atopic eczema, using the approaches of molecular genetic and cell biology.

Joint publications arising to date from the Barton/Brown collaborations are:

1. Filaggrin-stratified transcriptomic analysis of pediatric skin identifies mechanistic pathways in patients with atopic dermatitis. Cole C, Kroboth K, Schurch NJ, Sandilands A, Sherstnev A, O'Regan GM, Watson RM, McLean WH, Barton GJ, Irvine AD, Brown SJ. J Allergy Clin Immunol. 2014 Jul;134(1):82-91.
2. Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-Seq and ESTs. Schurch NJ, Cole C, Sherstnev A, Song J, Duc C, Storey KG, McLean WH, Brown SJ, Simpson GG, Barton GJ. PLoS One. 2014 Apr 10;9(4):e94270.
3. Tmem79/Matt is the matted mouse gene and is a predisposing gene for atopic dermatitis in human subjects. Saunders SP, Goh CS, Brown SJ, Palmer CN, Porter RM, Cole C, Campbell LE, Gierlinski M, Barton GJ, Schneider G, Balmain A, Prescott AR, Weidinger S, Baurecht H, Kabesch M, Gieger C, Lee YA, Tavendale R, Mukhopadhyay S, Turner SW, Madhok VB, Sullivan FM, Relton C, Burn J, Meggitt S, Smith CH, Allen MA, Barker JN, Reynolds NJ, Cordell HJ, Irvine AD, McLean WH, Sandilands A, Fallon PG. J Allergy Clin Immunol. 2013 Nov;132(5):1121-9.
4. Haploinsufficiency for AAGAB causes clinically heterogeneous forms of punctate palmoplantar keratoderma. Pohler E, Mamai O, Hirst J, Zamiri M, Horn H, Nomura T, Irvine AD, Moran B, Wilson NJ, Smith FJ, Goh CS, Sandilands A, Cole C, Barton GJ, Evans AT, Shimizu H, Akiyama M, Suehiro M, Konohana I, Shboul M, Teissier S, Boussofara L, Denguezli M, Saad A, Gribaa M, Dopping-Hepenstal PJ, McGrath JA, Brown SJ, Goudie DR, Reversade B, Munro CS, McLean WH. Nat Genet. 2012 Nov;44(11):1272-6.

The School of Life Sciences at Dundee was ranked as the top UK biological sciences university department and the School of Medicine was ranked top for the Clinical Impact of its research in the UK Research Excellent Framework (REF) 2014. As such, Dundee is a centre of excellence in life sciences and biomedical research that combines quality of life with quality of science. Staff of more than 50 different nationalities creates a vibrant international working environment, with a particularly active Post-Doc Association.

Principal Duties

The Wellcome Trust-funded post holder will:

• Contribute to the experimental planning and computational analysis of data from high throughput sequencing technologies
• Develop their own strategies for working with the bioinformatics data
• Participate in the development of novel methodologies for the assessment of eczema models in vitro
• Plan and manage their research activity, under the guidance of Profs Barton & Brown, whilst contributing to the ethos of our collaborative and supportive team
• Keep abreast of developments in the fields of sequencing and data analysis
• Be able to work to deadlines and meet targets, with careful attention to detail
• Understand the importance of treating human samples and data with due diligence and respect
• Attend and contribute to weekly and monthly laboratory meetings
• Write up results for publication
• Present work at conferences in the UK and abroad, with training and support from the grant-holder

Service Delivery

The post holder will deliver service in bioinformatics, research management and presentation, as well as supervision of technical staff and students when required.

Communication

The post holder will require excellent communication skills for multidisciplinary team working and the presentation of preliminary data at internal meetings and research findings at national/international meetings as well as writing for publication. Depending on the level of experience, these duties will be carried our independently or with support and guidance from Profs Barton & Brown.

Liaison & Networking

The post holder will liaise with collaborative groups within the UoD and other UK universities.

Decision Making, Planning and Problem Solving

The post holder will be expected to work in a team but taking independent decisions when appropriate to their level of experience. They will be required to plan their own workload and meet deadlines.

Team Development

The post holder will join our team of translational researchers, including clinical and non-clinical scientists. Funding is available for attendance at courses/conferences outwith Dundee (up to £2,000 per annum).

The Brown group also works closely with the lay public, in collaboration with the patient support group Eczema Outreach Scotland. Opportunities for innovative public engagement work will be provided and the post holder may participate according to their interest and skill-level.

Qualifications, Knowledge and Experience

Essential

• PhD in Bioinformatics; however we also welcome applicants without a PhD in Bioinformatics providing they have strong data analysis skills gained in other fields, e.g. physics
• 3-years research experience of programming/data analysis/development
• For appointment at the higher grade at least 3-years' relevant postdoctoral experience are required
• Skills in at least one of: Perl, Python, Java, C/C++ in a Unix/Linux environment
• Knowledge of statistical analysis of relevance to biological research & large datasets.
• Ability to work in a multidisciplinary team environment
• Ability to work independently with minimal supervision, but also operating as part of a team, where necessary, providing direction and guidance as required
• Demonstration of initiative and ability to conceive, design and execute appropriate experimental analyses and draw conclusions from the outcomes
• Excellent written/oral presentation skills
• Flexibility and willingness to work outwith regular hours if required

Desirable

• Familiarity with molecular biology/structural biology concepts and principles
• Evidence of interest in clinical/translational research
• Sound knowledge of standard bioinformatics tools, algorithms and techniques
• Knowledge of bioinformatics techniques commonly applied in high-throughput sequencing
• Major contribution to at least one paper in a peer-reviewed journal