THE WELLCOME TRUST CENTRE FOR HUMAN GENETICS
Job Title: HIGH THROUGHPUT SEQUENCING BIOINFORMATICIAN (Full-time 100%)
Salary: University Grade 7: £28,983 to £35,646 with a discretionary range to £38,951
Tenure: Fixed term contract for 2 years in the first instance, funded by the Oxford Bio Medical Research Centre
Reporting to: Dr Jenny Taylor
About the post:
An exciting opportunity has arisen for a high throughput sequencing bioinformatician within the Oxford Biomedical Research’s Centre’s (BRC) Genetics Theme, based at the Wellcome Trust Centre for Human Genetics. The Oxford BRC is a collaboration between the University of Oxford and the Oxford Radcliffe Hospitals NHS Trust, funded by the Department of Health to translate research into clinical practice (www.oxfordbrc.org/research/genetics). The emphasis of the Oxford BRC Genetics Theme’s programme is on clinical applications of novel genomics technologies, in particular next generation sequencing and array-based methods. The results of this programme are already being translated to the clinic. Particular focus is currently on cancer, cardiovascular and neurodegenerative diseases and pathogen analysis.
The post-holder will be responsible for the analysis of next generation sequencing data from a range of genetics research projects, encompassing de novo assembly, whole genome and targeted re-sequencing. The post-holder will apply analysis methods and, where appropriate, develop novel methods, and work on setting up and maintaining the necessary data processing pipelines. Relevant sequence data will be generated in-house, initially from a mixture of Roche/454 and Illumina/Solexa instruments. The post-holder will work closely with the BRC’s multi-disciplinary project teams, encompassing laboratory scientists and clinicians, and with the WTCHG high throughput sequence analysis group within the WTCHG bioinformatics core. Good interpersonal skills are required.
The interdisciplinary nature of the BRC Genetics Theme programme implies a diverse and stimulating array of challenges relating to biology, sequence analysis, statistics and computer programming and this, combined with the location in the WTCHG, provides an active and rich research environment.
Purpose of the job: The post-holder will work on analysing next generation sequencing data, applying and developing methods, and maintaining the data processing pipelines to support projects evaluating the clinical applications of next generation sequencing.
Main Responsibilities:
Analysis and Data Management
· To conduct analysis of next generation sequence data (DNA-seq, RNA-seq) from clinical patient samples being generated by BRC, to include de novo and targeted sequencing
· To develop novel methodologies for analysis of HT sequencing data in collaboration with colleagues in the WTCHG Core.
· To address any programming requirements inherent in the management of this data.
· To assist with bioinformatics aspects of translation of sequencing technology to NHS as appropriate
· To keep abreast of relevant literature and methodology developments relevant to the field
Communication
· To report to the Oxford BRC Genetics Theme Programme Director (based at the WTCHG), meeting regularly to review data and projects.
· To report to the Head of High-Throughput Sequencing Analysis to ensure that appropriate analysis methodologies are deployed and developed.
· To communicate frequently and effectively with the laboratory scientists generating the sequencing data
· To meet with BRC project PIs and teams, to discuss their requirements, reporting data and ensuring that the tasks are completed satisfactorily
· To hold frequent discussions with members of the HT Sequence Analysis group and other members of the Bioinformatics Core, to remain aware of ongoing developments
· To contribute ideas and communicate effectively with members of the BRC and HT Sequencing Group and Bioinformatics Core
· To assist in the conduct of research, under the direction of the Head of High-Throughput sequencing
· To perform any other comparable duties as may reasonably be required to ensure the efficient running of the group
· To participate in group meetings, generate publication-quality manuscripts and contribute to discussions of the aims and objectives of the group.
· To contribute ideas and communicate effectively with database experts and scientific programmers.
General Responsibilities:
· To be accountable for your professional conduct within the BRC and the Centre.
· To undertake such other duties as may be required from time to time that are commensurate with the grade and responsibilities of this post.
· To ensure such that all conduct is with due regard to the University Equal Opportunities and Data Protection policies.
Relationships:
· The post holder will be responsible to and meet routinely with Dr Jenny Taylor (BRC Genetics Theme Programme Director).
· For technical matters the post holder will be responsible to and meet routinely with Dr Gerton Lunter (WTCHG Head of High-Throughput sequencing).
· The post holder is to meet with the other members of the project to discuss progress, and with the BRC Genetics Theme Leader, Prof Andrew Wilkie, and Advisory Committee as required.
Education and Training:
· To continue to develop research interests in the area of bioinformatics and statistical genomics in keeping with the aims of the BRC, Bioinformatics Group and the Centre.
· To participate in the education and training of other staff as necessary and appropriate.
· Following the probationary period the post holder's performance will be continually monitored to ensure that the required standards of accuracy and efficiency are maintained.
Knowledge and Skills:
· A PhD degree in bioinformatics or statistical genetics
· A degree at grade 2.1 or 1st or equivalent in a numerical subject, (eg Statistics, Computer Science, Mathematics, Physics, Bioinformatics or similar)
· Strong post-doctoral experience in applied DNA sequence analysis is required
· Experience in the analysis of next generation sequencing data is highly desirable
· Excellent programming skills in languages such as Python, Java, C/C++, R or similar.
· High level of self motivation and ambition
· Ability to work as part of a team is essential and experience of supervising other scientists would be preferred.
· Strong communication skills; ability to communicate effectively with a wide range of people (at a variety of levels of technical knowledge), and enjoy working with a lively and motivated group of scientists
· Demonstrated ability to conduct independent research.
· Proven ability to write up scientific findings in peer-reviewed journals
Working for the University of Oxford
At the University of Oxford, we’re naturally very proud of our outstanding reputation for scholarship and research. But we’re also proud to say that we’re one of the region’s biggest and best-established employers, with a diversity of staff helping to sustain our success – from laboratory assistants, cleaners, technicians and secretaries, to IT, finance and administrative professionals. Join us, and you can expect to find yourself working in a friendly, open-minded atmosphere where your ideas will be welcomed, with an interesting and satisfying job to do, and with plenty of opportunities to learn new skills, or maybe even get some extra qualifications.
As well as pay and other benefits such as generous holidays and excellent pension scheme, we may be able to help you with:
· Training – We train our staff, both in the skills needed for starting the job, and to help them develop afterwards. If you don’t have all the skills we are looking for (e.g. computer packages), but you know you are a quick learner, its worth asking if training might be available.
· Working Hours – We may be able to be flexible about working patterns to help you combine work with responsibilities at home. Even for full-time jobs, we can often adjust starting and finishing times, or even sometimes consider term-time-only working: if this is important to you, let us know.
· Disability – If you have a disability, we have specialist staff who can help you to start and stay in work.
· Childcare – The University offers subsidised nursery places, and tax and National savings schemes. Please note that there is a long waiting list for nursery places. It is particularly important to refer to the website http://www.admin.ox.ac.uk/eop/child for further information including up to date information about the length of the waiting list and alternative sources of information about childcare in the Oxford.
· Parenting – The University has a generous maternity leave scheme and also offers paternity leave to expectant fathers and partners, and adoption leave.
· Cultural and Religious needs – We respect the cultural and religious lives of our staff. If you need time away from work, or special facilities, and can give plenty of notice for arrangements to be made, this will always be considered.
· Travel Arrangements – We offer an interest free-season ticket loan scheme for bus or train season tickets. Annual passes for Oxford Bus Company routes are available at discounted rates.
· Use of University Facilities – All University staff can use the study facilities provided by the University libraries and museums; join the University Club, a sports and social club which has its own bar, café, and reading room; and make use of the University Sports Complex and the Pulse fitness centre.
· Discounts – A number of discounts are available to University staff e.g. for insurance, holiday travel, and computer equipment.
The range of benefits is continuously reviewed and extended. For further information see www.admin.ox.ac.uk/ps/staff/benefits/
If you come from outside the area, you may be interested to know that as well as the famous tourist attractions such as the ‘dreaming spires’ of all the lovely old buildings, the river and a number of attractive parks and gardens, Oxford also has a busy shopping centre and a lively nightlife, particularly during term time. Housing is relatively expensive within the city, but nearby areas such as Didcot or Bicester are more reasonable priced. Although car parking is difficult during the day, there are good train and bus services, including several ‘Park and Ride’ routes; and of course, lots of cycle paths.
Pay and Benefits
The salary offered for full-time appointment to this job will be in the range, £28,983 to £35,646 with a discretionary £38,951 (Academic-Related Research Staff Grade 7), depending on qualifications and experience. If you are appointed at a salary below the top of this range, your salary will automatically be increased each year until you have reached the top point. There is also an annual ‘cost of living’ salary review, which normally takes place in summer each year. Pay and benefits for part-time appointments are worked out on a ‘pro rata’ basis.
For a full – time appointment, the annual holiday entitlement will be 38 days (including 8 public holidays). Your hours of work are such as are reasonably required to carry out your duties to the satisfaction of your head of department.
The appointment is subject to satisfactory completion of a 6 month probationary period, during which the notice period will be one month on either side. Once the appointment has been confirmed, the notice period will be three months either side.
The position is available for up to two years in the first instance and will be funded by the Oxford Bio-Medical Research Centre.
Staff
The age of retirement for university appointments is 65. Staff are eligible to join the University Superannuation Scheme (USS) which is a contributory scheme. Subject to the Statement of Pensions Policy, which will be issued to the successful candidate, the appointee will be deemed to be in membership of the USS until such time as he or she gives notice in writing to exercise the right not to be a member of the scheme.
The Wellcome Trust Centre for Human Genetics has a NO SMOKING policy.
How to apply
To apply, please write a letter of application and send a detailed CV and return it to:
Personnel Administrator
Wellcome Trust Centre for Human Genetics
Roosevelt Drive
Oxford
OX3 7BN
or by fax to 01865 287516 or email to by no later than Friday 25th June 2010. Applicants received after this date will not be considered. Please make sure you quote reference number H5-10-037-JT at the beginning of your application.
The list of duties and the ‘selection criteria’ for this job describe the sort of skills, experience, knowledge or abilities which we are looking for. We will interview those whose applications best meet these criteria, so it is very important that you should use your application to explain how you can match them. Remember that you will have gained abilities, experience and skills from many aspects of your life; some may come from education or work, and others from home or community life. Tell us about which schools or colleges you went to and any qualifications you have. List employment, voluntary work, hobbies, or family responsibilities which help to show you meet the selection criteria.
Please give the names, addresses and telephone numbers of two people you are prepared to give you a reference for this job. If you have previously been employed, your referees should be people who have direct experience of your work through closely working with you for a considerable period, and at least one of them should be your formal line manager in your most recent job. Otherwise they can be people who know you from recent college, school, or voluntary experience. It is helpful if you can tell us briefly how each referee knows you (e.g. ‘line manager’. ‘Work colleague’, ‘college tutor’).
Your referees will be asked to look at the job details and tell us if, in their opinion, you could do the job. We will assume that we can approach them at any stage unless you tell us otherwise when you apply. So, if you wish us to ask for your permission before approaching a particular referee, or to contact them only under your circumstances (for example if we are calling you for an interview, or if we have made you a conditional offer), you must state this explicitly alongside the details of the relevant referee(s).
Your appointment will be subject to (i) the return of a completed medical questionnaire which is acceptable to the University, (ii) the provision of original documentation which indicates your right to work in the UK, and (iii) the completion of an initial probationary period of 6 months.
Equal opportunities at the University of Oxford
As an Equal Opportunity employer, we positively encourage applications from people of different backgrounds. All our jobs are filled in line with our equal opportunities code of practice, which helps us make sure that men and women, people of different races, and those with disabilities are all treated fairly.