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Job Profile Job Description Job Details Job Title: Postdoctoral Research Fellow, Computational Biology School/Dept/Institute & Centre: Clinical Pharmacology/William Harvey Research Institute Reports to: Dr Damian Smedley, Senior Lecturer Grade: 6 Working hours per week: 37 Appointment period: Till 31st March 2018 Current Location: Charterhouse Square Job Context Briefly describe the setting of the post within the School/Dept/Institute. Please see guidance notes for additional instructions and working examples of job contexts for a variety of roles at QMUL. This post will be in Dr Smedley’s team in the Centre for Clinical Pharmacology whose research looks to utilise clinical and model organism phenotype data to better understand human disease. The researcher will contribute to Queen Mary’s national reputation for research by planning and managing innovative projects within Dr Smedley’s team as well as providing expert advice to other members of the William Harvey Research Institute. The holder will interact with our external collaborators on the PheneBank project to develop a new database of disease, gene and phenotype associations. Dr Smedley has a joint role as Director of Genomic Interpretation for Genomics England Limited, located on campus, and the utility of PheneBank to the 100,000 Genomes Project will be a major focus of this position. Job Purpose Provide an accurate and concise statement of why the job exists, summarising the overall purpose of the job in the context of QMUL. Please see guidance notes for additional instructions and working examples of job purposes for a variety of roles at QMUL. To participate in the newly funded PheneBank project that aims to apply a novel natural language processing approach to generating a database of disease, gene and phenotype associations. PheneBank involves partners at the University of Cambridge, European Bioinformatics Institute and Charite University, Berlin. This role will initially involve annotating disease, phenotype and gene relationships within biological literature to develop a gold standard test dataset that will be used by the Cambridge partner to develop their algorithms. In the second phase the role with involve assessing the utility of PheneBank in the clinical interpretation of rare disease patient genomes in projects such as the 100,000 genomes project. Main Duties & Responsibilities It is not necessary to list every task the jobholder will undertake. Job applicants will not read copious amounts of text. You should therefore focus on 12-15 of the primary duties and responsibilities of the jobholder. Duties should take the format: What is done, to what / to whom and with what outcome. Please see guidance notes for further instructions on how to complete this section. To participate in selecting an appropriate text corpus for the PheneBank project’s goal of identifying diseases, phenotypes and genes and the relationships between them. To manually curate disease, phenotype and genes relationships in a subset of this corpus to serve as gold standard test and training datasets for the natural language processing (NLP) team at the University of Cambridge. 1 Job Profile Job Description Main Duties & Responsibilities Assess the success of detecting the curated associations using the NLP approach. Deciding when the specificity and sensitivity of the NLP approach on the initial manually curated gold standard datasets is sufficient to apply more globally to the whole text corpus. Contribute to the design of the PheneBank database that will store the results of the NLP. Assess the research utility of the PheneBank database by comparison to existing manually curated disease, phenotype and gene databases such as OMIM and Orphanet. Assess the utility of the PheneBank database in a translational context by incorporating it into the clinical interpretation of unsolved cases from the 100,000 Genomes Project. Regular discussions with the main QMUL PI and participation in his group meetings. To participate in regular teleconference and face to face meetings with the lead partner at the University of Cambridge as well annual project meetings with the rest of the partners from Charité – Universitätsmedizin Berlin, the European Bioinformatics Institute and the University of Colorado. To plan and manage research projects and associated budget within Dr. Smedley’s team and contribute to the identifying and securing of future sources of funding. Supervising and taking responsibility for the research team. Disseminate research findings through publication in leading journals and presentations at conferences, establishing a national reputation for research. Collect data and undertake any appropriate analysis of data as requested. Undertake literature and database searches for the research project, and to be able to interpret and present the findings of the literature searches and advise the research teams appropriately regarding potential projects as required by the line manager/supervisor/PI. Keep up to date with subject related and professional issues, in particular, developments in the specific subject area. Monitor research findings with a view to commercial exploitation, and to inform the Head of Department (or line manager, as appropriate) and Head of Innovation & Enterprise of any appropriate novel research outcomes. To contribute to the research environment in the department through participation in seminars and discussion groups and providing expert advice. To undertake such other duties as may be reasonably expected by the line manager or Head of Department/Director of Institute. To carry out responsibilities with due regard to the College’s Equal Opportunities and Health & Safety Policies. The above list of responsibilities is not exhaustive and the jobholder may be required to undertake other duties commensurate with the level of the role, as reasonable requested by their line manager. This job description sets out the duties of the post at the time it was drawn up. Such duties may vary from time to time without changing the general character of the duties or level of the responsibility entailed. Such variations are a common occurrence and cannot in themselves justify a reconsideration of the grading of the post. 2 Job Profile Person Specification This table lists the essential and desirable requirements needed in order to perform the job effectively. Candidates will be shortlisted based on the extent to which they meet these requirements. Essential / Desirable Requirements Qualifications PhD or equivalent experience in a relevant biological and computational discipline. Essential Knowledge, Experience in identifying or utilising the relationships between diseases, phenotypes and genes in a Mendelian/rare disease research setting. Desirable Skills and Experience of literature curation Desirable Experience Working knowledge of disease databases Desirable Strong written and oral English communication skills Essential Ability to write analysis scripts in an appropriate language such as Perl, Python or R Essential Querying of relational databases managed using standard systems such as MySQL, PostGres or ORACLE Desirable Attention to detail Essential Ability to communicate effectively within a multidisciplinary team Essential Flexible and co-operative approach to colleagues Essential Professional attitude towards work Essential A demonstrable ability to cope under pressure and deliver to deadlines Essential Understanding of the research process Essential Experience of dissemination of information in relevant and high impact publications Essential 3 Job Profile Person Specification E – Essential: Requirements without which the job could not be done. D – Desirable: Requirements that would enable the candidate to perform the job well. 4