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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.
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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.
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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
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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.
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