Research Fellow, Centre for Cancer Research and Cell Biology

To work with the Stratified Medicine Group led by Professor Kennedy at the Centre for Cancer Research and Cell Biology. The aim of
this work will be to investigate the alterations which characterise the DDRD molecular subgroup within the research group of
Professor Richard Kennedy. The DDRD (the DNA damage response deficient- DDRD) was discovered through gene expression
profiling of breast cancer tumours, enriched for BRCA1/2 mutations. A 44 gene expression assay was developed to identify the
molecular subtype using formalin-fixed paraffin-embedded tissue and was shown to identify patients who had significantly more
benefit from DNA damaging chemotherapy such as anthracycline and cyclophosphamide based regimens in three independent
datasets. This project aims to gain more insight into the underlying biology driving the DDRD group by understanding the alterations
at the genomic, transcriptomic and proteomic level which associate with the DDRD molecular subgroup. This would be performed
using internally generated and external data e.g. The Cancer Genome Atlas datasets across multiple cancer types. The project would
involve the development of a bioinformatics pipeline in R or Matlab for interrogating omics datasets with gene expression signatures.
Using the DDRD assay as an example the software will classify the DDRD status of patients across cancer types using gene
expression data; it will then integrate this information with matched profiles from other data types and perform statistical tests to
uncover significant alterations associated with the DDRD group. The final output of the software will be to present integrated findings
(across cancer and data types) in an intuitive report format.

MAJOR DUTIES:

1. To design, develop and execute experiments related to the above titled project under the supervision of Dr Nuala McCabe and
Professor Richard Kennedy in order to obtain reliable data and to evaluate and interpret the results using methodologies and
other techniques appropriate to the area of the research.
2. To present regular progress reports on research to members of the research project team and, as appropriate, to other internal
or external audiences to disseminate and publicise research findings.
3. Initiate and maintain collaborative links with various project partners.
4. To work as part of a collaborative team of biologists, bioinformaticians and clinicians, including external partners, to ensure
optimal progression of the project at all times and to contribute to the achievement of project milestones.
5. To write up results in a timely manner and take a leadership role in writing research manuscripts for publication in high quality journals.
6. The appointed individual will be encouraged to formulate, write and submit grants for fellowship awards, project and travel support.
7. To attend and present new data at national and international meetings as appropriate.
8. To assist with the supervision of postgraduate students, honours or summer students on mini-projects, which will help develop their own supervisory skills.
9. Carry out routine administrative tasks associated with the research project/s to ensure that project/s are completed on time and within budget.
10. Read academic papers, journals and textbooks to keep abreast of developments in own specialism and related disciplines and
to maintain awareness of the context of the research project.
11. Any other reasonable duties within the general ambit of the post and competence of post holder.

Planning and Organising:

1. Plan own day-to-day activity within framework of the agreed research programme.
2. Plan up to a year in advance to meet deadlines for journal publications and to prepare presentations and papers for conferences.
3. Coordinate and liaise with other members of the research group over work progress.

Resource Management Responsibilities:

1. Support the development and training of support staff and students by making available their research experience and expertise.

Internal and External Relationships:

1. Communicate appropriately with lab colleagues the latest research findings/results.
2. Develop contacts with other labs within the research community at Queen’s and look to identify potential cross-discipline collaborations.
3. Work collaboratively with external academic/industrial partners.
4. Join national and international scientifically relevant societies.

ESSENTIAL CRITERIA:

1. Have or be about to obtain a PhD in either Bioinformatics, Maths, Stats or Computing or PhD in Natural Sciences with a significant bioinformatics component.
2. At least three years relevant experience to include experience of:
 • Experience of processing and analysing high-dimensional omics datasets;
 • Experience of curating and analysing clinico-pathological data;
 • Experience of presenting statistical results to multi-disciplinary audiences;
 • Experience in statistical programming eg R or Matlab
3. Must have published paper(s) in quality journals to a level commensurate with their research experience.
4. Evidence of proactive organisational capabilities.
5. Sufficient breadth and depth of specialist knowledge in the discipline and of research methods and techniques to work within established research programmes.
6. Evidence of communication skills.
7. Ability to communicate complex information clearly.
8. Ability to build contacts and participate in internal and external networks and research presentations.
9. Team worker, highly motivated, supportive of junior colleagues within the group.
10. Ability to assess and organise resources.

DESIRABLE CRITERIA:

1. MSc or BSc/BA in either Bioinformatics, Maths, Stats or Computing.
2. Experience of key statistical methods and approaches eg clustering, classification and survival analysis.
3. Experience of applying and evaluating classification accuracy measures.
4. Experience of developing analytical pipelines for analysis of omics data.
5. Experience of developing/evaluating and applying new biostatistical algorithms to omics data.
6. Experience of identifying and adapting for batch/technical effects.
7. Previous experience in cancer biology.
8. Previous track record of high quality research in the field of cancer biology.
9. Evidence of scientific writing skills.
10. Evidence of participation in training/mentoring of students or junior staff.
11. Commitment to professional development, as evidenced by Scientific memberships eg. AACR.