Download Faculty of Medicine and Health School of Medicine Leeds Institute of

--------------------Faculty of Medicine and Health
School of Medicine
Leeds Institute of Cancer and Pathology (LICAP)
Section of Experimental Haematology
Research Fellow – Bioinformatics
Project Title: Systems Understanding of Haematological Malignancies
This post is supported by four research groups within the Section of Experimental
Haematology and is immediately available, for two years in the first instance with a
possibility of extension subject to performance and available funding.
We are looking for an enthusiastic, highly motivated individual working in the area of
bioinformatics and systems biology. The Successful applicant will work on a range of
projects focussed on the molecular mechanisms of normal and diseased haematopoiesis
with a strong translational focus. These projects will generate large high-throughput data
sets from experiments incorporating techniques such as ChIP-Seq, microarray and gene
mutation analysis by NGS. The post holder will be responsible for the analysis of this data,
and the development of statistical and systems models to contribute to our understanding
of the molecular mechanisms underlying these processes.
You will have (or be about to be awarded) a PhD and research experience in
bioinformatics or systems biology. You will have substantial statistical and mathematical
skills, and a good grasp of the relevant biology.
The University of Leeds is committed to providing equal opportunities for all and
offers a range of family friendly policies (http://hr.leeds.ac.uk/homepage/4/policies).
The University is a charter member of Athena SWAN and holds the Bronze award.
The School of Medicine gained the Bronze award in 2013. We are committed to
being an inclusive medical school that values all staff, and we are happy to consider
job share applications and requests for flexible working arrangements from our
employees.
University Grade 7 (£31,342 - £37,394 p.a.) dependent upon qualifications and
relevant research experience. Please note that the maximum starting salary point
for this post is limited to £33,242 p.a. due to funding restrictions.
If you have any informal enquiries about the post please contact Dr Pascal Lefevre,
email: [email protected]
Any specific enquiries about your online application please contact Sharon Collins,
email [email protected] or Nicola Johnson, email: [email protected]
Job Ref:
MHCAP1024
Closing Date: 15 May 2015
Background
The Leeds Institute of Cancer and Pathology (LICAP)
Director: Professor Tim Bishop
http://medhealth.leeds.ac.uk/info/900/leeds_institute_of_cancer_and_pathology
The Leeds Institute of Cancer and Pathology addresses both laboratory based and clinical
research into cancer with a major focus on translational science. LICAP is one of the
largest cancer Institute’s in the country and has major financial support from the cancer
charities. The laboratories and clinical research are all based on the St James’s site with
laboratory activities being located in the Wellcome Trust Brenner Building and adjacent
buildings while the clinical work is based within Bexley Wing. The Institute consists of
eight Sections: Epidemiology & Biostatistics; Experimental Haematology; Experimental
Oncology; Oncology & Clinical Research (Clinical); Oncology & Clinical Research
(Laboratory); Patient Centred Outcome Research; Pre-cancer Genomics; and Pathology &
Tumour Biology.
Cancer Research UK Leeds Centre
http://www.cancerresearchukcentre.leeds.ac.uk
The Leeds Cancer Research UK Centre is a partnership between the University of Leeds,
Leeds Teaching Hospitals NHS Trust and Cancer Research UK, which aims to harness
the scientific power of Leeds-based cancer researchers to deliver improvements in cancer
care at local, national and international level. It fosters excellence in basic and
translational research and offers services to all cancer researchers in Leeds, irrespective
of their funding source. Beyond research, the Centre is also keen to build stronger
relationships with the local community, with patients undergoing cancer treatment, their
carers, cancer survivors and the wider public.
Section of Experimental Haematology – Professor Peter Hillmen
Research environment
Our department is led by Professor Peter Hillmen, an internationally renowned
haematologist who leads research into chronic lymphocytic leukaemia and PNH. Other
clinical researchers are Professor Gordon Cook, a leading expert in the treatment
of myeloma, and Dr Reuben Tooze, a haematopathologist leading research into the
diagnosis and molecular pathology of lymphoid cancers. Principal Investigators in the
department are Dr Gina Doody (signal transduction, gene regulation in B-cell
differentiation and tumours), Dr Peter Laslo (gene regulation in myeloid leukemias), Dr
Pascal Lefevre (signalling and chromatin structure), and Dr Darren Newton (PNH and
chronic lymphocytic leukaemia).
The Leeds Centre has had a worldwide impact on the treatment of patients with
haematological malignancies. For example, clinical trials designed and led in Leeds have
improved outcomes for patients with multiple myeloma, B-cell chronic lymphocytic
leukaemia and Paroxysmal Nocturnal Haemoglobinuria (PNH).
Leeds is a Leukaemia and Lymphoma Research (LLR) Centre of Excellence - these
Centres are chosen by the LLR charity for their expertise in blood cancer research. The
department of Experimental Haematology at the University of Leeds has close links with
the Haematological Malignancy Diagnosis Service (HMDS) and the Haematological
Malignancy Research Network (HMRN) - an LLR funded comprehensive population-
based register and research resource spanning the cancer networks of Yorkshire, and the
Humber and Yorkshire Coast. This provides an unparalleled resource for the integration of
tumour biology with patient epidemiology and treatment response.
Cancers of the immune system and blood are thought to arise principally as a
consequence of random aberrations, with relatively minor contributions from defined
behavioural/environmental factors or known genetic causes. They can affect people of all
ages and around 30,000 people are diagnosed with a blood cancer in the UK every year.
Haematological malignancies are generally diseases of adults and the elderly, but
childhood leukaemia is the most common form of cancer in children.
The broad categories of lymphoma and leukaemia encompass a wide range of different
diseases. These are important separations because the underlying causes, clinical
outcomes and treatment requirements are very different. Major advances have been made
in treatment, but many haematological malignancies remain difficult to treat. Challenges
reside both in identifying mechanisms of disease and new treatment options and in
identifying patient groups who respond best to existing and new therapies. Translating
such understanding into patient care is a major focus of the team in Leeds.
Our current research includes:
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Understanding normal cellular behaviour and pathways in the immune system and
how these are deregulated in lymphoma and myeloma (cancers of the
immune system).
Investigating faults in molecules leading to cells multiplying out of control in
lymphoma and myeloma.
Identifying genes associated with haematological malignancies and studying how
9these genes are regulated.
Investigating how myeloma cells interact with cells in the immune system.
Understanding the biology of monoclonal B-lymphocytosis (MBL) and its
relationship with CLL.
Investigating how cellular and genetic aberrations influence the response to both
conventional and novel targeted therapies in CLL.
Building on the Centre’s work in Oncolytic Virotherapy (OV) – enhancing
antibody-based immunotherapy using OV in haematological malignancies.
Leading national myeloma and CLL trials.
Investigating the pathophysiology of bone marrow failure and its association
with PNH.
Understanding and improving the therapy of PNH.
A principal collaboration is in place between groups within this section and with Professor
Westhead’s group in the Faculty of Biological Sciences in relation to the development of
systems level and genomic approaches to disease and diagnosis. Professor Westhead’s
group is interested in prediction methods for biological problems based on machine
learning and statistical methods. One of their major interests is functional genomics and
systems biology, where they are involved in predicting molecular networks using genome
sequence data and the use of large genomic data sets (such as DNA microarrays, ChIPseqand proteomics) in gene function analysis and gene network prediction. They have
worked extensively with next generation sequencing data in the context of genetic
regulatory network prediction.
Facilities
The applicant will be primarily located within the Westhead Group. Here, research workers
have personal workstations and access to an extensive LINUX network, maintained by the
local systems administration group. This is coupled with an effective system for data storage
and backup. High performance computing is provided through access to the University
ARC1 system comprising more than 2000 computer cores.
Main Duties & Responsibilities
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To use appropriate computational, statistical or mathematical methods for handing and
analysing large data sets.
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To contribute to the design of a successful programme of investigation.
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To provide expertise in computational, statistical and mathematical methods
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To use specialist knowledge to develop bespoke solutions to specific problems.
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To present findings of research effectively both within the group and at external
meetings (local, national and international)
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To generate relevant research output (publications, presentations).
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To evaluate methods and techniques used and results obtained by other researchers
and to relate such evaluations appropriately to your own work.
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To manage own workload effectively, ensuring requirements are delivered to agreed
timescales.
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To be an active member of the local bioinformatics community ensuring research
outputs are shared and providing specialist knowledge to others.
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To keep specialist knowledge and skills (including research methods and techniques)
up-to-date.
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To train other members of the group in bioinformatics methods as required
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To work with others to ensure compliance with relevant Health and Safety
requirements.
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You will be expected to support and adhere to the Institute’s commitment to Equality
and Diversity.
Person Specification
Education and Professional Training
Essential
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Relevant first degree and PhD (biological science, bioinformatics, statistics or a
closely related numerate discipline). If first degree or PhD is in a biological science,
evidence of further relevant training in bioinformatics or statistics.
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Experience in computer-based analysis of large-scale biomolecular or other data.
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Experience in the analysis of Next Generation Sequence Data
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Expertise in statistical and mathematical methods.
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Expertise in programming with strong ability in at least one language (e.g. Python,
Perl, C etc.).
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Knowledge of mathematical/statistical packages (e.g. Matlab, R etc.).
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Ability and motivation to understand experimental methods and the underlying
biology.
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Ability to design, execute and write up research work independently.
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Good organisational and time management skills.
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Good communication skills.
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Effective interpersonal
presentational.
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Effective organisational ability, including the ability to manage time effectively and
prioritise tasks.
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The ability to work effectively, independently, and to work under pressure.
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Enthusiasm for working within a multi-disciplinary environment.
and
communication
skills,
including
written
and
Desirable
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Expertise in the use of high performance computing clusters.
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Experience with commonly used software tools for next generation sequencing
data, including alignment to reference genomes and SNP analysis
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Experience in whole genome/exome sequence analysis
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Data management and analytical skills including experience of the use of database
and statistical software.
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Experience with commonly used genomic analysis tools that are used by local
research groups (Genespring, Partek, Affymetrix/Illumina proprietary software etc)
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Experience in analysis of biological networks (e.g. Ingenuity, Metacore, WGCNA,
MERLIN etc.)
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Experience in the analysis of microarray, ChIP-seq and gene expression data
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Good publication record
Relationships
The appointment will be made through the Section of Experimental Haematology, Leeds
Institute of Cancer and Pathology (LICAP). The appointee will be directly responsible to
Doctor Pascal Lefevre, and through him to Professor Tim Bishop, Head of Institute, the
Dean of the School of Medicine and Dean of Faculty of Medicine and Health.
University Values
All staff are expected to operate in line with the university’s values and standards, which
work as an integral part of our strategy and set out the principles of how we work together.
More information about the university’s strategy and values is available at
http://www.leeds.ac.uk/comms/strategy/
Further Information
Faculty Information
Faculty of Medicine and Health Information
With more than 6,000 students, 1,600 staff and annual research income of £60m, the
Faculty of Medicine and Health at Leeds is bigger than some universities. Leeds has one
of the largest medical and bioscience research bases in the UK, and is an acknowledged
world leader in cancer, cardiovascular, psychiatric, genetic, musculo-skeletal and health
services research. Treatments developed in Leeds are transforming the lives of people
around the world living with conditions such as HIV, TB, diabetes and malaria.
The School of Medicine
The School of Medicine at the University of Leeds is a major international centre for
research and education. Our ambition is to improve health and reduce health inequalities,
locally and globally, through excellent scientific research and the translation of that
research into healthcare practice, and through the education of future scientific and clinical
leaders who will advocate and practise an evidence-based approach. Our major strategic
aims are to:
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Deliver outstanding research including basic discovery science through to applied
health research that makes a significant difference to health.

Produce exceptional graduates, clinicians, educators, doctoral and post-doctoral
fellows whose learning has been informed and inspired by our research excellence
and who will form the next generation of academic and clinical leaders.

Develop and support knowledge transfer activities that flow from our academic
activities.
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Create and maintain an efficient and sustainable environment for research and
teaching within an organisational culture and management style that enacts and
supports the university’s core values of community, inclusiveness, integrity and
professionalism.
The School of Medicine is organised into seven Institutes. All are committed to high quality
research-led teaching, through their training of postgraduate research students, delivery of
postgraduate taught courses, and its leadership in undergraduate teaching. The School
works closely with the local NHS, having a number of jointly funded clinical posts to ensure
this relationship is effective and strong for both research and student education.
Additional Information
Terms and Conditions
Details of the terms and conditions of employment for all staff at the university, including
information on pensions and benefits, are available on the Human Resources web pages
accessible via the links on the right hand side, or at http://hr.leeds.ac.uk/policies
Disclosure and Barring Service Checks
A Disclosure and Barring Service (DBS) Check is not required for this position. However,
applicants who have unspent convictions must indicate this in the ‘other personal details’
section of the application form and send details to the Recruitment Officer
Disabled Applicants
The post is located both in the Garstang building main campus and on the St James’s
University Hospital site, Beckett Street, Leeds LS9 7TF. Disabled applicants wishing to
review access to the appropriate buildings are invited to contact the department direct.
Additional information may be sought from the Recruitment Officer, email
[email protected] or tel + 44 (0)113 343 1723.
Disabled applicants are not obliged to inform employers of their disability but will still be
covered by the Equality Act once their disability becomes known.
Further information for applicants with disabilities, impairments or health
conditions is available in the applicant guidance.