Job-Description - Gray Institute for Radiation Oncology and ...

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Oct 1, 2013 (4 years and 1 month ago)

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Job description and selection criteria

Job title

Bioinformatics Core Leader

Division

Medical Sciences

Department

Oncology


Location

Old Road Campus Research Building, Headington, Oxford OX3
7DQ

Grade and salary

Grade 10: £
49,689
-

£57,581 per
annum with a discretionary
range to £62,907

Hours

Full time


Contract type

Fixed
-
term
until 31 March 2017
in the first instance


Reporting to


Professor
Tim Maughan
,
Clinical Director

Vacancy reference

103049



Introduction


The University of Oxford

is a complex and stimulating organisation, which enjoys an
international reputation as a world
-
class centre of excellence in research and teaching. It
employs over 10,000 staff and has a student population of over 21,000.


Most staff are directly appoint
ed and managed by one of the University’s 130 departments or
other units within a highly devolved operational structure
-

this includes 5,
9
00 ‘academic
-
related’ staff (postgraduate research, computing, senior library, and administrative staff) and
2,8
2
0 ‘s
upport’ staff (including clerical, library, technical, and manual staff). There are also
over 1,600 academic staff (professors, readers, lecturers), whose appointments are in the
main overseen by a combination of broader divisional and local faculty board/
departmental
structures. Academics are generally al
l also employed by one of the 38

constituent colleges
of the University as well as by the central University itself.


Our annual income in 2010/11 was £919.6m. Oxford is one of Europe's most innovative an
d
entrepreneurial universities: income from external research contracts exceeds £376m p.a.,
and more than 70 spin
-
off companies have been created.


For more information please visit
www.ox.ac.uk



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Medical Sciences Division


The Medical Sciences Division is an internationally recognized centre of excellence for
biomedical and clinical research and teaching. We are the largest academic division in the
University of Oxford
.


World
-
leading programmes, housed in state
-
of
-
the
-
art f
acilities, cover the full range of
scientific endeavour from the molecule to the population. With our
NHS

partners we also
foster the highest possible standards in patient care.


Of particular relevance to this post, the Wellcome Trust Centre for Human Gen
etics is part of
the Medical Science Division and is located on the Old Road Campus adjacent to the Old
Road Campus Research Building within which the Department of Oncology is based. The
Wellcome Trust Centre is one of the leading international centres f
or the study of the genetic
basis of common human diseases. As well as hosting a number of high
-
profile groups
pursuing the genetic basis of diabetes, cardiovascular disease and neuropsychiatric
phenotypes (amongst others), the WTCHG has led the efforts of

the Wellcome Trust Case
Control Consortium and been responsible for advancing the application of large
-
scale
genetic analysis to the dissection of common human phenotypes.
The centre provides a
unique integrated environment


including core genomics facil
ities, bioinformatics and
statistical genetics.
Presently the WTCHG has around 470 scientists and support staff and
had a £19.2M grant turnover in 2009/10.

The Bioinformatics and Statistical Genetics
Core
of the WTCHG
provides support

and
services to Cent
re’s scientists, in the areas or bioinformatics, statistical genetics, functional
genomics, databases and scientific computing, and undertakes collaborative and
independent research. It is focused on next
-
generation sequencing (including pipeline
develo
pment, maintenance and delivery to include RNAseq, ChipSeq, Variant Calling,
structural variants, assembly), statistical genetics (including linkage, eQTLs, analysis of
genotype data, CNVs, association analysis, and some ‘omics’ analysis), functional genom
ics
analysis (including microarray and high
-
throughput sequencing data), databases and
bioinformatics infrastructure.

The Bioinformatics core of the department of oncology will have
close links with this core group within the WTCHG.

For more information p
lease visit:
http://www.ox.ac.uk/divisions/medical_sciences.html


Oncology
Department


The Department of Oncology
within the Medical Sciences Division
was created in October
2010, under the

headship of Professor Gillies McKenna, to enhance the coordination of
clinical and basic cancer research in Oxford. The Department incorporates the Cancer
Research UK
-
MRC Gray Institute for Radiation Oncology & Biology, the
Sections of Medical
Oncology

a
nd

of Clinical Pharmacology and the Surgical Oncology Group of the Nuffield
Department of Surgical Sciences.


The Department is the second largest in the University’s Medical Sciences Division. Its
activities currently cover four sites: the Old Road Cam
pus Research Building, science
facilities in the Weatherall Institute of Molecular Medicine at the John Radcliffe Hospital, the
Radiobiology Research Institute on the Churchill Hospital site, and clinical service and
facilities at the Cancer
Centre in the
Churchill Hospital
.


The creation of the new Department marks an exciting step towards truly multidisciplinary
and collaborative oncology research in Oxford and positions us to take this discipline to new
heights. Working closely with colleagues in the ne
w state
-
of
-
the
-
art NHS Oxford Cancer and
Haematology Centre, research can be rapidly and efficiently translated into cutting
-
edge
clinical treatment for cancer patients.




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The Bioinformatics core is a newly established core group within the
D
epartment of
O
n
cology
the staff of which will work with scientific and clinical investigators from the
D
epartment of
Oncology
.


For more information please visit:
http://www.oncology.ox.ac.uk


The Gray Institute for Radiation
Biology and Oncology


The CRUK/MRC Gray Institute for Radiation Oncology and Biology was established in 2008
with the purpose of establishing a centre of excellence for radiation research in the UK. The
Institute, under the Directorship of Professor Gillie
s McKenna, has expanded to include 17
research groups with more than 200 staff and students, of whom the majority are scientists,
clinicians and technologists. Professor Tim Maughan has recently been appointed as Clinical
Director of the Institute. The Ins
titute has core infrastructure groups in radiation physics, and
radiation sources, imaging, bioanalysis, high through
-
put screening
, clinical radiotherapy

and
clinical trials support. The principal research facilities of the Gray Institute sit on the Old R
oad
Campus of the University adjacent to the major Cancer Hospital of the Oxford University
Hospitals Trust. Co
-
located with the Institute on the Campus are the Wellcome Trust Centre
for Human Genetics, the Ludwig Institute, the Jenner Institute for Vaccci
ne Research, the
Institute for Biomedical Engineering and the Richard Doll Building for Epidemiology and
Biostatistics. The Nuffield Department of Medicine is developing a Target Discovery Institute
on this site and the Kennedy Institute of Rheumatology ha
s a new building currently under
construction.


The Gray Institute for Radiation Oncology and Biology is the

leading centre for the
identification and development of new approaches to the biological and physical targeting of
radiation to improve the cure a
nd control of cancer.



The Bioinformatics Core within the Department of Oncology


High throughput technology has
supported

a scientific revolution in molecular biology and
clinical research. It is now possible to routinely acquire a large quantity of
in v
ivo

and
ex vivo

data using techniques such as genotyping, gene expression microarray, proteomic and
tissue array, and anatomical and molecular imaging. Some of these technologies have

already provided useful information both in terms of laboratory and clin
ical research and
management. However, isolated analysis of data from each technology has some intrinsic

and practical limitations, and thus an integrative approach is more likely
to aid experimental
discovery and the clinical decision
-
making process
in co
mplex diseases like cancer. Such
integration provides challenging methodological issues and requires standardization of data

processing; semantic interoperability of data, analytical procedures and workflows;

visualization and presentation of information i
n readily understandable formats; development
of powerful statistical methods and novel approaches to efficiently mine and utilise the data
complexity. In response to this opportunity, we are now establishing a core resource in
bioinformatics to address t
hese issues in relation to the scientific work of our 23 group
leaders and fellows

in the Department of Oncology
. There is funding for 4 personnel, who will
be drawn from a range of backgrounds including mathematics / statistics to ensure accuracy
and appr
opriate design and execution of the analyses performed; biology to make sense of
the data and analyse appropriate data sets


functional genomics, methylation, pathways etc
and computer science to manage database, sample annotation, writing codes and scrip
ts,
ensuring

availability of the resource. This post is for the leader of the core who could be
drawn from

any of these background disciplines.
It is expected that the work of the
Bioinformatics core will be balanced between collaborative research wi
th in
vestigators in the
D
epartment of
O
ncology and some independent research funded by external grant income.



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Core Activity



Setting
-
up and manag
ing

the Oncology Department Bioinformatics core group



Advis
e on the Bioinformatics component of the design of laborat
ory studies,
clinical studies and trials.



Advise on, and facilitate
, the implementation of genomic assays and genomic
profiling in trial protocols



Develop
, maintain and overview an Oncology Bioinformatics Platform for
execution of

Bioinformatics analysis p
ipelines

for the Department



Work in collaboration with Bioinformatics and Statistics groups in
the
University

to exploit existing
Bioinformatics
resources, tools and methods to
their full potential



Work in collaboration to develop pipelines
which combine e
xisting tools
, tools
developed by the group and by other groups in the Department and the
University



Overview the
implementation and

maintenance of analyses pipelines,
software and databases

relating to new and existing methods for use within
the Departme
nt



Implement standards in genomic analyses in collaboration with
the senior
Statistician,
other groups in the Oncology department

and in the Wellcome
Trust Centre for Human Genetics (WTCHG).



Participate in national and international projects aiming at sta
ndardi
z
ing
Bioinformatics analyses and data management



Train

students, clinicians and scientists in
the Oncology
D
epa
rtment

using
either existing courses within the university, integrating where necessary with
lectures/new modules, or one
-
to
-
one tutorials
.

Research Activity



Conduct methodological and scientific research in Bioinformatics applied to
cancer, specifically in g
enomic profiling in
oncology

studies and trials
, and
drug development studies



Investigate new study designs

in collaboration with cancer

researchers

and
clinicians

a.

Work with wet
-
lab scientists to design and develop novel research
studies (e.g. in
-
vivo studies, multi
-
level functional studies, in
-
silico modelling
studies)

b.

Work with clinicians/statisticians to design
genomic and
(post)g
enomics clinical trials
, and novel studies that analyse retrospective
clinical series

c.

Collaborate with national and international projects developing new
software environments facilitating integration of bioinformatics and clinical
data.




Work in collab
oration with
groups in the
Oncology D
epartment
,
the Target
Discovery Institute
(TDI)
and
the WTCHG to

d
evelop
and assess pipelines
to
analyze

genomics

data
in the context of

clinical
, translational

and laboratory
studies



Develop
and assess approaches and
p
ipelines
for analysis of complex
and
multi
-
layered
cancer datasets
, with particular attention to
methods that apply
to
clinical
studies and
trials



5



Work in collaboration with groups in the department, the TDI and the WTCHG
to develop and assess new approach
es for integration of

genomic data,
clinical data and data from other technologies (e.g. imaging data
, shRNA
library data
)



Work in collaboration with the WTCHG groups to develop pipelines to analyze
data from novel genomic platforms (e.g. deep sequencing)

in the context of
cancer studies, with emphasis on clinical and translational studies and trials



Work in collaboration with the Senior Statistician and the WTCHG to
implement

pipelines for large scale meta
-
analyses of genomic/post
-
genomic
clinical studies

and trials



Work in collaboration with

groups in the Oncology Department to introduce
Bioinformatics and genomics into other areas of oncology research, such as
target discovery and tumour modelling studies



Obtain external funding for research in the area

of Bioinformatics and cancer,
and Bioinformatics and Clinical and Translational Oncology

Communication & Networking:



Communicate the scientific relevance of their activity within the broader
context of the

D
epartment of Oncology and the University at re
levant
meetings and seminars.




Report progress
es

in data analy
sis and software development to committee
meetings and other relevant meetings.




Write
, contribute to the writing and/or supervise the writing of

papers for peer
-
reviewed journals.




P
repare and/
or overview the preparation of scientific
materials for teaching

within and outside the University,

demonstration

and/or presentation at
scientific conferences
.




C
ommunicate
scientific and technical
information which needs careful
explanation
to help oth
er member of the team and department

on a
frequent

basis
.





Maintain and develop the group’s scientific reputation through participation in
internal and external networks
, conferences and meetings.




Build

relationships
with Data M
anagers,
Scientists, C
lin
i
cians and S
tatisticians
to foster
exchanges of information

and collaborations between groups within
the
Department of
Oncology and collaborate actively with the Target
Discovery Institute and the Wellcome Trust Centre for Human Genetics.

Decision Making,
Planning and Problem Solving:



Responsible for developing
analysis pipelines and
software solutions

to
integrate, manage and interpret biological
and clinical
data

in the
Department
of
Oncology
.




Take responsibility and organise work of the Bioinformatics t
eam
.




S
upervise students and organize Bioinformatics training in the
Department of
Oncology
u
sing existing courses within the
U
niversity, integrating where
necessary with lectures, or one
-
to
-
one tutorials
.




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Supervise core funded Post
-
d
octorals
.




Provide ad
vice on Bi
oinformatic analyses to P
ost
-
doctoral
Scientists and
C
linicians
.




Apply for external funding as a lead, co
-
lead or collaborator as required in the
areas of Bioinformatics, Clinical and Translational Oncology, and Cancer.


Analysis & Research:


S
ee
the

section
above
on Key objective
s, “Research Activity”
.

Further Research objectives:




Overview the deployment, development, implementation and maintenance of
software and algorithms for analysis of genomic data in collaboration with the
data managers,

the statisticians, the scientists and the clinicians in the
Department of Oncology
, groups at the Target Discovery Institute and groups
at Wellcome Trust Centre for Human Genetics




Overview Bioinformatics analyses of genomic data such as gene expression;
miRNA expression data; SNP array data; deep sequencing data and data
generated using shRNA libraries, in the context of clinical studies and clinical
trials.




Investigate methods and implement pipelines for the use of genomic profiling
in clinical studies

and trials, both as covariate and/or endpoint in the
study/trial, and as a mean to inform the study design/trial.




Investigate methods and pipelines for the use of genomic profiling in drug
target discovery studies




Investigate novel approaches to analysi
s of complex and multi
-
layer datasets,
with particular attention to methods that apply to clinical and translational
studies, and trials.




Implement and develop analysis pipelines to integrate genomic data, clinical
data and data from imagining modalities
used in clinical and laboratory
studies (e.g. Magnetic Resonance Imaging and Positron Emission
Tomography) in collaboration with groups in the Oncology Department and
Target Discovery Institute.



Work in collaboration with the Senior Statistician and the W
TCHG to develop
pipelines for large scale meta
-
analyses of genomic/post
-
genomic clinical
studies and trials

Team Work, Teaching & Learning Support:



Participate in meetings, both in the department and with external
collaborators
.




Supervise students and P
ost
-
docs
.





Work cooperatively as a member of the
D
epartment

of Oncology.



Attend and contribute to relevant scientific meeting, and generate high
-
quality


7

manuscript
s
.




Act as a point of referral on issues related to own work area.




Act as facilitator in
scientific collaborations with external groups
.




Train students, Clinicians and S
cientists in the use of bioinformatics to
analyse their data and to
improve for example, study efficacy.




Maintain confidentiality regarding research data when interacting wi
th non
-
collaborating researchers.




To be accountable for their own professional conduct within the Group.




Undertake duties as may be required from time to time that are
commensurate with the grade and responsibilities of the post.




Conduct him or herself
with due regard to the University Equal Opportunities
and Data Protection policies.


Sensory/Physical Demands & Work Environment:



Use of a keyboard and a monitor is required for more than 90% of working
time



Selection criteria


The successful applicant

will be expected to meet the following criteria
:

Essential




A PhD or Masters in a numerical
or biomedical science
subject
, including some
bioinformatics or statistical genetics,
and relevant postdoctoral experience.





Have a proven track record in trainin
g and developing staff, including the provision of
technical advice and intellectual support.




Demonstrable aptitude for conducting independent research and experience in
developing strategy and success in obtaining peer reviewed funding.




Have the skills
and confidence to conduct complex discussions and influence
negotiations with collaborators.




Experience in Cancer Clinical Bioinformatics
.




Significant experience in Bioinformatics infrastructure management.




Programming skills in low level languages such

as C/C++, Java or similar.




Excellent database programming skills.




Experience in informatics aspects of High
-
Throughput Sequencing technology.




Familiarity with the existing literature and research in the field.



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Working knowledge of statistical software

packages such as R/BioConductor.




An active interest in undertaking scientific research and the ability to learn new
techniques and apply them to a high standard.




The ability to work closely with others as part of a team, while taking personal
responsib
ility for assigned tasks.




Excellent interpersonal skills.




Good communication skills with good spoken and written English.


Desirable Criteria:




Experience of running a wet lab undertaking genomic analyses




Experience of working within an informatics serv
ice facility within a University setting.




Experience of taking the lead with a team of colleagues.


Working at the University of Oxford


For further information about working at Oxford, please see:

http://www.ox.ac.uk/about_the_university/jobs/research/


How

to apply


If you consider that you meet the selection criteria, click on the
Apply Now
button on the
‘Job Details’ page and follow the on
-
screen instructions to register as a user.

You will then be
required to complete a number of screens with your application details, relating to your skills
and experience. When prompted, please provide details of
two referees

and indicate whether
we can contact them at this stage.


You will also
be required to

complete a short application form,

upload a
CV and

supporting
statement.
The supporting statement should describe what you have been doing over at
least the last 10 years.


This may have been employment, education, or you may have taken
time

away from these activities in order to raise a family, care for a dependant,
or
travel

for
example
.


Your application will be judged solely on the basis of how you demonstrate that
that you meet the selection criteria outlined above and we are happy to co
nsider evid
ence of
transferable skills or

experience which you may have gained outside the context of paid
employment or education.


Please save all uploaded documents to show your name and the document type.


All applications must be received by
midday

on the closing date stated in the online
advertisement.


Should you experience any difficulties using the online application system, please email
recruitment.support@admin.ox.ac.uk

To return to the o
nline application at any stage, please click on the following link
www.recruit.ox.ac.uk



9

P
lease note that
you will be notified of the progress of your application by automatic e
-
mails
from our e
-
recruitment system
.
Please check your spam/junk mail

regularly to ensure that
you receive all e
-
mails.