Research Fellow in Bioinformatics - Cancer and Genomic Sciences

Страна: Великобритания;

Город: Birmingham

Добавлена: 04.10.2019

Работодатель: University of Birmingham

Дедлайн подачи: 10.11.2019

 

The post-holder will play a pivotal role in enabling the research to “Improve outcome for patients with Poor Risk Acute Myeloid Leukaemia” under the supervision of Prof Jean-Baptiste Cazier at the Centre for Computational Biology (CCB). It will include the selection, development and implementation of the optimal integrative mathematical/statistical/ computational framework, tools, and approaches for the project.

 

The post-holder will be specifically responsible for the integrative analysis of multi-modal Acute Myeloid Leukaemia (AML) data generated by the CRUK programme led by Prof Jude Fitzgibbon, Queen Mary University of London, in collaboration with numerous prestigious institutions.  This programme sets out to improve on existing treatments for patients with poor risk AML.  This will be achieved by combining the efforts of 5 established UK groups into a unified programme that focus on new knowledge generation through the integration of Genomic (WGS, RNA-seq) Cell Signalling (Proteomics and Drug testing) and stem cell profiling (CyTOF, normal HSC profiles) in a series of poor risk AML patients. 

 

AML is characterised by the accumulation of immature cells called myeloblasts within the bone marrow, with patients presenting with symptoms of Bone Marrow Failure (BMF). It is the most common form of leukaemia in adults, with seventy percent of patients dying from their disease; mostly within 12 months of diagnosis. Chromosomal abnormalities represent the best-established prognostic marker, dividing patients according to various outcome groups with a dismal 10 year survival. We believe that improvements in care for this patient group will not be achieved by focusing on any single deregulated pathway or actionable mutation. We need instead, to generate new knowledge on the mechanisms responsible for promoting and sustaining the pathophysiology of these leukaemia, and how these impact on both the bulk tumour, normal and leukaemic stem cell population. 

 

The results will provide new insight into the biology of poor risk disease, will inform our existing translational studies that include ‘targeting the phosphor-proteome’ and ‘reawakening normal stem cell function’, and will fuel new and innovative research projects based on our data integration. The programme will lead to new clinical trial activity in the area of poor risk disease and the capability to align patients to treatments based on their underlying biochemical profiles.

 

The CCB is a cross-college initiative combining multiple disciplines across the University and its partners to maximise the analysis and application of Big Data, focusing on Development, Application, and Training. The CCB aims to promote excellence in Computational Biology, Data Science for the Life Sciences, Systems Biology, and Bioinformatics across the range of fundamental and applied sciences, in both the University and allied Healthcare arenas. It federates expertise through world class, independent and collaborative research, as well as teaching to a broad audience, ranging from undergraduates to health care professionals. The CCB provides an environment, both physical and structural, to its ~60 members to foster collaborative work and cross-fertilisation such as the new Compute and Storage for Life Sciences (CaStLeS) infrastructure, a £2.3M initiative in the Birmingham Environment for Academic Research Cloud (BEARCloud).

 

The work involves:

  • Identify, and when necessary develop, the appropriate methods to perform a holistic analysis of the data provided using techniques such as AI and ML.
  • Integrative Analysis of the multi-modal datasets from pairs to the whole set
  • Conducting analysis on the data provided in liaison with the relevant experts
  • Participating to publications and presentations of data and resulted issued from the project
  • Participate in training and dissemination relevant to the project

 

Main Duties / Responsibilities:

  • Integrative Analysis of the multi-modal datasets from pairs to the whole set
  • Identify, and when necessary develop, the appropriate methods to perform a holistic analysis of the data provided
  • Select, deploy and apply mathematical, statistical and bioinformatics tools for individual and integrative analysis
  • Conducting analysis on the data provided in liaison with the relevant experts
  • Interact with partner researchers and analysts to optimise quality control and analysis relevant to the specific platform
  • Communicate research results through conference presentations, scientific publications or project reports
  • Compile data for use in activities such as gene expression, profiling, genome annotation and structural bioinformatics
  • Participate to the supervision and training of technicians and information technology staff applying bioinformatics tools or applications in areas such as proteomics, transcriptomics, metabolomics and clinical bioinformatics
  • Keep abreast of new methods, instrumentation, or software by reading scientific literature and attending professional conferences
  • To aid in the development of bioinformatics tools, pipelines and processes to acceptable standards of quality and accuracy suitable for the analysis and interpretation of NGS data for a broad range of clinical diagnostic and research applications

 

General:

  • Analyse and interpret data
  • Apply knowledge in a way which develops new intellectual understanding
  • Contribute to writing bids for research funding
  • Disseminate research findings for publication, research seminars etc
  • Supervise students on research related work and provide guidance to PhD students where appropriate to the discipline
  • Contribute to developing new models, techniques and methods
  • Undertake management/administration arising from research
  • Contribute to Departmental/School research-related activities and research- related administration
  • Contribute to enterprise, business development and/or public engagement activities of manifest benefit to the College and the University, often under supervision of a project leader
  • Present research outputs, including drafting academic publications or parts thereof, for example at seminars and as posters
  • Provide guidance, as required, to support staff and any students who may be assisting with the research
  • Deal with problems that may affect the achievement of research objectives and deadlines
  • Promote equality and diversity values, acting as a role model and fostering an inclusive working culture.

 

Person Specification:

  • The candidate should have a PhD (or have within 6 months of appointment), or equivalent experience in Bioinformatics, Mathematics, Statistics or Computer Sciences.
  • You'll need a relevant degree, at a minimum of a 2:1 classification or equivalent. Degree should have links with bioinformatics and data science e.g. biological, biomedical, natural sciences, mathematics and computer science.
  • Proven experience with Data Science, specifically Data Integration and Bioinformatics analyses
  • Knowledge of advanced Machine Learning methods such as iterative Random Forest, Topological Data Analysis.
  • Understanding of theoretical underpinnings of sequence alignment algorithms in use for next generation sequencing (NGS) data such as DNASeq, RNASeq or relatedGood Presentation skills and talent for technology and knowledge transfer
  • Knowledge of Bioinformatics resources such as annotation tools and databases
  • Staff and/or project management experience
  • Aptitude for international collaboration
  • Linux expertise including file systems, shell, hardware/software monitoring etc.
  • Knowledge of the protected characteristics of the Equality Act 2010, and how to actively ensure in day to day activity in own area that those with protected characteristics are treated equally and fairly.
  • Ability to:

o To demonstrate an understanding of both science and mathematics in a research setting.

o Innovate and develop ideas into grant proposals

o To learn and keep abreast of latest technological, methodological and software developments.

o Ability to write concise and timely scientific papers and reports

o Must be able to plan and prioritise work effectively to meet deadlines

o To interact with external partners and explain complex ideas to non- scientists in an understandable way

o To work in a heterogeneous environment of Clinicians, Biologist, Bioinformaticians, Computer ScientistsProficiency in: High level (e.g. python) and low level (C, C++) programming languages, Database (SQL) development, Maintaining code repositories (version control)

o To write concise and timely scientific papers and reports 

 

 

Further Particulars can be found here: http://www.download.bham.ac.uk/vacancies/jd/MDSFPs.pdf

 

Informal enquiries can be sent to CCB Centre Manager, Jessica Mylchreest, j.mylchreest@bham.ac.uk or +44 121 414 7012. 

 
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