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--------------------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: 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 To use appropriate computational, statistical or mathematical methods for handing and analysing large data sets. To contribute to the design of a successful programme of investigation. To provide expertise in computational, statistical and mathematical methods To use specialist knowledge to develop bespoke solutions to specific problems. To present findings of research effectively both within the group and at external meetings (local, national and international) To generate relevant research output (publications, presentations). To evaluate methods and techniques used and results obtained by other researchers and to relate such evaluations appropriately to your own work. To manage own workload effectively, ensuring requirements are delivered to agreed timescales. To be an active member of the local bioinformatics community ensuring research outputs are shared and providing specialist knowledge to others. To keep specialist knowledge and skills (including research methods and techniques) up-to-date. To train other members of the group in bioinformatics methods as required To work with others to ensure compliance with relevant Health and Safety requirements. You will be expected to support and adhere to the Institute’s commitment to Equality and Diversity. Person Specification Education and Professional Training Essential 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. Experience in computer-based analysis of large-scale biomolecular or other data. Experience in the analysis of Next Generation Sequence Data Expertise in statistical and mathematical methods. Expertise in programming with strong ability in at least one language (e.g. Python, Perl, C etc.). Knowledge of mathematical/statistical packages (e.g. Matlab, R etc.). Ability and motivation to understand experimental methods and the underlying biology. Ability to design, execute and write up research work independently. Good organisational and time management skills. Good communication skills. Effective interpersonal presentational. Effective organisational ability, including the ability to manage time effectively and prioritise tasks. The ability to work effectively, independently, and to work under pressure. Enthusiasm for working within a multi-disciplinary environment. and communication skills, including written and Desirable Expertise in the use of high performance computing clusters. Experience with commonly used software tools for next generation sequencing data, including alignment to reference genomes and SNP analysis Experience in whole genome/exome sequence analysis Data management and analytical skills including experience of the use of database and statistical software. Experience with commonly used genomic analysis tools that are used by local research groups (Genespring, Partek, Affymetrix/Illumina proprietary software etc) Experience in analysis of biological networks (e.g. Ingenuity, Metacore, WGCNA, MERLIN etc.) Experience in the analysis of microarray, ChIP-seq and gene expression data 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: 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. 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.