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    RESPONSIBILITIES

    The Faculty of Health Sciences (healthsci.queensu.ca) and the Department of Pathology and Molecular Medicine at Queen's University are seeking an international leader and innovator in the areas of bioinformatics and health analytics. Applicants should have an established research program focused on precision medicine, particularly in relation to the identification of cancer diagnostic and prognostic markers and potential therapeutic targets. The successful candidate will become the designated nominee for an approved Tier I Canada Research Chair (www.chairs-chaires.gc.ca/prog[...].aspx). This is a tenured appointment at the level of Professor.

    REQUIREMENTS

    Candidates must hold a PhD or MD/PhD (or equivalent). The main criteria for selection are an established record of global leadership and innovation in bioinformatics, and a track record of mentorship and training of high-quality personnel in various emerging areas in the field. Queen's University is committed to establishing an international reputation in health related informatics, building on existing assets that include: the Centre for Advanced Computing (CAC, cac.queensu.ca ), a cluster of computer systems and storage resources shared by five universities and three colleges; the biobank resources and ongoing capabilities of the Canadian Cancer Trials Group (CCTG, www.ctg.queensu.ca ), which is a major national and international cooperative oncology clinical trials organization, and the national database of chronic disease management developed by the Canadian Primary Care Sentinel Surveillance Network (cpcssn.ca ) , a trans-Canadian network of 11 primary care networks. In addition, robust linkages exist between CAC and the CCTG with the informatics programs of the Ontario Brain Institute (braininstitute.ca ) and the Ontario Institute for Cancer Research (oicr.on.ca ), respectively.

    The successful candidate will be expected to play a leadership role in: i) developing and applying modern data analytics concepts, methods and techniques to utilize an ever-growing wealth of biomedical data generated by existing and emerging world-class research programs at Queen's University (www.queensu.ca/research/centres ), ii) fostering collaborative links between existing researchers involved in health related analytics and informatics across the University, and iii) the recruitment and mentorship of new faculty in the informatics/analytics areas. Salary is commensurate with qualifications and experience.

    LOCALE

    Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada

    HOW TO APPLY

    The University invites applications from all qualified individuals. Queen's is committed to diversity and inclusion and has an employment equity program that meets the goals of the CRC program and the requirements of our collective agreement with the Faculty Association. Until such time as we have met our equity targets (queensu.ca/vpr/[...]-crcp), preference will be given to members of the Four Designated Groups under the Canada Research Chairs program: "women, Indigenous/Aboriginal peoples, persons with disabilities and racialized persons/visible minorities." All applicants will be invited to self-identify once they have applied; those who wish to be considered under our employment equity provisions are required to self-identify. Self-identification information will be held in confidence by the Equity Office and one member of the selection committee. All qualified candidates are encouraged to apply; however, in accordance with Canadian Immigration requirements, Canadian citizens and Permanent Residents of Canada will be given priority.

    To comply with Federal laws, the University is obliged to gather statistical information about how many applicants for each job vacancy are Canadian citizens / permanent residents of Canada. Applicants need not identify their country of origin or citizenship, however, all applications must include one of the following statements: "I am a Canadian citizen / permanent resident of Canada"; OR, "I am not a Canadian citizen / permanent resident of Canada". Applications that do not include this information will be deemed incomplete.

    A complete application consists of: (i) a cover letter (including one of the two statements regarding Canadian citizenship / permanent resident status specified in the previous paragraph), (ii) a full curriculum vitae (including a list of publications, awards and grants received), and (iii) a summary of the proposed plan of research. Please send your application electronically to Dr. Roger Deeley, Chair of the search committee (c/o Ms. Barbara Latimer bal[at]queensu.ca).

    The University will provide support in its recruitment processes to applicants with disabilities, including accommodation that takes into account an applicant's accessibility needs. If you require accommodation during the interview process, please contact: Ms. Barbara Latimer (bal[at]queensu.ca).

    Academic staff at Queen's University are governed by a Collective Agreement between the University and the Queen's University Faculty Association (QUFA), which is posted at queensu.ca/facu[...]ement and at www.qufa.ca.

    Appointments are subject to review and final approval by the Principal. Only nominees external to Queen's University will be considered. (Please note that, for the purposes of this competition, Queen's Term Adjuncts and Adjunct-1s will be considered as external nominees.) Review of applications will commence on 22 March 2018 and remain open until a suitable candidate is recruited.

    Submitter

    BACKGROUND

    Paramount are working in partnership with Genomics England to expand their team in order to deliver success Paramount are working in partnership with Genomics England to expand their team in order to with the 100,000 Genomes Project. This is a challenging and fast moving project with the aim to carry out whole genome sequencing on 100,000 participants. Genomics England works with key partners to collect, transport, store, quality check and sequence the samples from participants. The aim for this project is to create a new genomic medicine service for the NHS – transforming the way people are cared for. Patients may be offered a diagnosis where there wasn't one before. In time, there is the potential of new and more effective treatments.

    This is an ideal role for an experienced bioinformatician with software development experience to work as part of the team responsible for pipeline delivery. It's also an opportunity to work with some of the most established and smartest minds in the genomics world.

    RESPONSIBILITIES

    Key Accountabilities:
    • Produces high quality code
    • Liaises with internal and external parties to determine platform requirements
    • Implements workflows for high-throughput sequencing data analysis
    • Establishes general bioinformatics resources for day-to-day use by colleagues
    • Continues to the team's continuous improvement efforts

    REQUIREMENTS

    • MSc in Bioinformatics or related discipline
    • Python software development experience
    • Solid skillset in Bioinformatics in particular next-generation sequencing Bioinformatics ideally in humans
    • Solid exposure to Linux, Git, Postgres (or similar)
    • Expertise in developing software to analyse large data sets
    • Excellent technical writing skills
    • A demonstrable ability to cope under pressure and deliver to deadlines
    • Ability to communicate effectively within a multidisciplinary team and a flexible and co-operative approach
    • Ability to work independently and to show initiative within a team
    • Ability to prioritise and balance competing demands.
    • Experience of working on greenfield projects is desirable
    • A demonstrable ability to cope under pressure and deliver to deadlines

    COMPENSATION

    There are some great benefits on offer with this opportunity including a competitive salary, pension, generous holidays and more.

    HOW TO APPLY

    Please do not hesitate to contact Harvey Uppal at huppal[at]pararecruit.com or call (+44) 121 616 3407 to discuss this opportunity further.

    Keywords: Bioinformatician, Genomics, Pipeline, Development, Python, NGS, Linux, Git, RDBMS, PostgreSQL, Software, London.
    Opportunity: Python Developer @ Genomics England -- London, UK
    Submitted by Eugene Mc Daid; posted on Thursday, February 15, 2018

    Submitter

    BACKGROUND

    Paramount are working in partnership with Genomics England to expand their team in order to deliver success Paramount are working in partnership with Genomics England to expand their team in order to with the 100,000 Genomes Project. This is a challenging and fast moving project with the aim to carry out whole genome sequencing on 100,000 participants. Genomics England works with key partners to collect, transport, store, quality check and sequence the samples from participants. The aim for this project is to create a new genomic medicine service for the NHS – transforming the way people are cared for. Patients may be offered a diagnosis where there wasn't one before. In time, there is the potential of new and more effective treatments.

    This is an ideal role for an experienced Python developer responsible for creating web applications and utilising programming skills for the interpretation of genetic data from large databases.

    RESPONSIBILITIES

    The post holder is responsible for developing and operating computational pipelines, working on complex projects and custom tasks that span a wide variety of analysis problems and developing and maintaining a knowledge base of variants and annotations.

    It's also an opportunity to work with some of the most established and smartest minds in the genomics world.

    Key Accountabilities:
    • Develops and applies state of the art approaches to 100,000 whole genome sequences (WGS) in the areas of:
      • Quality assurance and sample provenance monitoring
      • Analysis of WGS in cancer and rare diseases
      • Sequence alignment and variant calling
    • Assists with the deployment, maintenance and troubleshooting of computational pipelines for WGS processing and analysis
    • Liaises with internal colleagues as needed to ensure the provision and smooth running of the computational pipelines for data processing and analysis

    REQUIREMENTS

    • Post-graduate degree or equivalent work experience in bioinformatics (desirable)
    • Experience in the development of NGS analysis pipelines for large numbers of samples (desirable)
    • Proficiency in Bash and a general purpose programming language such as Java or Python, and experience with APIs
    • Proficiency in collaborative development tools such as Github, Confluence and JIRA
    • Comfortable using of high performance computing clusters
    • Ability to work independently and to show initiative within a team
    • Ability to prioritise and balance competing demands
    • Ability to communicate effectively within a multidisciplinary team

    COMPENSATION

    There are some great benefits on offer with this opportunity including a competitive salary, pension, generous holidays and more.

    HOW TO APPLY

    Please do not hesitate to contact Harvey Uppal at huppal[at]pararecruit.com or call (+44) 121 616 3407 to discuss this opportunity further.

    Keywords: Python, Developer, Software, Engineer, Web, Backend, Frontend, Java, JavaScript, Bash, API, HPC, Jira, Confluence, Git, Bioinformatics, Genomics, NGS, WGS, Genome, Analysis, London.

    DESCRIPTION

    The World's Brightest Minds Always Innovate.

    At St. Jude Children's Research Hospital, we know what can be achieved when the brightest scientific minds face the fewest barriers. That's why we provide world-class facilities. State-of-the-art technologies. Extraordinary support. And a collaborative, bench-to-bedside environment where you can see, firsthand, how your science translates into survival for the children we serve. Quite simply, at St. Jude, we encourage you to dream big, and we give you everything you need to be the force behind our cures.

    Overview:
    The department of Computational Biology is seeking a highly motivated Bioinformatics Research Scientist to work on exciting gene discovery projects in conjunction with clinical and translational investigators from the Division of Cancer Predisposition, a newly formed program dedicated to the evaluation and management of children and families at increased genetic risk for cancer. As a part of this team, you will have the opportunity to apply innovative analytical and visualization approaches for studying and understanding the genetic variants and epigenetic modifications to cutting edge large-scale discovery projects using the latest sequencing technologies, including whole genome/exome sequencing, RNA-seq, CHIP-seq, ATAC-Seq and long read sequencing. You will also contribute ideas to automate and improve existing analysis methods, assist in preparing and submitting manuscripts for publication and assist with establishing and documenting protocols or best practices for common research tasks.

    Candidates with a strong background in population and/or statistical genetics, deep understanding of biological problems, critical thinking skills, and expertise in linkage analysis are highly encouraged to apply for this position. The study of familial cancers is a high priority area of investigation at St. Jude. Accordingly, it is expected that successful candidates will take a leading role in developing and implementing new computational pipelines, assisting with the discovery of novel cancer predisposing genes and/or genetic modifiers and coordinating multiple research projects that will further enhance our understanding of childhood cancer.

    Recognized as a world leader in mapping the genetic landscape of pediatric cancers, the St. Jude department of Computational Biology has developed state-of-art computational infrastructure, well-established analytical pipelines, and deep genomic analysis expertise with a track record of high-impact publications in top-tier biomedical journals such as Nature, NEJM, JAMA, Nature Genetics and Nature Methods. The department provides a highly interactive environment with collaborative opportunities across basic and clinical departments, access to high performance computing clusters, cloud computing environment, innovative visualization tools, highly automated analytical pipelines and mentorship from faculty scientists with deep experience in data analysis, data management and delivery of high-quality results for highly competitive projects. This position is located in Memphis, TN, and relocation assistance is available.

    Minimum Experience:
    • PhD in Molecular Biology, Biochemistry, Computer Science, Statistics, Mathematics, Bioinformatics or related field required. Prior experience must include research related to bioinformatics (such as analysis of DNA and RNA sequence data, microarray, SNPs, imaging data, proteomics data, or biological pathways; development of algorithms, statistical methods, or scientific software).
    ~OR~
    • If PhD training did not include bioinformatics research, will require a minimum of two (2) years of pre- or postdoctoral research experience in Computational Biology or Bioinformatics.
    • Experience with programming languages such as Perl, C, or Java required. Experience with Python and knowledge on statistical analysis package such as R, SAS and Matlab is highly desired.
    Minimum Education:
    • PhD in Molecular Biology, Biochemistry, Computer Science, Statistics, Mathematics, Bioinformatics or related field required.

    LOCALE

    Memphis – A Great Place to Live & Work.

    St. Jude is based in Memphis, TN with relocation assistance available if needed. Memphis is a family-friendly metropolitan area that more than one million people call home. Memphis is recognized for its world-class music, food and hospitality. Cost of living is one of the biggest attractions; in fact Money listed Memphis as one of the least expensive cities in which to raise a child.

    HOW TO APPLY

    Ready to join a team that is always innovating, because we believe anything is possible?

    Apply now at: bit.ly/2o1Rp2T

    POLICY

    St. Jude Children's Research Hospital is an Equal Opportunity Employer. St. Jude does not discriminate on the basis of race, national origin, sex, genetic information, age, religion, disability, sexual orientation, gender identity, transgender status, veteran's status or disabled veteran's status with respect to employment opportunities. All qualified applicants will be considered for employment. St. Jude engages in affirmative action to increase employment opportunities for minorities, women, veterans and individuals with disabilities.

    BACKGROUND

    LifeArc is pioneering new ways to turn great science into greater patient impact. We bring together a network of partners to tackle specific diseases and directly fund academic and early stage research.

    Our Centre for Therapeutics Discovery (CTD) in Stevenage operates at the interface between academic research and the drug discovery industry. We take novel academic targets and generate lead stage small molecules and therapeutic antibodies for indications with unmet medical need.

    We are looking for a highly motivated individual who will support a multidisciplinary team of Computational and Medicinal Chemists, Biologists and Antibody Engineers by maintaining and developing our scientific data platforms and helping to develop a truly bespoke informatics facility at LifeArc.

    RESPONSIBILITIES

    You will be responsible for maintaining and developing our Dotmatics Browser web-based interface which enables our scientists to query and visualise project data from the multiple data sources we maintain.

    This will require you to develop and support ODBC, API links and ETL protocols for extraction and cleansing information from all our corporate data repositories where our biological data on small molecules, proteins and antibodies is currently stored. These cover a multiple set of data sources including structured databases such as our Activity Base, Genedata and Bioregister, Electronic Lab Notebooks, Chemical Inventories and other unstructured legacy formats.

    Working with our team you will also help build and enrich our informatics platform by providing tools to enable dynamic access to and analysis of scientific data and up-to-date information from reliable public data sources. This includes annotations for our compounds from ChEMBL and protein targets, pathways and disease associations with information from Uniprot and the Human Protein Atlas.

    REQUIREMENTS

    The successful candidate will preferably have a BSc degree in Biological or Chemical Science and ideally have an MSc in Bioinformatics (or be close to completing). Applications from newly qualified PhD graduates in a relevant field are also welcome.

    You will be expected to demonstrate knowledge of a range of programming tools (such as Python/Perl, JavaScript, java, web-services, Pipeline Pilot or KNIME) and a good grasp of rational databases and some appreciation of statistical packages (e.g. R).

    Excellent communication skills, with the ability to work collaboratively with our scientists and IT specialists are key requirements of the role. In addition, you will have excellent time-management skills with the ability to prioritise and manage a busy workload.

    COMPENSATION

    Your salary will be determined by qualifications and experience. In addition, LifeArc offers a defined contribution pension scheme, private health insurance, a flexible benefits scheme and 31 days paid holiday per year.

    HOW TO APPLY

    To apply, please email your CV and covering letter explaining why you want to work for LifeArc to: recruitment[at]lifearc.org or by post to Recruitment, LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX (electronic applications preferred).

    DEADLINE

    Closing date: 11 March 2018

    POLICY

    LifeArc is committed to the principles and practices of equal opportunities and to encouraging the establishment of a diverse workforce. It is our policy to employ individuals on the basis of their suitability for the work to be performed and their potential for development, regardless of age, sex, race, colour, nationality, ethnic or national origin, disability, marital status, pregnancy or maternity, sexual orientation, gender reassignment, religion or belief. This includes creating a culture that fully reflects our commitment to equal opportunities for all.

    SUMMARY

    Applications are sought for a Data Manager/Scientist to contribute to the Pancreatic Cancer Research Fund Tissue Bank (PCRFTB) through the maintenance and expansion of its clinical data infrastructure, working closely with the PCRFTB key and collaborating centres. The post will be based in the Bioinformatics Unit, Centre of Molecular Oncology, Barts Cancer Institute, within the Barts and The London School of Medicine and Dentistry, Queen Mary University of London.

    REQUIREMENTS

    Essential requirements for this post include a MSc/PhD degree in Computer Science/Data Science/Computational Biology/Bioinformatics or a relevant discipline, and substantial experience in relational database design and implementation. The successful applicant also needs to be proficient in web application development. Experience of data management within a health environment and knowledge on contemporary data science technologies are desirable.

    The successful candidate will be responsible for maintaining and expanding an existing eb-based data infrastructure for the PCRFTB resource. Programmatically this post requires expertise in relational database management systems including MySQL, scripting language including Perl and R, and database-oriented web application development technologies. Experience of additional languages, e.g. Java or C, would be highly desirable. Familiarity with Linux network/server administration will be an advantage. Knowledge of Research Governance, data Protection Act and Good Clinical Practice is highly desirable. The post-holder will be required to work flexibly with various members in the PCRFTB team at the coordinating centre. A demonstrated ability to communicate well and working within a team are therefore essential.

    TERMS

    The post is full time and for January 2020, in the first instance.

    COMPENSATION

    Starting salary will be in the range £36,677 - £43,152 per annum inclusive of London Allowance. Benefits include 30 days' annual leave, defined benefit pension scheme and interest-free season ticket loan.

    HOW TO APPLY

    To apply, please visit the Human Resources website on ig24.i-grasp.com/fe/t[...]14079

    Application enquiries can be directed to recruitment[at]qmul.ac.uk

    Informal enquiries about this post, including arrangements to visit the Institute/Centre, can be made to Professor Claude Chelala (c.chelala[at]qmul.ac.uk) or Professor Hemant Kocher (h.kocher[at]qmul.ac.uk).

    Details about Barts Cancer Institute can be found at www.bci.qmul.ac.uk.

    DEADLINE

    The closing date is 4th March 2018 and interviews are likely to be held the week commencing 12 March 2018

    POLICY

    Valuing Diversity & Committed to Equality

    The Barts Cancer Institute requires that applicants invited for interview will need to provide all certificates to confirm their qualifications (specified in the job description).

    Candidates must be able to demonstrate their eligibility to work in the UK in accordance with the Immigration, Asylum and Nationality Act 2006. Where required this may include entry clearance or continued leave to remain under the Points Based Immigration Scheme.

    RESPONSIBILITIES

    Applications are sought for a Bioinformatician/Data Manager to develop, maintain, enhance and expand the Pancreatic Cancer Research Fund Tissue Bank's (PCRFTB) unique integrative bioinformatics portal and related data management system. The successful candidate will also be responsible for pancreas cancer data curation and release cycles of this platform. The post will be based in the Bioinformatics Unit, Centre of Molecular Oncology, Barts Cancer Institute, within the Barts and The London School of Medicine and Dentistry, Queen Mary University of London.

    REQUIREMENTS

    Essential requirements for this post include a PhD in Bioinformatics/Computational Biology or a related discipline, experience in molecular biology or pancreas cancer research, and significant experience in the use of relational databases. A demonstrated ability to communicate well, work within a team and maintain good laboratory records are also essential. The successful applicant needs to be proficient in the analysis and management of high throughput data, including microarrays and next-generation sequencing. A working experience in using the BioMart technology is also desirable.

    Programmatically this post requires expertise in relational database management systems, particularly in MySQL, and a scripting language, such as Perl or Python. Experience of additional languages, such as Java or C, is highly desirable. Familiarity with Linux network/server administration and web application development technologies would also be an advantage.

    TERMS

    The post is full time until December 2020, in the first instance.

    COMPENSATION

    Starting salary will be in the range £36,677 - £43,152 per annum inclusive of London Allowance. Benefits include 30 days' annual leave, defined benefit pension scheme and interest-free season ticket loan.

    HOW TO APPLY

    To apply, please click on ig24.i-grasp.com/fe/t[...]13873

    Application enquiries can be directed to recruitment[at]qmul.ac.uk

    Details about Barts Cancer Institute can be found at www.bci.qmul.ac.uk

    Informal enquiries about this post, including arrangements to visit the Institute/Centre, can be made to Professor Claude Chelala (c.chelala[at]qmul.ac.uk) or Professor Hemant Kocher (h.kocher[at]qmul.ac.uk).

    DEADLINE

    The closing date is 21 February 2018 and interviews are likely to be held the week commencing.

    POLICY

    Valuing Diversity & Committed to Equality

    The Barts Cancer Institute requires that applicants invited for interview will need to provide all certificates to confirm their qualifications (specified in the job description).

    Candidates must be able to demonstrate their eligibility to work in the UK in accordance with the Immigration, Asylum and Nationality Act 2006. Where required this may include entry clearance or continued leave to remain under the Points Based Immigration Scheme.

    BACKGROUND

    The aim of precision medicine is to guide patient treatment via profiling of individual tumours. To date, great advances have been made in the characterization and cataloguing of molecular aberrations associated with various cancers, however our ability to translate genomic information into clinical benefit has yielded mixed results. To complement these molecular analyses, we are generating cell culture models from each patient to functionally interrogate tumour biology, including drug response. The advent of advanced cell culture techniques offers tremendous promise in efficiently generating patient-relevant preclinical models in a timely manner, such that laboratory results may be fed back into the clinic to potentially affect clinical decisions.

    In collaboration with physicians at the Christie Foundation NHS Trust, we are generating a biobank of cultures that faithfully recapitulate the tumours from which they were derived. The aim of this post is to help molecularly characterize a library of patient-derived cultures from a variety of cancer types, which will be used to functionally interrogate tumour biology with the goal of translating laboratory results into clinical benefit.

    Why choose Cancer Research UK Manchester Institute?
    The Cancer Research UK Manchester Institute (www.cruk.manchester.ac.uk), an Institute of The University of Manchester (www.manchester.ac.uk), is a world-leading centre for excellence in cancer research. The Institute is core funded by Cancer Research UK (www.cancerresearchuk.org), the largest independent cancer research organisation in the world. We are currently situated at the internationally-renowned life sciences campus at Alderley Park in Cheshire England, 15 miles from Manchester, a vibrant and dynamic city surrounded by beautiful countryside.

    We are partnered with The Christie NHS Foundation Trust (adjacent to the CRUK MI Paterson Building) in South Manchester (www.christie.nhs.uk), one of the largest cancer treatment centres in Europe. These factors combine to provide an exceptional environment in which to pursue basic, translational and clinical research programmes.

    RESPONSIBILITIES

    About the role:
    We are seeking a highly motivated Computational Biologist within the Cancer Precision Medicine Advanced Cancer Cultures Team which is located within the Clinical and Experimental Pharmacology (CEP) Group to conduct cutting edge translational research on preclinical cancer models. The focus of our research is translational medicine with an emphasis on preclinical therapeutics and precision medicine in breast, lung, and colorectal cancers.

    REQUIREMENTS

    About you:
    You should have at least a BSc in Computational Biology, Mathematics or related discipline plus significant relevant experience analysing transcriptomics data sets. Additionally you should have experience writing complex code in at least one of the following: Perl, Python, R, Matlab, C, or C++.

    TERMS

    Duration: fixed term until 31 March 2022

    COMPENSATION

    Salary in the range of £23,800 - £36,000 per annum, dependent upon experience

    HOW TO APPLY

    To apply for this position, please visit our website: www.cruk.manchester.ac.uk/jobs

    For any informal enquiries about this post, please contact Kris Frese via email: kristopher.frese[at]manchester.ac.uk

    Job Ref: MI/17/80_2

    DEADLINE

    Closing date: 11 March 2018.

    SUMMARY

    We have an exciting opportunity for a talented bioinformatician to join a team led by Dr Stephen Sansom at the Kennedy Institute of Rheumatology (KIR).

    In this role, you will work in the computational genomics group to develop and run bioinformatics pipelines for the analysis of next-generation sequencing (NGS) data. Taking advantage of our state-of-the-art high-performance compute (HPC) facility you will collaborate closely with wet-lab scientists to analyse diverse types of data including those from RNA-seq, single-cell RNA-seq, ATAC/ChIP-seq, micobiome and CyTOF experiments. At the KIR – which is a world-class academic research Institute – researchers are now using such techniques to advance understanding and treatment of diseases such as rheumatoid arthritis, cancer and inflammatory bowel disease.

    You will hold a degree of direct relevance to bioinformatics data analysis (or equivalent experience). Strong programming skills and experience with analysis of next-generation sequencing data essential for this post. A PhD in bioinformatics or computational biology, record with collaborative scientific research and of Immunology would be desirable.

    Informal enquires to Dr Stephen Sansom are welcomed (stephen.sansom[at]kennedy.ox.ac.uk).

    BACKGROUND

    Research context:
    The Kennedy Institute of Rheumatology (KIR) is a world-class academic research Institute at the University of Oxford. It has a mission to advance understanding and treatment of inflammatory diseases such as Rheumatoid Arthritis and Inflammatory Bowel Disease. In the course of their investigations, scientists at the KIR are increasingly using high-throughput genome-scale approaches for which bioinformatics analysis is essential. Such techniques include next-generation sequencing (NGS) based methods such as RNA-seq, single-cell RNA-seq, ATAC/ChIP-seq and microbiome analysis, as well as mass cytometry (CyTOF). The KIR has two computational research groups and has recently invested in a state-of-the-art high-performance compute (HPC) facility.

    RESPONSIBILITIES

    Role overview:
    In this role, you will join our Computational Genomics research group to help develop and run bioinformatics analysis pipelines. You will work closely with students and post-docs from the KIRs' wet-lab research teams, taking responsibility for the routine analysis of next-generation-sequencing and CyTOF datasets. You will have the opportunity to develop and gain skills with a diverse range of bioinformatics techniques, to acquire knowledge of immunological research and to contribute (as a named author) to peer-reviewed research publications. Applicants at all career stages are encouraged to apply.

    Key responsibilities:
    • To develop, maintain and document bioinformatics pipelines in consultation with other members of the Computational Genomics research group
    • To use bioinformatics pipelines to perform analysis of genomic data generated by researchers within the KIR
    • To prepare project-specific data-analysis reports from pipeline results, and to present and discuss these with individual KIR scientists and research groups
    • To advise and assist other research staff with the design and bioinformatics analysis of genomic experiments as appropriate
    • To contribute to manuscripts, presentations and other means of disseminating results
    • To attend scientific seminars, meetings and training as appropriate
    • To help evaluate new methods of relevance to KIR researchers
    • To support and participate in the activities of the Computational Genomics team
    • To keep accurate, up-date and accessible records of project work and pipeline development
    Relationships:
    • You will be a member of the Computational Genomics team led by Dr Stephen Sansom at the KIR.
    • You will be supported in your role by the KIR HPC Systems Administrator and Research Informatics team.
    • You will also provide regular (i.e. monthly to quarterly) updates to the KIR Computational Genomics Strategy Group and this group will also contribute to setting priorities.

    REQUIREMENTS

    • A degree of direct relevance to bioinformatics data analysis (or equivalent experience)
    • Experience with the analysis of next-generation sequencing data
    • Demonstrated proficiency with scripting languages (including Python) and familiarity with a lower-level language such as Lisp, C or Java
    • Software development experience including expertise with version-control systems
    • Statistical expertise and experience with R or Matlab
    • Expert knowledge of Bash, Linux and High-performance computing
    • Excellent interpersonal skills, able to work independently and collaboratively
    • Excellent communication skills, both oral and written
    • Good working knowledge of office software
    • Excellent organisational skills – managing both time and records effectively
    • Able to use own initiative to solve problems

    PREFERENCES

    • A PhD in bioinformatics or computational biology
    • Successful track record with collaborative scientific research
    • Academic training or research experience in the field of Immunology
    • Experience with the use of SQL databases
    • Experience with the teaching of bioinformatics skills to others
    • Experience with automated report generation (e.g. via Latex, Sphinx or Rmd)
    • Experience with the development of pipelines for genomic data analysis
    • Good project management skills and a track record in meeting deadlines

    TERMS

    This is a full-time fixed-term appointment for 3 years.

    LOCALE

    Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Kennedy Institute of Rheumatology, Old Road Campus, Oxford

    COMPENSATION

    Grade 7: £31,604 - £38,883 p.a.

    A lower grade offer may be made (Grade 6: £28,098 - £33,518 p.a.) with commensurate reduction in responsibilities (and amendment in job title to Research Assistant in Bioinformatics) if a suitable candidate cannot be found to fill the Grade 7 position.

    HOW TO APPLY

    Please visit www.recruit.ox.ac.uk/pls/[...]33277

    Contact Person: Recruitment Team
    Vacancy ID: 133277
    Contact Phone: 01865 737843
    Closing Date: 05-Mar-2018
    Contact Email: personnel[at]ndorms.ox.ac.uk

    A satisfactory Disclosure Scotland check is required due to the nature of the research at the Kennedy Institute of Rheumatology.

    DEADLINE

    The closing date for applications is 12.00 noon on Monday 5 March 2018.

    Submitter

    BACKGROUND

    CSRA has an opportunity for a strong Unix / Linux Engineer to join our team of Scientific Systems / High Performance Computing [HPC] Engineers supporting the gene sequencing and bioinformatics needs of a scientific research environment at the National Human Genome Research Institute (NHGRI). This team is managing about 200-300 Linux servers, and supporting approximately 100 PhD scientists and their applications. In this role, you will use your experience with Linux engineering to manage large high performance supercomputers and the myriad of scientific and software applications that run on them.

    You will be hands on with the design, build, and configuration of services necessary for research computing, and underlying scripting capabilities. This role requires regular, close collaboration with Data Center, VmWare, Oracle, Storage, Backup, SQL Administrators, as well scientific investigators. This is a customer service focused environment with the associated business needs of an advanced research environment, requiring high reliability and 24 x 7 up time.

    Position is for full time employment with CSRA and will be based at our customers office located at 5635 Fisher Lane, Suite 1400; Rockville, MD.

    RESPONSIBILITIES

    • Provide hands on design, build, and configuration of services necessary for research computing, and underlying scripting capabilities.
    • Diagnose hardware and software problems, and replace defective components.
    • Perform data backups and disaster recovery operations.
    • Maintain and administer computer networks and related computing environments, including computer hardware, systems.
    • Collaborate with other Systems Administrators who oversee the Data Center, VmWare, Oracle, Storage, Backup, SQL Administration, as well scientific investigators.
    • Use strong analysis and decision-making skills to conduct briefings and participate in technical cross-functional meetings.
    • Focus on process and documentation with a demonstrated understanding of change and configuration management principles in support of a validated environment.
    • You'll be utilizing an exceptional Linux/UNIX scope and associated project management skillset as well.

    REQUIREMENTS

    Required Skills and Experience:
    • Bachelor's degree and 6+ years experience (equivalent professional experience may be considered in lieu of formal education)
    • In depth knowledge of UNIX/Linux systems, system administration tools, methodologies, and security practices; CentOS and Scientific Linux Knowledge
    • Experience managing multiple systems and in-depth understanding of one or more of the following – storage (FC, SAS, iSCSI, FCoE) or high speed interconnects (InfiniBand, 10Gig, etc), provisioning tools, etc.
    • Experience writing scripts to automate processes in a production *nix environment using any of the following languages – shell, Bash, Perl, or Python
    Competencies:
    • Proactive communication to manage scope and schedule for multiple priorities
    • Focus on Customer Service and Business Needs (Support Science), Reliability, Up Time (24 x7) etc.

    PREFERENCES

    Desired:
    • Certifications such as RedHat Certified Engineer – RHCE (RHEL 7), CCNA & MCP are preferred.
    • Domain knowledge in HPC and system software such as cluster management/provisioning tools, job schedulers, MPI, etc. is strongly preferred.
    • Knowledge of programming languages (C, Ruby, or R) is a plus.
    • Knowledge of a configuration management tool such as CF Engine, Puppet, Ansible, or Chef is preferred.
    • Knowledge and/or experience with cluster file systems (pNFS, Lustre, PVFS), and MPI
    • Experience with revision control software (such as Subversion, CVS, Git) is a plus.

    TERMS

    Full Time Employment

    LOCALE

    Rockville, MD

    COMPENSATION

    Negotiable

    HOW TO APPLY

    Please apply directly online via www.csra.com to job #RQ10223 or via this link: www.csra.com/care[...]linux

    DEADLINE

    ASAP

    POLICY

    EEOC

    Submitter

    BACKGROUND

    CSRA is seeking an experienced Storage & Backup Engineer to join our highly functioning IT consulting team supporting the scientific research environment at the National Human Genome Research Institute (NHGRI). In this role, you will have the opportunity to work across a wide breadth of storage and backup technologies, collaborating with all areas of the IT infrastructure team; as well as providing true IT consulting / expertise to our customers in order to engineer best practice solutions.

    In this role, you will support IT infrastructure storage/ backup needs; Isilon and 3Par storage environment leveraging Linux/UNIX/HPC, Windows OS and multiple databases (SQL/ Oracle); EMC Networker, EMC Data Domain and Quantum library backup environment. Expansive EMC Networker, EMC Data Domain and Quantum library experience is required. The preferred candidate will possess strong analytical and decision-making abilities; conduct stakeholder briefings and participate in technical cross-functional meetings; strong commitment to process, understands change and configuration management principles in support of a validated environment. You will also collaborate with multiple Data Centers and OS [Linux/ OSX/ Windows] as well Oracle/ SQL DBAs and associated project managers. This is a customer service focused environment with the business needs of a scientific environment, mandating high reliability and 24 x 7 up time.

    Position is for full time employment with CSRA and will be based at our customers office located at 5635 Fisher Lane, Suite 1400; Rockville, MD. Offers a flexible schedule Monday through Friday around core business hours.

    RESPONSIBILITIES

    • Responsible for configuration, layout and performance tuning of storage infrastructure
    • Responsible for storage infrastructure system management including capacity planning, snapshots, performance monitoring/ tuning, security management, etc.
    • Provide infrastructure support for projects including planning, installations, configurations, and upgrades; work with requisite teams to ensure smooth project deployments through completion
    • Plan, recommend and implement strategies around attached storage and load balancing
    • Setup and maintain fiber channel switches
    • Insure backups are in place using EMC Networker configured with EMC Data Domain and Quantum i6000 tape library as target storage
    • Participate and adhere to change management processes
    • Customer Service Focus; experience discerning/ balancing business need (support Science) with allied enterprise reliability and "up-time" requirements. Resolve escalated ticket issues, collaborating with desktop support services; manage/ provide Tier-2/3 assistance following incident management best practices (ITIL)
    • Design and implement disaster recovery plans; implement associated backups (EMC NetWorker)
    • Actively monitor IT maintained systems with monitoring tools such as Check_mk and Nagios
    • Be available as may be required to support monitoring alerts after hours
    • Rack/ stack servers and network equipment

    REUIREMENTS

    Required Skills and Experience:
    • 6+ years IT experience (to include a min of 4+ years storage / backup)
    • Solid hands-on experience with EMC Isilon
    • In depth understanding of protocols to include NFS and SAMBA
    • Experience with Data Domain for backup, RAID Inc, Brocade and Cisco technologies for SAN
    • Demonstrated documentation capabilities (such as using Visio and portal applications such as wiki)
    • Working knowledge of Linux (Scientific Linux, CentOS), Windows, and OSX multi-platform operating systems
    • Strong troubleshooting abilities
    • In depth understanding of one or more storage technology fields (Fiber Channel SAN, SAS, iSCSI, or FCoE) as well high speed interconnects (InfiniBand, 10GigE, etc)
    • Understanding of virtualized environments
    • Ability to earn/ hold Public Trust suitability
    Competencies:
    • Excellent interpersonal communication skills
    • Proactive, polished communication (verbal/ written) skillset
    • Ability to manage scope and schedule for multiple project priorities

    PREFERENCES

    Desired skills and experience:
    • Bachelor's degree in Computer Science, Information Systems, Engineering is a plus; equivalent professional experience may be considered in lieu of degree
    • EMC Isilon Certified Storage Professional (ICSP) is preferred. CSRA offers strong benefits for training and development and can help you obtain this certification or others of interest.

    TERMS

    Full Time Employment

    LOCALE

    Rockville, MD

    COMPENSATION

    Negotiable

    HOW TO APPLY

    Please go to our CSRA Careers site and apply to job # RQ10210 or via this link: www.csra.com/care[...]cisco

    DEADLINE

    ASAP

    POLICY

    EEOC
    Opportunity: Head of Bioinformatics @ Genomics England -- London, UK
    Submitted by Eugene Mc Daid; posted on Friday, February 02, 2018

    Submitter

    BACKGROUND

    100,000 Genomes Project – Central London – Research Services Team!

    Paramount are working in partnership with Genomics England to expand their team in order to deliver success with the 100,000 Genomes Project. This is a challenging and fast moving project with the aim to carry out whole genome sequencing on 100,000 participants.

    Currently they are heading up a new Research Services team and are looking for an experienced candidate with a strong background in Statistical Genetics/Genomics to provide high calibre research support to external researchers and industrial partners by delivering custom analyses, facilitating access to datasets and ensuring optimal use of their Research Data Centre. This role would suit someone with a strong background in Statistical Genetics (GWAS, cohort studies, population genetics) with team leadership/management experience.

    Genomics England works with key partners to collect, transport, store, quality check and sequence the samples from participants. The aim for this project is to create a new genomic medicine service for the NHS – transforming the way people are cared for. Patients may be offered a diagnosis where there wasn't one before. In time, there is the potential of new and more effective treatments.

    RESPONSIBILITIES

    Your main responsibilities will involve:
    • Leading a skilled team of around five people that supports academic and industrial partners by analysing the program's data to answer partner's questions
    • Ensuring the delivery of team's objectives, staff management and development, providing hands-on support as a Senior Genomics Data Analyst
    • Providing services to external clients, ensuring quality of data analyses are appropriate and the right methodologies are used
    • Internal collaboration, particularly with others in the Chief Scientist's team, Commercial team, Bioinformatics team and Software/Infrastructure Engineers to develop and deploy suitable solutions for customers
    • Understanding customer needs (NHS, academia and industry) and working with them to ensure their scientific projects are successful

    REQUIREMENTS

    The ideal candidate will meet the following requirements:
    • At least 3 years' postdoc work in fields related to statistical genetics/genomics with a strong quantitative background in Mathematics, Physics or Computer Science
    • Strong evidence of experience in data analysis and genomics research using large genomics datasets of NGS data alongside clinical data. This could be any involvement in GWAS, cohort studies, population genetics, etc.
    • Team leadership experience with proven ability to communicate with key customer and internal stakeholders from diverse backgrounds
    • Demonstrated knowledge and competence in relevant programming languages and applications (Python, R) and experience with statistical methodologies
    • Strong publication record in a relevant field

    COMPENSATION

    In return you will receive a competitive salary and the opportunity to make a real difference and contribute to the project at its most exciting phase. Due to growth they also have new modern offices.

    HOW TO APPLY

    If you'd like to know more about the position and apply, please feel free to contact Anna with an up-to-date CV (alauterjung[at]pararecruit.com or +44 (0) 121 616 3469).

    Keywords: Statistical Genetics, Statistical Geneticist, Statistical Genomics, Genomcis, Statistics, GWAS, genome wide association, cohort, population genetics, Genetic data, Clinical data, Data Analysis, Pharmaceutical, Python, R, genome sequencing, whole genome, WGS, NGS, Scientist, Bioinformatics, UK, London

    BACKGROUND

    The Institute for Genome Sciences (IGS) at the University of Maryland School of Medicine is seeking to recruit senior well-funded translational research scientists and their teams to accelerate the school's biomedical and clinical research enterprise to answer important "big science" questions underlying human health and disease. Individuals with an academic track record in the areas of Computational Biology and Genomics. are strongly encouraged to apply. Positions are available at the level of Associate Professor or above, and preference will be given to applicants holding a doctoral degree with a superb record of scholarly activity, who are also highly collaborative, and have multiple currently active NIH awards as principal investigator.

    IGS (www.igs.umaryland.edu) currently has 22 highly collaborative faculty members with research interests in the areas of the human microbiome, host/pathogen interactions, infectious diseases, human genome sequencing, genetic variation, cancer genomics, genomics and systems biology of disease, and other broad areas of genomics and bioinformatics applied to improving human health. IGS has established significant infrastructure to support both research-based and clinical high-throughput sequencing, as well as high-complexity bioinformatic analyses, including an extensive computational grid available to all faculty with ~4 PB of storage and a >2000 core cluster.

    REQUIREMENTS

    Ph.D., M.D. or equivalent in computational biology, biostatistics, computer sciences, genomics, genetics, microbiology or a related field, with relevant postdoctoral experience and a strong record of academic achievement as determined by publications and grant funding. Senior investigators who are currently funded with two (2) or more NIH (R01, PPG or Center grants) or equivalent awards are targeted for this position. A key requirement of this position is that the applicant must have a track record of fostering interdisciplinary team science with other groups.

    LOCALE

    IGS is located on the University of Maryland Founding Campus in Baltimore, MD (www.umaryland.edu), which houses the University System's Medical, Dental, Pharmacy, Nursing, Social Work and Law schools as well as the Graduate School. The University has vibrant communities with clinical, research and teaching activities in infectious diseases, genetics, genomics and personalized medicine that offer numerous opportunities for collaborative interdisciplinary research.

    COMPENSATION

    Initial salary commensurate with qualifications and experience.

    HOW TO APPLY

    Interested candidates must apply online through the UMB Online Recruitment System: umb.taleo.net/care[...]ng=en

    Please submit an initial application that includes a letter of interest, a current curriculum vitae, statement of research interests, and full contact information for three references.

    In addition to applying online, interested candidates may also send application materials to: IGS-jobs[at]som.umaryland.edu.

    Consideration of candidates will begin upon receipt of applications and will continue until June 1, 2018 or a suitable candidate is identified.

    POLICY

    The University of Maryland, Baltimore is an Equal Opportunity, Affirmative Action Employer. Minorities, women, veterans and individuals with disabilities are encouraged to apply.

    BACKGROUND

    The World's Brightest Minds Always Innovate!

    At St. Jude Children's Research Hospital, we know what can be achieved when the brightest scientific minds face the fewest barriers. That's why we provide world-class facilities. State-of-the-art technologies. Extraordinary support. And a collaborative, bench-to-bedside environment where you can see, firsthand, how your science translates into survival for the children we serve. Quite simply, at St. Jude, we encourage you to dream big, and we give you everything you need to be the force behind our cures.

    The department of Computational Biology is seeking a highly motivated scientist to join our Clinical Cancer Genomics team. As a clinical genome analyst, you will analyze and classify somatic and germline genetic alterations in pediatric cancer patients ascertained from whole-genome, whole-exome and transcriptome sequencing and present findings to pathologists, oncologists, and genetic counselors. This scientist will work closely with our bioinformatics pipeline and visualization teams to explore novel analysis approaches that aid molecular classification and clinical reporting, contribute ideas to automate and improve existing analysis methods, and assist in preparing and submitting manuscripts. The successful candidate will also have opportunities to participate in research projects to analyze the pediatric cancer genome and epigenome.

    RESPONSIBILITIES

    Our ideal candidate has a deep understanding of cancer biology and expertise in genomic and/or transcriptomic data analysis either through NGS or molecular pathology approaches. Prior experience within in a clinical environment and experience in clinical test development are highly desirable.

    Recognized as a world leader in mapping the genetic landscape of pediatric cancers, the St. Jude department of Computational Biology has developed state-of-art computational infrastructure, well-established analytical pipelines, and deep genomic analysis expertise with a track record of high-impact publications in top-tier biomedical journals such as Nature, NEJM, JAMA, Nature Genetics and Nature Methods. The department provides a highly interactive environment with collaborative opportunities across basic and clinical departments, access to high performance computing clusters, cloud computing environment, innovative visualization tools, highly automated analytical pipelines and mentorship from faculty scientists with deep experience in data analysis, data management and delivery of high-quality results for highly competitive projects. This position is located in Memphis, TN, and relocation assistance is available.

    REQUIREMENTS

    Minimum Education:
    PhD in Molecular Biology, Biochemistry, Computer Science, Bioinformatics or related field required. PhD in a field directly related to cancer biology with a strong desire to work in a clinical environment preferred.

    Minimum Experience:
    PhD in Molecular Biology, Biochemistry, Computer Science, Bioinformatics or related field required. Prior experience must include research related to bioinformatics (such as analysis of DNA and RNA sequence data, microarray, SNPs, proteomics data, or biological pathways; development of algorithms, statistical methods, or scientific software).

    ~OR~

    If PhD training did not include bioinformatics research, will require a minimum of two (2) years of pre- or postdoctoral research experience in Computational Biology or Bioinformatics.

    Experience with programming languages such as Perl, C, Python, Java, or R required.

    Job Preferences: PhD in a field directly related to cancer biology with a strong desire to work in a clinical environment AND experience with programming languages.

    Candidates at varying levels of their career will be considered.

    HOW TO APPLY

    Ready to join a team that is always innovating, because we believe anything is possible?

    Apply now at: bit.ly/2EsYoJ4

    BACKGROUND

    We seek a motivated bioinformatician to be involved in our studies of gene regulatory networks. Our laboratory at Memorial Sloan-Kettering Cancer Center combines computational and experimental approaches to annotate and functionally elucidate small RNA pathways, mRNA processing and modification pathways, and transcription factor networks. Towards this end, we produce small RNA, RNA-seq, CLIP-seq, RNA modification and ChIP-seq data, and analyze these with respect to the rich comparative genomic data available for Drosophila and mammals. There is a close exchange of ideas between dry and wet lab members to generate and test biologically-based hypotheses.

    Recent Studies involving genomics/bioinformatics approaches:

    Kan, L., A. V. Grozhik, J. Vedanayagam, D. P. Patil, N. Pang, K.-S. Lim, Y.-C. Huang, B. Joseph, C.-J. Lin, V. Despic, J. Guo, D. Yan, S. Kondo, W.-M. Deng, P. C. Dedon, S. R. Jaffrey and E. C. Lai (2017). The m6A pathway facilitates sex determination in Drosophila. Nature Communications 8: 15737, 1-16.

    Kondo S., J. Vedanayagam, J. Mohammed, S. Eizadshenass, L. Kan, N. Pang, R. Aradhya, A. Siepel, J. Steinhauer and E. C. Lai (2017). New genes often acquire male-specific functions but rarely become essential in Drosophila. Genes and Development 31: 1841--1846. (Highlighted in Genes and Dev 31: 1825-1826.)

    Sanfilippo P., J. Wen and E. C. Lai (2017). Landscape and evolution of tissue-specific alternative polyadenylation across Drosophila species. Genome Biology 18: 229 doi: 10.1186/s13059-017-1358-0.

    Mohammed, J., A. S. Flynt, A. M. Panzarino, M. Mondal, M. DeCruz, A. Siepel and E. C. Lai (2018). Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus. Genome Research 28: 52-65.

    Jee, D., J.-S. Yang, S. M. Park, D.'J. Farmer, J. Wen, T. Chou, A. Chow, M. T. McManus, M. G. Kharas and E. C. Lai (2018). Dual strategies for Argonaute2 Slicer-dependent miRNA biogenesis of erythroid miRNAs underlie conserved requirements for slicing in mammals. Molecular Cell 69: 265-278.

    Lab home: www.sloankettering.edu/rese[...]c-lai

    RESPONSIBILITIES

    The candidate will integrate into several related projects regarding post-transcriptional regulation, including mechanisms of miRNA biogenesis, tissue-specific alternative polyadenylation, and in vivo regulation by m6A/RNA methylation.

    REQUIREMENTS

    Relevant candidates will have strong computational skills and experience with analyzing deep-sequencing data, comparative genomics and statistics. In addition to utilizing standard NGS packages, programming proficiency is required to develop custom scripts for novel sequence analyses as well as to develop web-basted data displays. The successful candidate will be self-motivated and highly interactive to work with biologists to solve foundational questions in genome regulation. Postdoctoral fellows or BA/MS level candidates seeking experience before graduate school will be considered.

    LOCALE

    Memorial Sloan-Kettering Cancer Center, New York City

    HOW TO APPLY

    Please send letter of inquiry, research statement, CV and references to laie[at]mskcc.org.

    DEADLINE

    As soon as possible.
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