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    BACKGROUND

    We seek a highly motivated and independent computational biologist to develop innovative genomic tools to dissect principles of epigenetic cell memory in mammals.

    Our research/The group:
    Our research goal is to understand how chromatin is replicated and epigenetic information propagated in dividing cells, and how this impinges on epigenetic changes in disease. We are focusing on mechanisms involved in replication-coupled chromatin dynamics, propagation of DNA methylation and histone-based information. To this end we are applying innovative proteomic and genomic approa­ches in combination with cutting-edge cell biology, advanced imaging and biochemistry.

    Our key recent publications include:
    Saredi et al., Nature 534:714, 2016
    Alabert et al., Genes Dev 29:585, 2015
    Huang et al., Nat Struct Mol Biol 2015
    Alabert et al., Nat Cell Biol 16:29, 2014

    The research project:
    The successful candidate will join a multi-disciplinary team working on how epigenetic information is transmitted in self-renewing cells. In particular, the lab is currently developing a panel of genomic tools to interrogate the impact of DNA replication on epigenome composition and transcription. The candidate will develop bioinformatic pipelines for these tools and optimally also be engaged in the wet-lab application of those tool to fundamental questions in epigenetics including how DNA replication influence transcription factor occupancy and 3D genome organization.

    Start: 1 September 2017 or after agreement
    Duration: 2 years with possibility of extension

    REQUIREMENTS

    Qualifications and skills:
    We expect you to be a highly motivated and ambitious scientist with the following qualifications and skills:
    • A PhD in bioinformatics, computational biology or life sciences
    • Documented experience with NGS data workflow and analysis (e.g. ChIP-seq, ATAC-seq, HI-C, OK-seq, RNA-seq)
    • Experience including a combination of scripting, programming, and statistical analysis
    • Background in epigenomics / genomics
    • Previous experience in cell and molecular biology is an advantage
    • Ability to grasp complex problems and deliver creative, practical solutions
    • Proven ability to envision, plan and execute a research project
    • Excellent English skills written and spoken
    The ideal candidate will be a team player and have excellent communication skills.

    For further information regarding the position, please contact Professor Anja Groth (anja.groth[at]bric.ku.dk)

    TERMS

    Terms of salary and employment:
    Salary, pension and terms of employment will be in accordance with the agreement between the Ministry of Finance and The Academics Central organization. Currently, the monthly salary starts at 32.351 DKK/ca. 4.250 Euro plus pension. Depending on qualifications, a higher salary may be negotiated.

    Non-Danish and Danish applicants may be eligible for tax reductions, if they hold a PhD degree and have not lived in Denmark the last 10 years.

    The position is covered by the "Memorandum on Job Structure for Academic Staff at the Universities" of June 28, 2013.

    LOCALE

    Place of employment:
    The employment is at BRIC, University of Copenhagen. BRIC is located in the Biocenter, close to the centre of Copenhagen. We offer creative and stimulating working conditions in a dynamic and international research environment. Our research facilities include modern laboratories and a number of core facilities shared between the 23 research groups at BRIC and the neighboring Finsen Laboratory. We have weekly journal clubs, data clubs, seminars with invited speakers and a young researchers club ASAP and our own Postdoc Career Programme and PhD programme, MoMeD. BRIC actively participates in the European alliance, EU-life consisting of 13 excellent life science research institutions eu-life.eu

    Please read more about the Groth research group and BRIC on www.bric.ku.dk

    Part of the International Alliance of Research Universities (IARU), and among Europe's top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career.

    HOW TO APPLY

    Application:
    Your application must be submitted electronically by clicking `Apply now' below or via BRIC's website on www.bric.ku.dk/jobs/. The application must include the following documents/attachments – all in PDF format:
    • Motivated letter of application (max. one page)
    • CV incl. education, work/research experience, language skills and other skills relevant for the position
    • A certified/signed copy of a) PhD certificate and b) Master of Science certificate. If the PhD is not completed, a written statement from the supervisor will do.
    • List of publications
    Letters of recommendation:
    Furthermore, the applicant should provide two letters of recommendation. To be taken into consideration, the letter must be signed by the supporting person on paper with institutional letter head and in PDF-format. The letters should be received before deadline on jobs[at]bric.ku.dk with subject "name candidate-Groth-postdoc-2017"; preferably by the supporting person. Please make sure that an easy match between the recommendation letter and the individual applicant is possible.

    We reserve the right not to consider material received after the deadline, and not to consider applications or letters of recommendation that do not live up to the above-mentioned requirements.

    Apply online: ssl1.peoplexs.com/Peop[...]99366

    The further process:
    Shortlist: After expiry of the application deadline, the superior with power to appoint selects a number of applicants for assessment on the advice of the Appointments Committee. All applicants are immediately notified whether their application has been passed for assessment. Applicants who were not passed for assessment should not expect further with regard to their application unless the shortlist is revised.

    Assessment: The selected applications will be assessed according to the Ministry Order on the Appointment of Academic Staff at Universities 2012 and the University of Copenhagen's guidelines 2013. The Assessment Committee makes a non-prioritized assessment of the academic qualifications and experience with respect to the above mentioned area of research, techniques, skills and other requirements listed in the advertisement.

    You can read about the recruitment process at employment.ku.dk/faculty/

    BRIC and University of Copenhagen wish to reflect the diversity of society and welcome applications from all qualified candidates regardless of personal background.

    DEADLINE

    Application deadline: 15 May 2017

    BACKGROUND

    The Wellcome Trust Sanger Institute is seeking a highly motivated researcher with strong skills in computational genomics to fill a postdoctoral fellow position. The aim of the fellow is to develop a quantitative framework for predicting antimicrobial resistance spread in clinical bacterial isolates from diverse generated large-scale genetic and phenotypic data.

    The goal of the encompassing international collaborative project is to predict and map drug targets for cell-to-cell horizontal transmission of antibiotics resistance. To this end, we are generating data from three different types of bacterial strains. First, we are performing large-scale experimental evolution experiments to map de novo mutations that confer changes to transmission ability. Second, we are phenotyping comprehensive collections of knockout and overexpression mutants to identify determinants of adaptation. Finally, we will sequence full genomes of, gather gene expression and proteomics data for, and deeply phenotype thousands of clinical isolates from the largest collection in Europe to find variants likely to alter resistance transmission properties. The first sets of experiments have been executed, and the bulk of the assays are expected to complete in 2017.

    RESPONSIBILITIES

    The successful candidate will perform original research in quantitative modeling of these multimodal high throughput data to predict antimicrobial transmission for previously unobserved clinical isolates. It is important you have the ability to bridge from understanding the processes generating the measured data, to implementing computational pipelines to extract information, as well as creating and applying correct models for analysis. You are expected to make progress on your project as the first priority, while budgeting time for training in further skills, piloting new leads, and potentially collaborating on other related projects. To function effectively in a multidisciplinary, collaborative setting, you have to be able to communicate well with scientists from diverse backgrounds, and be a pleasant colleague.

    This position offers the opportunity to work at one of the world's leading genomic centres at the forefront of genomic research, in collaboration between computational groups with expertise in quantitative genomics (Parts, Sanger Institute) and evolutionary biology (Mustonen, University of Helsinki). You will have access to Sanger's computational resources, including a 15000+ core computational cluster, the largest in life science research in Europe, and multiple petabytes of high-speed cluster file systems. Our group also has laboratory space and access to core facilities, where we generate our own data with the help of dedicated staff. This provides an exciting opportunity for you to not only analyse the data, but to be actively involved in the planning and execution of large-scale experiments.

    We are part of a dynamic and collaborative environment at the Genome Campus and, although we seek someone who can work independently, you will have the opportunity to interact with researchers across many Programmes at the Institute. In particular, we often share interests with colleagues from other teams in the Cellular Genetics and Pathogen Genomics Programmes, as well as our neighbours at the European Bioinformatics Institute.

    REQUIREMENTS

    • Motivation to understand antibiotic resistance spread
    • PhD in a relevant subject area (Physics, Mathematics, Computer Science, Engineering, Statistics, Computational Biology, Bioinformatics, Molecular Biology)
    • Experience with bacterial genomics
    • Ability to devise novel quantitative models, use relevant mathematics-heavy literature
    • Experience in formulating the world in statistical models and applying them to real data
    • Full working proficiency in a scripting language (e.g. Python, R, Perl), and UNIX/Linux
    • Ability to work independently, organise workload, and communicate ideas and results
    • Strong publishing record

    PREFERENCES

    • Knowledge of genomics and molecular biology
    • Previous experience in creating finished software
    • Full working proficiency in a compiled language (e.g. C, C++, D, Julia, Fortran)
    • Previous experience with implementing – omics data analysis pipelines on a cluster
    • Proven independent working style, problem solving, data analysis and generation of novel ideas

    COMPENSATION

    £31,115 to £39,004 plus excellent benefits.

    Our Benefits include: Defined Benefit Pension Scheme, Group Income Protection, Healthcare scheme, Childcare Vouchers, Nursery and 25 days Annual Leave plus Bank Holidays. We also have a gym, two cafes, a nursery, dining facilities, and a free campus Bus service. Our thriving Sports and Social Club provides many opportunities to meet with people working across the campus.

    HOW TO APPLY

    Click on the following link jobs.sanger.ac.uk/wd/p[...]06961

    Please submit a cover letter and CV with your application.

    DEADLINE

    Closing date: 15/04/2017

    POLICY

    Wellcome Trust Sanger Institute welcomes applications from all candidates irrespective of age, disability, gender, gender identity, sexual orientation, race, religion or belief, or marital or civil partnership status.

    BACKGROUND

    Phenome Centre-Birmingham is a new major centre for providing national capability in state-of-the-art metabolic phenotyping applied to stratified medicine. The post holder will contribute significantly to the day-to-day operation of the Phenome Centre-Birmingham (PC-B) within the University of Birmingham, in particular by implementing an automated data processing pipeline, experimental design, and processing and statistical analysis of large scale MS and/or NMR based metabolomics datasets. In addition the post holder will collaborate with researchers within and external to the university (academic, industry, scientific instrument manufacturers), provide training and support in bioinformatics, and undertake independent research.

    RESPONSIBILITIES

    Main Duties:
    • To develop and conduct computational and statistical analyses of metabolomics datasets within the Phenome Centre-Birmingham, in particular of MS and/or NMR datasets analysed by both univariate and multivariate techniques
    • Implement an automated analysis pipeline for MS and/or NMR based metabolomics datasets
    • To undertake independent research in computational metabolomics, to develop the workflows for managing and analysing metabolomics datasets, for example using Galaxy software
    • To develop and maintain the computer hardware and software associated with the metabolomics laboratory
    • To train and assist postdoctoral researchers and PhD students in bioinformatics analyses of metabolomics datasets
    • To contribute to writing bids for research funding
    • Apply knowledge in a way which develops new intellectual understanding
    • Disseminate research findings for publication, research seminars, etc.
    • Undertake management/administration arising from research
    • Collect research data; this may be through a variety of research methods, such as scientific experimentation, literature reviews, and research interviews
    • 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

    REQUIREMENTS

    • PhD or equivalent experience in Bioinformatics, Biostatistics, Chemometrics or Computational Biology (all with metabolomics or related specialism)
    • Experience in the analysis of MS and/or NMR metabolomics datasets
    • Experience in statistical analyses, including multivariate and univariate methods
    • Experience in computer programming (e.g. python and R)
    • Experience in workflows, e.g. Galaxy
    • Experience in managing multiple projects simultaneously
    • Good communication and interpersonal skills
    • A high level of accuracy and attention to detail
    • Ability to work on own initiative, manage time effectively, progress tasks concurrently and work to deadlines
    • Detailed knowledge of office safety
    • Ability to communicate complex information clearly
    • Fluency in relevant models, techniques or methods and ability to contribute to developing new ones
    • Ability to assess resource requirements and use resources effectively
    • Understanding of and ability to contribute to broader management/administration processes

    LOCALE

    Birmingham, UK

    HOW TO APPLY

    Informal enquiries can be addressed to Professor Mark Viant (tel: +44 (0)121 414 2219 or email: M.Viant[at]bham.ac.uk) or Dr Warwick Dunn (tel: +44 (0)121 414 5458 or email: W.Dunn[at]bham.ac.uk).

    For further information and to apply visit atsv7.wcn.co.uk/sear[...]xNw==

    DEADLINE

    26th April 2017

    BACKGROUND

    We are seeking an experienced Senior Software Developer to join our development team providing informatics support for the High-Throughput Gene Editing team. We develop bioinformatics tools to assist in, for example, the design of genomic knockout constructs, CRISPR-Cas9 experiments and automated alignment analysis for quality control of targeted clones. Additionally, we develop web services to implement a LIMS (Laboratory Information Management System) for tracking scientific data generated in our stem cell engineering lab, as well as more bespoke support for our research groups in mouse and human stem cell engineering. See www.sanger.ac.uk/scie[...]atics for more information on the work we do.

    RESPONSIBILITIES

    You will become part of a relaxed but professional software development team, with access to world class computing resources and many opportunities for furthering your knowledge of programming for bioinformatics and genomics, whether within the web framework or on our extensive compute farm.

    This role involves gathering user requirements (in an informal way) and discussing the impact on current systems with the Senior Scientific Manager in the group and other members of the informatics team. We operate separate ticketing systems to manage user requirements and functional implementation. We develop primarily in modern Perl using a web stack based on PostgreSQL, Catalyst (for MVC support) and DBIx::Class. Legacy systems we still support use Oracle as the database layer. However, proficiency in programming any current language is more important than specific Perl experience.

    Our user interfaces rely more and more on JavaScript and we use the ExtJS framework for some of our views.

    There is substantial Perl expertise in the group and this opportunity could be a good way for appropriate candidates to get up-to-date with current Perl coding methodology.

    Our LIMS is used to support many other groups, both within the Sanger Institute and around the world. WGE is recognised as world class software for designing important genome editing experiments in many leading research groups.

    You will contribute code to our source code repositories on GitHub (github.com/htgt) as part of our collaborative and agile-enlightened approach to coding.

    We welcome applications equally from those who wish to work full time (37 hours) or for a minimum of 30 hours per week via a flexible working arrangement.

    REQUIREMENTS

    • Bachelor's degree or above in computer related sciences, or equivalent experience
    • Evidence of a high level of competence in a modern scripting language based on C-style syntax using a relational database
    • Ability to design and run complex database queries in SQL
    • Experience of developing and delivering a quality product within fixed deadlines
    • Ability to prioritise tasks to ensure the right things are done at the right time
    • Highly developed problem solving skills

    PREFERENCES

    • Programming in Modern Perl
    • Some experience with JavaScript programming and web development
    • Evidence of having successfully worked in a collaborative, project-focused software team
    • Evidence of having successfully created interfaces that link with and enable extraction/reporting/display of data from large, complex databases into a web environment
    • Experience and understanding of bioinformatics and familiarity with genome data

    LOCALE

    The Sanger Institute is a charitably funded research centre focused on understanding the role of genetics in health and disease. We use state of the art large-scale genomic approaches to drive world-leading projects to uncover the basis of genetic and infectious disease. Our goal is to provide results that can be translated into diagnostics, treatments or therapies that reduce global health burdens. The Institute is located near Cambridge, UK on the stunning Wellcome Genome Campus. This growing and dynamic site is the British hub of genomic science. It hosts the European Bioinformatics Institute (EBI), Open Targets, a Biodata Innovation Centre and will soon host Genomics England Limited's 100,000 Genomes Sequencing Centre. The Campus is also home to Wellcome Genome Campus Connecting Science. Connecting Science inspires new thinking, sparks conversation and supports learning by drawing on the ground-breaking research taking place on the Campus. Its mission is to enable everyone to explore genomic science and its impact on research, health and society. To help researchers to develop their skills and networks, the Institute hosts a range of scientific seminars with internal and invited speakers, scientific group meetings and skills development workshops.

    COMPENSATION

    £31,498 - £39,729 pa depending on experience

    Our Benefits include: Defined Contribution Pension Scheme, Group Income Protection, Healthcare scheme, Childcare Vouchers, Workplace Nursery and 25 days Annual Leave, increasing by one day per year up to a maximum of 30, plus Bank Holidays. We also have a gym, two cafes, dining facilities, and a free campus bus service. Our thriving Sports and Social Club provides many opportunities to meet with people working across the campus.

    HOW TO APPLY

    To apply click on the link: jobs.sanger.ac.uk/wd/p[...]08547

    Please include a covering letter and CV with your application.

    DEADLINE

    Closing date: 23rd April 2017

    POLICY

    Wellcome Trust Sanger Institute welcomes applications from all candidates irrespective of age, disability, gender, gender identity, sexual orientation, race, religion or belief, or marital or civil partnership status.

    BACKGROUND

    Two exciting Software Development opportunities have become available under the leadership of Professor Sir Mike Stratton as part of the CRUK Grand Challenge, Mutographs of Cancer project. This is an exciting opportunity for the successful candidates to apply novel bioinformatic algorithms to unravel the mutational signatures that will hopefully explain the major global differences in cancer incidence, to understand the biological mechanisms underlying cancer-causing mutational processes and to explore their application towards surveillance of mutagenic exposures in human populations.

    RESPONSIBILITIES

    The successful candidates will be embedded in a multidisciplinary team and will be tasked with further contributing towards developing the analysis pipelines for this project. These roles involve working at the interface between scientific and IT staff on this projects to ensure efficient analysis of the DNA sequencing data sets.

    These positions would suit a Bioinformatician/Software Developer who enjoys developing or enhancing software tools for analysis of complex NGS biological data sets and to make these efficient, visually appealing and interpretable by the scientific/clinical community. We are looking for individuals who enjoys working in a multi-disciplinary team environment to help solve complex IT issues which will ultimately aid our understanding of mutational processes in human cells.

    REQUIREMENTS

    • Good degree in Bioinformatics or Computer Science with a scientific background
    • Software development skills (using Perl and/or Python)
    • ORACLE/MySQL databases
    • Experience of handling Next Generation sequencing data LSF or Open Grid scheduling software
    • Experience working, developing and compiling software tools in a UNIX/LINUX environment
    • Enjoy working as part of a team

    PREFERENCES

    • Software development using a compiled language (C,C++,Java)
    • Experience of statistical analysis in a bioinformatics (in R)
    • Experience of workflow management IT systems
    • Experience of VMware, OpenStack or Amazon Web Services (AWS)
    • Experience of working in an Agile Software Development Group
    • Web development using Perl, Java, HTML(5), CSS, JavaScript
    • Background in cancer genetics

    COMPENSATION

    £31,498 to £39,729, plus excellent benefits.

    HOW TO APPLY

    Click on link: jobs.sanger.ac.uk/wd/p[...]08825

    Please include a covering letter and CV with your application.

    DEADLINE

    Closing date for applications: 19th April 2017, however applications will be considered and reviewed on an on-going basis and therefore the post may be filled before the deadline.

    POLICY

    Wellcome Trust Sanger Institute welcomes applications from all candidates irrespective of age, disability, gender, gender identity, sexual orientation, race, religion or belief, or marital or civil partnership status.

     

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