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    BACKGROUND

    The Wellcome Trust Sanger Institute are seeking to recruit a Data Scientist who can facilitate the scientific work of the Jones group by leading the computational data analysis support for the team and their collaborators.

    The group, led by Phil Jones, studies pre-cancer, how mutant cells evolve into cancers in humans and model systems (www.sanger.ac.uk/scie[...]group). We are interested in how mutant clones compete with each other and interact with the cancer promoting environment during epithelial cancer evolution in order to guide new cancer prevention therapy. Our cross disciplinary approach exploits quantitative methods to link mutation with changes in cell dynamics (see links 1-3 below). Recent work includes developing a new deep sequencing technique to reveal a high density of clonal mutations in normal human skin, basis of skin stem cell cell fate and developing new models of oesophageal cancer. The group is a mixture of experimentalists and quantitative biologists. The post holder will be able to exploit extensive bioinformatics and statistical expertise within the Institute.

    Many of our experiments involve the generation of large quantities of genome and exome sequencing and RNAseq including single cell transcriptomics which require strong computational skills to create high quality mutation calls, carry out statistical analysis to interpret the effects of mutation in varied samples and experiments and develop bespoke solutions to data visualisation. Collaborating within the experimental team to integrate genomic analysis with other types of data to resolve the cellular and tissue effects of mutations within tissues is an important part of what we do.

    RESPONSIBILITIES

    The post-holder must be a good communicator and be able to understand the scientific background and technical detail of the team's projects, and be to be proficient at devising and implementing software solutions and statistical analysis. This role would suit somebody with previous experience of next-generation sequencing technologies and their application to clonal evolution, although experience with next-gen data is highly desirable it is not essential as training can be provided. The successful candidate will work in conjunction with other computational biologists in the group and with other teams at the WTSI.

    1) Martincorena I, Roshan A, Gerstung M, Ellis P, Van Loo P et al. Science 2015;348; 880-6. Tumor evolution. High burden and pervasive positive selection of somatic mutations in normal human skin. PUBMED: 25999502; DOI: 10.1126/science.aaa6806

    2) Roshan A, Murai K, Fowler J, Simons BD, Nikolaidou-Neokosmidou V and Jones PH. Human keratinocytes have two interconvertible modes of proliferation. Nature cell biology 2016;18;145-56. PUBMED: 26641719; DOI: 10.1038/ncb3282

    3) Frede J, Greulich P, Nagy T, Simons BD and Jones PH. A single dividing cell population with imbalanced fate drives oesophageal tumour growth. Nature cell biology 2016;18, 967-78. PUBMED: 27548914; DOI: 10.1038/ncb3400

    REQUIREMENTS

    • A PhD level degree related to biology/genetics/computer science/mathematics
    • Experience of bioinformatics and familiarity with genome data
    • Evidence of proficiency in a modern computer language such as Perl or Python
    • Strong UNIX/LINUX skills
    • Experience of researching/using/supporting external software packages
    • Ability to rapidly attain new technical skills and understanding of new technical concepts
    • A high level of communication skills to be able to elicit complex requirements from, and convey complex information to, group members with different levels of technical knowledge
    • Ability to quickly adapt to new problems and ideas
    • Ability to work unsupervised
    • Excellent problem-solving skills

    PREFERENCES

    • R programming experience
    • Experience of working with biological analysis pipelines on multi-node compute clusters
    • Experience in pathway analysis software
    • Proficient in statistical analysis of genome-wide datasets

    COMPENSATION

    Salary Range: £31,498 to £39,729, plus excellent benefits.

    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.

    ABOUT US

    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.

    HOW TO APPLY

    Clicking on the link jobs.sanger.ac.uk/wd/p[...]16217

    Please include a covering letter and CV with your application. If you have any informal queries please contact Phil Jones pj3[at]sanger.ac.uk.

    DEADLINE

    22nd June 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. Please include a covering letter and CV with your application.

    BACKGROUND

    MeInBio is a newly established research training group at the University of Freiburg and the Max Planck Institute of Immunobiology and Epigenetics Freiburg. It aims at a dual education in bioinformatics and wet laboratory methods to explore the spatio-temporal dynamics of gene regulation using high-throughput and high-resolution methods. For further details concerning the positions, information on the individual research groups and the offered projects, as well as the application procedure please refer to
    www.anatomie2.uni-freiburg.de/en/g[...]x.htm

    We offer:
    • Exciting modern research projects in well equipped laboratories using state-of-the-art technologies (stem, cancer and prokaryotic cells, single cell and high-throughput sequencing, high-resolution imaging, bioinformatics)
    • Tandems between wet laboratory and bioinformatics groups with an at least three-month stay in the lab of the respective other field
    • Different model organisms for conceptual learning and scientific exchange
    • Professional and efficient supervision secured by a thesis advisory committee
    • Regular courses in bioinformatics and wet laboratory techniques
    • Additional "soft skills" courses and gatherings of all research training group members for scientific exchange

    REQUIREMENTS

    We are looking for junior researchers with expertise either in life sciences (molecular biology, cell biology, molecular medicine, biochemistry), or bioinformatics/informatics. Our dual education profile requires a strong interest for training in the respective other field.

    Candidates should:
    • Have an excellent recent university degree in one of the fields mentioned above
    • Be passionate about science and highly motivated
    • Have a strong affection to acquire both, biological and informatics knowledge
    • Be fluent in written and spoken English

    TERMS

    Positions are for three years, starting in September, 2017.

    LOCALE

    Freiburg, Germany

    COMPENSATION

    65% PhD positions (life sciences)
    100% PhD position (bioinformatics)
    100% Postdoc position

    HOW TO APPLY

    Only online applications through the web site www.anatomie2.uni-freiburg.de/en/g[...]x.htm will be considered.

    DEADLINE

    June, 8th, 2017

    BACKGROUND

    The Canadian Center for Computational Genomics (C3G) at McGill University provides bioinformatics analysis and high performance computing services for the life science research community. C3G develops customized and case-by-case bioinformatics solutions as well as an extensive suite of open-source software, including bioinformatics analysis pipelines (bitbucket.org/mugq[...]lines) used by multiple academic institutions, and many data access and analysis portals. We are seeking a Web Application Developer to engage in the development maintenance of a number of web applications, including the International Human Epigenome Consortium (IHEC) Data Portal (epigenomesportal.ca/ihec/), GenAP (genap.ca) and other online resources.

    Under the supervision of the Bioinformatics Manager, the Web Application Developer will implement and maintain client and server-side applications, extending the tools and technologies already in place using JavaScript, HTML, Python, MySQL, and so on. Short development cycles will involve small but frequent releases, and constant interactions with the bioinformatics platform team members.

    RESPONSIBILITIES

    • Design, build, test, deploy, monitor and maintain high-quality interactive web applications using Javascript, D3, HTML, and CSS
    • Iteratively write code to incorporate new concepts and test new designs
    • Focus on user experience, intuitive interfaces and interaction layers to create user-friendly web pages and applications
    • Ensure implementation is done using the best coding practices, including proper code commenting, unit testing, etc.
    • Develop server-side applications and scripts, such as data quality control pipelines
    • Contribute in the technological research and the prototyping
    • Make proper use of a revision control system such as BitBucket with Git
    • Setup and maintain automation tools for testing, continuous integration & delivery such as Selenium and Jenkins
    • Optimize code when needed while making use of good software practices
    • Make use of an issue tracking system such as Atlassian JIRA to document tasks, issues and bugs, and the resolution status of these
    • Ensure that all finished solutions work within a variety of browser types and screen settings along with the constraints set by development and design
    • Ensure that all Internet standards are met and that the company does not intentionally violate any standards or licenses that would place our domain in jeopardy

    REQUIREMENTS

    • Experience with Javascript in developing full-scale web applications is absolutely mandatory. Providing links to examples of web applications applicant has worked on is highly recommended.
    • Undergraduate degree in computer science, engineering or related field
    • Having an open mind towards new technologies, having at least basic knowledge of the various layers involved in web application development (full-stack)
    • Attention to detail, good communication and organizational skills and ability to work in a highly interactive group
    • Capable of getting multiple tasks assigned at once, and making sure that they all progress at a steady pace

    PREFERENCES

    • Experience with Javascript APIs and frameworks, for example jQuery, D3, ReactJS, AngularJS
    • Experience with relational databases (RDBMS), such as MySQL and Postgres
    • Experience with server-side scripting, such as Python, Perl, Bash
    • Experience with Python frameworks like Flask and Django
    • Experience with the Git version control system
    • Demonstrated sound intuition in making efficient and simple-to-use browser-based interactive tools and interfaces
    • Interest in the field of genetics and bioinformatics.
    • English and French (spoken and written)

    TERMS

    Contract renewable yearly.

    LOCALE

    McGill University, Montreal, Quebec, Canada

    HOW TO APPLY

    Please submit your application online at www.mcgill.ca/medh[...]y-now. Click on "APPLY NOW" and clearly indicate the reference number.

    DEADLINE

    June 2, 2017 at 5:00 PM

    POLICY

    McGill University is committed to equity in employment and diversity. It welcomes applications from indigenous peoples, visible minorities, ethnic minorities, persons with disabilities, women, persons of minority sexual orientations and gender identities, and others who may contribute to further diversification.

    RESPONSIBILITIES

    Position Context:
    Under the direction of the Bioinformatics Manager, the Bioinformatics Specialist will perform advanced analyses at McGill's Canadian Center for Computational Genomics (C3G). The chosen candidate will contribute to the development of analysis pipelines associated with Next-Generation Sequencing (NGS) instruments. The specialist will be a member of the technical development group and perform advanced statistical analyses that facilitate genomics data interpretation. The specialist will work closely both with other members of the C3G team and scientists at the McGill University and Génome Québec Innovation center. The chosen candidate will be exposed to a wide variety of novel sequencing technologies, bioinformatics approaches, and state of the art computing resources in facility dedicated to high-throughput sequencing and large-scale genomic studies.

    Primary Responsibilities:
    • Actively contribute to the Technical Development group efforts to create Standard Operation Procedures and perform on-demand analyses.
    • Mentor and guide Bioinformatics Consultants in the unit. Monitor their progress and insure quality of results delivered.
    • Use and develop analysis pipelines using in-house and third party tools or algorithms, and incorporate them into specialized analysis workflows.
    • Develop bioinformatics solutions for the analysis of complex genomic datasets.
    • Update and extend bioinformatics tools and software methods used or developed at the C3G.
    • Provide detailed reports with analysis results and descriptions of methods used.
    • Contribute to problem-solving discussions.
    • Provide regular internal reports regarding the progress of projects (oral presentations).
    • Keep online documentation up-to-date, explaining the services offered and the analysis methods used.
    • Stay informed of the most relevant bioinformatics practices in genomics.
    • Lecture in bioinformatics training workshops organized by the center.
    • Manage several analysis projects at the same time.

    REQUIREMENTS

    Education/Experience and Other Qualifying Skills and/or Abilities:
    • MSc in Bioinformatics, Statistics, Computer Science or related field (PhD is preferred).
    • Three (3) years of experience in bioinformatics or genomics research.
    • Excellent understanding of statistics is a must.
    • Experience with Python is a requirement.
    • Experience with data analysis in the research context is a plus.
    • Good knowledge of R, git, and bash is needed.
    • Additional programming experience (perl and java) is an asset.
    • Experience in using HPC environment.
    • Experience with Docker or VM environment for analysis is an asset.
    • Experience lecturing in training workshops is desirable.
    • Very good communication skills in English, spoken and written. French is an asset.

    LOCALE

    Canadian Centre for Computational Genomics
    McGill University
    Montreal, QC
    Canada

    Faculty/Unit: Faculty of Medicine, Department of Human Genetics

    HOW TO APPLY

    Please submit your application online at www.mcgill.ca/medh[...]y-now. Click on "APPLY NOW" and clearly indicate the reference number MT0294.

    We thank all applicants for their interest, however, only those applicants selected for an interview will be contacted.

    POLICY

    McGill University is committed to equity in employment and diversity. It welcomes applications from indigenous peoples, visible minorities, ethnic minorities, persons with disabilities, women, persons of minority sexual orientations and gender identities, and others who may contribute to further diversification.

    RESPONSIBILITIES

    Position Context:
    Under the direction of the Bioinformatics Manager, the software developer and HPC integration specialist will participate in the planning, development, co-ordination, implementation and maintenance of information systems and genomic analytical pipelines developed at the McGill's Canadian Center for Computational Genomics (C3G). This includes the integration of information systems strategy, policy and planning with all members of the projects, and the development and implementation of information system strategies that support the analytical needs of various projects. The chosen candidate will also work closely with members of McGill's High Performance Computing (HPC) centre and other Calcul Québec staff members for the efficient integration of tools developed by the C3G with the Compute Canada infrastructure and other cloud-computing systems. The chosen candidate responsibilities will also include troubleshooting and supporting a variety of users using these tools.

    Primary Responsibilities:
    • Contribute to the design and implementation of software pipelines for the processing of next generation sequencing data. Help maintain and document the pipelines code base and related procedures.
    • Participate in the continuous development of a virtual file system. This involves installing software, genomic databases and also monitoring and optimizing performance of the said system.
    • Contribute to project planning and establish project milestones.
    • Participate actively in discussions with other developers and users of the centre.
    • Ensure that pipelines run efficiently on C3G clusters as well as on Compute Canada HPC resources, and that all incoming data and analysis output is properly stored and maintained with appropriate user access.
    • Port current pipelines to cloud-computing infrastructures
    • Keep abreast of new developments in the field of parallel processing on HPC infrastructures, with the goal of increasing efficiency and accuracy of analytical pipelines.
    • Act as a primary contact person in supporting users seeking advice on how to access and execute the developed analysis pipelines on the HPC infrastructures. When appropriate, inform supervisors and formulate recommendations.
    • Provide IT support to users.
    • Troubleshoot system problems as necessary to ensure operational integrity.
    • Provide training and technical support services for all aspects related to the operation of the systems.
    • Develop training materials and documentation for the systems and analytical pipelines.

    REQUIREMENTS

    Education/Experience and other Qualifying Skills and/or Abilities:
    • M.Sc in Computer Science, Informatics or related field (Ph.D. is an asset).
    • 3 years of related experience. Experience with Python, git, and bash is a requirement.
    • Additional programming experience (Perl and Java) is an asset.
    • Experience in using HPC environment.
    • Experience with cloud computing and distributed applications is a must.
    • Experience with Docker, Singularity or other containers is an asset.
    • Very good communication skills in English, spoken and written. French is an asset.

    LOCALE

    Canadian Centre for Computational Genomics
    McGill University
    Montreal, QC
    Canada

    Faculty/Unit: Faculty of Medicine, Department of Human Genetics

    HOW TO APPLY

    Please submit your application online at www.mcgill.ca/medh[...]y-now. Click on "APPLY NOW" and clearly indicate the reference number (MT0293).

    We thank all applicants for their interest, however, only those applicants selected for an interview will be contacted.

    POLICY

    McGill University is committed to equity in employment and diversity. It welcomes applications from indigenous peoples, visible minorities, ethnic minorities, persons with disabilities, women, persons of minority sexual orientations and gender identities, and others who may contribute to further diversification.

    BACKGROUND

    A Postdoctoral Research Associate position is available in the Division of Epidemiology, Department of Medicine, at Vanderbilt University Medical Center. Our current research concentrates on population-based genetic epidemiologic studies for the exploration of novel genetic risk variants and genes for cancers. We will focus on numerous genetic epidemiology and large genomics studies using large population-based prospective cohort studies. In order to understand the underlying molecular mechanisms of carcinogenesis, we will apply and develop bioinformatics tools and build statistical models to process large whole genome sequencing and whole exome sequencing, RNA-seq, array-based genotype and epigenetic data to investigate all types of genetic variants, including noncoding and structure variants. The chosen candidate will lead independent research projects in the fields of genetics, epigenetics, functional genomics, and bioinformatics. They should also expect to participate in multiple collaborative projects in cancer-related genetic epidemiology studies.

    The Division of Epidemiology is committed to conducting research to enhance and expand our understanding of the distribution and determinants of disease, to promoting collaboration aimed at the translation of research into cost-effective strategies of disease prevention and health care delivery, and to training independent investigators in epidemiological research and disease prevention. Our group has a broad interest in the research of genetics and genomics for cancer. We concentrate on population-based genetic epidemiologic studies for the exploration of novel genetic risk variants and genes for cancer outcomes. These projects will primarily build from valuable cohort resources based at the Vanderbilt Epidemiology Center, i.e., the Asian Breast Cancer Consortium (ABCC) and the Asian Colorectal Cancer Consortium (ACCC). We are interested in developing and applying computational methods for processing high-throughput genomic sequencing data from the above population-based cohorts to identify various genetic variants, especially structure variants for cancer risk. In particular, we are also highly interested in studying the functional potential of risk coding or noncoding variants by integrating big experimental data from the next-generation sequencing (e.g., ChIP-seq, ATAC-seq, BS-seq and RNA-seq) from public databases (i.e. TCGA and ENCODE). Information about the Division of Epidemiology can be found at medicineandpublichealth.vanderbilt.edu/vec/[...]x.php.

    RESPONSIBILITIES

    Under guidance from Drs. Xingyi Guo and Wei Zheng, the candidate is expected to work on a wide range of bioinformatics projects. He/she should have:
    • A PhD in bioinformatics, computational biology, biostatistics, genomics, molecular biology or related fields. The candidate should have a strong background in processing high-throughput genomic and genetic data with biostatistics knowledge.
    • Strong experience with script languages such as Perl, Python or R. Experience with the Linux/Unix environment is required.
    • Experience in statistical computing (e.g. R/Bioconductor and Biopython).
    • Good interpersonal skills.
    • An excellent grasp of English, both in writing and speech.

    COMPENSATION

    Salary is commensurate with the NIH pay scale. The postdoc positions will be provided with benefits following Vanderbilt University Medical Center standards.

    HOW TO APPLY

    To apply, please send a cover letter, CV, summary of past work, and the names and email addresses of three references to Dr. Xingyi Guo at xingyi.guo[at]vanderbilt.edu. The position is for two years with the possibility of further extension.

    DEADLINE

    The deadline for applications is July 30, 2017. Any applications received after this time will not be considered. Incomplete applications will not be considered.

    POLICY

    Vanderbilt University Medical Center wishes to reflect the diversity of society and welcomes applications from all qualified candidates, regardless of personal background.

    BACKGROUND

    We are seeking an individual with a background in analytical chemistry/biochemistry or related discipline, and experience in the interpretation and analysis of novel mass spectrometry-based datasets. You will independently procure, review and curate lipid structures and associated mass spectral data from existing sources and user submitted datasets into databases for publishing on an internationally recognized lipidomics web resource. You will work independently as well as within a team on the implementation of software solutions for processing, searching, display and analysis of data and lipid structures.

    This role will work within a multidisciplinary team that includes scientists and informaticians, as part of the LIPID MAPS database.

    RESPONSIBILITIES

    Curating and uploading data to an online repository from multiple online sources, industry and private users and developing and supporting the efforts of a team of programmers/curators as part of the international database project, LIPID MAPS (www.lipidmaps.org).
    • Curation, review, and auditing of molecular structures and Mass Spectrometry (MS) data relating to lipidomics experiments. Curated databases will have international impact and will be made accessible via the LIPID MAPS portal (www.lipidmaps.org).
    • Support software development within an international, multi-centre team, through working with programmers to suggest and test solutions.
    • Ensure that the project milestones are met, proactively changing delivery according to user requirements
    • Establish working relationships with key contacts, developing appropriate communication links within the University and internationally recognised researchers within the field of lipidomics and other high-profile, international databases
    • Advise on informatics needs, suggesting projects for informaticians to develop as needed through working closely with a project coordinator and other programmers
    • Engage in cross-training within the team and provide a secondary support buffer for other team roles, where appropriate
    • Provide professional advice and guidance on the LIPID MAPS resource and database processes and procedures to internal and external customers that will have institute wide impacts, using judgement and creativity to suggest the most appropriate course of action where appropriate, and ensuring complex and conceptual issues are understood
    • Take responsibility for resolving issues independently along with the team of programmers/curators in the LIPID MAPS group where they fall within set role objectives
    • Investigate and analyse specific issues within LIPID MAPS, creating recommendation reports, supported by advances within the lipidomics research field
    • Ensure that the provision of LIPID MAPS objectives is delivered to the institution, proactively changing the delivery according to customer requirements
    • Create specific working groups from colleagues across the University to achieve School of Medicine and Division of Infection and Immunity objectives, if needed
    • Develop and deliver training within LIPID MAPS and lipidomics in general
    • Instruct and guide others within the LIPID MAPS team and other employees across the University within the field of lipidomics and in relation to the LIPID MAPS resource

    TERMS

    This post is full time (35 hours per week), is available immediately and is fixed term until 26th July 2020.

    HOW TO APPLY

    Please visit krb-sjobs.brassring.com/TGne[...]86138

    DEADLINE

    Saturday, 10 June 2017

    BACKGROUND

    The London Institute of Medical Sciences (LMS) is a large biomedical research Institute funded by the Medical Research Council, closely associated with Imperial College London at its Hammersmith Campus. The interests of research groups at the LMS are increasingly driven by the interface between experimental and computational biology. This post provides exciting opportunities to contribute to this growth area.

    RESPONSIBILITIES

    You will lead a team of Bioinformaticians and computational biologists providing support to diverse research projects within a dynamic academic environment. Working with IT/computing and other bioinformatics/computational biology research groups of the LMS, the main challenges for the future are: (1) high-level direction, planning and monitoring of bioinformatics strategy, oversight and development of the bioinformatics team; (2) active engagement in data analysis, the development of tools for data integration and visualisation; (3) support the demanding and rapidly changing computational biology needs of LMS research programmes (4) identify and harness for the benefit of the LMS's science the strengths in academic Bioinformatics and computing within Imperial College; (5) develop and oversee teaching of bioinformatics at the LMS; and (6) to identify, evaluate and exploit relevant cutting-edge Bioinformatics techniques and emerging technologies that will help keep the LMS at the scientific forefront.

    REQUIREMENTS

    You will:
    • Have a broad knowledge of Bioinformatics gained over a number of years probably in different environments, as well as in-depth knowledge of required computational technologies and programming environments.
    • Determine Bioinformatics strategy for the LMS in order to deliver the Institute's long-term scientific objectives and facilitate development of Bioinformatics within the Institute.
    • Have experience of managing a team of Bioinformaticians/computational biologists and provide high-level bioinformatics support to end-users within a complex and demanding environment, gained in either the commercial or academic sectors or both.
    • Have an empathy with research (some research experience at a postgraduate level is essential) and able to work constructively and effectively with academic staff, both within the LMS and more widely within Imperial College, putting ideas across convincingly and commanding respect.
    • Be able to demonstrate success as a motivator and manager of people.
    • Be experienced in defining and managing projects, with a track record of delivery to time and budget.

    LOCALE

    London, UK

    COMPENSATION

    £42,220 - £55,342 inclusive

    HOW TO APPLY

    The MRC has a final salary pension scheme and a generous annual leave allowance of 40.5 days (inclusive of bank holidays). For full details of this post and to complete an online application, visit mrc.tal.net/vx/l[...]en-GB and upload your CV, statement of research experience and goals, names and contacts of three scientific references along with a covering letter stating why you are applying for this role (providing evidence against the requirements of the job as per the job description and person specification). Please quote reference number LMS - 554.

    DEADLINE

    19th June 2017

    BACKGROUND

    Applications are sought for an exceptional Postdoctoral Research Assistant to undertake bioinformatical investigations into the evolution of Barrett's oesopahagus to cancer as a means to predict cancer risk. They will work under the supervision of Dr Stuart McDonald, the Principal Investigator (PI) of the Clonal Dynamics in Epithelia laboratory, and in collaboration with Prof Trevor Graham (Clonal evolution in Cancer laboratory) in order to realise the objectives of a Cancer Research UK funded programme grant predicting risk of cancer development in patients with Barrett's oesophagus. This is a multidisciplinary group that includes wet lab scientists, bioinformaticians and clinicians.

    Barrett's oesophagus is the only known precursor of oesophageal adenocarcinoma (OAC) in the UK. OAC has a poor survival rate and Barrett's is common but progression to cancer is rare (0.3% of patients). All Barrett's patients undergo regular endoscopic surveillance for signs of cancer, which is both invasive and expensive, but there are no prognostic biomarkers available to predict cancer risk. We believe that this is because we do not understand the evolutionary pathways of Barrett's to cancer. We are seeking an experienced post doctoral scientist to investigate how Barrett's glands evolve by generating and developing a predictive model of cancer risk using next generation sequencing data in combination with histological phenotyping. Experience in bioinformatics and modeling biological processes is desirable. The successful candidate will be expected to help drive the direction of the project and develop novel analytical approaches to answer the research question.

    The research will be based in the Centre for Tumour Biology, 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 a relevant bioinformatics, mathematics or biological subject (with a strong bioinformatical component) and an undergraduate degree in a relevant subject. Research experience in bioinformatics or genetic analysis or modelling is desirable. A demonstrable interest in the evolution of cancer would be an advantage. Furthermore, an appropriate publication record is essential. The applicant will have the ability to communicate well, work within a team and maintain good laboratory records.

    TERMS

    The post is full time, fixed term position for 3 years (with a further 3 years upon successful programme renewal). Starting salary will be in the range £32,405 - £42,431 per annum inclusive of London Allowance depending on experience. Benefits include 30 days annual leave, a defined benefit pension scheme and an interest free season ticket loan.

    HOW TO APPLY

    To apply, and for full job details, please visit the Human Resources website on www.hr.qmul.ac.uk/vacancies and search for reference QMUL9555.

    The Barts Cancer Institute requires applicants to provide all certificates at interview to confirm their qualifications (specified in the job description). Please be aware there are specific job descriptions for each post.

    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.

    Informal enquiries about this post, including arrangements to visit the Institute/Centre are encouraged and can be made to Dr Stuart McDonald Tel: +44 207 882 3800 or email s.a.mcdonald[at]qmul.ac.uk

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

    DEADLINE

    The closing date is the 26th May 2017 and the interviews are likely to be held shortly afterwards. It is expected the position will commence as soon as possible.

    POLICY

    Valuing Diversity & Committed to Equality

    Submitter

    BACKGROUND

    CSRA has an opportunity to make an impact in the cure for cancer. We are seeking a Bioinformatics Software Engineer with JAVA and statistical programming languages to join our team supporting the National Cancer Institute (NCI) Center for Cancer Research (CCR) Developmental Therapeutics Branch. This team is building web application and database tools in support of laboratory scientists and pharmacology groups who are searching for new cancer drugs and conducting cutting edge cancer research. This web-site is visited by over 8000 unique visitors a month from over 100 countries.

    In this role, you will be involved with maintaining and expanding a newly created data analysis tool; as well as supporting other JAVA based applications developed for this lab and then made public and used by researchers all over the world.

    Position is for full time employment with CSRA and will be based at the NIH main campus in Bethesda, MD (metro accessible); with the opportunity to telework one day a week once established and with manager approval. Typical schedule will be Monday through Friday around normal business hours.

    RESPONSIBILITIES

    • Design, develop, document, test and debug applications software and systems that contain logical, mathematical, and bioinformatics solutions in support of research science.
    • Collaborate with research investigators in the planning, design, development, and utilization of automated solutions for bioinformatics data analysis and processing.
    • Determine computer user needs; analyze system capabilities to resolve problems on program intent, output requirements, input data acquisition, programming techniques and controls; prepare operating instructions; design and develop utility programs.
    • Ensure software standards are met. These activities support the identification of new drug targets and biomarkers as well as data validation.
    • Utilize existing algorithms, techniques, and statistical methodologies but also be responsible for implementing and developing novel approaches from the group.
    • Emphasis is on developing cutting edge techniques such as gene or protein profiling analysis methods and implementing them successfully within project teams.

    REQUIREMENTS

    • Bachelors and 5+ yrs related experience, or MS + 3 yrs related experience, or equivalent combination of education and experience
    • Experience in bioinformatics application and tool development for Data Science analysis
    • Experience in Java software development, JavaScript, HTML, and JSP
    • Experience with statistical programming languages such R, Python, Matlab, Perl, or other
    • Experience with testing packages and writing test scripts
    • Knowledge of MySQL and database design and development
    • Knowledge of statistics, data mining, analytics and/or data sciences

    PREFERENCES

    • Experience with biological sequence, variant, and pathway databases and associated data mining software
    • Python, R Studio, Shiny, Docker, Apache POI, Struts, tiles, JDBC, CSS, XSLT, jUnit, Quartz, Ant, IntelliJ IDEA, CGI, etc.
    • Multi-platform environments (Windows, Mac OS X, Solaris and Linux)
    • Experience with microarray and next generation sequencing data preparation and analysis software
    • Experience with 508 compliance process and requirements
    • 10 plus years of experience desired

    TERMS

    Full time employment with CSRA

    LOCALE

    Bethesda, MD

    COMPENSATION

    Negotiable

    HOW TO APPLY

    Please apply directly online to job #14279 on our www.csra.com/careers site or to this link: jobs.csra.com/job/[...]76560

    DEADLINE

    Please apply by June 8; start date is ASAP.

    POLICY

    EEO

    BACKGROUND

    Do you want to fight malaria from your computer? Are you a motivated bioinformatician and want to work with the latest sequencing technologies and single cell sequencing?

    The Wellcome Trust Sanger Institute is taking on some of the most difficult challenges in genomic research, to push the boundaries of our understanding of life in ever new and exciting ways. We have an exciting opportunity for you to work within a team of bioinformaticians and biologists to use state-of-the-art genomic and transcriptomic datasets to understand the biology and evolution of malaria parasites.

    In the Parasite Genomics group we produce and analyse DNA sequence data to gain insights into parasite biology and to generate resources of lasting value to the Research community. We use the latest sequence technologies, like Oxford Nanopore, 10X to push the limits of single-cell analysis for parasite genomes.

    We seek to recruit a senior bioinformatician in to our malaria genomics team, to work with DNA and RNA sequencing data. The position would be ideal for an individual to gain valuable experience in using third generation sequencing data, as well as cutting edge single-cell approaches.

    RESPONSIBILITIES

    • Analyse and evaluate 3rd generation sequencing data with existing tools, and with new tools generated in house
    • Analyse single-cell datasets
    • Generate programs and pipelines to generate hundreds of high quality malaria-parasite genomes

    REQUIREMENTS

    • The position will involve both data analysis and programming.
    • Good knowledge of programming, demonstrated by a Masters or PhD degree in Computer Science or Bioinformatics, or PhD in another discipline (such as physics, maths or biology) with a large component of computational work
    • Must have experience in Java, Perl or Python programming and driving projects to completion

    PREFERENCES

    Experience with genome and next generation sequencing analysis or a background in malaria biology

    TERMS

    Fixed Term Contract for 3 years

    COMPENSATION

    Salary Range: £31,498 to £39,729 plus excellent benefits.

    HOW TO APPLY

    Clicking on link: jobs.sanger.ac.uk/wd/p[...]14748

    DEADLINE

    Closing date for applications: 16th June 2017, however applications will be considered and reviewed on an on-going basis.

    DESCRIPTION

    The research laboratories of Dr. Frank Pugh and Dr. Shaun Mahony, in the Department of Biochemistry and Molecular Biology at The Pennsylvania State University, are seeking a highly motivated, senior engineer with proven experience in developing open-source bioinformatic software and research applications. For the right applicant with software engineering experience, this could be filled as a telecommute position.

    The hired individual will be the technical team lead for development of bioinformatics software and database platforms for a lab of ~25 scientists, faculty and technicians. This position involves designing and identifying the requirements for interactive database applications and programming novel methods primarily for epigenomics data derived from next-generation sequencing (NGS).

    This position requires development experience on a UNIX platform; experience with high-performance computing parallel programming and a background in statistical methods is preferred. Also required is the ability to develop and support a codebase written with Python, JavaScript and Java; proficiency in other programming languages is expected. Professional software engineering training and experience with peer design, code reviews, source code management and deployment management will be part of the expectations for this position.

    This job will be filled as a level 3, or level 4, depending upon the successful candidate's competencies, education, and experience. Typically requires a Master's degree or higher in a field of study with focus on computational research methods, plus four years of related experience, or an equivalent combination of education and experience for a level 3. Additional experience and/or education and competencies are required for a level 4 job classification.

    HOW TO APPLY

    Applications must be submitted electronically at psu.jobs/job/68820 and include a cover letter and resume. A project portfolio and set of code samples from previous work will be requested for all applicants selected for an interview. This is a fixed-term appointment funded for one year from the date of hire with possibility of re-funding.

    BACKGROUND

    A postdoctoral position in the field of Bioinformatics/Systems Medicine is available for a talented and highly-motivated individual in the group of Dr. André Leier at the Informatics Institute, University of Alabama at Birmingham. The successful candidate will perform original research in biomedical data analysis, algorithm and tool development, predictive modeling, and machine learning. Sample projects include analyzing protein post-translational modification cross-talk, protein function prediction, genotype to phenotype mapping, and predicting outcomes of therapeutic interventions.

    REQUIREMENTS

    Applicants must have a PhD in Computer Science, Bioinformatics, Systems Biology or an equivalent field with a general background in molecular cell biology. Programming (C++, Matlab, R, and/or Python) and mathematical/analytic skills are expected. Previous experience in bioinformatics-related projects is a must. It is expected that the candidate is able to understand various types of omics data, to subsequently generate and implement computational pipelines for analysis and/or prediction.

    PREFERENCES

    Ideally, the candidate has additional hands-on experience in machine learning techniques and use of various bioinformatics tools and online databases.

    TERMS

    Appointment will be for one year with the possibility of extension contingent on satisfactory performance.

    LOCALE

    Birmingham, Alabama

    COMPENSATION

    Competitive salary (with benefits) will follow NIH guidelines commensurate with training and experience.

    HOW TO APPLY

    Please send
    1. A cover letter including a brief statement explaining fit, motivation and interest in the open position, summarizing past research and outlining career goals,
    2. A CV including a full list of publications and names and contact details of three references (with institutional mail/email addresses), and
    3. One sample authored publication/manuscript
    By email in one single PDF file to André Leier (aleier (at) uabmc.edu). Referees of short-listed candidates will be contacted directly.

    DEADLINE

    While the start date is negotiable, screening of applications will start immediately and will continue until the position is filled.

    For further details, see:
    www.uab.edu/post[...]70301

    OVERVIEW

    Arbor Diagnostics, Inc Laboratory at Dallas, TX (www.arbordiagnostics.org) is seeking a highly motivated, enthusiastic individual to join its Human Genetics Department's Bioinformatics team as a Bioinformatician. This individual will be responsible for Next-generation sequencing test validation and analyzing clinical genomics data generated in the facility for genetic carrier screening. In this role, you would be expected to have a level of knowledge to properly analyze results, especially where results are abnormal or atypical, while adhering to regulatory requirements. Our goal is to utilize next-generation DNA sequencing – based approach to yield the accuracy and completeness necessary for carrier screening tests and detection of variants in inherited diseases.

    RESPONSIBILITIES

    1. Implementation of computational tools and bioinformatics analysis pipelines for targeted gene panels
    2. Complete quality control analysis of NGS data from Illumina or similar platform along-with base calling, read alignment, variant calling, and variant annotation
    3. Variant filtering: Disease-targeted panels analysis of Exome Sequencing/ Genome Sequencing
    4. Comply with quality standards and regulatory requirements throughout all phases of testing and analysis, and maintain quality assurance documentation
    5. Understands and ensures HLI compliance in use of electronic record keeping with respect to health information
    6. Applies the informatics processes that connects sample requisition to wet lab processes, data analysis, report writing, and transmission of final reports to referring physicians
    7. Uses current software for next-generation sequencing variant calling and confirmations (e.g. BWA, GATK)
    8. Experience in bioinformatics resources such as BLAST, BWA, GATK, dbGaP, Clustalw, NCBI, EBI, Pfam, COG, GO, KEGG, etc.
    9. Identifies artifacts and trouble spots in genome sequence data as part of data interpretation, including the visualization of single nucleotide and copy number variation; basic biostatistical analysis of sequencing data; and analyzing and integrating data from orthogonal confirmation methods
    10. Observe uses the following bioinformatics tools as part of interpretation work- genome browsers (UCSC, IGV, ENSEMBL), human genome variation databases (e.g., ClinVar, 1000Genomes, ESP), variant analysis software, if available (custom software or vendor software), in silico algorithms for prediction of effects of missense changes (PolyPhen, GERP, SIFT, Alamut, etc.)
    11. Understands and applies basic biostatistical concepts, including case-control studies, odds ratios, use of different statistical measurements, appreciating outcomes of population studies

    REQUIREMENTS

    Special Knowledge, Skills, and Abilities:
    1. Must have strong computer skills including familiarity with online databases (ExAC, HGMD, dbSNP, etc.) and in-silico variant assessment tools (SIFT, PolyPhen, etc) to aid in variant interpretation in addition to excellent verbal and written communication skills.
    2. Candidates should have a strong background in the application of bioinformatics software for Illumina sequencing and utility programming in a UNIX environment.
    3. Strong computer programming skills is preferable: Perl, or Python, C, C++ and R.

    PREFERENCES

    • Education: Master's in bioinformatics or a related field
    • Experience: Six (6) years of experience with increasing responsibilities, next generation sequencing data analysis (preferably in a Clinical setting)
    • Strong analytical abilities and communication skills

    LOCALE

    Preferably located near Dallas TX

    COMPENSATION

    $75,000-150,000 annual salary

    HOW TO APPLY

    Please send your resume to mkorenvaes[at]doublehelixmgmt.com

    BACKGROUND

    Job Description:
    When you join us at Thermo Fisher Scientific, you'll be part of a smart, driven team that shares your passion for exploration and discovery. With revenues of $17 billion and the largest investment in R&D in the industry, we give our people the resources and opportunities to make significant contributions to the world.

    Position Summary:
    We are searching for a Bioinformatics Scientist to address our needs for assays design pipelines supporting innovative chemistries and focusing on bacterial, viral and metagenomics applications. The candidate will execute the implementation and documentation of algorithms and programs to support assay design, conduct troubleshooting analyses of design strategies and analyze experimental data with the goal to improve the design algorithms. QC activities are key in successful assay designs and part of the activities will include providing tools that allow in silico validation of assays. The candidate will also participate in core team meetings, help define requirements, and collaborate closely with biochemists and molecular biologists in the group.

    Thermo Fisher is a leader in the development of PCR based assays. Flagship product lines are TaqMan® , AmpliSeq™, and capillary electrophoresis primers which are used together with our instruments for genotyping, gene expression and mutation detection applications.

    RESPONSIBILITIES

    • Work with R&D scientists, and product managers to define the requirements of a design pipeline, focusing on identifying and curating target sequences.
    • Use existing pipelines and tools to design assays.
    • Implement new design algorithms taking advantage of an existing infrastructure.
    • Critically assess data to identify patterns that provide hypotheses to improve in silico and in vitro success rates.
    • Prepare technical reports, product summaries, protocols, quantitative analyses and code documentation.
    • Curate existing DNA/RNA sequence databases for periodic upgrades and releases to customers

    REQUIREMENTS

    Minimum Qualifications:
    • Minimum of 8 years of related experience with a Bachelor's degree; or 6 years and an advanced degree or equivalent work experience; industry experience preferred.
    • Degree in molecular biology, statistics, computational biology, bioinformatics, or related field.
    • Expert in usage and handling of public domain data of sequences and variations. Understanding of annotation data, bacterial and viral taxonomy and naming conventions.
    • Expertise in comparative genomics and mapping/comparison tools.
    • Experience with primer design.
    • Understanding of metagenomics algorithms and tools.
    • Experience in next gen sequencing and PCR based assays.
    • Linux/Unix work environment, Perl. We are also using Python and Java.

    PREFERENCES

    Preferred Qualifications:
    • Industry experience preferred.
    • Strong communication skills.

    LOCALE

    US - California - South San Francisco

    HOW TO APPLY

    Apply now: jobs.thermofisher.com/Show[...]tics/

    At Thermo Fisher Scientific, each one of our 50,000 extraordinary minds has a unique story to tell. Join us and contribute to our singular mission—enabling our customers to make the world healthier, cleaner and safer. Apply today: jobs.thermofisher.com.

    Job ID: 43769BR

    (*IND-LSG)
    (#LI-TH1)

    POLICY

    Thermo Fisher Scientific is an EEO/Affirmative Action Employer and does not discriminate on the basis of race, color, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, disability or any other legally protected status.
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