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    Opportunity: Scientists in Epigenomic Mapping by High-Throughput Sequencing @ McGill University--Montreal, Quebec, Canada
    Submitted by Tony Kwan; posted on Friday, April 06, 2012

    Three positions are available.


    The next frontier in human genomics explores its tissue specific function and the impact of the environment on the genome. The Canadian Epigenetics, Environment and Health Research Consortium (CEEHRC) has awarded McGill University five year funding (2012-2017) to establish one of two National Epigenomic Mapping Centres (EMCs) as well as an Epigenomic Data Coordination Centre (EDCC), which will operate under the principles of the International Human Epigenome Consortium (IHEC). These Epigenomic Centres are housed in the McGill University and Génome Québec Innovation Centre (Montreal, Canada), a world-class research facility for genomics and bioinformatics located on McGill University's main campus. The facility holds a number of high-throughput sequencing technology platforms, automated laboratory processes, and large-scale computing supporting an array of genome-wide epigenome mapping techniques (including MethylC-seq, ChIP-seq, RNA-seq).

    We are seeking a number of highly motivated and team-oriented individuals with good organizational, interpersonal, and communication skills to join the EMC and EDCC teams to tackle challenges in next-generation epigenomics within a dynamic, multi-disciplinary environment.


    1. Bioinformatics Specialists:
    Support and develop various analysis pipelines associated with Next-Generation Sequencing (NGS)-based epigenomics experiments. The relevant techniques include but are not limited to: 1) whole-genome bisulphite sequencing (MethylC-seq.), 2) transcriptomic analysis (RNA-Seq. and smRNA-Seq.), and 3) chromatin-immunoprecipitation sequencing (ChIP-Seq.). The work will involve developing and utilizing sequence analysis pipelines using in-house and 3rd party tools or algorithms, and incorporating these into specialized analysis workflows. The successful candidate will work closely with other members of the Epigenomic Centers and with the wider informatics team and collaborating scientists at the Innovation Centre and beyond.

    Duties/Responsibilities: To develop ad-hoc bioinformatics solutions for the analysis of complex genomic datasets, to analyze epigenome data using existing and extended software tools for collaborating scientists.
    1. Bioinformatics Software Developers:
    Create web-interfaces and software for a portal that will be developed as part of the EDCC. Data and meta-data from the CEEHRC initiative will flow into this portal, which will provide summary reports and tools for data visualization, distribution and advanced analysis. This portal will be build from two existing software resources, NANUQ and CBRAIN, which will be adapted for the CEEHRC initiative to facilitate access to epigenomics resources produced by the consortium.

    Duties/Responsibilities: Assisting in the design of repository software, protocols and web interfaces for the Epigenomics portal, working independently to implement and maintain bioinformatics software and repository, liaising with developers involved in other aspects of the project (LIMS, pipeline software) to achieve interoperability between modules.
    1. Post-Doctoral Fellows in Computational Epigenomics:
    A bioinformatics postdoctoral fellow will join a multidisciplinary team of biologists, genomicists, and bioinformaticians within the EMC. The project aims at mapping epigenetic marks (methylation, histone marks, gene expression) in healthy and patient-derived human tissue samples, and linking epigenetic variation to environmental, genetic and phenotypic variation.

    Duties/Responsibilities: Primary and higher order analysis of epigenomics data, deconvolve mixed signals due to imperfect sample collection, and integrate them in order to reveal the mechanisms at play and their phenotypic consequences. He/she will face a number of algorithmic and statistical challenges whose solutions will have the potential of being published as methods papers, while specific data analyses will be published in collaboration with the team.


    1. Bioinformatics Specialists:
    Qualifications: MSc (or BSc with 3+ years of work experience) in computational biology, mathematics, computer sciences, statistics or molecular biology. Demonstrated computer skills (e.g. programming in Perl, Python, C++, Java, mySQL) are required. Previous experience in processing and analyzing NGS data, genome annotation or in developing sequence analysis pipelines is necessary. Familiarity with databases and statistical computing programs, R and Matlab, would be useful.
    1. Bioinformatics Software Developers:
    Qualifications: BA or higher degree in computer science, software engineering or bioinformatics. Proficiency in Perl and Java. Demonstrated experience in web architecture and open source frameworks (Wicket Spring, WEB Services, Tomcat, Maven, Struts). Experience with relational database programming, including SQL, Hibernate, Ibatis, MySql). Familiarity with bioinformatics software tools is necessary.
    1. Post-Doctoral Fellows in Computational Epigenomics:
    Qualifications: The successful candidate will hold a Ph.D. in bioinformatics or closely related area and will have experience in regulatory genomics or epigenomics. Ability to manage and analyze large biological data sets coming from next generation sequencing is a must, as is working knowledge of algorithms and statistics, and the ability to interact and communicate with biologists.


    Start-date: immediate. Duration: up to 5 years.


    This opportunity is based in Montreal, Quebec, Canada at the McGill University and Genome Quebec Innovation Center.


    Applicants should submit a cover letter explaining their qualifications and their interest in these positions, a curriculum vitae and the names and contact information for three individuals who could provide letters of recommendation. Applications and any inquiries should be sent to emc.mcgill[at]

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