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    Opportunity: BIOINFORMATICS Systems Analyst 2/3 - Fungal Genomics (#74816) @ DOE Joint Genome Institute--Walnut Creek, CA (US)
    Submitted by Hannah Kuhns; posted on Friday, June 29, 2012


    Organization: GN-Genomics

    The DOE Joint Genome Institute (JGI) in Walnut Creek, CA (a division of the Lawrence Berkeley National Lab) has an exciting opportunity available for an experienced Bioinformatics Systems Analyst. Will serve as a Bioinformatics Analyst 2 or 3 to annotate and analyze genomes for the MycoCosm, Genomic Encyclopeda of Fungi, and 1000 Fungal Genomes projects ( and provide support to JGI user communities. Responsibilities include; collecting data for genome annotation, genome annotation and analysis using JGI annotation pipeline and other tools, assessing quality of input data and predicted genes and annotations. Will provide user support for internal and external collaborators at every stage of annotation projects to ensure communication, user training, data distribution and analysis. Will contribute to writing manuscripts and developing new tools and protocols for genome annotation and analysis. Position will report to the Fungal Genomics Program Head.

    Specific Job Duties
    • Responsible for large-scale annotation and analysis of fungal genomes.
    • Collect and assess quality of data for genome annotation (from internal or public databases, collaborators, etc) and determine appropriate annotation strategy
    • Configure, run, and troubleshoot genome annotation and analysis tools including JGI annotation pipeline.
    • Analyze produced predictions, perform manual curation and large-scale computational analysis of predicted gene models and annotations.
    • Improve protocols, methods and tools for genome annotation and analysis.
    • Develop, present, and contribute to publications reports for annotated genomes
    • Closely work with user communities to enable community-wide genome analysis, train users on the use of JGI Genome Portal MycoCosm and provide guidelines for genome analysis and manual curation.
    • Support internal and external collaborators with data exchange and custom data analysis.
    • Work on validation and optimization of the annotation process, annotation pipeline, tools and methods for gene prediction, annotation and analysis.
    • Develop protocols and scripts for custom data management, analysis, and distribution.
    Essential Duties for the Systems Analyst 3:
    In addition to the required duties for the Systems Analyst 2, the Systems Analyst 3 will:
    • Work at a higher level of independence and responsibilities in carrying out assignments.
    • Train new group members on use of annotation tools.
    • Directly contribute to genome publications through analysis of annotated genomes.
    • Develop and implement known or novel computational methods to improve gene prediction, annotation, and analysis of complete genomes and integrate them into production annotation process and tools.


    Key Success Factors:
    • Bachelor's degree in Biology, Life Sciences, Bioinformatics or related field with a minimum of two years of work experience, or an equivalent combination of education and experience.
    • Background in fungal biology, genomics and molecular biology.
    • Knowledge of standard bioinformatics methods and tools for gene and protein sequence analysis.
    • Demonstrated experience with biological databases.
    • Experience in annotation and analysis of genomes, pathways and families of genes and proteins.
    • Experience with databases and running programs in a UNIX environment.
    • Working knowledge of SQL, Perl or Python.
    • Strong problem-solving, decision-making, and analytical skills to independently make sound judgments and recommend creative solutions to moderately complex problems.
    • Strong interpersonal, communication, and presentation skills to effectively work with large user communities.
    • Detail-oriented with strong organizational skills to address user needs in an effective and timely manner.
    • Ability to work in a diverse team environment.
    Essential Qualifications for the Systems Analyst 3:
    In addition to the required qualifications for the Systems Analyst 2, the Systems Analyst 3 will have:
    • Bachelor's degree in Biology, Life Sciences, Bioinformatics or related field with a minimum of five years of work experience, or an equivalent combination of education and experience. Advanced degree (PhD and/or MS) preferred.
    • Experience processing and troubleshooting large volumes of data, whole-genome data analysis, phylogenetics, and comparative genomics.
    • Ability to troubleshoot complex systems and data analysis problems.


    Apply directly online at[...]atics and follow the instructions to complete the application process.


    Berkeley Lab is an Affirmative Action/Equal Employment Opportunity employer committed to the development of a diverse workforce.

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