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    Opportunity: Bioinformatics Systems Analyst 3 -- Sequencing Technology Group (#78623) @ DOE Joint Genome Institute -- Walnut Creek, CA (US)
    Submitted by Hannah Kuhns; posted on Tuesday, August 19, 2014


    The DOE Joint Genome Institute (JGI) in Walnut Creek, CA (a division of the Lawrence Berkeley National Lab) has an exciting opportunity available for a Bioinformatics Systems Analyst to perform large-scale data analysis and develop computational tools for R&D projects surrounding genome, transcriptome and chromatin characterization.

    This role will evaluate the nature of biological challenges, design of molecular biological approaches and short read sequencing data, as well as thoroughly analyze DNA sequence data produced by next generation sequencing machines and various library types. Will develop and implement analysis pipelines, and provide technical and analytical data interpretation. Will also be responsible for improving existing data analysis tools and implement new tools for general use.

    This position will have a significant role in defining biological significance of the data, will work with various JGI groups on data analysis projects and facilitate transfer of knowledge of technologies and applications to JGI staff. May also provide custom analysis support to external collaborators. Will report to the Sequencing Technology Group analysis work lead.

    Key Responsibilities:
    Sequence Analysis and Interpretation
    • Perform quality analysis of sequence data and assist others in interpretation of analyzed data.
    • Extract new biological insights and phenomenon from the analyzed results.
    • Independently and proficiently utilize assembled genomes, various alignment tools, visualization tools, and other genome interrogation and analysis software.
    • Be familiar with the different types of data and approaches for chromatin (epigenetic) interrogation, transcriptome characterization and genome assembly.
    • Provide data quality feedback to wet-lab scientists and sequencing team members.
    • Provide clear and concise professional reports on data analysis and results.
    • Present technical and analytical status in weekly meetings.
    • Contribute to publications on experimental data generated by the new sequencing approaches.
    Bioinformatics Tool Adaptation and Improvement
    • Adapt and improve bioinformatics tools to process sequencing data generated by various R&D library types and projects.
    • Participate in the design and development of new tools for new R&D projects.
    • Refine and improve existing analytical tools.
    • Design and build new tools to analyze sequences of various research projects.
    • Troubleshoot system and data analysis problems and provide feedback on areas of improvement for existing tools.
    • Provide technical support to detect issues and improve library protocols.
    • Provide high quality documentation for newly developed software and approaches.


    • Demonstrated experience processing large volumes of data, whole-genome data analysis, phylogenetics and comparative genomics.
    • Typically requires a B.S. in Bioinformatics, Computer Science, Biology or a related field and at least five years of experience in genome bioinformatics, or an equivalent combination of education and experience. Master's Degree / PhD preferred.
    • Experience with the collection, recording and analysis of large-scale experimental data.
    • Expertise with genome assemblers, DNA sequencing, short read alignment programs and large-scale data analysis.
    • Demonstrated knowledge and experience with standard bioinformatics methods and tools, including sequencing databases.
    • Familiarity with various molecular biology procedures, including DNA sequencing, PCR and cloning.
    • Proficiency with Perl/Python, C/C++, Java or others in a Unix environment; familiarity with software engineering and web-based interface.
    • Experience with SQL, MySQL, Oracle or other RDBMs.
    • Experience with database structure and management.
    • Familiarity with statistical tools, applied statistics and interpretation of data.
    • Experience applying machine learning, pattern recognition, or modeling to scientific problems.
    • Demonstrated analytical skills sufficient to troubleshoot system and data analysis problems and make recommendations.
    • Proficient organizational and record-keeping skills.
    • Effective oral and written communication and interpersonal skills.
    • Ability to work independently and as a team member in a diverse team environment.
    • Ability to handle multiple tasks in parallel while working on a large number of projects.
    • Ability to follow laboratory safety guidelines.
    • Preferred - Knowledge and experience with laboratory DNA sequencing technologies and genetics, or related field or equivalent experience preferred.
    • Preferred - Experience in a multi-disciplinary scientific or production environment.


    This is a 1-year term appointment with the possibility of renewal and with the possibility of conversion to career based upon satisfactory job performance, continuing availability of funds, and ongoing operational needs. Work will be performed at the DOE Joint Genome Institute (JGI) in Walnut Creek, CA. Job may require occasional travel, weekend, and after-hours work. A background check is required.


    Apply directly online at[...]13174 and follow the on-line instructions to complete the application process.


    Rapid technological advances in genomics have transformed modern biology. From its inception, the Department of Energy Joint Genome Institute has been at the forefront of large-scale sequence-based science. Learn more at This position is part of the Sequencing Technologies Group that provides end-to-end support for the DOE JGI production sequencing activities. Our group applies state-of-the-art automation-based processing technologies coupled with high throughput sequencing operation to support our global DOE research community. Learn more about Genomic Technologies at the JGI.


    Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, age or protected veteran status.

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