[Next-Generation Sequencing Book]
  • [Photo] Bill Cannan • April 30, 2012
    Organization: GN-Genomics

    RESPONSIBILITIES

    The DOE Joint Genome Institute (JGI) in Walnut Creek, CA (a division of the Lawrence Berkeley National Lab) has an exciting Software Developer position available to support the Genomic Technologies group. Will work with a team of computational biologists, software engineers and bioinformaticians and focus on the transcriptome related research projects from JGI internal and external collaborators. Main responsibilities will involve applying existing, or research developed novel bioinformatics solutions for various transcriptomics problems. Will work closely with research scientists to determine data analysis strategies, perform quality control tests and provide feedback to groups and collaborators.

    Will also collaborate with software engineers to improve the performance of software pipelines and organize results for presentations and publications to benefit a wider scientific community. This is a very exciting opportunity to apply one's bioinformatics expertise to great scientific problems, as well as learn cutting edge sequencing and computational technologies, including second and third-generation sequencing technologies, cloud computing, etc. Reference: Nature Reviews Genetics 12, 671-682 (October 2011) and Nature Reviews Genetics 10, 57-63 (January 2009).

    Specific Job Duties:
    Data Processing-
    • Apply existing open-source bioinformatics tools to solve transcriptome related problems.
    • Research and develop novel bioinformatics solutions for transcriptomics studies in plants and microbial communities.
    • Collaborate with software engineers to improve the stability and functionality of existing RNA-Seq software pipelines
    • Collaborate with new sequencing technologies group and develop novel informatics tools for transcriptomics.
    • Apply analytical skills and creativity to solve diverse and challenging problems.
    • Assess quality of input data and results and troubleshoot moderately complex systems issues.
    • Maintain a work log of analyses and configurations performed and present the results.
    User Support-
    • Communicate with internal and external users regarding current projects including timelines and updates.
    • Develop and present updates and reports for other groups.
    • Support internal and external collaborators with data exchange and custom data analyses.

    REQUIREMENTS

    Key Success Factors:
    Essential-
    • Bachelor's degree in Bioinformatics, Computational Biology, or Life Sciences with an emphasis in bioinformatics/genomics, or a related field with a minimum of five years of work experience, or an equivalent combination of education and experience
    • Proven understanding of genomics, transcriptomics, molecular and microbiology
    • Demonstrated expertise in bioinformatics tools for next-generation sequence analysis, including short read aligners, short read assemblers
    • Proficient in PERL and UNIX shell scripting languages
    • Strong problem-solving, decision-making, and analytical skills to independently make sound judgments and recommend creative solutions to solve diverse and challenging problems
    • Detail-oriented with strong organizational skills to address user needs in an effective and timely manner
    • Excellent communication skills, ability to work with a team with diverse experience
    Marginal-
    • Experience with statistical data analysis using R/Matlab
    • Experience in large scale data analysis and parallel computing
    • Experience in visualization genomics data using genome browsers
    • Knowledge in project management

    HOW TO APPLY

    Apply directly online at http://bit.ly/lbl74482Bioinformatics and follow the instructions to complete the application process.

    POLICY

    Berkeley Lab is an affirmative action/equal opportunity employer committed to the development of a diverse workforce.

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