The DOE Joint Genome Institute (JGI) in Walnut Creek, CA has an exciting opportunity available for an experienced Bioinformatics Analyst to support the transcriptome annotation and quantification of various projects within the JGI. Main responsibilities will involve running the in-house RNA-Seq pipeline for on-going RNA projects including working with research scientists to determine data analysis strategies, formatting input data for the pipeline, performing quality control tests and providing feedback to groups and collaborators. Will also collaborate with software engineers to make modifications to improve the pipeline and format and organize results for presentation and viewing by the JGI's collaborators and the wider scientific community. Will interact with internal and external collaborators to ensure efficient communication and project execution as well as thoroughly document analysis procedures and methods. Position reports to the Genome Analysis group leader.
The selected candidate will be hired at the Analyst 2 or 3 classification depending upon the candidate's level of experience and qualifications.
Specific Job Duties
Data Processing-
- Collect and organize RNA-Seq data from internal and public databases and from JGI collaborators, etc.
- Run the in-house developed RNA-Seq pipeline, format the output according to analysis needs.
- Quality control RNA-Seq data and provide feedback to data generator(s).
- Collaborate with software engineers to improve the stability and functionality of the RNA-Seq pipeline.
- Assess quality of input data and results and troubleshoot moderately complex systems issues.
- Maintain a work log of analyses and configurations performed and provide feedback to improve protocols, methods and tools for RNA-Seq analysis.
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 analysis
Essential Duties for the Bioinformatics Analyst 3 - In addition to the required duties for a level 2 Analyst, the level 3 Analyst will:
- Work at a higher level of independence and responsibility in carrying out assignments.
- Develop and implement novel algorithms to improve the analysis capabilities and output for the group.
- Troubleshoot more complex systems and data analysis problems.
- Report, in the form of peer-reviewed manuscripts, both the technical details in novel processing of the sequencing data, and the results of the analysis of such datasets.
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 two years of work experience, or an equivalent combination of education and experience.
- Proven understanding of genomics, molecular and microbiology.
- Expertise in standard bioinformatics tools for sequence analysis, including sequence alignment (BLAST, BLAT, etc) and sequence assembly (CAP3, etc.)
- Proficient with PERL and UNIX shell scripting languages.
- Strong problem-solving, decision-making, and analytical skills to independently make sound judgments and recommend creative solutions to moderately complex 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.
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 Bioinformatics, Computational Biology, or Life Sciences with an emphasis in bioinformatics/genomics, or related field with a minimum of five years of work experience, or an equivalent combination of education and experience (Master's or PhD degree preferred).
- Experience processing data from the Illumina sequencing platform, especially RNA-Seq.
- Ability to troubleshoot complex systems and data analysis problems.
Notes
This is a full-time two-year term appointment with the possibility of renewal and conversion to career contingent upon satisfactory performance, continued work, and funding availability. Classification will be at the 2 or 3 level depending upon the applicant's level of skills, knowledge, and relevant experience. The work schedule may include off-hours and/or weekends. Work will be performed at the DOE Joint Genome Institute (JGI), Production Genomics Facility (PGF) located in Walnut Creek, CA. Detailed information about the Joint Genome Institute can be found at: http://www.jgi.doe.gov.
How To Apply
To apply from this page, click the "Apply Now" link (above), and follow the on-line instructions to complete the application process. As part of the online application process, please submit a single attachment that includes both your resume and a cover letter. Please be sure to reference where you found out about the position.
Berkeley Lab is an affirmative action/equal opportunity employer committed to the development of a diverse workforce.
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