Bioinformatics Systems Analyst 3- Sequencing Technology Group

Lawrence Berkeley National Laboratory
Job Location: 
Walnut Creek, CA
Job Description: 

Bioinformatics Systems Analyst 3- Sequencing Technology Group - 78623
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 a motivated Bioinformatics Systems Analyst. As part of the Sequencing Technology group, will develop computational tools to perform sequence analysis for research and development projects surrounding genome, transcriptome and chromatin characterization. Duties will include evaluating the nature of the biological challenges, design of molecular biological approaches and short read sequencing data, as well as performing thorough analysis of DNA sequence data produced by next generation sequencing machines and various library types. Will be involved in the development and implementation of analysis pipelines, and providing technical and analytical interpretation of data. Will also be responsible for improving existing data analysis tools and implement new tools for general use. The 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. Position reports to the Sequencing Technology Group analysis work lead.

Specific Job Duties
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.
• Familiar with the different types of data and approaches for chromatin (epigenetic) interrogation, transcriptome characterization and genome assembly.
• Feedback data quality 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 the 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.

Key Success Factors
• Typically requires a B.S. in Bioinformatics, Computer Science, Biology or a related field and at least five years of experience in genome bioinformatics and an equivalent combination of education and experience. Master’s Degree / PhD preferred.
• Experience with the collection, recording and analysis of experimental data.
• Expertise with genome assemblers, DNA sequencing, short read alignment programs and 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.
• Demonstrated experience processing large volumes of data, whole-genome data analysis, phylogenetics and comparative genomics.
• Proficiency with programming languages including Perl/Python, C/C++, Java or others in a Unix environment with demonstrated familiarity with software engineering as well as 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.
• Strong 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.

• Knowledge and experience with laboratory DNA sequencing technologies and genetics, or related field or equivalent experience 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. Detailed information about the Joint Genome Institute program can be found on the World Wide Web at the following location:

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.

Contact Information: 

How To Apply
Apply directly online at and follow the on-line instructions to complete the application process.