Organization: GN-Genomics

RESPONSIBILITIES:
The Plant Genomics Program at the DOE Joint Genome Institute (JGI), in Walnut Creek, CA, has two openings for Bioinformatics Analysts to contribute to our Plant Genome Annotation efforts. Under broad supervision, will work within the Phytozome group to generate new as well as refined plant genome annotations and facilitate the acquisition, incorporation and display of functional, genetic and other genome-anchored data in Phytozome. Responsibilities include: collecting data for genome-specific tuning of the plant annotation pipeline, assessing the quality of input data, incorporating the data into the Phytozome visualization environment, running and troubleshooting the annotation pipeline, analyzing predicted genes and functional assignments. Will interact with internal and external collaborators and the JGI Project Management group at all stages of annotation projects to ensure accurate and timely completion of projects. Position will report to the Plant Annotation Group Lead.

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:
Genome Annotation-

• Responsible for annotation and analysis of plant genomes.
• Collect data for genome annotation (from internal or public databases, collaborators, etc).
• Configure, run and troubleshoot genome annotation tools.
• Assess quality of input data and produced predictions.
• Apply and refine methods for mapping annotations between assembly versions, for identifying gene splits and merges, and assigning gene family names and functions.
• Apply analytical skills and creativity to troubleshoot and solve problems of a moderate scope.
• Provide feedback to improve protocols, methods and tools for genome annotation.
• Develop and present reports for annotated genomes, and participate in writing of scientific articles describing the genome annotation and related analyses.

Data Management-

• Ensure integrity and up-to-date status of internal (results of pipeline analyses) and external (e.g., GO, PFAM, SuperFAM. UniProt databases, externally-generated genomic assemblies and annotations) data required for the genome annotation system.
• Work with internal and external collaborators to make genome-anchored data available via the Phytozome system.
• Troubleshoot data parsers.

Essential Duties for the Analyst 3 - In addition to the required duties for a level 2, the Analyst 3 will:

• Work at a higher level of independence and responsibilities in carrying out assignments.
• Develop and implement substantial, known or novel, computational methods to improve the analysis capabilities and output of the group.
• Troubleshoot more complex systems and data analysis problems.

REQUIREMENTS:
Key Success Factors:
Essential-

• Typically requires a Bachelor's degree in Biology, Life Sciences, Bioinformatics, Computer Science or related field with a minimum of two years of work experience, or an equivalent combination of education and experience.
• Demonstrable understanding of 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 and Perl
• Strong problem-solving, decision-making, and analytical skills to independently make sound judgments and recommend creative solutions to 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

Preferred-

• Master's degree or higher in Biology, Bioinformatics, Life Sciences, Computer Sciences, or related field preferred
• Experience configuring and troubleshooting Gbrowse/GMOD components
• Knowledge of Plant Genetics
• Knowledge of Python

Essential Qualifications for the Systems Analyst 3 - In addition to the required qualifications for a level 2, the Analyst 3 will have:

• Bachelor's degree in Biology, Life Sciences, Bioinformatics, Computer Science or related field with a minimum of five years of work experience, or an equivalent combination of education and experience
• Advanced SQL, Perl or Java software skills
• Experience deploying, configuring and debugging GMOD components such as Jalview, BioMart, GBrowse
• Ability to troubleshoot complex systems and data analysis problems

HOW TO APPLY:
Apply directly online at http://bit.ly/lbl73542Bioinformatics and follow the instructions to complete the application process.

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