RESPONSIBILITIES:
Organization: GN-Genomics Division

The DOE Joint Genome Institute (JGI) in Walnut Creek, CA (a division of the Lawrence Berkeley National Lab) has an exciting research opportunity available for an experienced Bioinformatics Systems Analyst. Will analyze data and develop software to support gene finding, gene model curation, and functional annotation of predicted genes. The work will focus on the pipeline for re-annotation of microbial genomes with the goal of identifying low-quality gene models, generating reports of gene models requiring manual curation, summarizing the results of reannotation and preparing the files for submission to IMG database. Will participate in the improvement of functional annotation by analyzing sequence-similarity based protein families in order to identify families of equivalogs and generate models to represent them. Will work independently and as a contributing member of a dynamic, multidisciplinary team of biologists, bioinformaticians, computer scientists and software developers. Position reports to the Functional 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:
Essential-
Design, implementation and maintenance of a re-annotation pipeline for microbial genomes:

• Work with the IMG team to collect sequence files from GenBank and submit files to IMG-ER annotation pipeline.
• Submit annotated files to GenePRIMP analysis pipeline, review the results of automated gene model curation and prepare detailed reports of the genes requiring manual curation.
• Summarize the results of reannotation and prepare the files for integration into IMG database.
• Develop software and computational tools to further support gene finding, gene model curation, and functional annotation of predicted genes.
• Analyze the results of reannotation.

Improvement of functional annotation of predicted gene models:

• Analyze sequence similarity-based protein families, such as COGs or Pfams with respect to their annotation consistency
• Perform alignments and phylogenetic tree reconstructions and identify subfamilies of equivalogs and develop hidden Markov models for such families.
• Develop and enhance the software and algorithms supporting functional annotation.

Marginal-

• Develop and present updates and reports at group meetings.
• Support internal and external users with data exchange and custom data analysis.
• Participate in preparation of publications.

Essential duties for the Analyst 3 - In addition to the required duties for the Analyst 2, the Bioinformaticist 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:

• Bachelor's degree in Biology, Computer Science, Bioinformatics or a related field with a minimum of two years experience or an equivalent combination of education and experience.
• Demonstrated experience developing applications in Perl, familiarity with BioPerl.
• Demonstrated knowledge of the software and algorithms for multiple sequence alignment, domain identification, phylogenetic tree reconstruction and analysis, functional annotation.
• Demonstrated experience with processing and analysis of genomic and genetic data.
• Strong problem-solving, decision-making, and analytical skills to make sound judgments and recommend creative solutions to moderately complex problems.
• Strong interpersonal skills with the ability to work with scientific and administrative customers to define needs and priorities.
• Detail-oriented with strong organizational interpersonal skills to address user needs in an effective and timely manner.

PREFERENCES:

• Working knowledge of PostreSQL.

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

• Bachelor's degree in Bioinformatics, Computer Science or related field with a minimum of five years of work experience, or an equivalent combination of education and experience. Advanced degree preferred.
• Demonstrated expertise whole-genome data analysis and comparative genomics.
• Ability to troubleshoot complex systems and data analysis problems.

HOW TO APPLY:
Apply directly online at http://www.jobclub.com/banman/a.aspx?ZoneID=0&BannerID=1025&AdvertiserID=43&CampaignID=4022&Task=Click&SiteID=1&RandomNumber=660443 and follow the on-line instructions to complete the application process.

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