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Information Technology
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JG-Joint Genome Institute
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92715 Requisition #

Lawrence Berkeley Lab’s (LBL) Joint Genome Institute (JGI) has an opening for a Genome Annotation Scientist (Data Scientist) to join the team.

 

Take advantage of an exciting opportunity to employ your scientific and computational skills as part of  the JGI Plant Science Program, the world’s largest producer of high-quality plant genome assemblies and annotations.  In this role, you will work at the JGI within the Plant Comparative Analysis group to generate new as well as improved plant genome annotations and facilitate the acquisition, incorporation, and display of functional, genetic, and other genome-anchored data in the Phytozome Genomics Portal (https://phytozome-next.jgi.doe.gov). Your responsibilities include the curation and assessment of relevant plant transcriptomic datasets and assembled genomes, running and troubleshooting the annotation pipeline, analyzing the resulting gene predictions in coordination with internal and external scientists, evaluating genome-specific modifications and tuning of the pipeline components,  and incorporating the data into the Phytozome portal.  

 

What You Will Do:

  • 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.
  • Assist with migration and deployment of annotation tools to available computational platforms.
  • Assess the quality of input data and the resulting gene predictions. 
  • Apply analytical skills and creativity to troubleshoot and solve problems of diverse scope.
  • Provide feedback to improve protocols, methods, and tools for genome annotation.
  • Develop and present reports for annotated genomes.
  • Ensure integrity and up-to-date status of internally generated and externally acquired datasets (assemblies, annotations, comparative datasets, etc.).
  • Work with internal and external collaborators to make data available via the Phytozome portal.
  • Troubleshoot data parsers.

 

Additional Responsibilities as needed:

  • Modify/extend gene prediction/filtering algorithms to accommodate changes in assembly and transcriptome quality, and organism-specific needs.
  • Train users on the use of the Phytozome suite of tools for Comparative Plant Genomics.
  • Provide internal and external users with custom data analyses.
  • Assist with annotation-related sections of manuscript preparation.
  • Take lead role migrating annotation tools to new computational platforms
  • Modify/extend gene prediction/filtering algorithms to accommodate changes in assembly and transcriptome quality, and organism-specific needs.
  • Publish papers describing JGI Plant program annotation methods and workflows, with comparison to other systems.

 

 

What is Required:

  • Typically requires a Bachelor’s degree in Biology, Life Sciences, Bioinformatics, Computer Science or related field with a minimum of five years of related experience, or an equivalent combination of education and experience. 
  • Demonstrable experience performing eukaryotic genome annotation.
  • Demonstrable understanding of genomics and molecular biology.
  • Demonstrated experience with biological databases such as UniProt, InterPro, NCBI, Ensembl, Gramene. 
  • Familiarity with major genomics ontologies such as SO (Sequence Ontology) and GO (Gene Ontology).
  • Experience with loading/querying databases and running programs in a UNIX environment.
  • Knowledge of standard bioinformatics methods and tools for gene and protein sequence analysis.
  • Solid working knowledge of SQL and Perl/Python.
  • 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 and the ability to prioritize and schedule across multiple projects.
  • Ability to work in a diverse team environment.

 

 

Desired Qualifications:

  • Master’s degree or higher in Biology, Bioinformatics, Life Sciences, Computer Sciences, or related field with a minimum of three years of related experience.  
  • Experience with GMOD components such as CHADO, JBrowse, BioMart.
  • Experience running workflows under Cromwell/WDL or NextFlow.
  • Experience running large-scale computations with SLURM, SGE or similar job schedulers 
  • Experience running data and compute intensive computations on AWS or Google Cloud.
  • Strong knowledge in Genetics in general, plant genetics in particular.
  • Knowledge of good SW development practices including version control and testing.
  • Master’s degree or higher in Biology, Bioinformatics, Life Sciences, Computer Sciences, or related field with a minimum of six years of related experience.
  • Extensive experience in the annotation of multiple plant genomes.
  • Experience supervising and coordinating the work of other team members.

 

 

Notes:

  • This is a full time, 2 year, term appointment with the possibility of extension or conversion to Career appointment based upon satisfactory job performance, continuing availability of funds and ongoing operational needs.
  • This position will be hired at a level commensurate with the business needs; and skills, knowledge, and abilities of the successful candidate.
  • This position may be subject to a background check. Any convictions will be evaluated to determine if they directly relate to the responsibilities and requirements of the position. Having a conviction history will not automatically disqualify an applicant from being considered for employment.
  • Berkeley Lab is committed to Inclusion, Diversity, Equity and Accountability (IDEA) and strives to hire individuals from different backgrounds, experiences, and perspectives who share these same values and commitments.
  • Work will be primarily performed at Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA.

 

Learn About Us:

JGI & Berkeley Lab: A View to Fuel Innovative Science in the Public Interest

They say it’s all about location and Berkeley Lab has it all: a view above the San Francisco Bay, cool breezes, and world-class multidisciplinary science within a diverse and respectful research ecosystem of 5,000 people. Nearly 90 years ago, Ernest Orlando Lawrence, the inventor of the cyclotron, brought physicists, biologists, engineers and mathematicians together in Berkeley above the University of California campus to tackle the most urgent scientific challenges. Today, after garnering 13 Nobel Prizes, Berkeley Lab has sustained and grown that tradition of open, interdisciplinary team science, exemplified by how the U.S. Department of Energy Joint Genome Institute (JGI) addresses the most pressing energy and environmental challenges using integrative genome science approaches. JGI is based in the new, state-of-the-art Integrative Genomics Building (IGB) alongside the U.S. Department of Energy Systems Biology Knowledgebase (KBase), working to expand the frontiers of energy and environmental science in partnership with the worldwide community of researchers. Will you join us and be a critical part of our next ground-breaking discoveries?

 

(LBNL) addresses the world’s most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science.

Working at Berkeley Lab has many rewards including a competitive compensation program, excellent health and welfare programs, a retirement program that is second to none, and outstanding development opportunities.  To view information about the many rewards that are offered at Berkeley Lab-

 

Equal Employment Opportunity: Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. Berkeley Lab is in compliance with the

 

Lawrence Berkeley National Laboratory encourages applications from women, minorities, veterans, and other underrepresented groups presently considering scientific research careers.

 

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Equal Employment Opportunity: Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. Berkeley Lab is in compliance with the Pay Transparency Nondiscrimination Provision under 41 CFR 60-1.4. Click here to view the poster and supplement: "Equal Employment Opportunity is the Law."

 

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The Lawrence Berkeley National Laboratory provides accommodation to otherwise qualified internal and external applicants who are disabled or become disabled and need assistance with the application process. Internal and external applicants that need such assistance may contact the Lawrence Berkeley National Laboratory to request accommodation by telephone at 510-486-7635, by email to eeoaa@lbl.gov or by U.S. mail at EEO/AA Office, One Cyclotron Road, MS90R-2121, Berkeley, CA 94720. These methods of contact have been put in place ONLY to be used by those internal and external applicants requesting accommodation.