Senior Bioinformatics Engineer

Berkeley Lab’s (LBNL) Department of Energy’s (DOE) Joint Genome Institute (JGI) is looking for a Senior Bioinformatics Engineer to join their Plant Comparative Analysis Group!

In this exciting role, you will develop and run state-of-the-art plant genome analysis pipelines, and optimize and maintain genomic databases, warehouses and data delivery capabilities that can accommodate hundreds to thousands of complete plant genomes and their associated data sets. You will be responsible for the design, development, testing and integration of existing as well as new database systems and downstream genome analysis pipelines. Reporting to the Phytozome Group Lead, you will provide technical interpretation and guidance on complex and broad reaching genomic data processing and storage problems.

The JGI’s mission is to provide the global research community with access to the most advanced integrative genome science capabilities in support of the DOE”s research mission to solve the world’s evolving energy and environmental challenges. The JGI supports projects in genome sequencing, synthesis, transcriptomics, metabolomics, and natural products in plants, fungi, algae, and microorganisms. This position is headquartered on the Lab’s main site at the Integrative Genomics Building (IGB) (Virtual Tour).

This position has an anticipated start date of May 15, 2024.

What You Will Do:

• Populate and maintain existing plant genome data warehouses and reference databases.
• Develop, run, and maintain plant genome data analysis pipelines to provide proteome classification, gene expression, and gene family analysis of newly annotated JGI genomes and newly integrated externally sourced genomes. 
• Refine and optimize data access application programming interfaces (APIs) to support the Phytozome website and internal analysis pipelines. 
• Ensure data is submitted to GenBank and shared with collaborators in a timely manner.
• Explore new database technologies in order to accommodate a potential 10x increase in plant genomics data footprint.
• Communicate effectively with Generic Model Organism Database (GMOD) and other open-source bioinformatics communities (e.g., InterMine, Chado) to influence development priorities in line with Plant Program needs.
• Deploy and maintain automated monitoring of Phytozome web components and backend data systems.

What is Required:

• A Bachelor’s Degree (or equivalent knowledge/training) in Bioinformatics, Computer Science, Data Science, or related field and a minimum of 8 years of demonstrated success implementing and maintaining large scale genome sequence data analysis systems with large complex technological programs or an equivalent combination of education and experience.
• Demonstrated experience with standard genome analysis workflows, integrating third party and internal software, and supporting genomic analysis across multiple projects. 
• Experience with Python including good software development practices and database design and optimization.
• Experience with database schema design, administration, and SQL optimization.
• Demonstrated analytical skills including problem-solving, decision-making, critical thinking to provide recommendations and creative solutions to complex problems.
• Excellent oral and written communication skills including experience organizing information and presenting to technical and non technical audiences.
• Demonstrated interpersonal skills including experience collaborating with multiple diverse technical and non-technical stakeholders internal and external to the organization to achieve project goals.

Desired Qualifications:

• An Advanced Degree (or equivalent knowledge/training) in Bioinformatics, Computer Science, Data Science, or related field.
• Experience with Eukaryotic genome annotation.
• Experience designing and deploying large scale genome data analysis systems on appropriate computational infrastructure.  
• Experience with genomic data warehousing systems.
• Programming experience in Java and/or Perl.
• Experience maintaining and debugging genomic data warehouse systems like InterMine and BioMart.
• Experience with PostgreSQL and MySQL, D3, and other data visualization libraries.
• Experience with system monitoring tools like Prometheus.
• Experience with Kubernetes and cloud computing environments like AWS and Google Cloud.

Notes:

• For full consideration, please apply with a resume by April 29, 2024.
• This is a full time, exempt from overtime pay (monthly paid), 2 year (benefits eligible), 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 is expected to pay $126,900 - $158,628 per year for job code C70.3, which fits within the full salary range of $126,900 - $174,480 per year. Salary for this position will be commensurate with the final candidate’s qualification and experience, including skills, knowledge, relevant education, certifications, and aligned with the internal peer group.
• 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.
• This position is eligible for a hybrid work schedule - a combination of teleworking and performing work on site at Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA 94720. Individuals working a hybrid schedule must reside within 150 miles of Berkeley Lab. Work schedules are dependent on business needs.

Learn About Us:

Berkeley Lab (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 16 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- Click Here.

Berkeley Lab is committed to Inclusion, Diversity, Equity and Accountability (IDEA) and strives to continue building community with these shared values and commitments.

Berkeley Lab is an Equal Opportunity and Affirmative Action Employer. We heartily welcome applications from women, minorities, veterans, and all who would contribute to the Lab’s mission of leading scientific discovery, inclusion, and professionalism. In support of our diverse global community, all qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. 

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