Genomics Data Scientist

Employer
Lawrence Berkeley National Laboratory
Location
Berkeley, California (US)
Salary
apply for more information
Posted
August 21 2020
Discipline
Life Sciences, Genomics
Position Type
Full Time
Organization Type
Govt.

Genomics Data Scientist - 90937

Organization: JG-Joint Genome Institute

Lawrence Berkeley National Lab’s (LBNL, https://www.lbl.gov/) Joint Genome Institute (JGI, https://jgi.doe.gov/) Division has an opening for an experienced Data Scientist to join the User Support Analysis group.

The User Support Analysis (USA) group performs custom analyses for research projects across the JGI. These include diverse experiment types (including resequencing, transcriptomics, epigenomics, single cell transcriptomics, nanopore sequencing, metabolomics, CRIPSR screens), and subject areas (plant, fungal, microbial and environmental genomics projects). Our group contributes to hundreds of projects from JGI’s user programs each year, and also provides substantial input on internal proof of principle projects using new technologies. Some recent examples include: population genomics in poplar (Nature genetics 46 (10), 1089-1096), functional genomics in bacteria (Nature 557 (7706), 503-509), single-cell transcriptomics in plants (Cell reports 27 (7), 2241-2247. e4).

The new Data Scientist will act as project lead within the USA group to implement custom analyses in support of new genomic technologies, and develop automated pipelines as projects scale. Work will be in one to two main subject areas, with a likely focus on resequencing analysis and epigenomics (though new technologies may take precedence). The Data Scientist will also use their expertise in computation and genome biology to contribute broadly to projects within the group and across the JGI in general. They will work closely with JGI experimental scientists to provide input on experiment design, develop analysis approaches, provide analysis reports and contribute to publications.

What You Will Do:

• Take a lead role in developing, debugging and managing an existing high throughput data analysis pipeline (e.g. resequencing, epigenomics)

• Serve as the project lead for implementing analysis software and pipeline development for new/emerging genomic technologies (e.g. single cell technologies, nanopore sequencing) as they are implemented at the JGI including set-up, troubleshooting and evaluation of new analysis tools.

• Perform custom analysis for research projects in led by scientists at both JGI and external institutions.

• Work with research scientists to understand project-specific analysis requirements and deliverables, implement custom analysis workflows and perform analyses in timely manner.

• Provide interpretation of analysis results and propose actions (both lab and analysis)

• Prepare analysis results for presentation and publication at internal meetings and to external

What is Required: 

• B.S. in a related technical/scientific field, or equivalent experience, and a minimum of 8 years related experience.

• Extensive experience in genomic analysis; sequencing analysis pipelines; significant research accomplishments, including a strong publication record.

• Proficiency in developing analysis software (Python/Perl/R) in a UNIX environment

• In-depth experience running high throughput analyses in a parallel computing environment (SGE, SLURM)

• Broad understanding of bioinformatics tools used for genome analysis, development of re-sequencing pipelines, and integration of varied large data sets.

• Demonstrated ability to troubleshoot highly complex technical problems; recommend and implement actions.

• Effective interpersonal, verbal and written communication skills, including public-speaking and presentation skills.

• Demonstrated ability to work well independently as well as a part of a diverse team.  

Additional Desired Qualifications:

Experience in experimental molecular biology and genomic technologies

• Web development experience

• Experience in MySQL database

• Java / C development experience

• Significant experience using AWS or other cloud platform

The posting shall remain open until the position is filled.

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.

• M-F, exempt (monthly paid) from overtime pay.

• 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.

• Work will be primarily performed at: Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA.

How To Apply

Apply directly online at http://50.73.55.13/counter.php?id=185068 and follow the on-line instructions to complete the application process.

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 takes up residence in the new, state-of-the-art Integrative Genomics Building (IGB) along with the U.S. Department of Energy Systems Biology Knowledgebase (KBase) 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?

Berkeley Lab (LBNL, http://www.lbl.gov/) 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- Click Here (https://hr.lbl.gov/).

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 (https://www.dol.gov/ofccp/PayTransparencyNondiscrimination.html).  Click here (https://www.dol.gov/ofccp/regs/compliance/posters/ofccpost.htm) to view the poster: "Equal Employment Opportunity is the Law".

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