Lawrence Berkeley National Lab's (LBNL) Joint Genome Institute (JGI) Division has an opening for a Staff Data Scientist to join the team.
In this exciting role, you will work in the JGI Division as part of the User Support Analysis (USA) group to perform custom analyses for research projects across the JGI. These include diverse experiment types including resequencing, transcriptomics, epigenomics, single cell transcriptomics, nanopore sequencing, metabolomics and CRISPR screens, and subject areas including plant, fungal, microbial, and environmental genomics projects. Some recent examples of projects 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).
You will act as a 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 possible focus areas including transcriptomics, epigenomics or metabolomics (though new technologies may take precedence). You 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., transcriptomics, 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 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 a timely manner.
Provide interpretation of analysis results and propose actions (both lab and analysis).
Prepare analysis results for presentation and publication at internal and external meetings.
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, and significant research accomplishments including a strong publication record.
In-depth experience running high throughput analyses in a parallel computing environment (SGE, SLURM).
Proficiency in developing analysis software (Python/Perl/R) in a UNIX environment.
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.
Experience in experimental molecular biology and genomic technologies.
Experience in metabolomics data analysis.
Web development experience.
Experience in MySQL database.
Java / C development experience.
Significant experience using AWS or other cloud platforms.
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 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.We are also open to fully remote workers.
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 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.
In the world of science, Lawrence Berkeley National Laboratory (Berkeley Lab) is synonymous with excellence. Thirteen scientists associated with Berkeley Lab have won the Nobel Prize. Fifty-seven Lab scientists are members of the National Academy of Sciences (NAS), one of the highest honors for a scientist in the United States. Thirteen of our scientists have won the National Medal of Science, our nation's highest award for lifetime achievement in fields of scientific research. Eighteen of our engineers have been elected to the National Academy of Engineering, and three of our scientists have been elected into the Institute of Medicine. In addition, Berkeley Lab has trained thousands of university science and engineering students who are advancing technological innovations across the nation and around the world. Berkeley Lab is a member of the national laboratory system supported by the U.S. Department of Energy through its Office of Science. It is managed by the University of California (UC) and is charged with conducting unclassified research across a wide range of scientific disciplines. Located on a 200-acre site in the hills above the UC Berkeley campus that offers spectacular... views of the San Francisco Bay, Berkeley Lab employs approximately 4,200 scientists, engineers, support staff and students. Its budget for 2011 is $735 million, with an additional $101 million in funding from the American Recovery and Reinvestment Act, for a total of $836 million. A recent study estimates the Laboratory's overall economic impact through direct, indirect and induced spending on the nine counties that make up the San Francisco Bay Area to be nearly $700 million annually. The Lab was also responsible for creating 5,600 jobs locally and 12,000 nationally. The overall economic impact on the national economy is estimated at $1.6 billion a year. Technologies developed at Berkeley Lab have generated billions of dollars in revenues, and thousands of jobs. Savings as a result of Berkeley Lab developments in lighting and windows, and other energy-efficient technologies, have also been in the billions of dollars. Berkeley Lab was founded in 1931 by Ernest Orlando Lawrence, a UC Berkeley physicist who won the 1939 Nobel Prize in physics for his invention of the cyclotron, a circular particle accelerator that opened the door to high-energy physics. It was Lawrence's belief that scientific research is best done through teams of individuals with different fields of expertise, working together. His teamwork concept is a Berkeley Lab legacy that continues today.