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 jgiThese 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 projectsSome 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), 2241-2247E4).
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 scaleWork 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 generalThey 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.sIn 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.
Desired qualifications:
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.
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 may be subject to a background checkAny convictions will be evaluated to determine if they directly relate to the responsibilities and requirements of the positionHaving 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, caWe 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 peopleNearly 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 challengesToday, after garnering 13 nobel prizes, berkeley lab has sustained and grown that tradition of open, interdisciplinary team science, exemplified by how the u.sDepartment of energy joint genome institute (jgi) addresses the most pressing energy and environmental challenges using integrative genome science approachesJgi takes up residence in the new, state-of-the-art integrative genomics building (igb) along with the u.sDepartment of energy systems biology knowledgebase (kbase) to expand the frontiers of energy and environmental science in partnership with the worldwide community of researchersWill you join us and be a critical part of our next ground-breaking discoveries?
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 employerWe heartily welcome applications from women, minorities, veterans, and all who would contribute to the lab’s mission of leading scientific discovery, inclusion, and professionalismIn 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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