Staff Data Scientist

Location: San Francisco Bay Area, CA

*** Mention DataYoshi when applying ***

Lawrence Berkeley National Lab’s (LBNL), Environmental Genomics and Systems Biology Division has an opening for a Data Scientist to join the team.

In this exciting role, you will develop methods for extracting information and knowledge from a variety of structured and semi-structured sources, building integrated ontologies and knowledge graphs. You will also develop methods for predicting the effects of genomic variants, leveraging genomic, phenomic, and pathway resources. You will work closely with software and infrastructure groups to integrate methods into production systems, including the Exomiser variant prioritization tool.

What You Will Do:
  • Design, lead and conduct computational approaches to information and knowledge extraction from heterogeneous methods, including relation extraction from literature, and advanced extract/transform/load (ETL) dataflows.
  • Develop and help operationalize methods to automatically align and merge ontologies and knowledge graphs.
  • Develop approaches that leverage ontologies and knowledge graphs for prediction and discovery of new gene functions and gene phenotype associations; methods that use causal mechanistic knowledge from the Gene Ontology and pathway databases to assist in variant prioritization.
  • Participate in and help guide the development of data and analysis portals, and help develop extensions to the Exomiser variant prioritization tool.
  • Help develop and coordinate core standards and ontologies with a broad range of stakeholders.
  • Prepare results for publication and make presentations at seminars and scientific meetings.
  • Independently provide creative problem solving and work within a larger group of analysts/scientists to address and resolve complex challenges, questions, and issues.

What is Required:
  • Bachelor’s degree in data science, bioinformatics, or related field and a minimum of 8 years of relevant experience; or a Master’s degree and a minimum of 6 years of relevant experience; or a Ph.D. and a minimum of 3 years of relevant experience; or equivalent experience.
  • Demonstrated experience in information extraction and automated knowledge graph construction from structured and unstructured data sources, including the literature, curated databases, and health record data / clinical reports.
  • Demonstrated experience building and applying biomedical ontologies.
  • Expertise with pathway or interaction databases and network analysis.
  • Demonstrated experience working in Python or similar languages.
  • Familiarity with version control and continuous integration tools, containers, databases, open software and open science principles, and the capability to learn and adapt to new technologies.
  • Experience in preparing information for publications, presentations, seminars, and scientific meetings.
  • Ability to work effectively both independently and in a diverse team environment.
  • Demonstrated ability to conduct and perform individual and collaborative research.
  • Knowledge of ontology and knowledge engineering frameworks, APIs, languages, and techniques (e.g., OWLAPI, Jena, SPARQL).

Desired Qualifications:
  • Experience with cloud compute environments and workflow systems.
  • Experience with modeling complex biological data.
  • Familiarity with genomics, transcriptomics, metabolomics, proteomics.
  • Familiarity with microbial genomics.

For full consideration, please apply by May 27, 2021.

  • This is a full time, 2 years, 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.
  • Berkeley Lab is committed to
  • This position is open to fully remote work as long as you are located in the US.

Learn about us!

Environmental Genomics and Systems Biology

Mission: Linking genome biology to ecosystem dynamics.
Vision: Sustainable solutions to energy and environmental challenges developed through mechanistic understanding of ecosystem dynamics.
Approach: We develop systems-level models using integrated molecular observation and controlled manipulation of model organisms and defined biomes to design and test interventions that promote beneficial outcomes.

Berkeley Lab
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 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.

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.

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

*** Mention DataYoshi when applying ***

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