Genome Analysis Data Scientist

Company: College of Charleston
Location: Berkeley
Posted on: November 18, 2023

Job Description:

Berkeley Lab's ( ) Joint Genome Institute ( ) is looking for a Genome Analysis Data Scientist to join their User Support Analysis (USA) Group! The USA Group performs custom analyses for research projects across the JGI including diverse experiment types such as resequencing, transcriptomics, epigenomics, single cell transcriptomics, nanopore sequencing, metabolomics, CRISPR screens, and subject areas such as plant, fungal, microbial, and environmental genomics projects. The Group contributes to hundreds of projects from JGI's user programs each year and 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), and single-cell transcriptomics in plants (Cell reports 27 (7), 2241-2247. e4). As a Data Scientist, you will implement custom analyses in support of new genomic technologies and contribute to the development and maintenance of automated pipelines as projects scale. Your work will be in one or two main subject areas, with a likely focus on resequencing analysis and metabolomics (though new technologies may take precedence). You will utilize their computational and genomic knowledge to contribute to broader JGI efforts and work collaboratively with JGI experimental scientists on design, analysis, and publication efforts. The '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) ( ). This position has an anticipated start date of December 1, 2023. What You Will Do:

• Maintain and develop an existing high throughput data analysis pipeline (e.g., resequencing, metabolomics).
• Implement analysis approaches for 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. In addition to the above, the Data Scientist 3 will also:
  • Take a lead role in developing, debugging, and managing an existing high throughput data analysis pipeline (e.g., resequencing, metabolomics).
  • 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. What is Required:
    • A Bachelor's Degree (or equivalent knowledge/training) in Bioinformatics, Biotechnology, Computer Science, or a related field and a minimum of 5 years of relevant experience in analysis of high throughput sequencing data and/or metabolomics data or an equivalent combination of education and experience.
    • In-depth experience running high throughput analyses in a parallel computing environment (SGE, SLURM).
    • Experience with experimental molecular biology and genomic technologies.
    • Experience with analysis of metabolomics data.
    • Demonstrated proficiency with developing analysis software (Python / R) in a UNIX environment.
    • Excellent oral and written communication skills including the ability to organize and present information to technical and non technical audiences.
    • Strong analytical skills including the ability to identify and solve complex technical problems.
    • Demonstrated interpersonal skills including the ability to conduct and perform collaborative research effectively with a broad range of colleagues with tact and diplomacy. Additional Qualifications for the Data Scientist 3:
      • A Bachelor's Degree (or equivalent knowledge/training) in Bioinformatics, Biotechnology, Computer Science, or a related field and a minimum of 8 years relevant experience in analysis of high throughput sequencing data and/or metabolomics data or an equivalent combination of education and experience.
      • Experience with database administration, AWS, or other cloud platforms.
      • Experience developing production standard software using best practices including git, CI/CD. Desired Qualifications:
        • An Advanced Degree in (or equivalent knowledge/training) in Bioinformatics, Biotechnology, Computer Science or a related field.
        • Broad understanding of bioinformatics tools used for genome analysis, development of re-sequencing pipelines, and integration of varied large data sets.
        • Demonstrated research accomplishments, including a strong publication record. Notes:
          • For full consideration, please apply with a resume by November 13, 2023.
          • This is a full time, career appointment, exempt (monthly paid) from overtime pay.
          • If hired at a level 2: This position has a targeted salary range of $106,596-$133,236 per year for job code C78.2. Salary for this position will be commensurate with the final candidate's qualifications and experience, including skills, knowledge, relevant education, certifications, plus also aligned with the internal peer group.
          • If hired at a level 3: This position has a targeted salary range of $126,900-$158,628 per year for job code C78.3. Salary for this position will be commensurate with the final candidate's qualifications and experience, including skills, knowledge, relevant education, certifications, plus also 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 onsite, hybrid, full time telework, or remote work. Remote workers are defined as individuals that reside within the United States, but 150 miles away from Berkeley Lab. There may be an expectation to intermittently conduct work, attend meetings, and train on site at Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA 94720. Work schedules are dependent on business needs. Learn About Us: (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- . Berkeley Lab is committed to 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. Equal Opportunity and IDEA Information Links: Know your rights, click for the supplement: "Equal Employment Opportunity is the Law" and the under 41 CFR 60-1.4.
            #J-18808-Ljbffr

Keywords: College of Charleston, Berkeley , Genome Analysis Data Scientist, Other , Berkeley, California