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Bioinformatics Research Scientist

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Research/Science
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JG-Joint Genome Institute
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85872 Requisition #
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Berkeley Lab’s Joint Genome Institute Division has an opening for a Bioinformatics Research Scientist. This position is for a Bioinformatics Research Scientist with strong background in computational biology, microbial genomics, metagenomics, and data science. Under general supervision, will work as part of the Prokaryotic Super Program and perform metagenomics research, with a strong emphasis on the development of new computational technologies for big data mining and discoveries from metagenomics data. Tasks also involve Research & Development activities such as development of computational methods and pipelines for the identification of plasmids from metagenomics and metatranscriptomics data and characterization of their functional content with emphasis on antibiotic resistance genes and understanding how plasmids mediate the spread of these genes within and between biomes. The successful candidate will be expected to take a leadership role in the plasmid discovery project. The candidate will also be expected to extend research activities to collaborations with other scientists in the areas of viral genomics research.  Will report to the Prokaryotic Super Program Head.


What You Will Do:

  • Develop and implement computational methods for the identification of plasmid genomes from metagenomics and metatranscriptomic data.

  • Perform large scale analysis of plasmid sequence data: build models for the detection of plasmids, develop methods to group and classify plasmid sequences, analyze metagenomics sequences, and perform comparative genome analyses.

  • Identify and analyze CRISPR elements from all isolate genome and metagenomes and compare these data with plasmid genome sequences.

  • Take a leadership role in the plasmid discovery project and contribute to research as part of a large multidisciplinary team.

  • Identify areas of improvement and efficiency and offer feedback.

  • Troubleshoot all stages of computational process and optimize Standard Operating Procedures (SOP).

  • Interface with other data scientists, JGI staff, management, and sponsors at other national laboratories.

  • Summarize research results and publish in peer-reviewed journals; contribute to scientific research papers and reports.

  • Prepare proposals.

  • Lead, mentor and train graduate students, technical staff and other group members as necessary.


Additional Responsibilities as needed:

  • Attend group meetings and present status reports and scientific findings.

  • Keep an accurate and detailed laboratory notebook and tracking spreadsheets.


What is Required:

  • PhD in Biology, Molecular Biology, Microbiology, Bioinformatics or related field.

  • Strong experience in methods and tools for next-generation sequencing, metagenome assembly and binning

  • Significant experience in large-scale analysis of microbial genomes and metagenomes with a proven track record in this area reflected in recent or pending publications

  • Substantial knowledge and understanding of bioinformatics tools for sequence similarity search, multiple sequence alignment, profile search, clustering and phylogenetic analysis

  • Experience in viral genomics and host-viral interaction is highly desirable

  • Experience in a scripting language (Perl, Python) is a must, knowledge of Unix tools, relational databases and R is desirable

  • Demonstrated ability to conduct and perform collaborative research and effectively interact with a broad range of colleagues with tact and diplomacy.

  • Demonstrated ability to independently carry out creative research with a proven record of publications and achievement.

  • Effective problem-solving and decision-making skills with the ability to troubleshoot experimental processes and provide analysis.

  • Excellent organizational, analytical, and record-keeping skills with the ability organize and present technical reports to collaborators, JGI staff, management, and sponsors.

  • Demonstrated ability to accurately and eloquently represent and promote scientific projects to audiences of diverse technical backgrounds.

  • Effective interpersonal skills with experience establishing effective collaborations and interacting with members of the scientific, instrumentation and informatics communities.

  • Excellent written communication skills with demonstrated experience preparing funding proposals and research publications.


Additional Desired Qualifications:

  • Some experience in synthetic biology.


The posting shall remain open until the position is filled.


Notes:

  • 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.

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

  • Salary is commensurate with experience.

  • 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 DOE Joint Genome Institute (JGI) — 2800 Mitchell Dr., Walnut Creek, CA.


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.


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."


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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."

 

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