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    Opportunity: Biologist Project Scientist (#91828) @ Lawrence Berkeley National Laboratory -- Berkeley, CA (US)
    Submitted by Bill Cannan; posted on Friday, January 15, 2021

    DESCRIPTION

    Lawrence Berkeley National Lab's (LBNL, www.lbl.gov) Joint Genome Institute (JGI, jgi.doe.gov) Division as part of the Microbiome Data Science group has an opening for a Biologist Project Scientist to join the team. The expected workload is ~100% computational.

    In this exciting role, you will perform analyses and develop new computational genomics tools to support JGI Users, with a strong emphasis on the development of automated workflows to identify and analyze novel viruses from metagenomes and metatranscriptomes. This workflow will aim to provide users with advanced computational tools in identifying the viral component of microbiome datasets and should include (i) identification of viral genomes from metagenomes, (ii) viral genome clustering, (iii) connecting viruses to host genomes, and (iv) implement existing and/or establish new methods for taxonomic assignment of viral genomes. Additional tasks will include Research & Development activities such as benchmarking and troubleshooting publicly available tools, as well as the development of new quality metrics and standardized computational approaches. You will be comfortable working with very large datasets in an interdisciplinary scientific group. You will be expected to exercise independent judgment in determining methods and approaches to solving complex issues across various technologies and must be familiar with databases and different types of sequence data.

    What You Will Do:
    • Work independently and as part of a team to develop computational workflows for viral genomics including viral genome identification, clustering, and host prediction.
    • Perform large scale analysis of viral sequence data: build models for the detection of viruses, develop methods to the group and classify viral sequences, analyze metagenomics sequences, and perform comparative genome analyses.
    • Develop computational tools in the context of the Integrated Microbial Genome (IMG) data management and analysis system.
    • Work in close collaboration with JGI's microbial genome and metagenome program scientists.
    • Perform custom analysis of viral genomes from metagenomics and metatranscriptomics data.
    • Generate detailed reports and data packages with extensive documentation.
    • Identify steps in analysis pipelines that could be automated and design possible frameworks/pipelines.
    • Troubleshoot existing computational processes and optimize Standard Operating Procedures (SOP).
    • Analyze results and provide feedback on potential flaws/improvements.
    • Summarize research results and publish in peer-reviewed journals; contribute to scientific research papers and reports.
    Additional Responsibilities as Needed:
    • Attend group meetings and present status reports and scientific findings.
    • Keep an accurate and detailed laboratory notebook and tracking spreadsheets.

    REQUIREMENTS

    What is Required:
    • A minimum of 2 years of relevant experience beyond the highest customary degree in Biology, Microbiology, Bioinformatics, or related field.
    • Experience in methods and tools for next-generation sequencing, metagenome assembly and binning.
    • Experience in large-scale analysis of microbial genomes and metagenomes with a proven track record in this area reflected in recent or pending publications.
    • Experience with common sequence analysis tools including genome assembly, genome binning, sequence clustering, phylogenetics, and remote homology searches such as HMMER and HHSearch.
    • Experience in a scripting language (Perl, Python).
    • Experience with source control revision management and object-oriented design.
    • Experience with current approaches used for viral detection and analysis, e.g., VirSorter, VirFinder, vContact2, VOGdb, IMG/VR.
    • Substantial knowledge and understanding of bioinformatics tools for sequence similarity search, multiple sequence alignment, profile search, clustering, and phylogenetic analysis.
    • 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.
    • Excellent problem-solving and decision-making skills with the ability to troubleshoot experimental processes and provide analysis.
    • Efficient organizational and record-keeping skills with the ability to organize and present analysis reports to JGI Users and staff.
    • 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 research publications.
    Desired Qualifications:
    • Ph.D. in Biology, Microbiology, Bioinformatics, or related field.
    • Experience with the IMG & IMG/VR system.
    • Experience in viral genomics and host-viral interaction.
    • Knowledge of Unix tools, relational databases, and R.
    • Experience with paired metatranscriptomic/metagenomic analyses.
    • Experience with large-scale data analysis (e.g., integrated analysis of > 50 datasets).

    TERMS

    • This is a full time, 1 year, term appointment that may be renewed to a maximum of five years.
    • 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.
    • Diversity, equity, and inclusion are core values at Berkeley Lab. Our excellence can only be fully realized by faculty, students, and staff who share our commitment to these values. Successful candidates for our faculty positions will demonstrate evidence of a commitment to advancing equity and inclusion.

    LOCALE

    • Work will be primarily performed at Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA.

    HOW TO APPLY

    Apply directly online at 50.73.55.13/coun[...]91951 and follow the on-line instructions to complete the application process.

    Organization: JG-Joint Genome Institute

    POLICY

    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 (www.dol.gov/agen[...]sters) 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.

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