Scientist Metagenomics

Lawrence Berkeley National Laboratory
Job Location
Walnut Creek, CA 94598
Job Description

Scientist Metagenomics - 82292
Organization:  JG-Joint Genome Institute

Berkeley Lab is Bringing Science Solutions to the World, and YOU can be a part of it!

In the world of science, Lawrence Berkeley National Laboratory (Berkeley Lab) is synonymous with "excellence." That's why we hire the best - whether in research, finance or other operations. This is a great opportunity to bring your top-notch skills to bear in support of world-class scientific research that addresses national and global challenges!

Position Summary:
The Department of Energy Joint Genome Institute (DOE JGI, a division of Berkeley Lab) is looking for a Research Scientist to join the Metagenome Program. The position will report to the Metagenome Program Group Lead.

This position has three primary roles:
• Design, conduct and publish independent research that pushes the boundaries of metagenomics. Current research cuts across ecosystems and includes projects like discovering new RNA viruses in metagenomes through machine learning methods, sequencing the first large-scale soil virus metagenomes, constructing large scale Bayesian ecological networks and exploring plant-microbe interactions.
• Develop new computational and molecular methods in metagenomics that can be applied by our production groups to thousands of metagenome samples per year.
• Assist scientists who have received user grants from the Joint Genome Institute in planning and implementing experiments.

Specific Responsibilities:
• Lead or assist in diverse 16S tag, metagenome and metatranscriptome sequencing efforts.
• Perform new and detailed analysis of ribosomal DNA sequence data, metagenomic shotgun sequence data, and metatranscriptome data: build phylogenetic trees, analyze annotated metagenomes, and perform comparative analyses.
• Work on the development of software for machine learning and network analysis of genomic data.
• Design and carry out experiments aimed at recovering microbial genome sequence from environmental samples.
• Create, design, and execute experiments to obtain metagenomic, metatranscriptomic and/or single cell genomic data from target functional and phylogenetic groups of interest
• Perform Research & Development experiments to improve and automate various aspects of metagenomic sequencing, assembly, annotation, and binning.
• Identify areas of improvement and efficiency and offer feedback.
• Troubleshoot all stages of experimental process and optimize Standard Operating Procedures (SOP).
• Interface with collaborators, JGI staff, management, and sponsors at other national laboratories.
• Publish in peer-reviewed journals; contribute to scientific research papers and reports.
• Prepare proposals.
• Lead, mentor and train postdoctoral fellows, technical staff and other group members as necessary.

Additional Desired Responsibilities:
• Attend group meetings and present status reports and scientific findings.
• Keep an accurate and detailed record of laboratory and analytical work.


Required Qualifications:
• Ph.D. in Molecular Biology, Biology, Genetics or a closely related discipline and/or normally less than 5 years related
• Demonstrated ability to independently carry out creative research with a proven record of publications and achievement
• Experience programming in Python, Bash scripting and familiarity with Linux/Unix
• Experience with environmental nucleic acid extraction and next generation sequencing technologies and with the R statistical analysis platform
• Familiarity with Molecular Biology Techniques such as: PCR, qPCR, cloning
• Familiar with command line sequence analysis tools e.g. Bbtools, Last, Hmmer, Megahit, Velvet, Samtools
• Familiar with databases, e.g. RefSeq, BioCyc, PFAM, IMG
• Experience in 16S rRNA sequence analysis tools and databases including QIIME, Greengenes, RDP, and Silva
• Demonstrated ability to conduct and perform collaborative research and effectively interact with a broad range of colleagues with tact and diplomacy
• 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 to 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:
• Experience with machine learning especially using using Apache Spark/MLlib, Scikit-learn and deep neural networks
• Experience in viral biology

The posting shall remain open until the position is filled.

Notes: This is a 1 year, career-track term appointment that may be renewed to a maximum of 5 years and that may be converted to career based upon satisfactory job performance, continuing availability of funds, and ongoing operational needs. This position requires completion of a background check.

Work will be performed at the DOE Joint Genome Institute (JGI) in Walnut Creek, CA.

Salary is commensurate with experience.

How to Apply

Apply directly online at and follow the on-line instructions to complete the application process.

About Our Organization

Berkeley Lab 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: "Equal Employment Opportunity is the Law".

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