Lawrence Berkeley National Lab's (LBNL) Joint Genome Institute (JGI) 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.
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.
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.
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.
Work will be primarily performed at Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA.
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. Clickhere 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.
Internal Number: 91828
About Lawrence Berkeley National Laboratory
In the world of science, Lawrence Berkeley National Laboratory (Berkeley Lab) is synonymous with excellence. Thirteen scientists associated with Berkeley Lab have won the Nobel Prize. Fifty-seven Lab scientists are members of the National Academy of Sciences (NAS), one of the highest honors for a scientist in the United States. Thirteen of our scientists have won the National Medal of Science, our nation's highest award for lifetime achievement in fields of scientific research. Eighteen of our engineers have been elected to the National Academy of Engineering, and three of our scientists have been elected into the Institute of Medicine. In addition, Berkeley Lab has trained thousands of university science and engineering students who are advancing technological innovations across the nation and around the world. Berkeley Lab is a member of the national laboratory system supported by the U.S. Department of Energy through its Office of Science. It is managed by the University of California (UC) and is charged with conducting unclassified research across a wide range of scientific disciplines. Located on a 200-acre site in the hills above the UC Berkeley campus that offers spectacular... views of the San Francisco Bay, Berkeley Lab employs approximately 4,200 scientists, engineers, support staff and students. Its budget for 2011 is $735 million, with an additional $101 million in funding from the American Recovery and Reinvestment Act, for a total of $836 million. A recent study estimates the Laboratory's overall economic impact through direct, indirect and induced spending on the nine counties that make up the San Francisco Bay Area to be nearly $700 million annually. The Lab was also responsible for creating 5,600 jobs locally and 12,000 nationally. The overall economic impact on the national economy is estimated at $1.6 billion a year. Technologies developed at Berkeley Lab have generated billions of dollars in revenues, and thousands of jobs. Savings as a result of Berkeley Lab developments in lighting and windows, and other energy-efficient technologies, have also been in the billions of dollars. Berkeley Lab was founded in 1931 by Ernest Orlando Lawrence, a UC Berkeley physicist who won the 1939 Nobel Prize in physics for his invention of the cyclotron, a circular particle accelerator that opened the door to high-energy physics. It was Lawrence's belief that scientific research is best done through teams of individuals with different fields of expertise, working together. His teamwork concept is a Berkeley Lab legacy that continues today.