The Department of Energy Joint Genome Institute- DOE JGI (a division of the Lawrence Berkeley National Lab) has an exciting Postdoctoral Research opportunity available for a Computational Biologist Postdoc to participate in ongoing research in Microbiome Data Science. JGI has been instrumental in microbiome big data integration and interrogation towards development of better understanding of the forces that shape microbial communities. We are looking for a talented, highly motivated candidate with a strong background in microbial ecology, metagenomics. computational biology and bioinformatics to join our team. The successful candidate will be expected to perform large-scale identification and characterization of expressed protein families from hundreds of metatranscriptome samples, associate expression patterns with habitats and other physiological conditions, and identify biosynthetic clusters expressed under certain environmental conditions, adding new functional information to protein families. The metatranscriptomic data could be also utilized for the generation of metabolic models for specific habitat/physiological condition using KBase technology. The candidate will work as part of the Prokaryotic Super Program and is expected to work independently, as well as contribute as a member of a dynamic, multidisciplinary team of biologists, bioinformaticians, computer scientists and software developers at the JGI. Position reports to the Prokaryotic Program head.
What You Will Do:
Perform large scale analysis of metatranscriptome data, analyze metatranscriptomic sequences, and perform comparative analyses.
Perform large-scale identification and characterization of expressed protein families from metatranscriptomes
Identify over-expressed protein families under particular environmental conditions/habitats
Interrogation and interpretation of publicly available metagenomic and metatranscriptomic datasets.
Utilize scripting language(s) and apply standard bioinformatics tools and pipelines for the analysis of microbiome data
Work in a high-performance computing environment and interact with a team of computer scientists, software developers and postdoctoral researchers to develop new methods and tools for large-scale metagenome/metatranscriptome data analysis
Perform comparative analysis across hundreds of metagenomic/metatranscriptomic data and billions of genes.
Develop statistical methods to compare different samples/communities.
Prepare research results for publication and for presentations at scientific meetings.
Application of standard bioinformatics tools for the analysis of metagenomic/metatranscriptomic data.
Contribute to research in the Microbiome Data Science Group as part of a large multidisciplinary team
Interact with Kbase scientists and explore the feasibility of development habitat/physiological condition specific metabolic models
Design and implementation of new approaches for metatranscriptomics data analysis.
Publish in peer review journals and deliver scientific presentations at scientific meetings
Additional Responsibilities as needed:
Development of software for organization and handling of metatranscriptomics data and automation of analytical procedures.
Develop and present updates and reports at group meetings.
Support the development of user interface for navigation and data comparisons across thousands of metagenomic/metatranscriptomic samples
What is Required:
Recent Ph.D. (within the last 4 years) in Bioinformatics, microbiology, virology, or a related discipline with training/experience in bioinformatics.
Experience in any of the following areas: viral genomics, metagenomics, microbial ecology
Strong experience in analysis of microbial/viral genomes and metagenomes is essential with a proven track record in this area reflected in recent or pending publications
Strong experience with UNIX utilities and filesystems.
Familiar with command line sequence analysis tools e.g. Last, Hmmer, Megahit, MetaSpades, etc
Strong experience in scripting tools in order to mine data files.
Good experience with processing and analysis of genomic/metagenomic data.
Good experience with using standard bioinformatics tools and databases.
Knowledge Biology/Biochemistry and understanding of key and complex biological concepts (genes, pathways, microbial phylogeny).
Ability to independently carry out creative research with tenacity and of the highest quality standards.
Demonstrated ability to conduct and perform collaborative research and effectively interact with a broad range of colleagues with tact and diplomacy.
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.
Additional Desired Qualifications:
Experience programming in Python, Bash scripting and familiarity with Linux/Unix.
Experience with the R statistical analysis platform.
Experience with machine learning.
The posting shall remain open until the position is filled.
This is a full time, three year postdoctoral appointment with the possibility of renewal based upon satisfactory job performance, continuing availability of funds and ongoing operational needs. You must have less than two years paid postdoctoral experience. Salary for Postdoctoral positions depends on years of experience post-degree.
Full-time, M-F, exempt (monthly paid) from overtime pay.
This position is represented by a union for collective bargaining purposes.
Salary will be predetermined based on postdoctoral step rates.
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."
Internal Number: 85333
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.