Metatranscriptome Analysis Postdoctoral Scholar

Lawrence Berkeley National Lab's (LBNL) Joint Genome Institute (JGI) Division has an opening for a Metatranscriptome Analysis Postdoctoral Scholar to join the team.

In this exciting role, you will work with metatranscriptomic data generated by the JGI. You will develop best practices and pipelines, optimize data model and analysis tools for metatranscriptome data in Integrated Microbial Genomes and Metagenomes (IMG/M) system. You will use JGI-generated metatranscriptome data to analyze patterns of antisense and intergenic expression looking for novel regulatory mechanisms. You will be responsible for the design of the analysis workflows, development and testing of the software, summarizing the results of the analysis in publications and contributing to the development of standards in collaboration with the scientific community and Genomics Standards Consortium.

What You Will Do:

• Compare the results of the mapping of metatranscriptomes to different reference datasets in order to inform further development of the JGI processing pipelines and community standards.

• Develop a workflow for assessment of the quality of gene models in metagenomes and metatranscriptomes by analyzing the expression data.

• Communicate the results of the assessment to pipeline developers, collaborate with IMG pipeline group on the pipeline improvements.

• In collaboration with IMG group and NMDC participate in the development of an optimal data model, visualization, and statistical tools to support large-scale metatranscriptome data analysis.

• Contribute to the analysis of antisense and intergenic expression patterns looking for novel regulatory mechanisms.

• Be substantially (and independently) responsible for the design, development, testing, and documentation of the software necessary to perform the above analyses.

• Summarize the results of the analysis in publications and contribute to the development of standards for metatranscriptome data processing, recording, and analysis.

Additional Responsibilities as needed:

• Participate in other bioinformatics projects within the JGI Microbial and Metagenome Programs.

• Assist the JGI internal and external customers with metatranscriptome data analysis.

• Develop training materials for IMG system users to inform them of the protocols, practices, and tools for metatranscriptome analysis.

What is Required:

• Ph.D. degree in Bioinformatics, Computational Biology or a related discipline.

• Good understanding of DNA and RNA sequencing methods and molecular biology.

• Good knowledge of tools commonly used in bioinformatics, such as short read aligners (bwa, bowtie); software for interaction with sequencing data (samtools); genome annotation tools (GeneMark, hmmsearch, pairwise alignment tools).

• Experience writing Unix scripts (python, bash).

• Excellent verbal and written communication skills.

• Experience working in a diverse team environment.

• Strong analytical, organizational, and interpersonal skills.

Desired Qualifications:

• Familiar with databases (Oracle, MySQL).

• Familiar with design and methods for statistical analysis of expression data.

Notes:

• This is a full-time, 3 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 2 years of paid postdoctoral experience. Salary for Postdoctoral positions depends on years of experience post-degree.

• 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 Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA.

Learn About Us:

JGI & Berkeley Lab: A View to Fuel Innovative Science in the Public Interest

They say it's all about location and Berkeley Lab has it all: a view above the San Francisco Bay, cool breezes, and world-class multidisciplinary science within a diverse and respectful research ecosystem of 5,000 people. Nearly 90 years ago, Ernest Orlando Lawrence, the inventor of the cyclotron, brought physicists, biologists, engineers and mathematicians together in Berkeley above the University of California campus to tackle the most urgent scientific challenges. Today, after garnering 13 Nobel Prizes, Berkeley Lab has sustained and grown that tradition of open, interdisciplinary team science, exemplified by how the U.S. Department of Energy Joint Genome Institute (JGI) addresses the most pressing energy and environmental challenges using integrative genome science approaches. JGI takes up residence in the new, state-of-the-art Integrative Genomics Building (IGB) along with the U.S. Department of Energy Systems Biology Knowledgebase (KBase) to expand the frontiers of energy and environmental science in partnership with the worldwide community of researchers. Will you join us and be a critical part of our next ground-breaking discoveries?

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.

Working at Berkeley Lab has many rewards including a competitive compensation program, excellent health and welfare programs, a retirement program that is second to none, and outstanding development opportunities. To view information about the many rewards that are offered at Berkeley Lab- Click Here.

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.

Lawrence Berkeley National Laboratory encourages applications from women, minorities, veterans, and other underrepresented groups presently considering scientific research careers.