In this exciting role, you will be part of the Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA) scientific focus area, a collaborative effort to investigate the structure and function of microbial communities in the environment and the TrIP project, "Precision editing of gut dysbiosis in inflammatory bowel disease for ameliorating inflammation". You will learn and assist researchers in resolving prophage sequences from already sequenced microbial genomes. Experimentally, you will extract DNA from bacterial cultures and fecal samples, prepare libraries for shotgun and long read sequencing, and isolate phages. Bacterial cultures may include isolates, enrichments, and synthetic communities. You will help with a variety of bioinformatics tasks such as genome assembly, gene annotation, and genetic interaction inference.
What You Will Do:
Learn and perform DNA extractions, library preparations, sample submissions for sequencing.
Perform standard microbiology tasks to culture bacteria and phages.
Learn and adapt genomic and metagenomic workflows from Illumina sequencing data.
Perform gene function annotation.
Compare gene, genome, and protein sequences and derive scientific conclusions and hypotheses.
Assess bioinformatics workflow performance criteria such as run time and assembly quality.
Develop a database of prophage sequences within key microorganisms.
Keep detailed computational and experimental notebooks, and upload data in relevant databases.
Follow strict documentation routines and communicate them such that they can be repeated by others.
Communicate and collaborate with other bioinformaticians to debug complex computational workflows.
Contribute to scientific writing and publication.
What is Required:
Bachelor's degree with a course load that emphasized the physical or life sciences, math, and engineering preferred or equivalent experience.
Familiarity with sterile technique, bacterial culturing, and molecular biology techniques.
Familiarity with sequence alignment algorithms and variations such as bwa-mem and progressive mauve.
Excellent oral and written communication skills and capacity to contribute to scientific papers.
Proficient in UNIX, Python, and familiar with Jupyter notebook documentation.
Good organizational skills and attention to detail.
Strong interpersonal skills to effectively work within a diverse team environment.
Understanding of phage and molecular biology - used in drawing conclusions from genomic data.
Interest in scientific methodology or biology.
Ability to be self-starters who can learn new material rapidly.
Ability to quickly read scientific literature and discuss findings.
Understanding of nuances between experimental and bioinformatics workflows and how they can complement each other.
For full consideration, please apply by March 2, 2021.
This is a full time, term appointment with the possibility of extension or conversion to Career appointment based upon satisfactory job performance, continuing availability of funds and ongoing operational needs.
This position is represented by a union for collective bargaining purposes.
Salary will be determined based on range by collective bargaining agreement.
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 West Berkeley Biocenter (Potter St.) -- Bldg. 977, 717 Potter St., Berkeley, CA
Learn about us!
Environmental Genomics and Systems Biology
Mission: Linking genome biology to ecosystem dynamics.
Vision: Sustainable solutions to energy and environmental challenges developed through mechanistic understanding of ecosystem dynamics.
Approach: We develop systems-level models using integrated molecular observation and controlled manipulation of model organisms and defined biomes to design and test interventions that promote beneficial outcomes.
(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-
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
Lawrence Berkeley National Laboratory encourages applications from women, minorities, veterans, and other underrepresented groups presently considering scientific research careers.
Internal Number: 92058
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.