Research Scientist - NGS Methods Developer - 90775
Organization: JG-Joint Genome Institute
Berkeley Lab’s Joint Genome Institute (https://jgi.doe.gov/) has an opening for a Research Scientist to join the Sequencing Technologies group. The Research Scientist will develop new methods and implement published methods for both short and long read sequencing platforms (Illumina, PacBio, Oxford Nanopore) to identify and understand gene regulatory sequence in plants, fungi, and bacteria. The Research Scientist will play a central role in developing both laboratory and computational approaches.
The successful candidate will interact with JGI collaborators to develop genomic applications tailored to their research using sequencing technologies. The Scientist will be required to prepare detailed experimental plans, reports for presentation within and outside the JGI, and contribute/lead on scientific publications. To accomplish this the Research Scientist will be expected to work both independently, as well as interact with a multidisciplinary team of biologists, bioinformaticians, laboratory automation experts, computer scientists and software developers. This position will also manage research and technical staff.
What You Will Do:
• Responsible for designing and managing quantitative large-scale analyses of genomes with a focus on developing maps of gene regulatory DNA (TF binding site, open chromatin, 3D chromosomal interactions) for large number of plants, fungi and microbes, and interpreting the results to draw meaningful biological conclusions.
• Develop, optimize, and standardize sample preparation and library construction methods for functional genomics and epigenomics applications (DAP-seq, single cell RNA-seq and ATAC-seq) across a range of plant, fungal and bacterial species.
• Develop, optimize, and standardize sample preparation and library construction methods for short and long read sequencing platforms (Illumina, PacBio, Oxford Nanopore) across a range of plant, fungal and bacterial species.
• Apply scientific, engineering and/or other technical concepts in molecular biology and next generation sequencing technologies to develop new functional genomics approaches.
• Identify appropriate computational software and packages, develop computational pipelines, and apply appropriate statistical analysis to interpret results from new functional genomics approaches.
• 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 gene regulatory sequence data analysis.
• Remain at the cutting edge of research in the field through studies of the current literature and regular attendance of relevant seminars, conferences, and meetings.
• Interact with JGI microbial, fungal, plant, metagenomics, and other scientific programs to provide scientific and technical support.
• Collaborate with JGI community sequencing users and bioenergy research centers to assist with specific research needs.
• Work with the JGI Project Management Office to provide support and guidance on various scientific research projects.
• Attend, present, and represent the JGI at key meetings, workshops, and societies.
• Identify and implement partnerships with key vendors and/or academic labs.
• Keep detailed and accurate records and develop Standard Operating Procedures (SOPs).
• Publish in peer review journal; contribute to scientific research papers and reports.
Additional Responsibilities as needed:
• Supervise team and plan, direct and assign work to team members for complex and broad ranging initiatives and projects including the design, development, and implementation of molecular biology approaches and applications for overall sequencing technology improvement.
• Work with groups from JGI Production and Informatics department to optimize processes.
• Provide assistance and guidance to post-docs.
The posting shall remain open until the position is filled, however for full consideration, please apply by close of business on August 18, 2020.
• This is a full time career appointment.
• M-F, exempt (monthly paid) from overtime pay.
• 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.