Sample Preparation Group Lead

📁
Research/Science
💼
JG-Joint Genome Institute
📅
88125 Requisition #

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.


Berkeley Lab’s Joint Genome Institute (JGI) Division has an opening for a Sample Preparation Group Lead. The person  will serve as a Research Scientist in the Genomics Technologies Department to lead the Sample Management and Library Creation group. This person will design and conduct scientific research with a focus on sequencing technologies and their application to address a wide range of outstanding questions in biology. This person will serve as a Sequencing Technologies Research Scientist expert and apply scientific and technical expertise to develop new genomics capabilities at the JGI. This person will provide scientific and technical support to JGI’s Microbial, Fungal, Plant and Metagenomics, external collaborators, and other scientific research programs and interact with JGI collaborators to develop sequencing applications tailored to their researchers. This person will develop, optimize and standardize sample preparation and library construction methods for short and long read sequencing platforms (Illumina, PacBio, Oxford Nanopore) and transfer methods to liquid handling robotic automation for high throughput processing. This person will develop, optimize and standardize sample preparation and library construction methods for functional genomics and epigenomics applications (ChIP-seq, DAP-seq, ATAC-seq, methylSeq, single cell RNA-seq) and when possible transfer methods to liquid handling robotic automation for high throughput processing. This person will evaluate and validate next-generation sequencing technologies, develop molecular biology approaches for overall sequencing technology improvement, and develop new genomic applications utilizing these new technologies. This person will manage the Sample Management and Library Creation team to coordinate with internal and external collaborators to process samples to produce high-quality and timely results  and identify and implement improvements to scientific, technical or operational processes. This person will coordinate with work lead to plan and monitor production capacity and weekly throughput. Will be required to prepare detailed experimental plans, reports for presentation within and outside the JGI, and contribute/lead on scientific publications. Position reports to the Sequencing Technology Group Lead.


What You Will Do:

Production and Research and Development 

  • Apply scientific, engineering and/or other technical concepts in molecular biology and next-generation sequencing technologies to develop new functional genomics and production sequencing capabilities.

  • 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.

  • 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 and transfer methods to liquid handling robotic automation for high throughput processing.

  • Develop, optimize and standardize sample preparation and library construction methods for functional genomics and epigenomics applications (ChIP-seq, DAP-seq, ATAC-seq, single-cell RNA-seq) across a range of plant, fungal and bacterial species, and when possible transfer methods to liquid handling robotic automation for high throughput processing.

  • Innovate novel nuclear and chromatin extraction methods for a wide range of plant and fungal species for application in a diverse set of functional genomics assays.

  • Coordinate with work lead to manage day-to-day library production pipeline including planning, scheduling and coordinating as well as sample management, library creation, library QC and submission of libraries via integrated tracking system.

  • Coordinate implementation of new sequencing, quality control assessment or liquid handling robotics technologies, or new protocols into production.

  • Work closely with software developers to establish Laboratory Information Management Systems (LIMS) to support new protocols/workflow or to improve/ streamline existing workflow in the tracking system.

  • Work with informatics groups for data analysis and provide scientific input for development of new analysis software.

  • Generate reports and present findings to collaborators within and outside of the JGI.

  • Publish in peer review journals; contribute to scientific research papers and reports.

  • Keep detailed and accurate records and develop Standard Operating Procedures (SOPs).

 

Collaboration of Scientific Efforts 

  • Interact with JGI’s 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, guidance, and troubleshooting on various scientific research projects.



What is Required: 

  • PhD or equivalent experience in a life science field, and a clear understanding and extensive experience with high-throughput sequencing, genomics and/or other biological programs.

  • Experience utilizing high-throughput automated systems and equipment and proficiency in process optimization methodologies.

  • Experience exercising judgment and expertise to identifying and resolving complex and broad-reaching conflicts and problems.

  • Experience working with internal and external users of genomic/sequencing data.

  • Experience to hire, train, coach and performance manage employees.

  • Strong computer experience including strong database skills and use of the internet, email, and standard office software

  • Experience providing technical training and technology transfer.

  • Experience in developing and updating standard operating procedures. 

  • Technical expertise in high-throughput next-generation sequencing and supporting molecular biology techniques and laboratory technology. A proven track record for:     

    • Extensive experience with next-generation sequencing platforms

    • Extensive experience in molecular and cellular biology 

    • Expertise in high molecular weight DNA isolation and preparation of high quality long read libraries and large insert paired-end libraries including 20kb PacBio, 40kb fosmid, and 200kb BAC.

    • Expertise in isolation of plant and fungal protoplast/spheroplast, nuclei and intact chromatin, and preparation of genomic and epigenomics sequencing libraries (ChIP-seq, scRNA-seq, DAP-seq, ATAC-seq).

  • Validated operator for high throughput robot such as Hamilton SAM/StarLet/Vantage and expertise in high throughput method development collaborating with ITS and automation teams.

  • Proven ability to lead a scientific team through designing,  implementation, monitoring and completion of project goals.


Additional Desired Qualifications:

  • Ability to set priorities and works effectively with diverse technical, scientific and operational teams.

  • Strong verbal and written communication skills and the ability to write clear and concise technical descriptions.

  • Ability to organize and present reports to collaborators, JGI staff, management, and sponsors.

  • Effective interpersonal skills necessary for working in a diverse team environment.

  • Detail-oriented excellent record-keeping organization skills and follow through.

  • Excellent customer service experience and proven experience working with internal and external staff, collaborators and end-users.


The posting shall remain open until the position is filled.


Notes: 

  • This is a full-time career appointment.

  • Full-time, M-F, exempt (monthly paid) from overtime pay.

  • Salary is commensurate with experience.

  • 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) — 1 Cyclotron Road, Berkeley, CA.


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 science within a diverse, 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 Institute (JGI)  addresses the most pressing energy and environmental challenges. This summer, 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 the next ground-breaking discoveries in the public interest?


JGI is comprised of highly-skilled and diverse talent founded on a culture of scientific excellence, trust, curiosity, passion, and collaboration.


Working at Berkeley Lab has many rewards including a competitive compensation program, excellent health and welfare programs, paternal leave, a retirement program that is second to none, and outstanding employee 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."


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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."

 

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The Lawrence Berkeley National Laboratory provides accommodation to otherwise qualified internal and external applicants who are disabled or become disabled and need assistance with the application process. Internal and external applicants that need such assistance may contact the Lawrence Berkeley National Laboratory to request accommodation by telephone at 510-486-7635, by email to eeoaa@lbl.gov or by U.S. mail at EEO/AA Office, One Cyclotron Road, MS90R-2121, Berkeley, CA 94720. These methods of contact have been put in place ONLY to be used by those internal and external applicants requesting accommodation.