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Research Scientist - Single Cell Technology

Lawrence Berkeley National Laboratory
Job Location
1 Cyclotron Road
Berkeley, CA 94720
United States
Job Description

Research Scientist - Single Cell Technology - 90782

Organization: JG-Joint Genome Institute


Berkeley Lab’s Joint Genome Institute ( has an opening for a Term Research Scientist to join the Sequencing Technologies group. The Research Scientist will develop and optimize single cell methods (scRNA-seq, scATAC-seq) for a wide-range of plant species and carry out computational analysis to elucidate the molecular underpinnings of gene regulation of important bioenergy crop traits. The Research Scientist will integrate other relevant functional genomic and epigenomic data sets (DAP-seq, HiC, histone modifications, DNA methylation) to fully elucidate the complex interactions underlying gene regulation. 


The successful candidate will develop comparative genomics approaches to reveal conserved and novel gene regulation and gene networks underlying important plant traits. The Scientist will collaborate with other JGI scientists to establish standardized laboratory and analysis approaches for single cell RNA-seq and ATAC-seq, and spatial transcriptomics to share with the larger scientific community. The Research 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.  As this role expands, this position will manage research and technical staff. 


What You Will Do:

• Develop tissues, protoplast, nuclear and chromatin preparation methods for a wide-range of plant and fungal species for application in single cell assays (scRNA-seq, scATAC-seq, spatial transcriptomics).

• Develop computational pipelines for plant and fungal single cell transcriptomes (scRNA-seq) and open chromatin (scATAC-seq) analysis.

• Innovate comparative genomic analysis approaches for single cell transcriptomes and open chromatin, as well as integration with other relevant genomics and epigenomic data sets (DAP-seq, ChIP-seq, HiC). Goal is to identify conserved and branch-specific gene regulatory networks. 

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

• 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’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 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 journals; 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 25, 2020.



• This is a full time, 1-year 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.

• 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.


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: "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.



What is Required: 

• 5 years of experience with high-throughput sequencing, genomics, and/or other biological programs beyond the highest customary degree in a life science, bioinformatics, biotechnology or other relevant fields.

• Demonstrated experience in the analysis of next-generation sequencing data sets with a proven track record in this area reflected in recent or pending publications.

• Demonstrated experience with Python, PERL, R or similar programming languages.

• Demonstrated experience with Unix/Linux including working on the command line, Bash scripting, and installing programs and packages. 

• Substantial knowledge and understanding of bioinformatics tools for analysis of scRNA-seq, scATAC-seq, ChIP-seq/DAP-seq, HiC genomic feature clustering, gene regulatory network analysis, phylogenies, and comparative genomics.

• Ability to independently carry out high-quality research with creativity.

• Technical expertise in high-throughput next-generation sequencing and supporting molecular biology techniques and laboratory technology.

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

• Expertise in computational genomics.

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

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

• Strong analytical and organizational skills.

• Excellent interpersonal, oral, and written communication skills.

• Ability to work independently as well as part of a diverse team.

• A commitment to and demonstrated ability to perform collaborative research in a team environment.


Additional Desired Qualifications:

• PhD in life science, bioinformatics, biotechnology or other relevant field.

• Postdoctoral experience.

• Background in plant biology.


How to Apply

How To Apply

Apply directly online at and follow the on-line instructions to complete the application process.


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