Job:Bioinformatics Research Scientist
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2.2 years ago
BerkeleyLab ▴ 70

Bioinformatics Research Scientist - 93904

Organization: JG-Joint Genome Institute

Lawrence Berkeley National Lab’s (LBNL, Joint Genome Institute Division ( has an opening for a Bioinformatics Research Scientist to join the team.

In this exciting role, you will develop new computational methods to investigate gene regulation and regulatory sequence properties in plants, fungi, and bacteria. Specifically, the Research Scientist will develop approaches for integrating single cell ‘omics information (scRNA-seq, scATAC-seq) and high-coverage TF binding site maps (DAP-seq) with a focus on understanding gene and epigenome regulatory dynamics underlying important environmental and agricultural traits. The Research Scientist will work independently to drive research projects and with a larger team to develop complementary laboratory and computational approaches. The position will support and consult on the development of high-throughput implementation of new technologies and will collaborate with JGI Users to apply these novel genomics approaches to a wide-range of agricultural, environmental, and synthetic biology problems.

What You Will Do:

  • Develop integrative computational methods for functional characterization of plant and algal genomes and epigenomes using single cell genomics approaches (10x), TF binding site information (DAP-seq) and phenotype analysis (GWAS, eQT).
  • Develop cross-species comparative software tools to characterize conservation of functional gene regulatory circuits in important plant traits.
  • Design and manage 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.
  • 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:

  • Work with groups from JGI Production and Informatics department to optimize processes.
  • Provide assistance and guidance to post-docs.

What is Required:

  • 5 years of experience in computational genomics beyond the highest degree in life science, bioinformatics, computer science, or another relevant field.
  • Demonstrated experience in 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.
  • Some experience with bioinformatics tools for analysis of single cell genomic, ChIP-seq/DAP-seq, ATAC-seq, HiC, feature clustering, gene regulatory network modeling, phylogenetics, and comparative genomics.

Desired Qualifications:

  • PhD in life science, bioinformatics, computer science or another relevant field.
  • Background in plant biology.
  • Experience in pan-genome or comparative genomics, single cell genomics approaches (10x).
  • Experience in TF binding site analysis with DAP-seq.
  • Ability to independently carry out high-quality research with creativity.
  • Proven ability to lead scientific team through design, implementation, monitoring and completion of project goals.
  • Ability to set priorities and works effectively with diverse technical, scientific, and operational teams.
  • 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.


  • This is a full time 2 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.
  • 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.

How To Apply

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

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 is committed to Inclusion, Diversity, Equity and Accountability (IDEA, and strives to continue building community with these shared values and commitments

Berkeley Lab is an Equal Opportunity and Affirmative Action Employer. We heartily welcome applications from women, minorities, veterans, and all who would contribute to the Lab’s mission of leading scientific discovery, inclusion, and professionalism. In support of our diverse global community, all qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status.

Know your rights, click here ( for the supplement: "Equal Employment Opportunity is the Law" and the Pay Transparency Nondiscrimination Provision ( under 41 CFR 60-1.4.

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