Computational Biologist Postdoctoral Fellow

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.
Position Summary:
The DOE Joint Genome Institute (JGI) in Walnut Creek, CA has an exciting position available for a Computational Biologist Postdoctoral Fellow which offers excellent opportunities for interdisciplinary training in genetics, genomics, epigenomics, and systems biology. You will participate in research focused on developing approaches to identify and characterize conserved cis-regulatory elements genome-wide across many species. We are looking for a talented, highly motivated candidate with a strong background in computational biology and bioinformatics preferable with background in comparative and/or functional genomics. You will be expected to develop approaches to integrate published and internally generated functional genomic datasets with comparative sequence analysis methods to characterize conserved regulatory DNA sequences. This position will work as part of the Genomics Technologies group and is expected to work independently, as well as contribute as a member of a dynamic, multidisciplinary team of biologists, bioinformaticians, computer scientists and software developers and will report to the lead of the Sequencing Technologies group.
Specific Responsibilities:
Analyze next generation sequencing data such as TF ChIP-Seq, ATAC-seq, BS-seq, RNA-Seq, etc.
Analyze DAP-seq data, a rapid and inexpensive in vitro TFBS discovery approach for rapid cistrome and epicistrome mapping (see O'Malley et al, Cell 2016).
Perform large scale comparative genomic analysis of plant and animal sequence data (i.e. multi-species sequence alignments).
Develop software to integrate functional and comparative genomics to identify conserved non-coding regulatory sequences.
Incorporate statistical genetics including GWAS and 1000 Genomes data sets to support and extend conclusions
Implement software tools and best-practices (e.g. ENCODE standards) to develop functional genomics analysis pipelines.
Explore existing literature to support and extend conclusions.
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 metagenome data analysis
Prepare research results for publication and for presentations at scientific meetings.
Visualization of genomic data using tools such as Circos, IGV, Jbrowse, UCSC Genome browser.
Additional Required Responsibilities:
Provide general support to the Sequencing Technologies group.
Required Qualifications:
Ph.D. in bioinformatics, computer science, biology, genetics, molecular biology or a related discipline.
Experience in analysis of eukaryotic genomes with a proven track record in this area reflected in recent or pending publications.
Substantial knowledge and understanding of bioinformatics tools for sequence similarity search, multiple sequence alignment, clustering and phylogenetic analyses.
Significant experience in methods and third-party tools for next-generation sequence analysis €“ tools for alignment as well as secondary NGS analysis (peak calling, differential gene expression, differential methylated regions etc).
Excellent written and oral communication skills.
Ability to independently carry out high-quality research with tenacity and creativity.
Additional Desired Qualifications:
Experience in a scripting language (e.g. Perl, Python) is a must, knowledge of Unix tools, relational databases and R or MATLAB.
Good knowledge of online resources for plant or animal genome annotation.
Experience in or familiarity with statistical analysis.
The posting shall remain open until the position is filled.
This is a full time 2 year postdoctoral appointment with the possibility of renewal based upon satisfactory job performance, continuing availability of funds and ongoing operational needs. You must have less than 3 years paid postdoctoral experience. Salary for Postdoctoral positions depends on years of experience post-degree.
Full-time, M-F, exempt (monthly paid) from overtime pay.
This position is represented by a union for collective bargaining purposes.
Salary will be predetermined based on postdoctoral step rates.
This position is contingent on the successful completion of a background check.
Work will be primarily performed at DOE Joint Genome Institute (JGI) €” 2800 Mitchell Dr., Walnut Creek, CA.
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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