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Opportunity: BIOINFORMATICIST Research Scientist -- single cell genomics (#75274) @ DOE Joint Genome Institute -- Walnut Creek, CA (US)
Submitted by Bill Cannan; posted on Wednesday, November 14, 2012
Organization: GN-Genomics

The DOE Joint Genome Institute (JGI) in Walnut Creek, CA (a division of the Lawrence Berkeley National Lab) has an exciting research opportunity available for an experienced Bioinformaticist. Will work within a small scientific team as part of the Microbial Genome and Metagenome program and serve as a Bioinformaticist Research Scientist and perform research relevant to the analysis of single cell genomes. Strong emphasis will be placed on the development of new bioinformatics tools and approaches for analyzing and visualizing single cell data sets including co-assemblies of single cell and environmental data. Will distribute results to the scientific community by publication, scientific presentations, and over the web and collaborate with a team of software developers to implement bioinformatics tools as part of the JGI QC pipeline and Integrated Microbial Genomes System (IMG). Position will report to the Microbial Genomics Program lead.

Specific Job Duties:
* Design and implement gene and genome analysis methods, develop and apply computational algorithms for the characterization and comparison of large-scale DNA sequence datasets (single cell genomes, metagenomes) to study the evolution of genes and genomes and their relationship to organismal complexity and diversity.
* Devise and perform tests to assess the quality of input and output data and troubleshoot moderately complex systems and data analysis issues.
* Compare different assembly strategies and sequencing platforms and summarize the findings concisely.
* Contribute to the development of visualization tools for complex biological data and novel algorithms to solve bioinformatics problems relating to single cell datasets.
* In collaboration with scientific programmers and software developers in at the JGI, work on pipeline development for microbial single cell genome data QC and analysis, to automate some of the commonly used data processing steps.
* Interact with peers within and outside of the JGI to ensure efficient communication and completion of analysis projects.
* Store and organize results for presentation and viewing by JGI collaborators and the wider scientific community.
* Publish in peer review journals and deliver scientific presentations at scientific meetings

* Attend and present status reports at JGI meetings.
* Keep and maintain accurate and detailed records of all research and experiments performed.
* Attend group meetings and present technical status reports and scientific results.

Key Success Factors:
* Ph.D. in Bioinformatics or a related field
* Familiarity with molecular biology, comparative genomics, metagenomics, and microbial ecology
* Experience in biological data analysis using programming languages such as Perl, C/C++, Java, or equivalent
* Expertise in developing computational algorithms and building and using computer tools and databases for bioinformatics research and visualization
* Broad understanding of bioinformatics tools used for genome and metagenome analysis (i.e., assembly, binning, gene calling, etc.) and gene function prediction (i.e. sequence alignment, database search, etc.)
* Experience with statistical data analysis using R, visualization of (comparative) genomics data and phylogenetic analysis
* Experience with HPC environments/distributed computing such as Sun Grid Engine (SGE) or equivalent
* Ability to document and summarize research results for presentation and publications; must have a strong record of publications in peer-reviewed journals
* Strong analytical and organizational skills
* Excellent interpersonal, oral, and written communication skills
* Ability to work independently as well as part of a diverse team
* Proficient computer skills, including experience using UNIX/Linux, Mac and/or PC operating systems


To apply, please click "apply online" and follow the application instructions.

Berkeley Lab is an affirmative action/equal opportunity employer committed to the development of a diverse workforce.

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