DOE-JGI Call for LOIs for Large-Scale Genomics Proposals due April 10, 2014

The DOE Joint Genome Institute (DOE JGI) Community Science Program (CSP) is now accepting Letters of Intent for large-scale sequence-based genomic science projects that address questions of relevance to DOE missions in sustainable biofuel production, global carbon cycling, and biogeochemistry. Priority for this call will be given to projects that address the following areas of special emphasis and exploit the diversity of DOE JGI capabilities. The CSP data is immediately made publicly available, without exception.

A summary of the 2015 CSP Call is below. The full Call can be found here:

I. Functional Genomics and Microbiomes of DOE JGI Flagship Plants: Emphasis will be on proposals related to DOE JGI’s “flagship” plant genomes, including poplar, sorghum, Brachypodium, Chlamydomonas, soybean, foxtail millet, Physcomitrella, switchgrass, and miscanthus. These species are of special interest as biofuel feedstocks or as comparators that provide insight into feedstock evolution and phenotype. Projects may fall into the following categories:

a) Gene Atlas and ENCODE-like projects;

b) Large-scale resequencing projects;

c) Plant microbiomes.

II. Probing functional diversity of microbes: To complement its Genomic Encyclopedia of Bacteria &Archaea (GEBA) and 1000 FungalGenomes initiatives, the DOE JGI has begun to explore microbial functional diversity. Proposals are encouraged that extend this effort using high-throughput sequencing, and the DOE JGI’s DNA synthesis capabilities and are expected to use one or a combination of the DOE JGI’s (meta-) genome, (meta-) transcriptome, single-cell and isolate sequencing and resequencing pipelines. ENCODE-like projects for functional genomics that could serve as model organisms for DOE-relevant problems are encouraged and could include new DOE JGI capabilities for genome-wide transcriptomics, including non-coding and small RNAs, and epigenomics, including methylation detection and ChIP-seq.

III. Microbial emission and capture of greenhouse gases in terrestrial systems: Proposals are encouraged that will provide insight into global carbon (including methane) and nitrogen cycles, and/or suggest novel strategies for carbon capture, nitrogen processing, or methane reduction through gene/genome engineering.

IV. Discovery and expression of natural product pathways relevant to energy-related and environmental processes: The DOE JGI has developed a platform that enables the discovery of novel natural products based on technology combining computational genomics, pathway refactoring, host engineering, and high-throughput analytics.


Letters of intent (LOI) will only be accepted electronically and should be submitted at

· LOI due: April 10, 2014

· Full proposals invited: April 24, 2014

· Full proposals due: June 5, 2014

· Projects begin: October 2014

Questions? Contact:

Axel Visel (avisel), DOE JGI Strategic Planning-Science Lead.

About Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis
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