Cooperative Ecosystem Studies Unit, Souther Appalachian Mountains CESU | Apply Online

Opportunity Summary:

The Cooperative Ecosystem Studies Unit, Southern Appalachian Mountains CESU funding opportunity (Funding Opportunity Number 10HQPA0022) is a US Geological Survey (USGS) discretionary research award offered as a cooperative agreement under CFDA 15.808 (USGS Research and Data Collection). The project is focused on advanced bioinformatics support for analyzing laboratory-generated DNA/RNA sequence data, with an emphasis on transcriptome assembly across multiple taxonomic groups, including both invertebrates and vertebrates, and across multiple species within those groups. The work sits squarely in the science and technology research and development category and is framed as collaborative, hands-on technical and analytical assistance rather than a simple, stand-alone research grant.

The core purpose of the award is to fund expertise needed to take large-scale gene expression and sequencing outputs and turn them into interpretable biological results. The announcement highlights a need for specialists who can analyze data related to microarrays and transcriptomics, including identification and interpretation of splice variants, SNP discovery and characterization, regulatory sequence features such as cis elements, and small RNA biology such as miRNAs. A major component is the use of contemporary data mining methods to build and refine gene models, assign gene names, classify paralogous gene families, align assembled sequences to related species, and carry out gene ontology annotation so that downstream ecological or evolutionary inferences can be made from the data.

From a technical standpoint, the opportunity expects strong computational capability and familiarity with practical bioinformatics infrastructure. The work likely involves relational database design and use, writing and optimizing SQL queries, operating in UNIX environments, and developing scripts in PERL. Beyond basic analysis, the award calls for setting up automated or semi-automated processing systems that can handle very large volumes of raw and derived data, supporting repeatable workflows for data processing, data mining, statistical analysis, and results reporting. In other words, the project is not just about running a few tools; it is about building reliable pipelines and quality-controlled analysis cycles that can be reused and scaled.

The scope also emphasizes end-to-end support for microarray data analysis projects, explicitly mentioning a "full cycle" of analysis using a mix of public, licensed, and in-house bioinformatics tools. The successful team or partner is expected to be comfortable with experimental research design and with software used across multiple gene expression profiling approaches. The cooperative agreement format signals close collaboration with the USGS Principal Investigator, including troubleshooting, helping implement and verify laboratory quality control measures, and interpreting outcomes in light of those QC checks. The work is designed to be integrated with a broader interdisciplinary environment, where the bioinformatics contributor interacts routinely with bioinformatics analysts and engineers, molecular biologists, immunologists, statisticians, and computer programmers.

In terms of broader impact, the opportunity ties this analytical capability to federal resource management needs, particularly research that helps identify ecological and evolutionary processes affecting threatened and endangered species or invasive species. The project is positioned as a collaborative research support effort that can directly inform conservation and management decisions by improving how genomic and transcriptomic evidence is processed, annotated, and interpreted for species and systems of management concern.

Administratively, the opportunity anticipated a single award (Expected Awards: 1) with an estimated total funding amount of $70,000. No cost sharing or matching requirement is listed. The posted date was December 9, 2009, with an original and current closing date of December 19, 2009, and an archive date of January 18, 2010. Eligibility is restricted to partners within the Southern Appalachian Mountains CESU Program, reflecting the CESU model as a formal partnership network that provides research, technical assistance, and education. The listed agency contact for access issues is Faith Graves, Contract Specialist, at 703-648-7356.

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Previous opportunity: Cooperative Ecosystem Studies Unit, Piedmont South Atlantic CESU

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