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NIH Grants in Bioinformatics Awarded Feb. 2006 -- March 2006

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Evolutionary Modeling/Prediction of ncRNA Genes in Flies. Start date: Feb. 1, 2006. Expires: Jan. 31, 2011. FY 2006 amount: $224,366. Principal investigator: Ian Holmes. Institution: University of California, Berkeley. NIH institute: NIGMS.

Funds development of evolutionary models to identify non-coding RNA genes by comparative analysis of twelve fruit fly genomes. All software will be freely available online.


Predicting protein flexibility and stability. Start date: March 1, 2006. Expires: Feb. 28, 2010. FY 2006 amount: $365,930. Principal investigator: Donald Jacobs. Institution: University of North Carolina Charlotte. NIH institute: NIGMS.

Supports development of a Distance Constraint Model (DCM) to accurately predict protein stability in aqueous solution under specified thermodynamic conditions from known three-dimensional structure. A proof of concept, minimal DCM, will be extended in this project to include explicit modeling of essential entropy-compensation mechanisms that include hydration, hydrophobic interactions, and electrostatic interactions with a residue-specific parameterization.


Efficient Analysis of SNPs & Haplotypes with Applications in Gene Mapping. Start date: March 15, 2006. Expires: Feb. 28, 2009. FY 2006 amount: $402,001. Principal investigator: Jing Li. Institution: Case Western Reserve University. NIH institute: NLM.

Proposal to develop new algorithmic approaches and software tools to address some of the fundamental issues in the analysis of SNPs and haplotypes with applications in gene association mapping. The investigators plan on developing algorithms to infer haplotypes from genotypes on a pedigree, impute missing SNPs, discover the haplotype structure, and select informative (tag) SNPs.


The Transporter Classification Database (TCDB). Start date: April 1, 2006. Expires: March 31, 2010. FY 2006 amount: $293,313. Principal investigator: Milton Saier. Institution: University of California, San Diego. NIH institute: NIGMS.

Supports development of the Transporter Classification Database, a curated repository compiled from more than 10,000 references, including around 3,000 transport proteins and putative transporters, classified into about 400 families. Primary goals include automating text-classification and information-extraction software to facilitate the continual updating of TCDB as newly published information about transporters becomes available and developing software for the "semiautomatic prediction of transport functions for putative transporters for which complete sequence data but little or no experimental data are available," according to the grant abstract.


Bioimage Suite: A structural, functional and metabolic image analysis platform. Start date: April 1, 2006. Expires: Jan. 31, 2010. FY 2006 amount: $362,732. Principal investigator: Xenophon Papademetris. Institution: Yale University. NIH institute: NIBIB.

Funds development of the Bioimage Suite, a collection of software development efforts in image processing and analysis at Yale. The grant will enable the developers to "extend, document, and further test this software in order to provide a practical software suite for imaging researchers and enable us to freely disseminate it to researchers both at Yale and at other research institutions," according to the abstract.

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