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BioInform s Funding Update: Some Recent NIH Awards in Bioinformatics: Nov 3, 2003

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Integrated SNP, Gene Expression, and Proteomic Analysis. Start date: Sept. 2003. Expires: March 2004. Amount: $68,876. Principal investigator: Jonathan Buckley. Institution: Epicenter Software. NIH institute: NHGRI.

SBIR funds development of a software suite (Genetrix) comprised of tools for data management, visualization, machine learning, statistical analysis, and biologic interpretation of data from large-scale biological platforms in conjunction with ancillary clinical, demographic, epidemiological, laboratory, and outcome data.


Computational Tools for Bayesian Mixture Modeling. Start date: Sept. 2003. Expires: June 2005. Amount: $148,199. Principal investigator: Mario Medvedovic. Institute: University of Cincinnati. NIH institute: NHGRI.

Project to develop computational tools to extract biologically significant patterns from functional genomics data. Proposed computational procedures will be based on the Bayesian infinite mixture model. The software will also incorporate other relevant statistical techniques for correlating gene expression and cis-regulatory elements data.


A Statistical Computing Framework for Genomic Data. Start date: Sept. 2003. Expires: June 2006. Amount: $770,540. Principal investigator: Robert Gentleman. Institute: Dana-Farber Cancer Institute. NIH institute: NHGRI.

Supports development of a software infrastructure based on the R programming language to enable the integration of experimental data with biological metadata. In particular, computational methods will address visualization, computational inference, multiple comparisons, and specialized analytic methods for microarray data.


ACT Database: Protein Structure-Function Relationships. Start date: Sept. 2003. Expires: Sept. 2006. Amount: $206,212. Principal investigator: James Bowie. Institution: University of California Los Angeles. NIH institute: NLM.

Supports the ACT Database, which describes in machine-readable form the functions and molecular interactions of 680 proteins selected from the Protein Data Bank. Goals include doubling the size of the database so that all structures currently in PDB will be homologous to at least one ACT entry.


Representing and Acquiring Knowledge of Genome Regulation. Start date: Sept. 2003. Expires: Sept. 2007. Amount: $335,521. Principal investigator: David States. Institution: University of Michigan at Ann Arbor. NIH institute: NLM.

A pilot project to develop automated knowledge extraction technology for the research literature. The regulation of gene expression in hematopoiesis will be used as a test domain.


Computational Biology Core for the Texas Regional Center of Excellence. Start date: Sept. 2003. Expires: Feb. 2008. Amount: NA. Principal investigator: Harold Garner. Institution: University of Texas Southwestern Medical Center Dallas. NIH institute: NIAID.

Funds bioinformatics support for the Texas Regional Center of Excellence (RCE) in biodefense. Deliverables include bioinformatics tools, custom databases, experimental designs, data acquisition/archival/access methods and data analysis/interpretation methods.


Data Integration and Bioinformatics. Start date: Sept. 2003. Expires: Feb. 2008. Amount: NA. Principal investigator: Mitchell Brittnacher. Institution: University of Washington. NIH institute: NIAID.

Supports a central integrated data system and bioinformatics and computational support group at the University of Washington in connection with the Regional Center of Excellence for biodefense. The database will include DNA microarray expression ratios, peptide identification results from mass spec analysis, sequence data for bacterial strains, mutagenic and phenotypic data, and experimental conditions.


Integrated Proteome Technologies for Pathway Mapping. Start date: Sept. 2003. Expires: July 2008. Amount: $2,496,891. Principal investigator: Philip Andrews. Institution: University of Michigan at Ann Arbor. NIH institute: NCRR.

Proposal to develop improved technologies for proteome mapping, as well as methods to query changes in signal transduction, identification of protein interactions, and improved algorithms and computational tools for analyzing proteomics data.


Implications of Haplotype Structure in the Human Genome. Start date: Sept. 2003. Expires: Aug. 2008. Amount: NA. Principal investigator: Michael Waterman. Institution: University of Southern California. NIH institute: NHGRI.

Project to develop efficient algorithms to improve the accuracy of polymorphism detection by both DNA sequencing and hybridization chips and develop efficient computational algorithms for haplotype block partitions and tag SNP selection.

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