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NIH Grants in Bioinformatics Awarded January — March 2007

Computational Studies of Histone Modifications. Start date: Feb. 1, 2007. Expires: Jan. 31, 2012. Amount: $251,752 . Principal investigator: Yingkai Zhang. Institution: New York University. NIH institute: NIGMS.
Supports development of theoretical approaches that will combine ab initio quantum mechanical and molecular mechanical methods for modeling the catalytic mechanism for class I and II histone deacetylases. The project will also investigate histone lysine methyltransferases “to provide detailed insights into how the product specificity of histone lysine methylation is achieved,” according to the grant abstract.

Experimental and Computational Studies of Exit from Mitosis in Budding Yeast. Start date: Feb. 1, 2007. Expires: Jan. 31, 2011. Amount: $400,242. Principal investigator: John Tyson. Institution: Virginia Polytechnical Institute and State University. NIH institute: NIGMS.
Proposal to measure the molecular correlates of mitotic-exit events in budding yeast and to build detailed models of the signaling pathways that control these events — “the mitotic-exit network, the FEAR1 pathway, the DNA-damage checkpoint, and the spindle assembly checkpoint,” according to the grant abstract. The models will be used to make predictions about cell division under controlled conditions that will be tested by experimental collaborators.

Bioinformatics for Protein Microarrays. Start date: Feb. 1, 2007. Expires: Jan. 31, 2010. Amount: $316,487. Principal investigator: Richard Zangar. Institution: Battelle Pacific Northwest National Laboratories. NIH institute: NIBIB
Funds the development of protocols and software for analyzing protein microarray data. The investigators plan to create “protocols for the use of internal and external standards, develop the statistical foundation for evaluating data quality at all stages of data collection and analysis, and develop a sophisticated bioinformatics tool for rapid data analysis, including advanced quality control features,” according to the grant abstract.

Software Maintenance for Biomolecular Complexes. Start date: Feb. 15, 2007. Expires: Jan. 31, 2011. Amount: $298,350. Principal investigator: Chandrajit Bajaj. Institution: University of Texas, Austin. NIH institute: NIBIB.
Funds continued development of the Molecular Visualization and Processing (MVP) software package, which includes volumetric image processing, finite element meshing, analysis and rendering libraries and software tools. Specific aims include enhancing the volumetric and geometry processing, meshing, analysis, and rendering capabilities of the software. “These algorithms include new developments in fast and automatic identification of folds and structure units in 3D maps, hierarchical data structures that support multiresolution molecular surfaces, quality and topologically accurate finite element meshing, and automatic region of interest identification,” according to the grant abstract.

Database of Functional SNPs in Cancer-Related Environmentally Responsive Genes. Start date: March 1, 2007. Expires: Feb. 28, 2010. Amount: $272,254. Principal investigator: Yong Zhu. Institution: Yale University. NIH institute: NCI.
Funds a project that will “explore the application of available bioinformatic methods in functional SNP selection by focusing on genes responsible for environmental responses,” according to the grant abstract. The investigators plan to create a functional SNP database by identifying SNPs with potential functional importance in around 700 environmentally responsive genes using SNPs collected from public databases and screened by available bioinformatics tools. They will then “determine to what extent the predictive value of SNP functionality is mirrored in findings from molecular epidemiologic studies.”

Computational Assembly of Beta Barrel Membrane Protein. Start date: March 1, 2007. Expires: Feb. 29, 2012. Amount: $274,324. Principal investigator: Jie Liang. Institution: University of Illinois at Chicago. NIH institute: NIGMS.
Supports a project that plans to identify sequence and spatial motifs and anti-motifs in beta-barrel proteins for stability analysis; perform evolutionary analysis of beta-barrel membrane proteins to detect remote structural homologs and functional regions; and carry out large-scale prediction of three-dimensional structures and assembly of beta-barrel proteins. Aims of the project include developing computational algorithms, software, and databases that will be made publicly available for further studies.

64-Bit High Performance Computing. Start date: April 1, 2007. Expires: March 31, 2008. Amount: $402,523. Principal investigator: Edward Suh. Institution: Translational Genomics Research Institute. NIH institute: NCRR.
Supports the acquisition of a 64-bit SMP computing system at the Translational Genomics Research Institute. The grant abstract notes that TGen’s bioinformatics tools “require considerable computing power and large amount of memory to examine the enormous complexity of the solution space,” but adds that “conventional 32-bit computing architectures cannot address memory above 4 GB” — a memory limitation that “imposes suboptimal analytical approaches due to the prohibitively protracted computer analysis time needed for optimal mathematical models and computational algorithms.”

Computer Cluster for Computational and Structural Biology. Start date: April 1, 2007. Expires: March 31, 2008. Amount: $290,913. Principal investigator: Ronald Levy. Institution: Rutgers University, New Brunswick. NIH institute: NCRR.
Supports the purchase of a 150-processor Linux cluster to support nine NIH-funded investigators carrying out research in computational and structural biology, structural genomics, and proteomics. The cluster will use Opteron 280 AMD 64-bit dual-core processors.

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