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NIH Grants in Bioinformatics Awarded Sept. 2005 -- Nov. 2005

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Computational and Structural Biology in Biodefense. Start date: Sept. 1, 2005. Expires: July 31, 2010. Amount: $103,542. Principal investigator: David Gorenstein. Institution: University of Texas Medical Branch, Galveston. NIH institute: NIAID.

Funds a multidisciplinary pre-doctoral and post-doctoral training program in computational and structural biology in biodefense, which will span the fields of biochemistry, biophysics, molecular biology, structural biology, bioinformatics, genomics, proteomics, database management, chemical biology, cell biology, immunology, virology, and pathology.


Improved Protein Mapping for Fragment-Based Drug Design. Start date: Sept. 15, 2005. Expires: Sept. 14, 2006. Amount: $100,000. Principal investigator: Sandor Vajda. Institution: Solmap Pharmaceuticals. NIH institute: NIGMS.

Phase I SBIR funds development of a solvent-mapping algorithm that eliminates spurious local energy minima that are generated by current methods, which place molecular probes on a protein surface in order to identify the most favorable binding positions. The major applications of the method are in delineating the active sites of enzymes and other proteins, and detecting minor conformational changes in ligand-binding sites. The grantees intend to develop the mapping algorithm into the first step of a fragment-based drug design procedure, and apply the method to drug targets that are known to be difficult.


Computational Prediction of Biomolecular Dynamics. Start date: Sept. 15, 2005. Expires: Aug. 31, 2008. Amount: $324,097. Principal investigator: Ivet Bahar. Institution: University of Pittsburgh. NIH institute: NIGMS.

Supports improvements on the Gaussian Network Model, which was recently developed to predict protein dynamics. In the present proposal, the grantees will develop a new method to overcome the limitations of GNM and predict the collective dynamics of proteins and larger complexes.


Establishment of the RPI Exploratory Center for Cheminformatics. Start date: Sept. 23, 2005. Expires: July 31, 2007. Amount: $375,639. Principal investigator: Curtis Breneman. Institution: Rensselaer Polytechnic Institute. NIH institute: NHGRI.

Funds the Exploratory Center for Cheminformatics Research, which will support pilot projects in cheminformatics-related fields, including methods of encoding and capturing molecular information; machine learning and data mining techniques; and predictive model development, validation, interpretation, and utilization.


National Center for Integrative Biomedical Informatics. Start date: Sept. 25, 2005. Expires: Aug. 31, 2010. Amount: $3,758,966. Principal investigator: Brian Athey. Institution: University of Michigan at Ann Arbor. NIH institute: NIDA.

Funds the National Center for Integrative Biomedical Informatics, which will "develop problem-posing computational architectures within a managed software and data infrastructure that will permit the facile manipulation and analysis of today's massive data sets," according to the grant abstract. NCIBI will support research projects in Type I and Type II diabetes, prostate cancer, and the genetics of bipolar disorders.


National Center: Multi-Scale Study of Cellular Networks. Start date: Sept. 26, 2005. Expires: July 31, 2010. Amount: $3,758,967. Principal investigator: Andrea Califano. Institution: Columbia University Health Sciences. NIH institute: NCI.

Supports the National Center for the Multiscale Analysis of Genomic and Cellular Networks (MAGNet), which will "provide an integrative computational framework to organize molecular interactions in the cell into manageable context-dependent components and will develop interoperable computational models and tools that can leverage such a map of cellular interactions to elucidate important biological processes," according to the grant abstract.


Novel Algorithms and Organisms for Onto-Tools. Start date: Sept. 26, 2005. Expires: Aug. 31, 2008. Amount: $300,000. Principal investigator: Sorin Draghici. Institution: Wayne State University. NIH institute: NHGRI.

Supports continued development of Onto-Tools, an open-access gene-expression analysis package originally launched in 2001. The current grant supports development of Onto-Analyzer, a set of novel data analysis techniques based on latent semantic indexing and statistical analysis, which will be able to discover previously unknown interactions and phenomena at the genetic level, according to the grantees. Onto-Tools will also be enhanced by adding support for 17 new organisms.


Data Management, Statistics, and Informatics Core. Start date: Sept. 30, 2005. Expires: March 31, 2010. Amount: $1,059,525. Principal investigator: Heping Zhang. Institution: Yale University. NIH institute: NICHHD.

Proposal to establish a data management, statistics, and informatics core at Yale University as a part of the Genomic and Proteomic Network for Premature Birth Research. The core will be responsible for the central database, data analysis, and management; information technology; and coordination of the administrative activities of the network.


Polarity in Networks and Pathways. Start date: Sept. 30, 2005. Expires: July 31, 2010. Amount: $2,464,680. Principal investigator: Leslie Loew. Institution: University of Connecticut School of Medicine and Dentistry. NIH institute: NCRR.

Proposal to establish a Technology Center for Networks and Pathways that will integrate microscope technologies for making quantitative in vivo live cell measurements with new computational tools that will produce spatially realistic quantitative models of intracellular dynamics. These technologies will be developed and disseminated by the Center for Cell Analysis and Modeling at the University of Connecticut Health Center, the home of the Virtual Cell project, which is a computational environment for cell biological modeling.


New Tools for Exploring the Dynamic Interactome. Start date: Sept. 30, 2005. Expires: July 31, 2010. Amount: $2,775,587. Principal investigator: Michael Rout. Institution: Rockefeller University. NIH institute: NCRR.

Supports a proteomics project that includes the development of software to integrate data and represent "the actions of the macromolecular players in many dynamic subcellular assemblies," according to the grant abstract.


Comparative Bioinformatics and TP53 Expression. Start date: Sept. 30, 2005. Expires: Sept. 29, 2010. Amount: $295,387. Principal investigator: Peter Waddell. Institution: University of South Carolina at Columbia. NIH institute: NLM.

Funds a project to perform a "dense" comparative alignment of the TP53/GBN5 cis-regulatory region across 14 mammals and experimentally verify the hypotheses generated from the results of the alignment.

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