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NIH Grants in Bioinformatics Awarded May — June 2006

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Development of the www.EcoliCommunity.org Information Resource. Start date: June 1, 2006. Expires: May 31, 2009. Amount: $1,077,550. Principal investigator: Barry Wanner. Institution: Purdue University West Lafayette. NIH institute: NIGMS.

Supports development of an integrated E. coli community information resource, called EcoliHub. EcoliHub will build on a prototype database designed to be integrated with cooperating resources, including EcoCyc, Genobase, and the OU microarray DB. The resource will include a chat room, computational tools, and related E. coli informatics from specialized databases including Brenda, GeneMark, GenProtEC, GO, LipoP, MEROPS, PORES, RegulonDB, Superfamily, and TransportDB.


Searching Genomes for Non-Coding RNAs by Their Structure. Start date: June 1, 2006. Expires: May 31, 2009. Amount: $232,552. Principal investigator: Liming Cai. Institution: University of Georgia. NIH institute: NIGMS.

Proposal to develop computational tools to model the structures of RNAs, to perform RNA structure alignment and database searches, and then to experimentally test these predictions. "Our approach is based upon conformational graph models and graph theoretic techniques, which can describe both stem-loop and pseudoknot structures," according to the grant abstract.


Statistical Methods for Genome-wide Association Studies. Start date: June 1, 2006. Expires: May 31, 2009. Amount: $206,253. Principal investigator: Peter Donnelly. Institution: University of Oxford. NIH institute: NIGMS.

Funds development of a general statistical framework and associated methodology for the analysis of genome-wide association studies. Aims include the development of experimental designs for genome-wide association studies; statistical methods for genome-wide multi-marker association testing; a methodology for the detection of interacting disease genes; and analysis tools for the joint analysis of multiple related genome-wide scans.


Robust Computational Framework for Predictive ADME-Tox. Start date: June 1, 2006. Expires: May 31, 2009. Amount: $349,361. Principal investigator: Alexander Tropsha. Institution: University of North Carolina, Chapel Hill. NIH institute: NIGMS.

Proposal to develop a predictive ADME-tox modeling framework based on rigorous quantitative structure activity/property relationships modeling. The project will focus on the design of optimized QSPR protocols for the development of reliable predictors of important ADME-tox properties, including water solubility, membrane permeability, P450 metabolism inhibition and induction, metabolic stability, human intestinal absorption, bioavailability, transporters and PK data. The goal of the project is to provide these tools via a web-based Predictive ADME-Tox Portal.


TM4: Software for High-Dimensional Data Analysis. Start date: June 1, 2006. Expires: May 31, 2010. Amount: $539,999. Principal investigator: John Quackenbush. Institution: Dana-Farber Cancer Institute. NIH institute: NLM.

Supports continued development of TM4, an open-source software system for the analysis of microarray data. TM4 currently has more than 10,000 registered users. Goals include code improvements, and regular, stable, well-documented updates.


Phylogenetic Analysis with Complex Genome Rearrangement Events. Start date: June 2, 2006. Expires: May 31, 2009. Amount: $220,145. Principal investigator: Jijun Tang. Institution: University of South Carolina at Columbia. NIH institute: NIGMS.

Funds the development of methods for mathematical modeling and theoretical analysis of complex evolutionary events such as gene duplication and loss, as well as algorithm design and implementation for phylogenetics and gene order reconstruction. These algorithms will be assessed "through extensive testing on simulated and biological datasets," and implemented via "a flexible approach to parallelization."


Software to Facilitate DNA Cloning. Start date: June 26, 2006. Expires: Dec. 25, 2006. Amount: $100,000. Principal investigator: Aline Glick. Institution: GSL Biotech. NIH institute: NCRR.

Proposal to develop commercial software that will "streamline the design and documentation of DNA cloning projects." Aims include the development of easy-to-use software designed to prevent cloning errors.


Accelerating Metabolic Discovery Using Characterization Data. Start date: July 1, 2006. Expires: June 30, 2008. Amount: $149,778. Principal investigator: Timothy Lilburn. Institution: American Type Culture Collection. NIH institute: NIAID.

Funds development of statistical tools for integrating data and inferring metabolic networks for "data-poor" bacteria. "This approach can eliminate the need for genome sequencing, gene expression experiments and the like for thousands of gram-negative facultative rod bacteria," according to the grantees.


New Scoring, Assembly and Evaulation Techiniques for Protein Structure Prediction. Start date: July 1, 2006. Expires: June 30, 2008. Amount: $142,256. Principal investigator: Dong Xu. Institution: University of Missouri, Columbia. NIH institute: NIGMS.

Proposal to develop models, scoring schemes, and techniques based on the mini-threading approach for protein structure prediction. Aims include developing new statistical models and computational methods to identify useful fragments in the Protein Data Bank for a query protein. The methods will identify these fragments using statistically significant matches instead of limiting the fragments to 9-mers as practiced by existing methods. The grantees will also use optimization techniques, such as semidefinite programming and evolutionary algorithms, to find efficient methods of assembling local structures.


Computer-aided Design of Anti-cancer Drugs Targeting Protein Kinases. Start date: July 1, 2006. Expires: June 30, 2009. Amount: $55,248. Principal investigator: Chung Wong. Institution: University of Missouri, St. Louis. NIH institute: NCI.

Supports development of a computational model to help develop therapeutic drugs targeting protein kinases. Immediate goals include developing a five-tier hierarchical computational screening model that "balances theoretical rigor and speed at different tiers to shorten the time and expense needed to select the most promising drug candidates from large chemical libraries and to further optimize them for potency, selectivity and drug-like properties," according to the grant abstract. The model will be used to identify new anti-cancer drug candidates for the protein kinase targets EGFR, HER2, CDK2, and BCR-ABL.


Systems Biology of Sporulation in Bacillus Subtilis. Start date: July 1, 2006. Expires: June 30, 2010. Amount: $322,880. Principal investigator: Jun Liu. Institution: Harvard University. NIH institute: NIGMS.

Funds development of methods that will apply mathematics and statistics to study developmental gene control in sporulation in the bacterium Bacillus subtilis. The grantees will develop biochemical and molecular genetic experiments to probe DNA sequence features responsible for protein binding "so as to feed to the development of computational strategies." Computational predictions will be tested experimentally to improve computational models.


Supporting RNAstructure: Software for RNA Analysis. Start date: July 1, 2006. Expires: June 30, 2010. Amount: $214,800. Principal investigator: David Mathews. Institution: University of Rochester. NIH institute: NIGMS.

Funds development of RNAstructure, a software package for RNA secondary structure prediction and analysis. The software, available at http://rna.urmc.rochester.edu, has been downloaded by more than 11,000 users. Aims include the development of enthalpy nearest neighbor parameters for RNA secondary structure formation to allow structure prediction and analysis at other temperatures, the construction of a web server to provide RNA secondary structure nearest neighbor parameters and offer tutorials on their use, and other improvements.


Methods for Analysis of High Throughput Assay Data. Start date: June 1, 2006. Expires: March 31, 2009. Amount: $225,000. Principal investigator: David Rocke. Institution: University of California, Davis. NIH institute: NHGRI.

Supports the development of methods of analysis and software implementations for gene expression data, proteomics data, and metabolomics data that are "informed by research on the statistical characteristics of the data that are to be analyzed," according to the grant abstract. the grantees will apply methods and software developed for gene expression data to the analysis of proteomics and metabolomics data by mass spectrometry and NMR spectroscopy.

 

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