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NSF Bioinformatics Grants, May 14 — June 17 2006

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Computational Studies of Dynamic Molecular Search Mechanisms. Start date: June 15, 2006. Expires: May 31, 2007. Expected total amount: $538,624. Principal investigator: Aaron Dinner. Sponsor: University of Chicago.

Funds development of computational tools for characterizing the dynamics of molecular recognition, which will be applied to the human protein O6-alkylguanine-DNA alkyltransferase (AGT). The research will "promote application of state-of-the-art methods for studying activated dynamics to biomolecular systems, and their use to treat the dynamics of AGT and DNA will provide atomic-level insight into the kinetic strategies molecules use to control their interactions," according to the grant abstract.


Computational Methods for Exploring the Geometry of Large Data Sets. Start date: June 1, 2006. May 31, 2009. Expected total amount: $212,855. Principal investigator: Gilad Lerman. Sponsor: University of Minnesota, Twin Cities.

Funds development of a computational and theoretical framework to analyze large data sets with low-dimensional intrinsic structure. Applications include the identification of protein-binding genomic regions and quantitative exploration of the functional domain in the gene ontology and its relation with structural properties.


Computational Biology Facility for Western Massachusetts. Start date: June 1, 2006. Expires: May 31, 2007. Expected total amount: $185,015. Principal investigator: Oliver Brock. Sponsor: University of Massachusetts, Amherst.

Supports the acquisition of a computer cluster for research in bioinformatics and computational biology.


Characterization of the Tomato Secretome Using Integrated Functional and Computational Strategies. Start date: June 1, 2006. Expires: May 31, 2007. Expected total amount: $3,627,035. Principal investigator: Jocelyn Rose. Sponsor: Cornell University.

Funds an integrated project to catalog the tomato "secretome" — the composition and dynamic properties of the cell wall proteome. The project will combine a suite of new functional screens with sequencing of purified wall protein extracts, bioinfomatic tools, and computational prediction. A publicly accessible tomato secretome database, called SecreTom, will be developed to house the project data, to provide access to all associated computational tools, and to act as a hub for plant wall proteome research.


WebFusion — Autonomous Data Integration Tools for Biotechnology. Start date: July 1, 2006. Expires: Dec. 31, 2006. Expected total amount: $99,992. Principal investigator: Khaled Jababo. Sponsor: OishiiTech.

Phase I SBIR supports development of a graphical front-end database interface that will allow biologists to manage data on a local computer as well as remotely. The proposed product, called WebFusion, will provide "faster and more accurate data management tools to fully exploit the large commercial and public databases available online and through other sources," according to the grant abstract.


Machine Learning Software for Viral Sequence Analysis and Diagnostics. Start date: July 1, 2006. Expires: Dec. 31, 2006. Expected total amount: $100,000. Principal investigator: Gary Fogel. Sponsor: Natural Selection.

Phase I SBIR funds development of computational tools for viral sequence analysis that can be used to understand the relationship between sequence variations and phenotypic behavior and or response. The software will help predict the effect of viral mutations on infectivity and efficacy of the virus as well as aid in the development of antivirals and predict the effect of treatments.


Developing a Bioinformatics Database for Stoichioproteomics. Start date: July 1, 2006. Expires: June 30, 2007. Expected total amount: $1,027,900. Principal investigator: William Fagan. Sponsor: University of Maryland, College Park.

Supports the exploration of how the availability of nutrients in the environment affects proteins by modulating their amino acid composition. To do so, the project will create a bioinformatics database, the Genomics Resource Access for Stoichio-Proteomics (GRASP), which will contain an integrated ecological dataset for insect species and a database of protein composition.


MultiMedia Information Retrieval for Biological Research. Start date: July 1, 2006. Expires: June 30, 2007. Expected total amount: $1,198,998. Principal investigator: Linda Shapiro. Sponsor: University of Washington.

Supports development of a "unified methodology" for the organization and retrieval of biological data, particularly image data and related measurements from scientific experiments. The grantees will develop a probabilistic query framework for multimedia data that will provide users with a unified way to access multiple types of data.


Characterization, Quantification, and Management of Sequence-Alignment Errors with Emphasis on Molecular Phylogenetic Reconstructions. Start date: July 1, 2006. Expires: June 30, 2007. Expected total amount: $723,859. Principal investigator: Dan Graur. Sponsor: University of Houston.

Supports a project that will classify errors in multiple sequence alignment and develop tools and protocols through which alignment errors and uncertainties can be accounted for and properly managed. "The practical effects of alignment-error management will be assessed on real databases and real phylogenetic problems," according to the grant abstract. All software, data, and protocols will be made freely available.


Bioinformatics Tools Enabling Large-Scale DNA Barcoding. Start date: July 1, 2006. Expires: June 30, 2009. Expected total amount: $399,602. Principal investigator: Ion Mandoiu. Sponsor: University of Connecticut.

Proposal to develop bioinformatics tools and design methodologies that will enable large-scale species identification based on universal DNA arrays. The work will include efficient combinatorial algorithms for optimization problems in the design of large-scale identification assays.


Computational Methods and Software for Structured Multiscale Models of Tumor Invasion. Start date: Aug. 1, 2006. Expires: July 31, 2008. Expected total amount: $120,641. Principal investigator: Bruce Ayati. Sponsor: Southern Methodist University.

Proposal to develop computational methods and software to solve systems of partial differential equations in multiscale models of tumor invasion. The software will be developed with cancer biologists at Vanderbilt University and will handle "the complicated situation where the different genetic profiles of the multitudes of individual cells within a tumor, and the different stages in the cell-division cycle of each of these cells, are linked to the physically larger complete tumor," according to the grant abstract. This is expected to be useful in studying the effects of chemotherapy when using drugs that affect cells differently depending on their genetic type or what part of the cell-division cycle they are in.


Automated Annotation of Function in Protein Structures from Evolutionary-based 3D-Templates. Start date: Sept. 1, 2006. Expires: Aug. 31, 2007. Expected total amount: $1,288,463. Principal investigator: Olivier Lichtarge. Sponsor: Baylor College of Medicine.

Project will develop automated algorithms to identify functional sites in protein structures and to characterize protein function on a genome scale. The approach will build on the Evolutionary Trace method to locate functional sites in structures.

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