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BioInform s Funding Update: NSF Bioinformatics Awards through August 30, 2003

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Some Algorithmic Issues in Computational Biology. Start date: Aug. 15, 2003. Expires: July 31, 2004. Expected total amount: $80,685. Principal investigator: S. Rao Kosaraju. Sponsor: Johns Hopkins University.

Supports investigation of algorithmic issues in computational biology, including gene networks, DNA sequence assembly, and DNA sequence analysis.


BioText: Improving Search over Bioscience Literature via Language Analysis and User Interface Design. Start date: Aug. 15, 2003. Expires: July 31, 2007. Expected total amount: $840,027. Principal investigator: Marti Hearst. Sponsor: University of California Berkeley.

Award to design a new search system for bioscience literature using a computational linguistics technique called “statistical semantic grammars.”


Plant Evolutionary Genomics: Develop and Test Bioinformatic Tools to Automate Ortholog Identification for Phylogenomics and Functional Genomic Studies. Start date: Sept. 1, 2003. Expires: Aug. 31, 2004. Expected total amount: $83,201. Principal investigator: Gloria Coruzzi. Sponsor: New York University.

Supports development of new informatic tools for high-throughput ortholog identification using known genes from rice and Arabidopsis.


Learning through Associations in a Grid-based Bioinformatics Digital Library. Start date: Sept. 1, 2003. Expires: Aug. 31, 2005. Expected total amount: $449,563. Principal investigator: Javed Mostafa. Sponsor: Indiana University.

Project to apply digital library technologies to bioinformatics, and develop interaction tools to visualize associations among bioinformatics resources.


A Power and Sample Size Atlas for Microarray Research. Start date: Sept. 1, 2003. Expires: Aug. 31, 2005. Expected total amount: $97,835. Principal investigator: Jode Edwards. Sponsor: University of Alabama Birmingham.

Grant to develop a “power atlas” for microarray data sets for use in the determination of sample size requirements that meet criteria set by a researcher.


The Plant Ontology Consortium. Start date: Sept. 1, 2003. Expires: Aug. 31, 2006. Expected total amount: $1,672,411. Principal investigator: Lincoln Stein. Sponsor: Cold Spring Harbor Laboratory.

Supports the Plant Ontology Consortium, which is developing a controlled vocabulary to describe anatomic- and developmental-stage terms in plants.


Semantic Map of Biological Data Sources: Entity Identity and Path Characterization. Start date: Sept. 1, 2003. Expires: Aug. 31, 2006. Expected total amount: $325,000. Principal investigator: Zoe Lacroix. Sponsor: Arizona State University.

Project aims to construct a semantic map of biological data sources including unique identifiers, links between sources, and query capabilities. Tools will be accessible at http://www.umiacs.umd.edu/research/CLIP/BFEnt02/.


Iterative Hybrid Alignment: Improving the Sensitivity of Biological Database Searches. Start date: Sept. 1, 2003. Expires: Aug. 31, 2006. Expected total amount: $350,139. Principal investigator: Ralf Bundschuh. Sponsor: Ohio State University Research Foundation.

Grant to develop a sensitive homology search algorithm. The first implementation is proposed as a redesign of Psi-Blast but “it amounts to a complete replacement of the core algorithm,”according to the investigators.


A Protocol For Computational Protein Design. Start date: Sept. 1, 2003. Expires: Aug. 31, 2008. Expected total amount: $500,000. Principal investigator: Chen Zeng. Sponsor: George Washington University.

Project to develop a computational protocol based on the principle of designability in order to address the problem of designing novel protein folds.


Enhancing Access to the Bibliome for Genomics. Start date: Sept. 15, 2003. Expires: Aug. 31, 2008. Expected total amount: $1,206,377. Principal investigator: William Hersh. Sponsor: Oregon Health and Science University.

Project to improve information retrieval systems for the biomedical literature by developing tools that allow system developers to evaluate retrieval capabilities.


Reconstruction and Simulation of Genome-Scale Regulatory Networks. Start date: Oct. 1, 2003. Expires: Sept. 30, 2006. Expected total amount: $432,697. Principal investigator: Bernhard Palsson. Sponsor: University of California San Diego.

Project to establish an integrated framework for building models of transcriptional regulatory networks and incorporating them into genome-scale models of metabolism in microbial organisms.

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