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BioInform s Funding Update: NSF Bioinformatics Awards to Feb. 21, 2004

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A Scalable Framework for Mining Scientific and Biomedical Data. Start date: Jan. 15, 2004. Expires: Dec. 31, 2008. Expected total amount: $497,775. Principal investigator: Srinivasan Parthasarathy. Sponsor: Ohio State University Research Foundation.

Supports development of a scalable framework for mining large biomedical and scientific datasets. This project will develop graph-based methods to model the spatial or structural relationships embedded in such data, and will also develop parallel and incremental algorithms, along with cluster file system support, to mine such data.


Computational Methods for Learning Dynamic Networks of Biological Regulation and Control. Start date: Feb. 1, 2004. Expires: Jan. 31, 2009. Expected total amount: $487,344. Principal investigator: Alexander Hartemink. Sponsor: Duke University.

Project will develop new computational network-inference methods for elucidating the underlying mechanisms of complex biological systems, and also create a series of computational biology courses for the undergraduate and graduate curricula.


Prediction and Validation of Phospho-Regulatory Sites in Crop Plant Proteomes. Start date: Feb. 1, 2004. Expires: Jan. 31, 2006. Expected total amount: $691,501. Principal investigator: Jeffrey Harper. Sponsor: Scripps Research Institute.

Funds development of bioinformatics tools to predict a subset of potentially important sites of phospho-regulation in the rice proteome. A peptide array-based experimental strategy will validate those predictions.


Composition Patterns in Nucleotide Sequences. Start date: Sept. 1, 2003. Expires: June 30, 2004. Expected total amount: $86,623. Principal investigator: Gary Benson. Sponsor: Boston University.

Supports an investigation of computational problems that arise for the composition pattern — “a new type of discrete pattern in DNA sequences,” according to the grantees, which describes the frequency of occurrence of each alphabet letter in a particular string. The project will develop algorithms for three problem areas related to understanding composition variation: pattern matching, pattern detection, and sequence segmentation.


Critical Issues for Biomolecular Simulations: Organic Solvents, Protein-Protein and Nucleotide-Protein Interactions. Start date: March 1, 2004. Expires: Feb. 28, 2009. Expected total amount: $400,000. Principal investigator: Celeste Sagui. Sponsor: North Carolina State University.

Award supports research and education in computational biophysics, focusing on aspects of nucleic acid recognition and on protein-protein interactions.


Statistical Research in Drug Discovery and Development. Start date: Feb. 15, 2004. Expires: Jan. 31, 2007. Expected total amount: $398,828. Principal investigator: C. F. Jeff Wu. Sponsor: Georgia Tech Research Corp.

Project will explore the use of a new graphical procedure to address the issue of multiplicity in testing for microarray-based gene expression studies. The project will look into accurate estimation of false positive and false negative errors in high-throughput screening.


TRDB: A Multi-genome Database of Tandem Repeats. Start date: Sept. 1, 2003. Expires: Aug. 31, 2005. Expected total amount: $704,967. Principal investigator: Gary Benson. Sponsor: Boston University.

Supports development of a multi-genome tandem repeats database that will bring together information about repeats as well as serving as the platform for development of new tools. These include algorithms to compare and cluster repeats, as well as for identifying predictive criteria for copy number polymorphisms.


Biologically Inspired Computation to Understand Regulatory Gene Networks. Start date: Feb. 15, 2004. Expires: Jan. 31, 2005. Expected total amount: $100,000. Principal investigator: Bhubaneswar Mishra. Sponsor: New York University.

Funds a project to apply computational and mathematical methods to understanding gene networks. The researchers will study various topics dealing with genetic circuits, including the development of novel artificial circuits out of regulatory genes, RNAs, and proteins. The team also plans to infer gene networks with techniques analyzing time-course data.


Computational Biology at Howard University. Start date: May 1, 2004. Expires: April 30, 2007. Expected total amount: $999,997. Principal investigator: Louis Shapiro. Sponsor: Howard University.

Supports development of a concentration in computational biology in Howard University’s current doctoral programs in biology and mathematics. The concentration will consist of six courses plus the dissertation. Interdisciplinary research teams with faculty and Ph.D. students in mathematics and biology will also be formed.

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