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NSF Bioinformatics Awards to Dec. 31, 2005


Four-Dimensional Subcellular Structure Tracking and Modeling for Cell Dynamics Study. Start date: Jan. 1, 2006. Expires: Dec. 31, 2006. Estimated total amount: $558,077. Principal investigator: Jean Gao. Sponsor: University of Texas, Arlington.

Proposal to develop a web-based open access Cell Dynamics Analysis System (CellDAS) for automating subcellular particle motion estimation, tracking, and mobility analysis. The researchers will first develop a divergence filter to detect directed motion and then use a Markov chain Monte Carlo sampling framework for multi-object tracking, which "overcomes the exponential complexity problem," according to the grant abstract.

Bayesian Signal Processing for Uncovering Gene Regulatory Networks. Start date: Dec. 15, 2005. Expires: Nov. 30, 2007. Estimated total amount: $400,000. Principal investigator: Yufei Huang. Sponsor: University of Texas, San Antonio.

Project will investigate Bayesian signal processing solutions for uncovering gene regulatory networks. The researchers will investigate a novel graphical modeling framework for accurate and robust modeling of gene regulation; investigate a novel Bayesian framework for systematic and efficient data integration; investigate systematic procedures for effective results validation and error analysis; and apply the developed solutions to uncover the cell cycle gene regulatory networks of yeast and Plasmodium falciparum.

Next Generation Computer-Assisted Thinking Tools for Plant Scientists. Start date: Dec. 1, 2005. Expires: Nov. 30, 2006. Expected total amount: $166,533. Principal investigator: Nina V. Fedoroff. Sponsor: Pennsylvania State University, University Park.

Proposal to create computational tools that will allow experimental biologists "to explore accumulated information about biological systems without precluding access to contradictory information," according to the grant abstract. The approach will store ingredients for model building at the evidence level and enable biologists "to continuously and actively participate in model-building through the familiar device of formulating and testing hypotheses." The tools will be integrated into the Arabidopsis Information Resource database (

An Investigation of Biomolecular Graphs. Start date: Dec. 15, 2005. Expires: Nov. 30, 2006. Expected total amount: $100.000. Principal investigator: Debra Knisley. Sponsor: East Tennessee State University.

Proposal to develop graphical models of biomolecules, including both nucleic acids and proteins. Primary areas of focus include secondary and tertiary RNA structures, nucleotide excision repair, and tertiary protein structures and protein folding.

Reconstruction and Annotation of Transcribed Sequences in Plants. Start date: April 1, 2005. Expires: June 30, 2006. Expected total amount: $622,025. Principal investigator: John Quackenbush. Sponsor: Dana-Farber Cancer Institute

Grant supports expansion and continued development of the TIGR Plant Gene Indices (, including the development of a plant version of the Resourcer tool.

Combinatorial Algorithms for High-Throughput Collection and Analysis of Genomic Diversity Data. Start date: Jan. 15, 2006. Expires: Dec. 31, 2006. Estimated total amount: $554,572. Principal investigator: Ion I. Mandoiu. Sponsor: University of Connecticut.

Proposal to develop a high-throughput SNP genotyping assay along with novel likelihood maximization algorithms for addressing the computational problems that arise in two-stage sampling design association studies, including haplotype tagging SNP selection and haplotype reconstruction from genotype data. The researchers will also develop open-source software implementations and methodologies for evaluating the proposed algorithms, as well as curriculum and educational materials, including the creation of a new textbook on computational genomics.

Mathematical Modeling and Computer Simulation for Gene Expression and Regulation. Start date: Dec. 1, 2005. Expires: Nov. 30, 2006. Expected total amount: $100,000. Principal investigator: Chichia Chiu. Sponsor: Michigan State University.

Project will focus on mathematical modeling and computer simulation for gene expression and regulation, with the goal of integrating modeling approaches with quantitative determinations of transcriptional switch activity for a limited set of relatively well-characterized transcriptional regulators in the Drosophila blastoderm embryo.

Theoretical and Computational Studies of Pressure Induced Denaturation of Proteins. Start date: Jan. 1, 2006. Expires: Dec. 31, 2006. Estimated total amount: $946,933. Principal investigator: Angel Garcia. Sponsor: Rensselaer Polytechnic Institute.

Proposal to establish the relationship between the thermodynamics and the structural properties of pressure-induced changes in proteins using molecular simulations. The project will study the effect of high pressure on the stability of peptides that are known to form alpha and beta hairpin structures to determine the effect that high pressure has on the secondary structure stability.

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