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BioInform s Funding Update: Recent NIH Awards in Bioinformatics: Dec 6, 2004


Validating and Translating Array Signatures. Start date: Sept. 2004. Expires: Feb. 2005. Amount: $99,999. Principal investigator: Joseph Monforte. Institution: Althea Technologies. NIH Institute: NCI.

SBIR grant supports development of quantitative assays using microarray-derived gene signatures —sets of genes that can be used to classify cancer types. The investigators plan to validate the combined use of artificial neural network analysis for identification of small gene signatures with universal-primer-driven rtPCR for translating these signatures into high-throughput assays.

A Bioinformatic Approach to Inferring Protein Contacts. Start date: Sept. 2004. Expires: Aug. 2006. Amount: $203,950. Principal investigator: Marcella McClure. Institution: Montana State University (Bozeman). NIH Institute: NIAID.

Funds development of a computational approach for predicting amino acid contacts for the three proteins of the replication/transcription complex of the order Mononegavirales (e.g. ebola, rabies, measles, etc.). The method will comprise three steps: prediction of disorder; determination of compensatory mutation; and assessment of evolutionary dynamics. Bayesian networks will be used to correlate the results.

The Carolina Center for Exploratory Genetic Analysis. Start date: Sept. 2004. Expires: July 2007. Amount: $563,799. Principal investigator: Daniel Reed. Institution: University of North Carolina, Chapel Hill. NIH Institute: NCRR.

Supports the new Carolina Center for Exploratory Genetic Analysis, which will establish an interdisciplinary infrastructure for identifying the complex genetic traits underlying human diseases. To accommodate the diverse, multi-investigator databases necessary for this research, the center plans to develop a prototype, extensible data model and provide access to data via a portal constructed using the Open Grid Computing Environment toolkit. New techniques will be developed for linkage analysis , subspace clustering, and association analysis. The project will also “explore new visualizations and develop high-performance implementations.”

Development of Virtual Tumor. Start date: Sept. 2004. Expires: Aug. 2007. Amount: $450,782. Principal investigator: Thomas Deisboeck. Institution: Massachusetts General Hospital. NIH Institute: NCI.

Supports a multi-institutional, interdisciplinary project to develop a computational model of a tumor. The investigators will first establish an efficient infrastructure and workflow between the multiple teams; then collect, classify, and archive existing modeling tools and techniques; and finally initiate a pilot project to connect and integrate three distinct modeling modules and platforms in order to test the hypothesis that molecular heterogeneity can quantitatively affect multicellular patterns. To accomplish these goals, the team is structured into three cores: the administrative core, the computational modeling core (responsible for algorithm development and design of the digital model repository), and the biomedical data core (responsible for data collection and evaluation).

Modeling of Chemotactic Sensing in Dictyostelium. Start date: Sept. 2004. Expires: Aug. 2008. Amount: $413,558. Principal investigator: Pablo Iglesias. Institution: Johns Hopkins University. NIH Institute: NIGMS.

Proposal to integrate mathematical analysis with quantitative measurements of the temporal and spatial changes in chemotaxis-related enzymes to model gradient sensing in Dictyostelium.

Training in Pharmacoinformatics. Start date: Sept. 2004. Expires: Aug. 2009. Amount: $276,318. Principal investigator: George Stancel. Institution: University of Texas Health Science Center. NIH Institute: NIDDK.

Supports nine predoctoral and six postdoctoral positions to establish a training program in the interdisciplinary area of pharmacoinformatics. Students will be trained in the use of informatics approaches to identify biomolecules that are candidates for drug targeting; the use of structural genomics, chemoinformatics, and structure-based design to develop families of chemicals to target selected biomolecules and structures; and the use of ADMET profiling and computational predictions of efficacy to select viable drag candidates prior to biological testing.

Graduate Training in Computational and Systems Biology. Start date: Sept. 2004. Expires: Aug. 2009. Amount: $166,097. Principal investigator: Bruce Tidor. Institution: Massachusetts Institute of Technology. NIH Institute: NIDDK.

Supports a new interdisciplinary postdoctoral training program in computational and systems biology at MIT’s Computational and Systems Biology Initiative.


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