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BioInform s Funding Update: NSF Awards in Bioinformatics through May 20, 2003

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DIMACS Exploratory Postdoctoral Program in Computational Epidemiology. Start date: April 15, 2003. Expires: April 30, 2004. Expected total amount: $100,000. Principal investigator: Fred Roberts. Sponsor: Rutgers University.


Project will support computational epidemiology research at the Center for Discrete Mathematics and Theoretical Computer Science. The effort will focus on control theory models of virus dynamics, chemostat models describing the competition of several organisms for a single nutrient, and influenza modeling. Additionally, data mining technology will be developed for public health data and bioterrorism sensor location data.

Genetic and Proteomic Analyses of Ralstonia Solanacearum Secreted Proteins.
Start date: April 15, 2003. Expires: Feb. 28, 2006. Expected total amount: $360,000. Principal investigator: Timothy Denny. Sponsor: University of Georgia Research Foundation.

Research to carry out proteomic analysis of more than 100 exoproteins (EXPs) secreted by the Ralstonia solanacearum phytopathogen. Bioinformatic analyses and comparative genomics will characterize the nature, function, and importance of the genes encoding EXPs. A catalog of secreted proteins and their predicted amino acid sequences will be assembled to determine common structural characteristics of secreted proteins that can be used to predict which genes encode EXPs.


Comparative Genomic Analysis Using Evidence Integration Frameworks. Start date: May 1, 2003. Expires: April 30, 2006. Expected total amount: $560,392. Principal investigator: Simon Kasif. Sponsor: Boston University.

Project to develop a prototype modular gene identification system that can be trained on different species. The architecture will include a compositional organization to allow global model training for cross-species sequence analysis; a mechanism to perform Bayesian adaptation of the model to the specific pair of orthologous genes being compared; and the ability to integrate other sources of evidence for comparative gene identification.

Algorithmic Challenges in Computational Biology. Start date: May 15, 2003. Expires: April 30, 2005. Expected total amount: $75,000. Principal investigator: Bruce Donald. Sponsor: Dartmouth College.

Proposal to design algorithms to identify and characterize the properties of rhythmic genes from DNA microarray hybridization time-series data. The approach, called Rhythmic Analysis of Gene Expression, will address issues of computational complexity and statistical significance.

A Next-Generation Biological Database Management System for Search Intensive Discovery in Genomics and Proteomics. Start date: May 15, 2003. Expires: April 30, 2006. Expected total amount: $929,716. Principal investigator: Daniel Miranker. Sponsor: University of Texas, Austin.

Proposal to create an extendable database management system designed specifically to support complex queries on biological data types, including sequence and mass spectrometry data for proteomics. The system will use tree-based storage structures to speed database retrieval. The project will also develop SQL extensions to enable better use of protein identification algorithms.

Evaluating Bioinformatics Technology. Start date: May 15, 2003. Expires: April 30, 2004. Expected total amount: $271,028. Principal investigator: Lynette Hirschman. Sponsor: Mitre Corporation.

Supports an international “challenge evaluation” for biological text data mining. Two tasks are defined for evaluating technologies: identification of biologically significant entities, and extraction of relation information such as interactions or identification of Gene Ontology terms in the literature.

Physical Mapping: Models, Complexities, and Algorithms. Start date: July 1, 2003. Expires: June 30, 2006. Expected total amount: $90,000. Principal investigator: Li Sheng. Sponsor: Drexel University.

Project will explore the application of graph theoretic models to problems of molecular biology, with the goal of improved algorithms for the probe interval graph model and the tagged probe interval graph model used to construct physical maps of genomes.

Exact Computational Biology Algorithms with Small Parameters. Start date: September 1, 2003. Expires: August 31, 2006. Expected total amount: $200,000. Principal investigator: Sing-Hoi Sze. Texas Engineering Experimental Station, Texas A&M University.

Project aims at applying fixed-parameter tractability (FPT) — a computational technique developed for intractable problems with small parameters — to computational biology. Objectives include identifying important computational biology problems that can be addressed by the FPT framework and developing algorithms for these problems.

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