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BioInform s Funding Update: Some Recent NSF Awards in Bioinformatics: Sep 23, 2002


SGER GeneBeans: A Modular System that Makes Genomic-Scale Analysis Accessible to Biologists. Start date: September 1, 2002. Expires: August 31, 2004. Expected total amount: $91,882. Investigator: Ann Stapleton. Sponsor: University of North Carolina, Wilmington.

Supports development of an environment for constructing a series of queries and analyses. The system will use Enterprise Java Beans to import sequence data from a variety of sources and store it in a relational database. Other EJBs will handle workflow, query the database, and analyze results.


Comparative Genomic Analysis of Signal Transduction in Prokaryotes. Start date: September 1, 2002. Expires: August 31, 2003. Expected total amount: $142,000. Investigator: Igor Jouline. Sponsor: Georgia Tech.

Supports research to significantly improve prediction of biological functions for signal transduction proteins using a “systematic computational approach” that integrates analysis of functional elements of individual proteins with genomic information.


Southern California Bioinformatics Summer Institute. Start date: October 1, 2002. Expires: September 30, 2006. Expected total amount: $699,708. Investigator: Jamil Momand. Sponsor: California State, Los Angeles.

Supports eight research institutions that will offer lectures, workshops, research training, and career counseling to selected college students with a background in molecular life sciences and/or computer sciences and who have completed their second year of college but have not entered their third year of graduate school.


Computational Learning and Discovery in Biological Sequence, Structure, and Function Mapping. Start date: September 15, 2002. Expires: August 31, 2007. This is a collaborative grant. Funding breakdown is as follows:

• $5,660,476. Investigator: Raj Reddy. Sponsor: Carnegie Mellon University.

• $1,954,500. Investigator: Judith Klein. Sponsor: University of Pittsburgh.

• $1,135,291. Investigator: Jonathan King. Sponsor: Massachusetts Institute of Technology.

• $90,000. Investigator: Catherine Costello. Sponsor: Boston University.

Supports collaborative research in computational biolinguisics. The goal is to apply tools and methods that computer scientists have developed for dealing with human language, such as statistical language modeling, machine learning methods, and high-level language processing, to elicit the structure and function of proteins.


Distributed Hybrid Optimization Techniques with Applications to Proteomics and Genomics. Start date: September 1, 2002. Expires: July 31, 2005. Expected total amount: $300,000. Investigator: Alberto Segre. Sponsor: University of Iowa.

Supports the development of scalable, fault-tolerant, distributed search techniques and their application to construct hybrid optimization systems.


Computational and Experimental Studies of Pathways in Yeast. Start date: July 1, 2002. Expires: June 30, 2005. Expected total amount: $499,931. Investigator: Christodoulos Floudas. Sponsor: Princeton University.

This research combines experimental molecular genetics with computational systems biology to develop new approaches for mapping signal transduction pathways in eukaryotic cells. The project will investigate a new computational systems approach based on a superstructure representation and a mixed integer linear optimization framework for the prediction of the topology of complex pathways.


Mining the Bibliome — Information Extraction from the Biomedical Literature. Start date: September 1, 2002. Expires: August 31, 2007. Expected total amount: $3,499,759. Investigator: Aravind Joshi. Sponsor: University of Pennsylvania.

Supports development of methods for automatically extracting information from the biomedical literature, relying on recent research in high-accuracy parsing and shallow semantic analysis. The project is a collaboration with researchers in the Knowledge Integration and Discovery Systems group at GlaxoSmithKline.


Center for Computational Biophysics. Start date: October 1, 2002. Expires: September 30, 2007. Expected total amount: $5,000,000. Investigator: Herbert Levine. Sponsor: University of California, San Diego.

Supports the creation of a center for computational biophysics that will be operated as a partnership between UC San Diego, the San Diego Supercomputer Center, the Scripps Research Institute, and the Salk Institute for Biological Studies.

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