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BioInform s Funding Update: NSF Bioinformatics Awards to Oct. 4, 2003


A Post-Genomics Approach to Understanding E. coli Network Architecture. Start date: Sept. 1, 2003. Expires: Aug. 31, 2005. Amount: $199,971. Principal investigator: Ryan Gill. Sponsor: University of Colorado Boulder.

Project to develop a combined experimental and computational approach to discover genes whose over-expression has the strongest affect on cell behavior and to determine if these genes display biological network connectivity values that are characteristic of “small-world” network architectures in Escherichia coli.

A High-Speed Network Connection for Genomics Research. Start date: Sept. 15, 2003. Expires: Aug. 31, 2005. Amount: $164,732. Principal investigator: Steven Salzberg. Sponsor: The Institute for Genomic Research.

Proposal to establish a dark-fiber high-performance connection from the Institute for Genomic Research to the MidAtlantic Crossroads GigaPoP in College Park, Md., and then to the Abilene/Internet2 network. The Abilene/Internet2 connection will also be shared with the Joint Technology Center, the Center for the Advancement of Genomics, and the Institute for Biological Energy Alternatives.

Simulation and Analysis of Large Scale Complex Systems. Start date: Sept. 15, 2003. Expires: Aug. 31, 2005. Amount: $155,969. Principal investigator: Malik Magdon-Ismail. Sponsor: Rensselaer Polytechnic Institute.

Supports a shared computational infrastructure for the simulation of large-scale complex systems. The first project develops a general learning paradigm for designing efficient algorithms to solve large-scale optimization problems, such as DNA assembly and alignment and protein folding.

Subnanometer Structure Based Fold Determination of Biological Complexes. Start date: Sept. 15, 2003. Expires: Aug. 31, 2006. This grant is awarded to three investigative teams:

  • University of Texas, Austin. Principal investigator: Chandrajit Bajaj. Amount: $749,999.
  • University of California, San Francisco. Principal investigator: Andrej Sali. Amount: $749,999.
  • Baylor College of Medicine. Principal investigator: Wah Chiu. Amount: $750,002.

Project to develop computation and visualization methodology to deduce the folds of the domain components of large macromolecular complexes. Research team will explore different algorithms to enhance the signal through “denoising“ of the three-dimensional structure, visualize these maps, extract the individual protein components and their structural features, and construct atomic models using protein sequence and structure considerations as constraints.

Machine-Learning Approaches to Protein Sequence Comparison: Discriminative, Semi-Supervised, Scalable Algorithms. Start date: Sept. 15, 2003. Expires: Aug. 31, 2006. Amount: $300,000. Principal Investigator: Christina Leslie. Sponsor: Columbia University.

Proposal to train a model using examples from available proteins so that it can accurately predict which database sequences are related to a query protein sequence. Learning algorithms such as constrained clustering, neighborhood averaging, hierarchical labels and ensembles of classifiers, will be explored, as well as techniques for dimensionality reduction such as non-negative matrix factorization and kernel-based semi-supervised approaches.

Algorithms for Folding and Detection of RNA Genes. Start date: Sept. 15, 2003. Expires: Aug. 31, 2006. Amount: $450,000. Principal investigator: Serafim Batzoglou. Sponsor: Stanford University.

Proposal to develop a collection of algorithms and tools for the fold prediction of noncoding RNA genes. The method will explore the structural properties of RNA genes to exclude a large set of “unlikely structures” from the search space of possible configurations.

Combinatorial Algorithms for Biological Data Clustering. Start date: Sept. 15, 2003. Expires: Aug. 31, 2008. This grant is awarded to two investigative teams:

  • University of Tennessee, Knoxville. Principal investigator: Ying Xu. Amount: $1,295,000.
  • Cold Spring Harbor Laboratory. Principal investigator: Michael Zhang. Amount: $455,000.

Project has five goals: to develop a general framework for biological data clustering based on a minimum spanning tree representation of a data set; to demonstrate the effectiveness of this framework; to implement the clustering framework as a set of library functions; to provide insight on biological problems through clustering analysis; and to train students how to build biological data analysis tools using the clustering framework.

Acquisition of Cluster and Server for Computational Biology at the University of California, Irvine. Start date: Oct. 1, 2003. Expires: Sept. 30, 2006. Amount: $269,989. Principal investigator: Pierre Baldi. Sponsor: University of California Irvine.

Supports a compute cluster to serve computational biology research needs.

Oryza Map Alignment Project. Start date: Oct. 1, 2003. Expires: Sept. 30, 2007. Amount: $9,743,546. Principal investigator: Rod Wing. Sponsor: University of Arizona.

Project to map and align twelve wild genomes of rice to the public finished rice genome sequences derived from Oryza sativa ssp. japonica and ssp. indica, the major cultivated rice varieties grown throughout Asia and India. The Oryza Map Alignment Project (OMAP) resource will contain representatives of all extant wild rice genomes.

New Approaches to Experimental Design and Statistical Analysis of Genomic and Structural Biologic Data from Multiple Sources. Start date: Oct. 1, 2003. Expires: July 31, 2008. This grant is awarded to three investigative teams:

  • Massachusetts Institute of Technology. Principal investigator: Sanjoy Mitter. Amount: $836,000.
  • New York University. Principal investigator: Bhubaneswar Mishra. Amount: $572,242.
  • Purdue University. Principal investigator: Peter Doerschuk. Amount: $792,031.

Project will apply principles from information and systems theory, along with computational methods for statistical inference and numerical optimization, to create a unified approach to planning and analysis of complex quantitative experiments in the biological sciences, such as the determination of gene expression using gene chips and the determination of 3D viral structure from scattering and electron microscopy experiments.

PlantGDB Plant Genome Database and Analysis Tools. Start date: Jan. 1, 2004. Expires: Dec. 31, 2005. Amount: $978,683. Principal investigator: Volker Brendel. Sponsor: Iowa State University.

Supports the development of integrated databases and analytical tools to aid in the organization and interpretation of plant sequence data. When the project is underway, results will be accessible via the PlantGDB website for the NSF-funded project (


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