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NSF Bioinformatics Awards to Oct. 15, 2005

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Endowing Biological Databases with Analytical Power: Indexing, Querying, and Mining of Complex Biological Structures. Start date: Sept. 15, 2005. Expires: Aug. 31, 2008. This grant is awarded to two investigative teams:

  • University of Southern California. Principal investigator: Xianghong Zhou. Cumulative award amount: $228,616.
  • University of Illinois, Urbana-Champaign. Principal investigator: Jiawei Han. Cumulative award amount: $271,385.

Funds development of scalable indexing, query processing, and data-mining methods for constructing scalable, efficient, and analysis-based, heterogeneous biological database systems. The project will focus on a set of "typical" genomic and biological databases, according to the grant abstract, and will work on several major research themes, including the development of methods for indexing and accessing of complex biological structures, and the development of mechanisms for mining across heterogeneous, multi-relational biological databases.


Development of a Closed-Loop Identification Machine for Bionetworks (CLIMB) and its Application to Nucleotide Metabolism. Start date: Oct. 1, 2005. Expires: Sept. 30, 2006. Cumulative award amount: $183,417. Principal investigator Herschel Rabitz. Sponsor: Princeton University.

Proposal to develop a closed-loop identification machine for molecular bionetworks (CLIMB), which will "enable reliable and cost-effective model identification through iterative rounds of computation and computation-guided experimentation," according to the grant abstract. CLIMB involves two core computational components: a control module that designs "optimized chemical fluxes for application to the target network for the purpose of parameter identification;" and an inversion module that calculates feasible parameter values based on the experimental results. The technique will be used to study the nucleotide metabolism of Escherichia coli and Saccharomyces cerevisiae.


Assembling the Beetle Tree of Life. Start date: Oct. 1, 2005. Expires: March 31, 2007. This grant is awarded to three investigative teams:

  • Harvard University. Principal investigator: Brian Farrell. Awarded amount to date: $742,149.
  • University of Arizona. Principal investigator: David Maddison. Awarded amount to date: $479,813.
  • Brigham Young University. Principal investigator: Michael Whiting. Awarded amount to date: $399,991.

Supports an "extensive" study of beetle (insect order Coleoptera) phylogeny. According to the grant abstract, "novel bioinformatics tools will be developed to streamline data processing for the molecular and morphological data, and will allow for greater efficiency, accuracy, and reproducibility of the data and associated results, while providing an online framework for collaboration by participants throughout the world."


Marine Biotechnology and Bioinformatics. Start date: Oct. 1, 2005. Expires: Sept. 30, 2008. Cumulative award amount: $996,955. Principal investigator: Simona Bartl. Sponsor: San Jose State University.

Supports a collaboration between San Jose State University, California State University at Monterey Bay, and Moss Landing Marine Laboratories to incorporate biotechnology and bioinformatics into the biology curriculum at the middle school and high school levels. The project currently involves 60 teachers and 45 students, "and will ultimately reach approximately 6,000 students indirectly by project end," according to the grant abstract.


Assembling the Liverwort Tree of Life: A Window into the Evolution and Diversification of Early Land Plants. Start date: Jan. 1, 2006. Expires: Dec. 31, 2010. This grant is awarded to seven investigative teams:

  • Southern Illinois University at Carbondale. Principal investigator: Karen Renzaglia. Awarded amount to date: $358,356.
  • Southern Illinois University at Carbondale. Principal investigator: Barbara Crandall-Stotler. Awarded amount to date: $304,663.
  • Yale University. Principal investigator: Reed Beaman. Awarded amount to date: $378,176.
  • Duke University. Principal investigator: Jonathan Shaw. Awarded amount to date: $290,000.
  • University of Michigan Ann Arbor. Principal investigator: Yin-Long Qiu. Awarded amount to date: $105,000.
  • Field Museum of Natural History. Principal investigator: John Engel. Awarded amount to date: $101,348.
  • University of Connecticut. Principal investigator: Bernard Goffinet. Awarded amount to date: $200,000.

Funds a project to resolve phylogenetic relationships across the entire spectrum of liverworts (phylum Marchantiophyta), which were the first green plants to diversify on land and are considered to be the oldest living lineage of terrestrial organisms. Three general types of data will be compiled: conservative morphological and genome characters to resolve deep "backbone" relationships; anatomical/developmental data to resolve intermediate-depth lineages; and morphological and DNA sequence characters to resolve relationships among a sample of 800 taxa representing all genera of liverworts. A second major goal of the project is to integrate phylogenetic inferences and bionformatic efforts between this and other on-going NSF-supported projects.

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