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NSF Bioinformatics Awards to Sept. 11, 2005

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Ab Initio Gene Finding in Maize. Start date: Aug. 1, 2005. Expires: July 31, 2007. Awarded amount to date: $622,027. Principal investigator: William Barbazuk. Sponsor: Donald Danforth Plant Science Center.

Supports a project to improve gene prediction in maize by identifying a comprehensive training set of complete and annotated maize gene models that will be used to optimize the TwinScan gene-prediction algorithm to accurately identify maize genes in un-annotated maize genome sequence. Maize-trained TwinScan will be benchmarked and used to re-annotate available pubic maize genomic sequence. The results of the benchmarking and re-annotation, as well as the maize-trained TwinScan program, will be made publicly available at http://www.maizegenome.org/.


Cyberinfrastructure for Next Generation Biomolecular Modeling. Aug. 15, 2005. Expires: July 31, 2006. This grant is awarded to two investigative teams:

  • University of California, Berkeley. Principal investigator: Teresa Head-Gordon. Awarded amount to date: $431,174.
  • Stanford University. Principal investigator: Vijay S. Pande. Awarded amount to date: $312,700.

Funds the development and validation of polarizable force fields for use in biomolecular simulations and the public distribution of resulting software components and parallelized computer codes. Outcomes of the project include publicly available parameter sets and software, along with workshops for dissemination.


From Cellular and Gene Networks to Principles of Robust Communication and Distributed Systems Design. Start date: Aug. 15, 2005. Expires: July 31, 2006. Awarded amount to date: $200,001. Principal investigator: Vwani Roychowdhury. Sponsor: University of California, Los Angeles.

Supports development of an integrated analytical and software platform for analyzing several types of biological and social networks, including DNA-protein, protein-protein, metabolic, and inter-cellular signaling networks, and the design of information and computational networks, including fault-tolerant and attack-resistant federated databases and ad hoc communication networks, and distributed systems such as national power grids. The methodologies and software tools developed will be made available as a nationwide resource for the analysis of biological and social networks, and through interdisciplinary undergraduate and graduate courses and training programs on complex networks and their applications.


Novel Algorithms for ncRNA Discovery and RNA Structure Prediction. Start date: Aug. 1, 2005. Expires: July 31, 2008. Awarded amount to date: $488,774. Principal investigator: Vineet Bafna. Sponsor: University of California, San Diego.

Funds development of algorithms for discovering non-coding RNAs. The investigators will develop computational filters to rapidly eliminate much of the sequence database, while retaining the true homologs to be evaluated using more expensive functions. "Similar to Blast for DNA/protein database search, filter-based comparative ncRNA search has the potential to greatly accelerate discovery of novel ncRNA," the grantees write in their abstract.


Collaborative Research: Development of Vector Space based Methods for Protein Structure Prediction. Start date: July 1, 2005. Expires: June 30, 2006. Awarded amount to date: $233,622. Principal investigator: Donglin Liang. Sponsor: Georgia Tech Research Corp.

Proposal to design knowledge-based prediction systems based on optimal vector space representations of proteins that have previously been represented by character strings. Kernel-based nonlinear classifiers and nonlinear dimension reduction as well as visualization methods will be developed to provide scalable and elective prediction systems. The prediction systems will be tailored for several problems related to protein structure discovery such as protein secondary structure, relative solvent accessibility and disulfide connectivity, as well as prediction of protein-protein interaction.


Algorithms for Predicting Protein Function Using Interaction Maps. Start date: Sept. 1, 2005. Expires: Aug. 31, 2006. Awarded amount to date: $150,000. Principal investigator: Mona Singh. Sponsor: Princeton University.

Project to develop algorithms for analyzing protein interaction maps, in order to make novel predictions about a protein's biological process. "The goal is to provide a framework for moving from individual pairwise linkages to exploiting entire interaction networks, where each interaction may arise from either experimental and/or other computational methods," the grantees write in the grant abstract. The proposed work will develop methods using interaction maps for baker's yeast and fruit fly. Predictions and software will be made available at www.cs.princeton.edu/mona/software.html.


An Extensible Knowledge-Base and Visual Programming Environment for the Community Annotation of Multiple Genomes. Start date: Sept. 1, 2005. Expires: Aug. 31, 2006. Awarded amount to date: $379,208. Principal investigator: Jeff Elhai. Sponsor: Virginia Commonwealth University.

Funds development of a graphical programming environment based on the textual language BioLingua, along with representational tools that will enable biologists to see novel patterns "that computers are incapable of recognizing without human guidance." These tools will be integrated with the community-based annotation resource, the SEED, and the annotation of all available cyanobacterial genomes by the community of cyanobacteriologists will serve as a test case.


DAPLDS — a Dynamically Adaptive Protein-Ligand Docking System Based on Multi-Scale Modeling. Start date: Sept. 1, 2005. Expires: Aug. 31, 2008. This grant is awarded to three investigative teams:

  • University of Texas, El Paso. Principal investigator: Michela Taufer. Awarded amount to date: $655,626.
  • University of California, Berkeley. Principal investigator: David Anderson. Awarded amount to date: $198,720.
  • The Scripps Research Institute. Principal investigator: Charles Brooks. Awarded amount to date: $267,690.

The DAPLDS (Dynamically Adaptive Protein-Ligand Docking System) aims to enable adaptive multi-scale modeling in a distributed computing environment in order to study protein-ligand interactions. The goals of the project are to explore the multi-scale nature of algorithmic adaptations in protein-ligand docking and to develop infrastructures based on computational methods and models that efficiently accommodate these adaptations.


The Genome Properties: Metabolic Reconstruction System. Start date: Aug. 15, 2005. Expires: July 31, 2008. Awarded amount to date: $674,361. Principal investigator: Owen White. Sponsor: Institute for Genomic Research.

Supports development of the Genome Properties system (www.tigr.org/Genome_Properties), a relational database system that includes a set of tools and web interfaces for the investigation of the metabolism, phenotypes, qualitative and quantitative measures, and other biological properties of microbial life.


Integrated Analysis of Genetic and Cellular Networks. Start date: Sept. 15, 2005. Expires: Aug. 31, 2009. Awarded amount to date: $719,197. Principal investigator: Peter Bates. Sponsor: Michigan State University.

Supports a research training project for undergraduates in biological and mathematical sciences that will be directed towards qualitative and quantitative approaches to understanding molecular structures and mechanisms.


Acquisition of DNA Sequencing and Bioinformatics Resources for the Molecular Research Core Facility at Idaho State University. Start date: Sept. 1, 2005. Expires: Aug. 31, 2008. Awarded amount to date: $140,290. Principal investigator: Marjorie Matocq. Sponsor: Idaho State University.

Funds the expansion of the sequencing capacity at Idaho State University's Molecular Research Core Facility through the upgrade of the current DNA sequencer and the purchase of a robotics unit and a bioinformatics integration package.


MetNet: Integrated Software for Arabidopsis Systems Biology Research. Start date: Sept. 1, 2005. Expires: Aug. 31, 2007. Awarded amount to date: $969,634. Principal investigator: Eve Wurtele. Sponsor: Iowa State University.

Funds development of an open-source integrated software platform, MetNet, for visualization and analysis of experimental data and metabolic networks in the context of Arabidopsis systems biology. The MetNet platform will include graph visualization and modeling, interactive displays, graph-theoretic computations for determining biological distances, a multivariate display and analysis tool with functionality to do statistical analyses, graph modeling using the open source statistical analysis language, R, and text mining. Software will be made available at http://www.public.iastate.edu/~mash/MetNet/homepage.html.


Bioinformatic Data Mining for AIDS Resistance Genes. Start date: Sept. 15, 2005. Expires: Aug. 31, 2007. Awarded amount to date: $499,961. Principal investigator: Walter Messier. Sponsor: Evolutionary Genomics.

Phase II SBIR supports the use of evolution-based data-mining software to discover targets for the development of human therapeutics. Phase I "demonstrated that the evolution-based data-mining software was useful for dramatically narrowing the search for proteins that make chimpanzees resistant to the progression of AIDS after infection by HIV-1," the investigators note in their grant abstract. In Phase II, the impact on in-vitro HIV-1 infectivity of a human cell line transfected with the gene encoding one of the adapted chimpanzee proteins will be assessed.


Computational Exploration of Molecules in the Context of Biological Pathway Networks. Start date: Sept. 15, 2005. Expires: Aug. 31, 2006. Awarded amount to date: $195,038. Principal investigator: Joanne Luciano. Sponsor: Massachusetts General Hospital.

Supports development of methods to study biomolecules in the context of networks of biological pathways. The methods are built upon a combination of the BioPAX pathway data exchange standard and Instance Store, which uses an ontology and the data it describes to make inferences about data.


Cyberinfrastructure Demonstration Through Project-Centric Bioinformatics. Start date: Jan. 1, 2006. Expires: Dec. 31, 2007. Awarded amount to date: $250,000. Principal investigator: Oswald Crasta. Sponsor: Virginia Polytechnic Institute and State University.

Supports development of a multidisciplinary bioinformatics course for the students of Bluefield State College in Bluefield, West Virginia, and Galileo Magnet High School in Danville, Virginia.


Gene Ontology Terms for Standardized Annotation of Plant-Associated Microbe Genomes. Start date: Oct. 1, 2005. Expires: Sept. 30, 2008. Awarded amount to date: $1,128,817. Principal investigator: Brett Tyler. Sponsor: Virginia Polytechnic Institute and State University.

Funds development of an ontology for describing the functions of genes used by microbes that live in or on plants, including pathogenic microbes. The work of establishing the terms will be carried out in collaboration with the Gene Ontology Consortium.


Mesoscale Modeling of Protein-DNA Assemblies. Start date: Sept. 1, 2005. Expires: Aug. 31, 2008. Awarded amount to date: $64,094. Principal investigator: David Swigon. Sponsor: University of Pittsburgh.

Supports development of a computational procedure for analyzing the structure of protein-DNA assemblies, in which the DNA elastic energy, the electrostatic repulsion of charged residues, and the protein-DNA binding energy are the main components of the assembly energetics. The procedure will include new algorithms for calculating DNA configurations, determination of the free energy of DNA segments and polypeptide tethers, and analysis of protein-DNA binding states. The procedure will be applied to the study of the transcription of the lac operon in Escherichia coli.

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