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BioInform s Funding Update: NSF Bioinformatics Awards to Sept. 24, 2004

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Data Portal Enabling New Protein Structure Collaboration. Start date: Aug. 1, 2004. Expires: June 30, 2007. Expected total amount: $100,000. Principal investigator: Daniele Fabris. Sponsor: University of Maryland.

Project to construct a data-centric collaboration infrastructure with data management and analysis capabilities for mass spectrometric analysis that enables the determination of the three-dimensional structure of proteins, RNA, and macro-molecular assemblies. The computer infrastructure will incorporate emerging middleware standards for data/metadata management, security, application integration, and collaboration.


The Populus Genome Portal. Start date: Aug. 1, 2004. Expires: July 31, 2006. Expected total amount: $706,392. Principal investigator: Gerald Tuskan. Sponsor: University of Tennessee Institute of Agriculture.

Funds a resource to integrate all Populus genomic information and resources into a web-based portal, accessible at http://bahama.jgi-psf.org/prod/bin/populus/home.populus.cgi.


Center for Research Excellence in Bioinformatics and Computational Biology. Start date: Aug. 1, 2004. Expires: July 31, 2009. Expected total amount: $1,000,000. Principal investigator: Desh Ranjan. Sponsor: New Mexico State University.

Funds the establishment of a Center for Bioinformatics and Computational Biology at New Mexico State University. The center will combine the expertise of a team of researchers from computer science, biology, chemistry, and agriculture.


Free Energies in Biomolecular Systems: Theoretical Development and Application of Computational Approaches. Start date: Sept. 1, 2004. Expires: Aug. 31, 2008. Expected total amount: $312,825. Principal investigator: Benoit Roux. Sponsor: Weill Medical College of Cornell.

Proposal to extend current theoretical and computational approaches used in the modeling of biomolecular systems and to develop and test protocols that will provide increased accuracy and reliability in estimating free energies while remaining computationally tractable.


Multiscale Modeling of Gene Regulatory Modules. Start date: Sept. 1, 2004. Expires: Aug. 31, 2007. Expected total amount: $141,070. Principal investigator: Yiannis Kaznessis. Sponsor: University of Minnesota-Twin Cities.

Supports the integration of a number of simulation algorithms into a single multiscale algorithm for modeling biological regulatory processes, which extend from a stochastic low-copy number regime to a high-concentration “continuous” regime. The simulation algorithms to be integrated include a stochastic simulation algorithm, a chemical Langevin algorithm, and a multiscale deterministic simulation algorithm.


Bayesian ANOVA for Microarrays. Start date: Aug. 15, 2004. Expires: July 31, 2007. This grant is awarded to two investigative teams:

  • Cleveland Clinic Foundation. Principal investigator: Hemant Ishwaran. Expected total amount: $118,120.
  • Case Western Reserve University. Principal investigator: Jonnagadda Rao. Expected total amount: $53,880.

Supports development of a new methodology called Bayesian ANOVA for Microarrays for reliably detecting differentially expressed genes in complex experimental settings. The method rests on a high-dimensional variable selection method that exploits a rescaled spike-and-slab hierarchical model.


Enabling Pathway Queries in Large Molecular Interaction Networks. Start date: Aug. 15, 2004. Expires: July 31, 2007. Expected total amount: $167,571. Principal investigator: Trey Ideker. Sponsor: University of California, San Diego.

Project to develop methods and computational infrastructure for launching two major types of queries on the interaction network of cellular signaling and regulatory pathways: queries to identify network regions that are conserved across multiple species, conditions, or points in time; and queries to match observed genetic interactions, such as synthetic lethals, suppressor mutations, and complex genetic disease linkages, with the underlying pathways of physical interactions that best explain them.


Computing Life and the Kinetics of the Cell. Start date: Sept. 1, 2004. Expires: Aug. 31, 2007. Expected total amount: $499,994. Principal investigator: Jonathan Arnold. Sponsor: University of Georgia Research Foundation.

Supports an approach toward quantitative functional genomics, called the “computing life paradigm,” which integrates experimental probes of time-dependent intra-cellular kinetics with a recently proposed ensemble-based kinetics modeling technique.


Bioinformatics: The Rutgers Initiative in Teacher Enhancement. Start date: Sept. 1, 2004. Expires: Aug. 31, 2007. Expected total amount: $975,874. Principal investigator: William Sofer. Sponsor: Rutgers University New Brunswick.

Proposal to implement a project for teachers and students to integrate bioinformatics and structural biology into existing high school programs. The program will train up to 55 teachers in a local project at the Waksman Institute and over 100 teachers in a regional project conducted through distance learning on the Internet.


Acquisition of the Notre Dame Biocomplexity Computer Cluster. Start date: Aug. 1, 2004. Expires: July 31, 2006. Expected total amount: $160,160. Principal investigator: Mark Alber. Sponsor: University of Notre Dame.

Proposal to establishing a Beowulf-type Biocomplexity Cluster to serve as a computer infrastructure for the Notre Dame Interdisciplinary Center for the Study of Biocomplexity, where it will support the development of quantitative predictive models of biological processes ranging from subcellular to multicellular and ecological.


Efficient Representation and Manipulation of Large-Scale Biological Sequence Data. Start date: Sept. 1, 2004. Expires: Aug. 31, 2007. Expected total amount: $440,494. Principal investigator: Srinivas Aluru. Sponsor: Iowa State University.

Proposal to design storage structures, algorithmic techniques, and software for disk-resident sequence data, and apply it to applications in computational biology.


BioTagger — Biological Entity Tagging Using Online Resources and Machine Learning. Start date: Sept. 1, 2004. Expires: Aug. 31, 2007. Expected total amount: $411,555. Principal investigator: Hongfang Liu. Sponsor: University of Maryland, Baltimore County.

Project will use online resources (e.g., genetic databases, free-text corpora, or machine-readable dictionaries) and machine learning techniques to construct a biological entity tagging system that associates terms mentioned in text with entries in databases.


In Silico De Novo Protein Design: A Dynamically Data Driven, (DDDAS), Computational and Experimental Framework. Start date: Sept. 15, 2004. Expires: July 31, 2007. This grant is awarded to three investigative teams:

  • University of Pennsylvania Research Services. Principal investigator: John Lambris. Expected total amount: $220,000.
  • University of California, Riverside. Principal investigator: Dimitrios Morikis. Expected total amount: $334,069.
  • Princeton University. Principal investigator: Christodoulos Floudas. Expected total amount: $396,000.

Proposal to create a dynamically data-driven application systems effort that will integrate computational, physicochemical, and biochemical approaches for the in silico de novo design of peptides and proteins.


Computational Models for Gene Silencing: Elucidating a Pervasive Biological Defensive Response. Start date: Sept. 1, 2004. Expires: Aug. 31, 2008. Expected total amount: $1,100,000. Principal investigator: Lenwood Heath. Sponsor: Virginia Polytechnic Institute.

Proposal to develop Computational Models for Gene Silencing, a system that will blend molecular modeling, sequence analysis, data representation, and inferencing algorithms into a single methodology for studying complex systems biology frameworks.


Virtual Screening Algorithms for Bioactive Compounds Based on Frequent Substructures. Start date: Sept. 1, 2004. Expires: Aug. 31, 2007. Expected total amount: $405,498. Principal investigator: George Karypis. Sponsor: University of Minnesota, Twin Cities.

Funds the development of algorithms to analyze large chemical compound databases and identify the compounds that are the most probable for displaying the desired drug-like behavior. These virtual screening algorithms are based on a substructure-based classification framework.


Research Training Group in Mathematical and Computational Biology. Start date: Sept. 1, 2004. Expires: Aug. 31, 2009. Expected total amount: $1,800,000. Principal investigator: James P. Keener. Sponsor: University of Utah.

Proposal to develop and use mathematical and computational models to study complex biological processes, organized around four major research themes of biofluids, ecology and evolutionary biology, neuroscience, and physiology.


Rational Genomic Annotation Systems: Integration, Mining and Modeling of Biological Data. Start date: Sept. 15, 2004. Expires: Aug. 31, 2007. Expected total amount: $1,951,201. Principal investigator: Simon Kasif. Sponsor: Boston University.

Supports development of a Rational Genomic Annotation System for integration, mining, and modeling of biological data. The system will be an information-integration framework based on probabilistic graphical models, with a modular interface that will support different data types.


TAIR: The Arabidopsis Information Resource. Start date: Sept. 1, 2004. Expires: June 30, 2005. Expected total amount: $1,600,000. Principal investigator: Seung Rhee. Sponsor: Carnegie Institute of Washington.

Funds the second phase of TAIR (the Arabidopsis Information Resource), which includes maintaining the data and tools currently existing in TAIR and adding new efforts in key areas, including maintaining and improving the genome annotation, extracting phenotype and gene expression data from the literature, and improving accessibility of TAIR’s resources to all biologists, teachers, students and the general public.


Natural Language Processing Technology for Guided Study of Bioinformatics. Start date: Sept. 15, 2004. Expires: Aug. 31, 2008. Expected total amount: $270,000. Principal investigator: Dan Roth. Sponsor: University of Illinois Urbana-Champaign.

Supports development of an “intelligent tutor” — a human-computer interactive environment in which the computer is able to detect and track the user’s cognitive and academic state, and act based on this knowledge to aid the student in identifying and accessing relevant knowledge. The testbed domain in this project involves high school and undergraduate level students studying concepts in bioinformatics.


Computational Modeling of Genome-wide Transcriptional Regulation. Start date: Sept. 15, 2004. Aug. 31, 2007. Expected total amount: $163,118. Principal investigator: B. Franklin Pugh. Sponsor: Pennsylvania State University, University Park.

Proposal to construct a computational model that replicates changes in gene expression in response to experimental perturbations of the transcription machinery.


Acquisition of a Cluster Computer for Digital Biology. Start date: Sept. 1, 2004. Expires: Aug. 31, 2007. Expected total amount: $300,000. Principal investigator: Olivier Lichtarge. Sponsor: Baylor College of Medicine.

Funds the acquisition of a 220-CPU Opteron distributed memory computing cluster for the Structural and Computational Biology and Molecular Biophysics program at Baylor College of Medicine, Rice University, the University of Houston, the University of Texas MD Anderson, the University of Texas Health Sciences Center-Houston, and the University of Texas Medical Branch-Galveston.

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