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BioInform s Funding Update: NSF Bioinformatics Awards to July 30, 2004


Nonparametric Bayesian Models for Genetic Variations and Their Associations to Diseases and Population Demography. Start date: Aug. 1, 2005. Expires: July 31, 2006. Cumulative award amount: $100,000. Principal investigator: Eric Xing. Sponsor: Carnegie Mellon University.

Proposal to build statistical models of time series data, with the goal of using Bayesian methods to reverse-engineer an organism's genetic regulatory networks from gene expression and metabolite data. The investigators will apply their techniques to Escherichia coli. The method relies on a technique called Automatic Relevance Determination to simplify the models so that only those genes and metabolites that are participating players in the process are retained in the final model. The Bayesian framework will also enable information about known network connections and interactions, derived from the literature or commercial databases, to be included in the model.

Computational Population Genomics: Using Variation to Connect Genotypes to Phenotypes. Start date: Aug. 1, 2005. Expires: July 31, 2008. Cumulative award amount: $699,989. Principal investigator: Daniel Gusfield. Sponsor: University of California, Davis

A proposal to address computational problems that arise in population-scale genomic data acquisition and analysis. The main biology-based algorithmic problems concern the computational deduction of the frequency, location, and the full temporal structure of historical recombination, gene-conversion and lateral gene- transfer. The main technology-based problems are concerned with important problems of missing data or error-prone data, and with the deduction of haplotype data from genotype data. The investigators will develop algorithms and software that will allow biologists to better understand the history and role of recombination, gene-conversion and lateral gene transfer, and to cope with problems in the data.

P Systems: Theory and Applications to Modeling and Simulation of Cells. Start date: Aug. 1, 2005. Expires: July 31, 2006. This grant is awarded to two investigative teams:

  • University of California, Santa Barbara. Principal investigator: Oscar Ibarra. Cumulative award amount: $50,000.
  • Louisiana Tech University. Principal investigator: Andrei Paun. Cumulative award amount: $50,000

Proposal to simulate cells using concepts from P systems (membrane computing) implemented in the E-cell package. The project will also define models of P systems that mimic the processes in the cell. The project will "help explore, model, and simulate differential gene expression during various biological processes and transcriptional and signaling networks on a larger scale than the current capabilities," according to the grant abstract.

Bayesian Support Vector Machines for the Prediction of Molecular-Genetic Network Motifs Across Organisms. Start date: Aug. 1, 2005. Expires: July 31, 2008. Cumulative award amount: $249,999. Principal investigator: Alpan Raval. Sponsor: Keck Graduate Institute.

Funds development of computational methods that use high-throughput data from a variety of sources to predict biological interactions, and to assign confidence levels to each prediction in a systematic manner. The project uses Bayesian support vector machines to predict molecular interactions at the whole-genome level. The prediction system will be applied to the genomes of several organisms, including the budding yeast, worm, and fly.

Acquisition of a 512-node BlueGene/L Supercomputer for Large-Scale Applications in Genomics and Systems Biology. Start date: Aug. 1, 2005. Expires: July 31, 2008. Cumulative award amount: $600,000. Principal investigator: Srinivas Aluru. Sponsor: Iowa State University.

Funds the purchase of a supercomputer to support a number of projects, including assembly, validation, and annotation of the maize genome; large-scale EST clustering with applications to gene identification; detection of functional and regulatory clusters of proteins through whole-organism protein network analysis; and design and simulation of FPGA-based engines for computational genomics.

Acquisition of a Hybrid System and Research Infrastructure for Large-Scale Integration of Biomedical Data. Start date: Aug. 1, 2005. Expires: July 31, 2008. Cumulative award amount: $900,000. Principal investigator: George Zouridakis. Sponsor: University of Houston.

Proposal to develop methodologies for extracting information and integrating heterogeneous information systems, and mining multimodality data collected in real time. The data are generated locally by thermal cameras, 3D stereo video cameras, and brain activity scanners. The system may also include MRI and CT scans or live neurophysiological activity.

Integrated Process for Functional Site Feature Analysis. Start date: Aug. 1, 2005. Expires: July 31, 2006. Cumulative award amount: $168,390. Principal investigator: Jacquelyn S. Fetrow. Sponsor: Wake Forest University.

Funds a project to characterize the molecular function sites of six protein superfamilies, focusing on the following objectives: characterizing the sequence and structure of functional-site features and using the results to develop methods for clustering the peroxiredoxin family; analyzing the electrostatics at peroxiredoxin functional sites and testing them experimentally; integrating the electrostatic, sequence, and structural information to create a robust profiling method that can identify peroxiredoxin subfamilies; and using it to create active-site signatures and profiles for a well-studied and important set of protein superfamilies.

Probing Protein-Based Molecular Recognition through Computation and Simulation: Multicentered Hybrid Methods for the Reliable Characterization of pi-pi Interactions. Start date: Aug. 1, 2005. Expires: July 31, 2008. Cumulative award amount: $375,000. Principal investigator: Gregory Tschumper. Sponsor: University of Mississippi.

Proposal to study pi-pi stacking interactions through the development of a series of hybrid quantum-mechanical computational methods.

Theory of Biomolecular Structure and Dynamics. Start date: Dec. 1, 2005. Expires: Nov. 30, 2006. Cumulative award amount: $152,032. Principal investigator: James McCammon. Sponsor: University of California, San Diego.

Project to develop and apply methods for using computers to understand the activity of biological molecules. Computational tools that will be developed include enhancements to several widely used software packages to allow molecular dynamics simulations at constant pH, enhanced sampling via accelerated molecular dynamics, and more accurate calculations of free energy.

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