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Recent NIH Awards in Bioinformatics

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Integration and Visualization of Diverse Biological Data. Start date: April 1, 2005. Expires: March 31, 2005. Amount: $254,093. Principal investigator: Olga Troyanskaya. Institution: Princeton University. NIH Institute: NIGMS.

Supports a project to develop a generalizable bioinformatics framework for integrated analysis and visualization of heterogeneous biological data. The system will enable full-scale data integration and function prediction system for Saccharomyces cerevisiae and will be incorporated with the Saccharomyces Genome Database. According to the investigators, the technology developed for this project "will form a basis for systems that address the same set of issues for other organisms, including the human."


Informatics of GPCR Dimers in Drug Abuse Mechanisms. Start date: April 1, 2005. Expires: March 31, 2010. Amount: $126,000. Principal investigator: Marta Filizola. Institution: Weill Medical College of Cornell University. NIH Institute: NIDA.

Funds a project to use bioinformatics methods to determine homo- and hetero-dimerization interfaces of G-protein coupled receptors relevant to mechanisms of drugs of abuse, and to construct an information management system designed to store such data and its context in a manner that will facilitate the design and interpretation of pointed physiological and pharmacological experiments. In order to identify the most likely dimerization interfaces of GPCRs involved in mechanisms of drugs of abuse, the investigators will use a recently developed bioinformatics approach that identifies correlated mutations on the receptor lipid-facing region from multiple sequence alignments of specific GPCR subfamilies. The predicted interfaces will then be used to guide the molecular modeling of GPCR homo- and hetero-dimers involved in mechanisms of drugs of abuse.


The TINKER Modeling Software for Biomolecular Simulation. Start date: April 1, 2005. Expires: March 31, 2009. Amount: $256,156. Principal investigator: Jay Ponder. Institution: Washington University. NIH Institute: NIGMS.

Funds development of the TINKER molecular modeling package, a modular, extensible set of computational biology programs intended to serve as a test-bed for empirical potentials (force fields) and algorithm development. TINKER is able to perform energy calculations with a number of alternative present-generation force field parameter sets. The current project will extend this comparative capability to emerging polarizable energy models for biomolecular simulation.


Molecules in Motion Software to Study Live Cell Images. Start date: April 1, 2005. Expires: Sept. 30, 2005. Amount: $119,166. Principal investigator: Pamela Thuman-Commike. Institution: QED Labs. NIH Institute: NIGMS.

Phase I SBIR supports development of software called Molecules in Motion (MiM) that will enable biomedically relevant knowledge to be extracted from live cell images. MiM will provide several innovative features compared to existing software, according to the developers, including detailed user guidance and extensive quantitative capabilities.


High Precision Retrieval from Molecular Data Resources. Start date: Feb. 1, 2005. Expires: Jan. 31, 2006. Amount: $99,354. Principal investigator: Jisheng Liang. Institution: Insightful. NIH Institute: NLM.

Phase I SBIR funds a project to develop a natural-language search technology that will allow users to access biological information stored in heterogeneous data resources by entering queries in explicit sentences or questions. The technology is expected to offer higher precision than conventional keyword-based search engines.


The NEW Biology Workbench. Start date: April 1, 2005. Expires: March 31, 2009. Amount: $558,086. Principal investigator: Mark Miller. Institution: University of California San Diego. NIH Institute: NIGMS.

Funds further development of the Biology Workbench, which is used by 28,000 researchers and students for sequence analysis software, data storage, and data retrieval. This user base "has now grown larger than the original architecture of the Biology Workbench can support, and its rate of growth remains constant," according the developers. Project will "refactor" the existing Biology Workbench to create a more modular, more stable platform with better scalability.


Identifiability of Nonlinear Biological Models. Start date: March 1, 2005. Expires: Feb. 28, 2009. Amount: $222,282. Principal investigator: Paolo Vicini. Institution: University of Washington. NIH Institute: NIGMS.

Supports development of an algorithm and a software tool to test a priori global identifiability of nonlinear compartmental models, a very inclusive class of ordinary nonlinear differential equation models based on conservation of mass. These models are widely used to study the kinetics of endogenous and exogenous substances in living systems. The software is expected to be very useful in clinical studies where "severe constraints exist on experiment design, i.e. the number of inputs and outputs is limited for ethical and practical reasons," the developers note.


New Hydropathy-Based Computer Tools for Drug Discovery. Start date: April 1, 2005. Expires: March 31, 2010. Amount: $237,890. Principal investigator: Glen Kellogg. Institution: Virginia Commonwealth University. NIH Institute: NIGMS.

Project aims to develop an integrated suite of software applications for predicting, refining, and manipulating biomacromolecular structure, particularly with respect to computational virtual screening of drug candidates. The two main goals of the proposed research are: to improve the accuracy and reliability of free-energy scoring of putative protein-ligand complexes; and to enhance the quality of low-resolution structural models from x-ray, NMR, or comparative modeling to make them useful as targets for virtual screening. The core technology for this research plan is based on the HINT (Hydropathic INTeractions) program.


Pseudomonas aeruginosa Outer Membrane Protein Modeling. Start date: March 1, 2005. Expires: Feb. 28, 2010. Amount: $374,655. Principal investigator: Tjerk Straatsma. Institution: Battelle Pacific Northwest Laboratories. NIH Institute: NIAID.

Project to develop new modeling and simulation capabilities for the study of the outer-membrane proteins of Pseudomonas aeruginosa and Escherichia coli. The project's focus will be on the outer membrane of P. aeruginosa in comparison with the outer membrane of E. coli to determine the role of elements that are specifically found in the lipopolysaccharide membrane structure of the outer membrane of P. aeruginosa.


Bayesian Methods for Genomics with Variable Selection. Start Date: April 1, 2005. Expires: March 31, 2009. Amount: $216,067. Principal investigator: Marina Vannucci. Institution: Texas A&M University System. NIH Institute: NHGRI.

Funds development of new Bayesian methodologies for the analysis of genomic data. Specific aims include clustering of high-dimensional data, analysis of high-dimensional data with censored survival outcomes, application to microarray studies, application to proteomic data, and software development.


Reconstructing Regulatory Network Dynamics. Start date: Oct. 10, 2005. Expires: NA. Amount: $48,296. Principal investigator: Jason Suen. Institution: University of California Los Angeles. NIH Institute: NIGMS.

Funds development of techniques for reconstructing transcriptional regulatory networks and deducing the underlying dynamics of transcription factors from gene expression measurements. The project will extend the Network Component Analysis method developed in the sponsor's laboratory to reconstruct network models where limited or incomplete connectivity information of the underlying network is available.


Hierarchical Methods for Large Biomolecular Complexes. Start date: April 1, 2005. Expires: March 31, 2008. Amount: $239,355. Principal investigator: Chandrajit Bajaj. Institution: University of Texas Austin. NIH Institute: NIGMS.

Proposal to develop an enhanced and automated computational processing pipeline, once a volumetric cryo-electron microscopy map of a large biological complex has been reconstructed. In particular, the developers propose creating hierarchical computational representations, algorithms, and software to automate structural feature determination of large biomolecular complexes, as well as speed up fitting techniques between large biomolecular complexes and relevant proteins and/or nucleic acids.


Phylogeny and Genomic Inference for Quantitative Traits. Start date: April 1, 2005. Expires: March 31, 2009. Amount: $235,125. Principal investigator: Joseph Felsenstein. Institution: University of Washington. NIH Institute: NIGMS.

Proposal to develop statistical methods for analyzing data on phenotypic traits within populations, between populations, and between species, in an integrated way. Computer programs will be written and distributed to compare inferences at these levels and test whether divergence of characters among species shows different patterns of divergence when compared to the same characters observed between populations.

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