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NSF Bioinformatics Grants March 4 – June 1, 2007

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Shared Genome Database Informatics and Cyber Infrastructure.  Start date: April 1, 2007. Expires: March 31, 2008. Awarded amount to date: $225,757. Principal investigator: Donald Gilbert. Sponsor: Indiana University.
 
Funds development of integrated, shared database tools, such as those built under the umbrella of the collaborative Generic Model Organism Database project. “Software tools to fully assembly, analyze and compare these genomes are available, but the ability to employ them is limited to those with extensive computational resources and engineering talent,” according to the grant abstract. The investigators plan to develop new methods for use by existing and emerging model organism databases that will address genome database access needs and middleware for comparative analyses. The grant also supports the maintenance and improvement of the Bionet news service and the Bio-mirror project for distributing large genomic and biology databanks.
 

 
Quantitative Proteomics Using All-Against-All Biological Data Analysis. Start date: April 15, 2007. Expires: March 31, 2008. Awarded amount to date: $241,069. Principal investigator: Daniel Miranker. Sponsor: University of Texas at Austin.
 
Funds development of new algorithms and a new software system for large-scale protein identification and measurement of protein expression level by mass spectra look-up. These algorithms will be integrated into MoBIoS, a metric-distance database management system. Mass spectral data will be integrated into the existing Open Proteomic Database in order to build a reference library of experimental peptide mass spectra that can be used to supplement or supplant the use of computationally predicted peptide mass spectra currently used for spectral look-ups in proteomics, according to the investigators. “The ultimate goal of this project is to integrate OPD and MoBIoS to create a MoBIoS-based spectral matching application and enable spectral queries of OPD,” the grant abstract states.
 

 
Graph Theoretical Inference and Predictive Dynamic Modeling of Signal Transduction Networks. Start date: April 15, 2007. Expires: March 31, 2009. Awarded amount to date: $160,000. Principal investigator: Reka Albert. Sponsor: Pennsylvania State University, University Park.
 
Funds a project that will integrate graph inference, network analysis, and dynamic modeling approaches into a general framework for reconstructing and modeling biological signal transduction networks from partial and indirect knowledge. The methodology is expected to enable predictive modeling of partially characterized signaling networks where current methods cannot be applied.
 

 
OpenWetWare: A Collaborative Tool for Biological Knowledge Management and Dissemination. Start date: May 1, 2007. Expires: April 30, 2008. Awarded amount to date: $345,015. Principal investigator: Drew Endy. Sponsor: Massachusetts Institute of Technology.
 
Supports a project to enhance the existing Open WetWare database, which allows researchers to organize and disseminate protocols, interim and negative results, and contextual metadata generated during bench biology research. Goals of the project include developing additional tools for expanding the types and organization of knowledge that is managed by the system and implement a wiki-based framework for distributing and supporting the software.
 

 
Interrogating the pathogen-host relationship with genome-scale network analysis. Start date: May 15, 2007. Expires: April 30, 2012. Awarded amount to date: $400,000. Principal investigator: Jason Papin. Sponsor: University of Virginia Main Campus.
 
Supports an effort to develop a multi-scale model of the human pathogen, Leishmaia major, based on the integration of intracellular networks. The investigators propose reconstructing metabolic, regulatory, and signaling networks with the goal of developing a model that will link genome-scale reconstructions of L. major to tissue responses in host organisms.
 

 
Linking Evolution to Genomics Using Phenotype Ontologies. Start date: June 1, 2007. Expires: May 31, 2008. Awarded amount to date: $607,026. Principal investigator: Paula Mabee. Sponsor: University of South Dakota Main Campus.
 
Funds the development of tools to integrate evolutionary and model organism phenotype data using ontologies. The project will develop and apply ontologies for taxa and phenotypes in the Ostariophysi clade of fishes and will develop a suite of database and web-interface tools to enable researchers to investigate relationships between evolutionary phenotypes and developmental mutants of zebrafish.
 

 
Computational Comparative Genomic Approaches to Identifying Functional and Neutral DNA. Start date: June 1, 2007. Expires: May 31, 2008. Awarded amount to date: $50,000. Principal investigator: Jeffrey Chuang. Sponsor: Boston College.
 
Funds a proposal to perform computational sequence analyses to characterize the neutral mutation rate in several large eukaryotic phylogenies, including mammals, flies, and yeasts. “By computationally identifying and characterizing neutral sequences, it will be possible to clarify the molecular processes that are likely to affect much of eukaryotic DNA,” the investigators note in the grant abstract.
 

 
Algorithm and Software Development for MS-Based Glycomics. Start date: June 1, 2007. Expires: May 31, 2008. Awarded amount to date: $100,542. Principal investigator: Haixu Tang. Sponsor: Indiana University.
 
Funds algorithm and software development for mass spectrometry-based glycomics, the study of characterizing all functional oligosaccharides inside a cell. The proposal has three primary aims: to continue developing algorithms and software for characterizing oligosaccharide structures, including their sequences, branchings, and linkages, from tandem mass spectra; to develop algorithms and software for characterizing site-specific glycosylations in glycoproteins from their LC/MS/MS analyses; and to develop new educational courses in glycoinformatics and proteome informatics.
 

 
A New MCMC Framework with Applications to Protein Bioinformatics. Start date: July 1, 2007. Expires: June 30, 2008. Awarded amount to date: $117,341. Principal investigator: Jun Liu. Sponsor: Harvard University.
 
Supports the development of a new Markov chain Monte Carlo framework for use in protein bioinformatics. The grantee plans to develop a unified framework to generalize the standard Metropolis-Hastings approach to design Markov chains. The approach is expected to have applications in multiple sequence alignment, protein function annotation, protein-protein interaction analysis, and protein structural modeling, among others.
 

 
Regularization and Optimization for High Dimensional Regression and Classification with Biological Applications. Start date: June 1, 2007. Expires: May 31, 2010. Awarded amount to date: $180,001. Principal investigator: Chunming Zhang. Sponsor: University of Wisconsin-Madison.
 
Supports development of new regularization and optimization techniques for high- dimensional data in biological, medical, and scientific research. A “major goal” of the proposal is to improve the analysis of high-dimensional data, like spatio-temporal fMRI brain images, functional data objects, and gene expression profiles, according to the grant abstract.

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