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Funding Update: Jul 23, 2010

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NSF Bioinformatics Grants Awarded June 25 — July 22, 2010

Theory of Biomolecular Structure and Dynamics
Start date: Dec. 1, 2010
Expires: Nov. 30, 2012
Awarded amount to date: $171,803
Principal investigator: James McCammon
Sponsor: University of California, San Diego

Supports development of improved molecular dynamics tools, including more accurate models for the watery solvent around simulated biological molecules, and more powerful methods for sampling the shapes and energetic properties of biological molecules. "Challenging new applications include exploration of the biophysics of protein kinases and Ras proteins, and new studies of cytochrome P450s and protein-assisted membrane fusion," according to the grant abstract.


Structural Interpretation of the Protein Interactome
Start date: Aug. 1, 2010
Expires: July 31, 2011
Awarded amount to date: $138,994
Principal investigator: Robert Jernigan
Sponsor: Iowa State University

Funds a project that will use protein structural modeling to provide a better understanding of protein-protein interaction data. "The aim is to test the data and discover missing interactions, to develop molecular models of most pairs of interactions, and in this way to learn about the compatibilities of the pairs of interactions," the grant abstract states. "Physical overlaps in binding sites will be used to determine whether interaction sites overlap and are thus incompatible or whether they can coexist in assemblages of multiple proteins."


Comparative Microbial Genomics — Beyond the Genes
Start date: Aug. 1, 2010
Expires: July 31, 2013
Awarded amount to date: $477,761
Principal investigator: Jan Mrazek
Sponsor: University of Georgia Research Foundation

Funds the development of new computational tools that will enable the investigation of microbial genome features "beyond the protein-coding and RNA-coding genes," according to the grant abstract. These genome features include G+C content, codon usage, amino acid usage, oligonucleotide composition, sequence motifs, repeat structures, sequence patterns that can promote unusual DNA conformations, or sequences that locally affect physical characteristics of DNA or RNA molecules. "Computational tools will be designed for analyses of these features in microbial genomes, and subsequently these tools will be applied in systematic examination of prokaryotic genomes." The new software will be distributed under the GPL.


Large-Scale Multinomial Inference and Its Applications in Genome-Wide Association Studies
Start date: Aug. 1, 2010
Expires: July 31, 2011
Awarded amount to date: $79,297
Principal investigator: Chuanhai Liu
Sponsor: Purdue University

Supports an effort to study the so-called "large K and small n" problem in statistics, in which there are a large number (K) of categories and a small number (n) of samples, such as genome-wide association studies with a large number of genotypes. The investigators plan to develop methods that are "probabilistic and have desirable frequency properties," according to the grant abstract.


Plant Genomics Data Computational Interface
Start date: July 1, 2010
Expires: June 30, 2011
Awarded amount to date: $359,816
Principal investigator: Eva Huala
Sponsor: Carnegie Institution of Washington

Supports the development of an application programming interface that will provide web-based computational access for plant genomics data. The project will include "a new, open technology for generating computational data web services; an open, portable, optimized data warehouse that supports very fast queries of plant biology data; and a plant biology query language, query builder, and query optimizer that will provide a simple way to limit query results to only the required data," according to the abstract.


The De Novo Discovery of Transposable Elements for the Study of Neutral Substitution Rate Variation in Plant Genomes
Start date: July 1, 2010
Expires: June 30, 2015
Awarded amount to date: $588,345
Principal investigator: John Karro
Sponsor: Miami University

Funds the development of algorithms for the automatic annotation of transposable elements. According to the grant abstract, there are effective algorithmic methods for identifying transposable elements that have retained sufficient sequence similarity to their progenitor, but "the capability of these methods quickly diminishes when searching for transposable elements that have experienced a higher level of sequence decay due to age or presence in more evolutionary volatile genomic regions." The investigators plan to develop an algorithm that will underlie a comprehensive de novo generation of transposable element libraries, and then develop a sensitive search tool for transposable elements based on that library.


G-SESAME Cloud: A Dynamically Scalable Collaboration Community for Biological Knowledge Discovery
Start date: July 1, 2010
Expires: June 30, 2013
This grant was awarded to two investigative teams:
• $322,555, Philip Yu, University of Illinois at Chicago
• $545,536, Zijun Wang, Clemson University

Supports development of G-SESAME Cloud, a dynamically scalable collaboration community for biological knowledge discovery. The investigators first aim to enhance the existing G-SESAME (Gene Semantic Similarity Analysis and Measurement Tools) "in terms of methodology, functionality, accuracy, efficiency, and scalability to address the immediate needs of researchers who utilize G-SESAME tools in their daily biological research," according to the grant abstract. The "ultimate goal," however, "is to build a community-based scalable cloud computing infrastructure … to help the biological researchers disseminate their research results."


Systems Bioinformatics Approaches to Modeling and Deciphering Plant Transcriptional Regulatory Networks
Start date: July 1, 2010
Expires: June 30, 2013
Awarded amount to date: $1,183,305
Principal investigator: Patrick Xuechun Zhao
Sponsor: Samuel Roberts Noble Foundation

Funds a project that will use systems bioinformatics approaches to decipher plant transcriptional regulatory networks. Specific aims include developing graphical models to model and simulate plant transcriptional regulatory networks; developing computational algorithms to infer large-scale gene regulatory networks from high-throughput functional genomics data in model plants; constructing gene regulation networks specific to several model plants; and developing web systems to host these regulation networks.


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