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Funding Update: Feb 11, 2011

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NSF Bioinformatics Grants Awarded Jan. 12, 2011 — Feb. 10, 2011

Unlocking Organism's Potential Using Computational and Experimental Approaches
Start Date: June 1, 2011
Expires: May 31, 2016
Awarded Amount to Date: $402,346
Principal Investigator: Jennifer Reed
Sponsor: University of Wisconsin, Madison

The grant abstract states that the funds will be used to create new computational tools that will enhance the understanding of bacteria that are important in biotechnology and the environment. The investigators plan to use bacterial genome information to generate computational models of metabolism and transcriptional regulation that can be used to design experiments that improve the understanding of these activities in these microbes.


Sparse Modeling Driven by Large-Scale Genomic Data
Start Date: June 1, 2011
Expires: May 31, 2012
Awarded Amount to Date: $65,484
Principal Investigator: Qing Zhou
Sponsor: University of California, Los Angeles

The funds will be used to develop three sparse modeling methods "driven by large-scale gene expression data, protein binding data, and DNA sequence data." According to the abstract, the first method "motivated by modeling the relationship between protein binding and gene expression, constructs linear regression models on the terminal nodes of a decision tree;" the second method "concerns the construction of tight clusters for gene expression data by penalizing the difference in grouped parameters between two tight clusters and between a tight cluster and the null cluster;" and the third method aims at sequence pattern discovery.


Time Traveler
Start Date: June 1, 2011
Expires: May 31, 2012
Awarded Amount to Date: $29,866
Principal Investigator: Warren Porter
Sponsor: University of Wisconsin, Madison

The funds will be used to develop a bioinformatics computational platform, called Time Traveler, that connects 3D object animation with computational fluid dynamics, heat and mass transfer engineering, morphology, physiology, behavior, ecology, evolution, earth sciences, remote-sensing and GIS technologies. The investigators will use the platform to address the role of climate, topography, and plant environments in defining animal body sizes, shapes, and distributions in the geological past, the present, and future.


Computationally Generated Biomarkers
Start Date: Feb. 1, 2011
Expires: Jan. 31, 2012
Awarded Amount to Date: $99,433
Principal Investigator: Zeeshan Syed
Sponsor: University of Michigan, Ann Arbor

The funds will be used to develop a computational framework that allows for the "systematic exploration of the growing human 'physiome' for clues to predict and prevent major diseases."


Modeling the Equilibria of Marcomolecules
Start Date: Feb. 1, 2011
Expires: Jan. 31, 2013
Awarded Amount to Date: $99,909
Principal Investigator: Marvin Thrash
Sponsor: Miami University

Supports the development of a mathematical model that describes the binding equilibria of large biological macromolecules. The investigators anticipate that the work "will lead to a robust model capable of simulating single and multicomponent isotherms for biomolecules interacting with a variety of adsorbents ... and will have a transformative effect in the areas of chromatographic separations and material development for biomedical applications."


Comparative Genomics of Environmental Stress Responses in North American Hardwoods
Start Date: Feb. 1, 2011
Expires: Jan. 31, 2012
Awarded Amount to Date: $841,279
Principal Investigators: John Carlson, Jeanne Romero-Severson, Scott Schlarbaum, Mark Coggeshall, Haiying Liang
Sponsor: Pennsylvania State University

Supports an interdisciplinary team that will work together to "develop new genomic resources for important species that represent the major taxonomic groups of eastern hardwood trees." The project will produce sequence databases for expressed genes, genetic markers, genetic linkage maps, and reference populations in order to provide "lasting genomic and biological resources for the discovery and conservation of genes in hardwood trees for growth, adaptation and responses to environmental stresses such as drought, heat, insect pests, and disease."


Automated Proteogenomic Annotation for Prokaryotic Genomes
Start Date: Nov. 1, 2010
Expires: Aug. 31, 2012
Awarded Amount to Date: $469,988
Principal Investigator: Samuel Payne
Sponsor: Battelle Memorial Institute

The grant abstract states that the funds will be used to build a proteogenomics software pipeline that will "enable and improve primary genome annotation."


Multi-study Genomic Data Analysis
Start Date: Sept. 1, 2009
Expires: Oct. 31, 2011
Awarded Amount to Date: $212,427
Principal Investigator: Giovanni Parmigiani
Sponsor: Dana-Farber Cancer Institute

Supports the development of statistical approaches to multi-study genomic data analysis. The researchers aim to develop data analysis tools for "comparison and integration of genomic information across studies, across measurement technologies, and across biological systems." According to the abstract, "specific targets include generalization of meta-analysis tools used in medicine and social sciences to the genomics context, metrics for evaluating reproducibility of expression measurements across platform in the absence of a gold standard, approaches for deriving and validating common expression scales across platforms, and a novel reformulation of the combination problem based on constructing 'coexpression matrices' in which an element represents the coexpression of a subset of genes in a given study."


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