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Funding Update: Jun 26, 2009

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NSF Bioinformatics Grants Awarded May 20 — June 22, 2009

A Bayesian Framework for Analyzing Genetic And Gene Expression Architecture Of Complex Phenotypes
Start date: Sept. 1, 2009
Expires: Aug. 31, 2012
Awarded amount to date: $516,392
Principal investigator: Jason Mezey
Sponsor: Cornell University

This award, funded under the American Recovery and Reinvestment Act of 2009, supports the development of statistical methods to help discover DNA sequences that alter the expression of genes operating during development and various physiological processes. The project will develop a method called structural equation modeling that relies on computational Bayesian statistics "to overcome computational difficulties posed by the scale and complexity of genomic data, which make extracting relevant biological information difficult," the grant abstract states. The software developed in this project "will be used as a starting point for investigating why and how DNA sequences produce differences among individuals in both appearance and susceptibility to genetic diseases."


Collaborative Research: Statistical Inference for High-Dimensional Data: Theory, Methodology and Applications
Start date: Aug. 1, 2009
Expires: July 31, 2010
This grant was awarded to three investigative teams:
• T. Tony Cai, University of Pennsylvania, $278,043
• Huibin Zhou, Yale University, $77,850
• Tianxi Cai, Harvard University, $42,055

Funds development of "a comprehensive theoretical framework and general methodologies for estimating a large covariance matrix … for functional data regression where the predictors and/or the responses involve functional measurements, and to address a wide range of important applications in biomedical studies," the grant abstract states. The project aims to develop inference procedures and algorithms for analyzing high-dimensional data that will be applicable to astronomy, biology, chemistry, bioinformatics, and medicine.


Efficient Signal Processing Algorithms for Inference of Gene Regulatory Networks
Start date: July 1, 2009
Expires: June 30, 2012
Awarded amount to date: $313,175
Principal investigator: Erchin Serpedin
Sponsor: Texas Engineering Experiment Station

This, award funded under the American Recovery and Reinvestment Act of 2009, supports the development of a computationally efficient signal processing framework for global understanding of the structure and functionality of gene regulatory networks. Project aims include developing information theoretic tools for efficient inference of causal regulations between gene expressions, determination of global topologies for gene regulatory networks, and the development of a Bayesian information theoretic framework for inference of gene regulatory networks based on the integration of many heterogeneous data sources.


Hugebrow Lite, a Participatory Human Genome Browser for Mobile Devices
Start date: July 1, 2009
Expires: Dec. 31, 2009
Awarded amount to date: $100,000
Principal investigator: Beatriz Perez-Sweeney
Sponsor: Hugebrow

This Small Business Innovation Research Phase I project, funded under the American Recovery and Reinvestment Act of 2009, supports the development of a three-dimensional human genome browser. The platform will be "a 3D visualization software toolkit designed to explore the genome's structure and function in the context of the entire body," according to the grant abstract. "Currently, no genomic software incorporates the molecular movement capability of software tools into animated processes of gene expression. In addition, no software takes the powerful dataset integration of applications to create powerful 3D visuals," the abstract states. The project team aims to develop "a tool that will accept keyword search terms, like a trait name, and show all related regulatory molecules and pathways."


Achieving Long Timescale Sampling in Biomolecular Simulations
Start date: July 1, 2009
Expires: June 30, 2012
Awarded amount to date: $443,588
Principal investigator: Wei Yang
Sponsor: Florida State University

This award, funded under the American Recovery and Reinvestment Act of 2009, supports the development of simulation methods to "quantitatively describe complex biomolecular phenomena that usually occur in longer timescale than what conventional methods can achieve," according to the grant abstract. The investigators plan to develop efficient generalized ensemble simulation methods to enhance the sampling power of biomolecular simulations. These methods will be based on the orthogonal space random walk algorithm, "which can uniquely realize collective environmental relaxation in a robust and efficient manner."


Computational Infrastructure for Full-Sequence Association Studies with Pooled Individuals
Start date: June 1, 2009
Expires: May 31, 2014
Awarded amount to date: $399,999
Principal investigator: Itshack Pe'er
Sponsor: Columbia University

This award, funded under the American Recovery and Reinvestment Act of 2009, supports development of a Bayesian scoring method for recovering individual identity of mutation carriers from pooled sequencing data. The investigators will design overlapping pools for recovering mutation carrier identity. "Each individual will be sequenced in a unique combination of pools. Mutations observed in such a set of pools will be inferred to be carried by the corresponding individual," according to the grant abstract.


RCN for Genomic and Metagenomic Standards
Start date: June 1, 2009
Expires: May 31, 2010
Awarded amount to date: $100,000
Principal investigator: John Wooley
Sponsor: University of California-San Diego

Funds the creation of a research coordination network "to promote and integrate standards for genomic and metagenomic data and metadata within an international community," the grant abstract states. The network is based on the existing Genomic Standard Consortium, which will be extended to include ecological data standards such as Ecological Metadata Language, biodiversity standards such as Darwin Core, and environmental research programs such as the Global Lake Ecological Observatory Network and Long Term Ecological Research.

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