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Funding Update: Sep 23, 2011

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NSF Bioinformatics Grants Awarded Aug. 25 — Sept. 21, 2011

Developing an Effective, Portable Annotation Engine for Plant Genomes
Start Date: Nov. 1, 2011
Expires: Oct. 31, 2013
Awarded Amount to Date: $1,834,128
Principal Investigators: Mark Yandell, Shin-Han Shiu, Ning Jiang, Yanni Sun, Kevin Childs
Sponsor: University of Utah

Supports a project that aims to adapt and extend Maker, an established annotation tool, for use on plant genomes. According to the investigators, the overarching goal of the project is to produce a plant-genome-optimized annotation pipeline that can be widely used by the plant research community and will be incorporated as part of the iPlant Cyberinfrastructure.


Improving Analysis of Microbial Mixtures through Sparse Reconstruction Algorithms and Statistical Inference
Start Date: Sept. 15, 2011
Expires: Aug. 31, 2014
Awarded Amount to Date: $666,322
Principal Investigators: Simon Foucart, Gail Rosen, Loni Tabb
Sponsor: Drexel University

The funds will be used to improve microbial identification and comparison from next-generation sequence data. The investigators plan to improve a method of identification from short reads that uses a Bayesian classifier with "a zero-inflated negative binomial and Poisson models." They also aim to be able to "model and fit functions to microbial population changes in a gradient ... especially when many of the data points are missing."


Algorithms for the Analysis of Microbiomes
Start Date: Sept. 15, 2011
Expires: Aug. 31, 2013
Awarded Amount to Date: $246,367
Principal Investigators: Khalid Sayood, Steven Hinrichs
Sponsor: University of Nebraska, Lincoln

The investigators plan to use the funds to create a set of algorithms that are "explicitly developed to function in the complex context of microbiomes" in humans and the environment.


Mathematical Models and Adaptive Algorithms for Tumor Growth
Start Date: Sept. 15, 2011
Expires: Aug. 31, 2014
Awarded Amount to Date: $319,987
Principal Investigators: Serge Prudhomme, J. Tinsley Oden
Sponsor: University of Texas, Austin

According to the abstract, the funds will support the development of mathematical models to study tumor growth as well as to design "time-stepping schemes and finite-element discretization algorithms, build the computer software implementing these algorithms, and to develop solution-verification methods based on a posteriori error estimation."


Algorithms for Threat Detection via Geometry of Virus Genome Space
Start Date: Sept. 15, 2011
Expires: Aug. 31, 2012
This grant is awarded to two investigative teams:
Rong He, Chicago State University, $319,987
Stephen S. Yau, Jie Yang, University of Illinois, Chicago, $485,860

According to the abstract, the investigators will use the funds to collect available genome sequences for different types of viruses and compute their natural vectors; "explore the necessary number of dimensions of the natural vector" that allow it to accurately cluster the viral genomes; and classify or identify any given new virus based on its genome sequence and predict its functions or behavior pattern. They also plan to set up and maintain a "natural vector bank" for viruses.


An Approach to Inferring Networks from Complex Phenotypes
Start Date: Sept. 15, 2011
Expires: Aug. 31, 2013
Awarded Amount to Date: $500,000
Principal Investigator: Toni Kazic
Sponsor: University of Missouri at Columbia

The funds will support efforts to develop and test new mathematical and computational methods to infer networks that produce complex phenotypic traits using top-down approaches. The investigator will use two model systems from corn to test the methods. The first is a small set of biochemical pathways that determine the colors of corn kernels, which will be used to validate the approach. The second system, comprised of approximately 200 genes that are involved in the plant's defenses against pathogens, will be used to characterize responses to infection as well as to infer the underlying genetic network that causes these responses.


National Center for Genome Analysis Support
Start Date: Sept. 15, 2011
Expires: Aug. 31, 2012
Awarded Amount to Date: $488,842
Principal Investigators: Craig Stewart, Michael Lynch, Geoffrey Fox, Matthew Hahn, William Barnett
Sponsor: Indiana University

This award is to establish the National Center for Genome Analysis Support at IU in partnership with the Texas Advanced Computing Center. According to the abstract, the center will provide cluster-based genome analysis software, storage for submitted data sets, and a repository of open source genome analysis software for users.

It will also support the analysis of next-generation sequence data for de novo assembly, metagenomic, and resequencing projects and will provide compute power on the Mason large memory computer cluster at IU, the TACC Gordon system, and the San Diego Supercomputer Center Dash system.


A Systems Biology Platform for Protein Function Prediction
Start Date: Sept. 01, 2011
Expires: Aug. 31, 2014
Awarded Amount to Date: $240,000
Principal Investigator: Ameet Talwalkar

These funds will support the development of Sifter, a systems biology platform to predict protein function from high-throughput data. According to the abstract, the investigators intend to incorporate interaction networks as well as to explore techniques for function prediction based on low-rank matrix factorization and novel sampling-based approaches to help speed up computation. They also plan to develop algorithms to quantify uncertainty in Sifter's predictions.


Novel Computational Techniques for Cardiovascular Risk Stratification
Start Date: Sept. 01, 2011
Expires: Aug. 31, 2015
This grant is awarded to two investigative teams:
Zeeshan Syed, University of Michigan, Ann Arbor, $562,415
John Guttag, Massachusetts Institute of Technology, $637,585

These funds support the development of computational methods to assess patients' cardiovascular risk and match them to the treatments that are most likely to be effective. According to the abstract, these methods will be able to identify new markers of disease, improve the ability to measure new and existing markers, and construct personalized models that can provide individual assessments of risk.


Integrating the BioExtract Server with the iPlant Collaborative
Start Date: Sept. 1, 2011
Expires: Aug. 31, 2014
Awarded Amount to Date: $725,789
Principal Investigator: Carol Lushbough
Sponsor: University of South Dakota

Using these funds, the investigator and her colleagues aim to make it possible for researchers to execute iPlant analytic tools within the BioExtract Server, create iPlant workflows through the server, and manage analysis and provenance data across both platforms.


UniformMu: A Transposon Resource for Functional Genomics of Maize
Start Date: Sept. 1, 2011
Expires: Aug. 31, 2013
Awarded Amount to Date: $2,111,109
Principal Investigators: Donald McCarty, Karen Koch
Sponsor: University of Florida

These funds will support the development of a public resource of next-generation sequence data for functional genomics studies of maize based on the UniformMu population — a large inbred maize population developed specifically for transposon mutagenesis of the maize genome.


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