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Funding Update: NSF Bioinformatics Grants Awarded July 10 — Aug. 22, 2012

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Mining local correlations in extremely high-dimensional data: models, algorithms, and applications
Start Date: Sept. 1, 2012
Expires: Aug. 31, 2015
Awarded Amount to Date: $471,187
Principal Investigators: Xiang Zhang; Xiaofeng Zhu
Sponsor: Case Western Reserve University

The funds will support the development of computational and statistical tools for mining correlations in high-dimensional datasets such as gene expression, genetic variation, and protein and DNA sequence data.


Statistical methods for functional metagenomics in biothreat detection
Start Date: Aug. 15, 2012
Expires: July 31, 2015
Awarded Amount to Date: $722, 978
Principal Investigators: Lingling An; Hongmei Jiang; Jiannong Xu
Sponsor: University of Arizona

The funds will support the development of a probabilistic framework for characterizing gene content in “metatranscriptomic samples;” compare samples to detect significant functional patterns associated with biothreats; identify biothreat markers based on these patterns; and develop an R-based software tool dubbed FunctionMeta that implements the aforementioned algorithms. The investigators will also develop FunctionSim, a tool for generating synthesized sequencing data.


Integrated statistical algorithms with ultra-high performance computing for discovering SNPs from massive next-generation metagenomic sequencing data
Start Date: Aug. 15, 2012
Expires: July 31, 2016
This grant is awarded to two investigative teams:
Ping Ma; University of Illinois, Urbana-Champaign; $372,098
Xinping Cui; University of California, Riverside; $532,114

The funds will be used to develop algorithms to detect SNPs in metagenomic data. These tools are expected to find use in national security and biodefense agencies for detecting biothreat agents as well as in microbiology, where they can be used to analyze microbial diversity and evolution.


Synergistic application of cheminformatics and computational geometry approaches for predicting protein-protein interactions
Start Date: Aug. 1, 2012
Expires: July 31, 2015
Awarded Amount to Date: $289,892
Principal Investigators: Alexander Tropsha; Diane Pozefsky; Denis Fourches
Sponsor: University of North Carolina, Chapel Hill

The investigators will use the funds to develop software for analyzing protein-protein interactions, using an approach that combines structural bioinformatics, computational geometry, and cheminformatics.


Dynamic regulatory modeling of the iron deficiency response in Arabidopsis thaliana
Start Date: Aug. 15, 2012
Expires: July 31, 2017
Awarded Amount to Date: $847,368
Principal Investigators: Cranos Williams; Joel Ducoste; James Tuck; Terri Long
Sponsor: North Carolina State University

According to the abstract, these funds will support the development of a computing and modeling paradigm for identifying “previously uncharacterized regulatory components involved in the control of iron homeostasis in A. thaliana across multiple cell types.”


Secondary active membrane transporters: determining protein structure and transport mechanisms with a new hybrid simulation
Start Date: Aug. 1, 2012
Expires: July 31, 2017
Awarded Amount to Date: $252,419
Principal Investigator: Jeffery Klauda
Sponsor: University of Maryland, College Park

These funds will support the development of a simulation tool for use in investigating transport mechanisms and protein conformation changes of secondary active transporters — a type of membrane protein.


Statistical methodology for network-based integrative analysis of omics data
Start Date: Aug. 1, 2012
Expires: July 31, 2016
This grant is awarded to two investigative teams:
George Michailidis; University of Michigan, Ann Arbor; $447,651
Arun Sreekumar; Baylor College of Medicine; $191,348

According to the abstract, these funds support the development of network-based methods for integrating data from multiple 'omics platforms for pathway analysis; and computational algorithms for estimating large scale network-based models. The investigators also intend to develop hypergraph models for assessing differential activity in pathways and a method of detecting active members of pathways as part of biomarker discovery.


Statistical methods for enabling medical and population genomics of admixed human populations
Start Date: Aug. 1, 2012
Expires: July 31, 2016
Awarded Amount to Date: $774,315
Principal Investigator: Carlos Bustamante
Sponsor: Stanford University

These funds will support the development of population genetic models of admixed human populations and of statistical tools for estimating historical admixture in these models.


Bayesian factor modeling of context-specific gene regulation
Start Date: Aug. 1, 2012
Expires: July 31, 2014
Awarded Amount to Date: $296,859
Principal Investigators: Yufei Huang; Yidong Chen
Sponsor: University of Texas, San Antonio

These funds will support the development of a computational model dubbed the Semi-parametric Bayesian Factor Regulatory Model, or SB-FARM, for studying transcription factor and miRNA regulation of gene expression in Escherichia coli and human cancer.


Multi-domain, workflow driven computation system for microbial ecology research and analysis
Start Date: Aug. 1, 2012
Expires: July 31, 2013
Awarded Amount to Date: $299,999
Principal Investigator: Mark Ellisman
Sponsor: University of California, San Diego

These funds will support the development of a new application for the Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis, or CAMERA, which is a software tool used for depositing, locating, analyzing, visualizing, and sharing data about microbial biology. According to the abstract, the investigator will develop “heuristic-based dynamic resource scheduling approaches,” which will enable the “distribution of workflow tasks among heterogeneous computing domains such as local systems, a variety of commercial clouds, and multiple national resources.” The addition is being made to support next generation sequence data analysis using CAMERA’s tools.


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