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Funding Update: NSF Bioinformatics Grants Awarded Jan. 24 — Feb. 20, 2013

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PRUGC — Phylogenetic Reconstructions with Unequal Gene Contents
Start Date: Feb. 1, 2013
Expires: Jan. 31, 2018
Awarded Amount to Date: $549,529
Principal Investigator: Max Alekseyev
Sponsor: University of South Carolina, Columbia

According to the abstract, the funds will support the development of software for reconstructing ancestral genomes. Specifically, the PRUGC software will use multiple breakpoint graphs to address "algorithmic challenges arising from genomes having unequal gene contents" resulting from things like genome rearrangements and gene duplications.


Advanced Computational Algorithms for Deep Interrogation of Microbial Communities Using Millions of 16S rRNA Pyrosequences
Start Date: Nov. 30, 2012
Expires: April 30, 2014
Awarded Amount to Date: $519,222
Principal Investigator: Yijun Sun
Sponsor: The State University of New York, Buffalo

According to the abstract, the funds will be used to develop a suite of computational tools and statistical methods for analyzing large numbers of 16S rRNA sequences from microbial communities. Specifically, the investigator will develop web-based applications that can be used for "large-scale taxonomy independent analysis" and "comparative community analysis."


Annotating the Microbiome Using Machine Learning Methods
Start Date: March 30, 2013
Expires: Feb. 28, 2018
Awarded Amount to Date: $550,000
Principal Investigator: Huzefa Rangwala
Sponsor: George Mason University

According to the abstract, the funds for this project will be used to develop algorithmic methods that can "combine information across multiple hierarchical databases associated with annotation problems." Specifically, the PI will develop data fusion classifiers that can integrate "heterogeneous, incomplete data sources" such genomic, proteomic, and metabolic data, in order to predict phenotypes.


Co-evolution of Domains, Genes and Species: Models, Algorithms, and Software
Start Date: March 1, 2013
Expires: Feb. 29, 2016
Awarded Amount to Date: $717,566
Principal Investigator: Marie Dannie Durand
Sponsor: Carnegie-Mellon University

According to the abstract, these funds will be used to develop models, algorithms, and software for analyzing multidomain protein families.


Developing Biochemoinformatics Tools for Large-Scale Metabolomics Applications
Start Date: July 1, 2013
Expires: June 30, 2018
Awarded Amount to Date: $222,619
Principal Investigator: Hunter Moseley
Sponsor: University of Louisville Research Foundation

According to the abstract, these funds will be used to develop computational tools that can analyze large datasets generated by technologies such as stable isotope-resolved metabolomics.


Predicting the Combined Impact of Multiple Mutations on Protein Functional Adaptation
Start Date: April 1, 2013
Expires: March 31, 2016
Awarded Amount to Date: $238,779
Principal Investigators: Rachel Karchin, Manel Camps
Sponsor: Johns Hopkins University

According to the abstract, these funds will be used to develop a computational method for modeling higher order mutation interactions in proteins.


Differentially Private Machine Learning with Applications to Biomedical Informatics
Start Date: July 1, 2013
Expires: June 30, 2018
Awarded Amount to Date: $98,670
Principal Investigator: Kamalika Chaudhuri
Sponsor: University of California, San Diego

According to the abstract, these funds will be used to develop machine learning-based computational tools that can query, cluster, classify, and analyze medical databases in a way that ensures patients' privacy.


Methods for the Analysis of Population-Genomic Data
Start Date: Feb. 15, 2013
Expires: Jan. 31, 2016
Awarded Amount to Date: $1,049,851
Principal Investigator: Michael Lynch
Sponsor: Indiana University

The funds will be used to develop a statistical framework for analyzing genomic data from populations. According to the abstract, the investigators will also use the funds for several subprojects. These include measuring patterns of variation and covariation among nucleotide sites and the development of methods that can facilitate genome assembly and refine genetic maps.


Biochemical Network Models with Next Gen Sequencing
Start Date: Jan. 8, 2013
Expires: Sept 30, 2014
Awarded Amount to Date: $118,182
Principal Investigator: Grzegorz Rempala
Sponsor: Ohio State University

The funds will support the development of mathematical and statistical tools that can analyze biochemical network models. According to the abstract, the investigators will develop "likelihood-based estimates of the biochemical network parameters and structure from the data consisting of longitudinal species counts." They will also test the performance of their algorithms on real sequence data.


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