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Funding Update: NSF Bioinformatics Grants Awarded May 25 — June 26, 2013

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Expanding the Dimensions of Computational Epigenomic Modeling and Analysis
Start Date: July 1, 2013
Expires: June 30, 2018
Awarded Amount to Date: $230,167
Principal Investigator: Jason Ernst
Sponsor: University of California, Los Angeles

According to the abstract, the funds will be support computational methods of modeling and analyzing epigenomic data. Specifically, the investigator will work on methods that can model epigenomic changes over time, methods that can predict "the genome-wide signals of epigenetic marks in cell types in which a mark is not mapped," and methods that can "associate putative distal regulatory elements identified by epigenomic maps with the target genes they regulate by integrating multiple partially informative data sources to these interactions."


Bioinformatics Tools for Biology Education
Start Date: July 1, 2013
Expires: Dec. 31, 2013
Awarded Amount to Date: $150,000
Principal Investigator: Sandra Porter
Sponsor: Digital World Biology

These funds will support the creation of a tablet-based toolkit to help student conduct molecular investigations such as why some mutations affect protein function while others don't. The abstract states that the toolkit will contain "an application for viewing and manipulating structures, an interactive digital lab manual that supports bioinformatics investigations related to genetic disease, an instructor guide, and a dataset with superimposed and annotated structures."


A Novel Protein Fragment Assembler for Metagenomic Data Analysis
Start Date: June 15, 2013
Expires: May 31, 2016
Awarded Amount to Date: $486,116
Principal Investigator: Shibu Yooseph
Sponsor: Craig Venter Institute

The funds will be used to develop novel methods for analyzing metagenomic sequence data. Specifically, the investigator will develop "a sequence assembly framework for reconstructing full-length protein sequences directly from short peptide fragments identified on nucleotide reads," the abstract states.


Querying Massive Dynamic Biological Network Databases
Start Date: July 1, 2013
Expires: June 30, 2016
Awarded Amount to Date: $492,584
Principal Investigator: Tamer Kahveci
Sponsor: University of Florida

According to the abstract, the investigator aims to develop scalable algorithms and tools that enable comparative analysis of large biological network databases. Specifically, these algorithms will enable comparisons of pairs of biological networks which "ensuring mathematically provable confidence bounds on the optimality of the results;" efficiently mine the data to find "small sets of representative subnetworks in massive sets of alternative biological network topologies;" and search for "subnetworks … that can adapt to changes in the database and the query network structure."


Algorithms for Haplotype Assembly from Next-Generation Sequencing Data
Start Date: Sept. 1, 2013
Expires: Aug. 31, 2016
Awarded Amount to Date: $400,000
Principal Investigator: Haris Vikalo
Sponsor: University of Texas, Austin

These funds will support the development of algorithms for haplotype assembly from NGS data.


Quantifying and Exploiting the Structure of Phylogenetic Tree Space through Network Analyses
Start Date: June 15, 2013
Expires: May 31, 2016
This grant is awarded to two investigative teams:
James Wilgenbusch, Kyle Gallivan; Florida State University; $256,012
Jeremy Brown; Louisiana State University; $190,333

The investigators intend to develop a mathematical framework for quantifying information about genealogical relationships among organisms.


New Theorems and Algorithms for Comprehensive Analysis of Metagenomic Data via Statistical Phylogenetics
Start Date: Mar. 1, 2013
Expires: Aug. 31, 2017
Awarded Amount to Date: $315,914
Principal Investigator: Aaron Darling
Sponsor: Fred Hutchinson Cancer Research Center

According to the abstract, these funds will support efforts to develop methods that can "reconstruct the cellular compartmentalization of DNA in environmental samples, … detect synthetic genomes and evidence of directed evolution within a metagenomic sample, … detect combinations of genetic material that are anomalous given their location or time of observation, [and] statistically distinguish meaningful shifts in microbial community composition from noise."


Information and Complexity in the Analysis of Biological Datasets and Networks
Start Date: July 1, 2013
Expires: June 30, 2015
Awarded Amount to Date: $299,740
Principal Investigator: David Galas
Sponsor: Pacific Northwest Research Institute

These funds will support efforts to develop improved mathematical methods for biological network analysis.


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