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Funding Update: NSF Bioinformatics Grants Awarded May 17 — June 26, 2014

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Algorithms for Single Molecule Sequence Analysis
Start Date: June 1, 2014
Expires: May 31, 2019
Awarded Amount to Date: $293,574
Principal Investigator: Michael Schatz
Sponsor: Cold Spring Harbor Laboratory

The funds will be used to develop analysis algorithms for long read single molecule sequence data and associated error models. "Specific objectives of the research include working towards assembling entire plant and animal chromosomes into complete, haplotype-phased sequences; identifying fusion genes and complex alternative splicing patterns responsible for diseases or adaptability; and searching for structural variations associated with improved crop yield or human diseases such as cancer or autism," the abstract states.


High Performance Algorithms and Implementations for GenomeAlignment
Start Date: Sept. 15, 2013
Expires: Aug. 31, 2015
Awarded Amount to Date: $145,664
Principal Investigator: Ashfaq Khokhar
Sponsor: Illinois Institute of Technology

According to the abstract, the funds will be used to develop "high performance algorithms and implementations for aligning genomes using innovative sampling and domain decomposition strategies."


High Performance Algorithms and Implementations for Genome Alignment
Start Date: Sept. 15, 2013
Expires: Aug. 31, 2015
Awarded Amount to Date: $145,664
Principal Investigator: Ashfaq Khokhar
Sponsor: Illinois Institute of Technology

According to the abstract, the funds will be used to develop "high performance algorithms and implementations for aligning genomes using innovative sampling and domain decomposition strategies."


Exact Algorithms for Learning Latent Structure
Start Date: July 1, 2014
Expires: June 30, 2019
Awarded Amount to Date: $499,981
Principal Investigator: David Sontag
Sponsor: New York University

According to the abstract, the funds will be used to develop improved algorithms for inferring causal relationships between variables. "Based on a classical idea in statistics called the method-of-moments, the new algorithms will be applied in bioinformatics to discover regulatory modules from disease expression profiles, and in health care to predict a patient's clinical state using data from their electronic medical record," the abstract states.


Bioinformatic Analysis of Metal-complexing Domains in Dinoflagellate Genome
Start Date: June 1, 2014
Expires: May 31, 2015
Awarded Amount to Date: $5,070
Principal Investigator: Lindsay Rutter
Sponsor: Lindsay Rutter

According to the abstract, the funds will support a project that aims to "investigate the molecular mechanisms underlying coral symbiosis, using genomic information from both coral host and algae symbiont."


Computational Analysis of microRNA Binding
Start Date: June 1, 2014
Expires: May 31, 2017
Awarded Amount to Date: $416,456
Principal Investigator: Haiyan Hu
Sponsor: University of Central Florida

The funds will be used for a project that aims to develop computational methods and tools for studying microRNA binding interactions and microRNAs' role in gene regulation, according to the abstract.


Sequence Optimization for Synthetic Biology
Start Date: June 1, 2014
Expires: May 31, 2017
Awarded Amount to Date: $499,881
Principal Investigator: Steven Skiena
Sponsor: SUNY at Stony Brook

Researchers will use these funds to "generalize and expand computational approaches for designing gene sequences into a coherent set of tools for three areas of molecular biology: sequence design for optimized gene expression; signal identification and location; and self-assembly," according to the abstract.


Advanced Informatics and Effective Algorithms to enable CryoEM Protein Structure Prediction and Density Analysis
Start Date: July 1, 2014
Expires: June 30, 2017
Awarded Amount to Date: $182,869
Principal Investigators: Jing He, Mohammad Zubair, Desh Ranjan, Shuiwang Ji
Sponsor: Old Dominion University Research Foundation

These funds will be used to develop "efficient computational methods and tools for determination of protein structures from 3D images in the presence of errors," according to the abstract. These tools will be useful for interpreting "large molecular assemblies that have important biological functions such as viruses, membrane-bound channels, and cellular machines."


Integrated Statistical Algorithms with Ultra-high Performance Computing for Discovering SNPs from Massive Next-generation Metagenomic Sequencing Data
Start Date: Aug. 1, 2013
Expires: July 31, 2016
Awarded Amount to Date: $263,328
Principal Investigator: Ping Ma
Sponsor: University of Georgia Research Foundation

According to the abstract, the researchers will use the funds to develop efficient algorithms for detecting SNPs in metagenomic data with an eye towards characterizing "microbial diversity in natural environments."


A Platform for Biological Information Integration and Knowledge Discovery
Start Date: July 1, 2014
Expires: June 30, 2015
Awarded Amount to Date: $225,000
Principal Investigators: Jinfeng Zhang, Adrian Barbu
Sponsor: Insilicom

According to the abstract, the researchers will use the funds to develop three commercial products. These are "software for bio-entity relationship extraction based on a novel, proprietary method for extracting bio-entity relationships from unstructured texts; a commercial database for context-specific molecular interaction information based on the integrated molecular interaction database (IMID) developed previously; … [and] a platform for biological information integration and data mining with applications in drug repurposing and drug side effect prediction."


Methods for Analyzing Sequencing Data from Repetitive Genomes
Start Date: May 15, 2014
Expires: April 30, 2019
Awarded Amount to Date: $425,546
Principal Investigator: Benjamin Langmead
Sponsor: Johns Hopkins University

According to the abstract, the researchers will use the funds to develop "improved computational and statistical methods for analyzing DNA sequencing data, providing faster, more accurate, and more interpretable results to scientists studying organisms with repetitive genomes."


A Probabilistic Approach to Meta-analysis of Biological Network Interface
Start Date: July 1, 2014
Expires: June 30, 2017
Awarded Amount to Date: $689,713
Principal Investigator: Su-In Lee
Sponsor: University of Washington

According to the abstract, the researchers will use the funds to develop "a computational framework, based on statistical and machine learning techniques, for effectively integrating multiple heterogeneous data sets to infer gene networks accurately."


Resources for Mixed Model Association Mapping of Complex Traits
Start Date: June 1, 2014
Expires: May 31, 2019
Awarded Amount to Date: $109,203
Principal Investigator: Alkes Price
Sponsor: Harvard University

According to the abstract, the goal of this project is to "devise new statistical methods for identifying genetic variants associated to disease resistance and other traits in plants, livestock, and model organisms such as fruit flies and mice."


A Novel Framework for Detecting Genomic Structural Variation
Start Date: June 1, 2014
Expires: May 31, 2017
Awarded Amount to Date: $733,316
Principal Investigator: Paul Medvedev
Sponsor: Pennsylvania State University

The funds will be used for a project that aims to develop tools for identifying genomic structural variation.


Deciphering Functionality of Mutations across the Human Genome with Respect to Parental DNA Contribution
Start Date: June 1, 2014
Expires: May 31, 2015
Awarded Amount to Date: $5,070
Principal Investigator: Danjuma Quarless
Sponsor: Danjuma Quarless

Researchers will use these funds to develop "computational methods to uncover features dependent on the diploid nature of the human genome."


Computational Analyses of the Interactions between DNA and Chromatin Structure
Start Date: Jan. 1, 2014
Expires: Sept. 30, 2016
Awarded Amount to Date: $367,839
Principal Investigator: Jun Song
Sponsor: University of Illinois at Urbana-Champaign

The project investigator will use these funds to develop mathematical methods for analyzing "high-throughput nucleosome mapping data in yeasts" as well as "computational tools for studying the relations among DNA sequence, nucleosome stability, and nucleosome positioning," the abstract states.


Bayesian Model Checking for Phylogenetics in the Post-genomic Era
Start Date: Aug. 1, 2014
Expires: July 31, 2017
The grant is awarded to two investigative teams:
Jeremy Brown; $418,252; Louisiana State University
Robert Thomson; $181,956; University of Hawaii

According to the abstract, these funds will be used to develop improved open-source software for determining phylogenetic relationships.


Estimating the Bayesian Phylogenetic Information Content of Systematic Data
Start Date: Sept. 1, 2014
Expires: Aug. 31, 2017
Awarded Amount to Date: $600,000
Principal Investigators: Paul Lewis; Ming-Hui Chen; Lynn Kuo; Louise Lewis
Sponsor: University of Connecticut

The investigative team will use these funds to develop and test methods of "estimating the quality and information content of biological data sets used to determine genealogical relationships (phylogenies) among species," according to the abstract.

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