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Funding Update: Apr 29, 2011

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NSF Bioinformatics Grants Awarded April 1 — April 27, 2011

A Unified Statistical Framework for the Identification of Rare Variants Implicated in Complex Diseases
Start Date: July 1, 2011
Expires: June 30, 2012
Awarded Amount to Date: $130,598
Principal Investigator: Iuliana Ionita
Sponsor: Columbia University

Supports the development of statistical methods, implemented in a software package, that can be applied to high-dimensional and sparse datasets generated by high-throughput genomic experiments. The scientists will use the software to investigate rare genetic variants.


Bridging the Gap between the Transcriptome and the Proteome to Study Inter-cellular Signaling
Start Date: June 1, 2011
Expires: May 31, 2012
Awarded Amount to Date: $333,348
Principal Investigators: T. Murali, Richard Helm, Padmavathy Rajagopalan
Sponsor: Virginia Polytechnic Institute and State University

The grant abstract states that the funds will be used to develop an approach that prioritizes expensive and time-consuming proteomic experiments based on data collected from transcriptional experiments. The investigators plan to use the method to discover how different cell types communicate with each other in the complex environment found in tissues and organs and they plan to address the question using an in vitro three-dimensional liver mimic that contains two different hepatic cell types in a layered configuration. Furthermore, the researchers plan to develop a combined computational-experimental pipeline that integrates new proteomic data with existing measurements in order to refine the models and algorithms.


Computational Methods for Interpreting Epigenomics Datasets
Start Date: May 1, 2011
Expires: April 30, 2012
Awarded Amount to Date: $302,193
Principal Investigator: Olivier Elemento
Sponsor: Joan and Sanford I. Weill Medical College of Cornell University

Supports the development of computational methods that perform integrative analysis of epigenomics and chromatin interaction datasets obtained from ChIP-seq and Hi-C experiments, including tools for ChIP-seq peak detection, Hi-C interaction detection, information-theoretic discovery of sequence regulatory codes, information-theoretic cellular pathway analysis, graph theoretical analysis of chromatin interaction networks, and data visualization including immersive 3D visualization. The investigators plan to use these methods to “discover and characterize the principles by which regulatory elements situated far away from genes contribute to the regulation of transcription in cells.”


Algorithms and Software for Discovery of Non-sequential Protein Structure Similarities
Start Date: May 1, 2011
Expires: April 30, 2014
This grant was awarded to two investigative teams:
$408,140, Bhaskar DasGupta, Jie Liang, University of Illinois, Chicago
$200,001, Mona Singh, Princeton University

The grant abstract states that the funds will be used to develop scalable computational methods for comparing protein structures. The tools will enable the discovery of sequence-order-independent substructure similarity with a long-term goal of doing a large-scale comparison over all protein structures.


Theoretical Studies of Protein Folding
Start Date: May 1, 2011
Expires: April 30, 2012
Awarded Amount to Date: $205,000
Principal Investigator: Harold Scheraga
Sponsor: Cornell University

The funds will be used to improve biomolecular algorithms to gain an understanding of how inter-residue interactions determine three-dimensional structure. The abstract states that the main focus of the project is the “extension of the united-residue (UNRES) methodology to treat protein-DNA and protein-protein enzyme-substrate complexes.”


Advanced Computational Algorithms for Deep Interrogation of Microbial Communities Using Millions of 16S rRNA Pyrosequences
Start Date: May 1, 2011
Expires: April 30, 2014
Awarded Amount to Date: $657,287
Principal Investigators: Yijun Sun, Volker Mai
Sponsor: University of Florida

Supports the development of a suite of computational tools and statistical methods that allow researchers to analyze tens of millions of 16S rRNA sequences for microbial community analysis and to extract biologically relevant patterns from massive sequence data.

Specific aims of the project include the development of algorithms for large-scale taxonomy-independent analysis; the development of a collection of statistical and computational methods for comparative community analysis, including discriminant analysis, topology analysis, and microbial network analysis; and to establish a web application based on the proposed algorithms to provide researchers with a complete package of tools for comparative microbial community analysis.


Algorithms and Applications for Next Generation High-Throughput Sequencing Technologies
Start Date: April 15, 2011
Expires: March 31, 2016
Awarded Amount to Date: $503,509
Principal Investigator: Jinze Liu
Sponsor: University of Kentucky

The investigators will use the funds to develop a computational method for characterizing the transcriptome from the hundreds of millions of random short sequences sampled from messenger RNA samples. The tool will use a maximum likelihood approach to identify novel and known splicing and fusion events; a genome-wide transcriptome comparison method to detect statistically significant differential alternative splicing patterns; and data-mining algorithms to reconstruct co-regulated splicing networks that carry out specific biological functions.


Representation, Visualization, and Modeling of Signaling Pathways in Higher Plants
Start Date: April 15, 2011
Expires: March 31, 2012
Awarded Amount to Date: $254,754
Principal Investigators: Andy Pereira, Lenwood Heath, Ruth Grene
Sponsor: Virginia Polytechnic Institute and State University

The grant abstract states that the funds will be used to build the Beacon system, which will provide computational support for biologists' questions about signaling pathways.


Commoditizing Data-Intensive Biocomputing in the Cloud
Start Date: April 15, 2011
Expires: March 31, 2013
Awarded Amount to Date: $370,000
Principal Investigators: Wuchun Feng, Joao Setubal, Heshan Lin
Sponsor: Virginia Polytechnic Institute and State University

Supports the development of the MetaRx software environment to address issues associated with computing large quantities of DNA sequence data by transforming and commoditizing cloud computing infrastructures, such as Microsoft Azure, to massively accelerate the discovery process for scientists and engineers.