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Funding Update: NSF Bioinformatics Grants Awarded June 26 — Aug 6, 2013

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Gini-based Methodologies to Enhance Network-scale Transcriptome Analysis in Plants
Start Date: Sept 1, 2013
Expires: Aug 31, 2016
Awarded Amount to Date: $399,168
Principal Investigator: Xiangfeng Wang
Sponsor: University of Arizona

These funds will support the development of a software package called the Gini Network Analysis Toolkit, or GNAT, that is based on a family of mathematical solutions used for "analyzing non-normally distributed data" in fields such as economics, physics, and social networks. According to the abstract, the GNAT will help address computational problems such as "how to derive non-linear relationships between transcription factors and targets, how to properly decompose a network into individual sub-network modules, how to predict biologically significant genes via network-scale comparisons, how to integrate and use the heterogeneous forms of biological interaction data to facilitate network analysis, and how to seamlessly visualize a large-scale network for interactive data mining." The investigator also intends to develop a tool called BioNetscape, which will be used to organize and visualize network data generated from the GNAT.


Scalable Statistical Computing for Emerging Omics Data Streams
Start Date: Aug 1, 2013
Expires: July 31, 2016
Awarded Amount to Date: $1,000,000
Principal Investigator: Martin Morgan
Sponsor: Fred Hutchinson Cancer Research Center

These funds will support efforts to develop new approaches to solve problems in statistical analysis and interpretation of omics data using a combination of capabilities from the Bioconductor and Galaxy projects. According to the abstract, the project will involve three components: The first will focus on developing R programming paradigms that are appropriate for scalable analysis; the second will focus on developing high performance statistical methodologies for analyzing genomic data; and the third component will provide integration of R / Bioconductor workflows into Galaxy.


Novel Directions for Biological Network Alignment
Start Date: July 1, 2013
Expires: June 30, 2016
Awarded Amount to Date: $444,863
Principal Investigator: Tijana Milenkovic
Sponsor: University of Notre Dame

According to the abstract, these funds will support a project that aims to address issues with biological network alignment. Specifically, the investigators intend to develop a framework for evaluating existing network alignment methods; "redefine the problem of network alignment to allow for directly optimizing the amount of conserved network topology, which current methods fail to do;" and "extend the proposed methods to allow for alignment of heterogeneous networks encompassing the different [biological network] types."


Supporting Efficient Discrete Box Queries for Sequence Analysis on Large Scale Genome Databases
Start Date: Sept 1, 2013
Expires: Aug 31, 2016
This grant is awarded to two investigative teams:
Qiang Zhu; University of Michigan, Ann Arbor; $222,277
Sakti Pramanik, Charles Brown; Michigan State University; $273,419

According to the abstract, these funds will support efforts to investigate techniques for storing and querying "large scale k-mer data sets — overlapping k-length subsequences obtained from genome sequences — for sequence analysis in bioinformatics."


Modeling and Querying of Probabilistic Biological Networks
Start Date: Aug 1, 2013
Expires: July 31, 2015
Awarded Amount to Date: $174,925
Principal Investigator: Tamer Kahveci
Sponsor: University of Florida

These funds will support the development of computational techniques that "characterize and compare probabilistic networks," according to the abstract. Specifically, the investigators will develop "mathematical models that characterize topological properties of probabilistic networks" and a framework that lets users compare biological networks "when at least one of them is probabilistic."


Matrix Variate Modeling and Analysis of Large-scale Biological Data with Complex Dependencies
Start Date: Aug 1, 2013
Expires: July 31, 2016
Awarded Amount to Date: $166,661
Principal Investigators: Kerby Shedden, Shuheng Zhou
Sponsor: University of Michigan, Ann Arbor

These funds will support efforts to "assess the extent to which accounting for relationships among samples allows more accurate estimates to be made of relationships among variables." According to the abstract, the investigators have developed a "statistical procedure that uses inferred relationships among the units of observation to more accurately estimate physical and biological unknowns." In this project, they plan "to develop the theory behind their technique … [to] build software for carrying out the analyses, and to work with scientists in cancer biology, genomics, and neuroscience to assess the potential for using this approach to obtain novel scientific insights."


Dynamics and Function of Proteins by NMR and Computation
Start Date: Aug 1, 2013
Expires: July 31, 2017
Awarded Amount to Date: $685,063
Principal Investigator: Rafael Bruschweiler
Sponsor: Florida State University

These funds will support efforts to develop new algorithms, web servers, and software for "accurate and realistic characterization of proteins in their native environment," the abstract states.


New Software Tools for Genome Comparisons of Non-model Organisms
Start Date: Aug 1, 2013
Expires: July 31, 2016
Awarded Amount to Date: $657,009
Principal Investigator: Jian Ma
Sponsor: University of Illinois, Urbana-Champaign

These funds will support the development of methods to compare more than 10 new bee genomes. Specifically, the investigators will work on developing software to "better annotate the gene models by incorporating both RNA-seq data and information from genome sequences of related organisms," the abstract states. Furthermore, they will develop methods for building "cross-species sequence alignments for both coding and non-coding regions in the bee genomes."


Integrated Bayesian Deterministic and Probabilistic Modeling of Phenotype-Genotype Networks in the Metabolic System
Start Date: Aug 1, 2013
Expires: July 31, 2016
Awarded Amount to Date: $51,303
Principal Investigator: Rachael Hageman Blair
Sponsor: State University of New York, Buffalo

These funds will support the development of Bayesian methodology for mathematical modeling that "integrates across diverse data types, accounts for model uncertainty, and incorporates existing prior knowledge about the biological system," the abstract states. This approach, according to the investigators, will address limitations experienced by two modeling paradigms: "deterministic mathematical models of cellular metabolism; and causal graphical models of phenotypes and genotypes."


Mathematical Models and Computational Methods for the Tumor Microenvironment
Start Date: Aug 1, 2013
Expires: July 31, 2016
Awarded Amount to Date: $380,938
Principal Investigators: Robert Dillon, Prashanta Dutta
Sponsor: Washington State University

According to the abstract, these funds will support the development of computational methods for modeling breast cancer microenvironments "based on integrated second-order finite volume methods for each of the system components — fluid mechanics, chemical and ion transport in the bulk fluid, reactions on the cell membrane, transport through the cell membrane, and fluid/structure interaction of the elastic biological cells."


Algorithms and Statistical Methods for Personalized Diagnosis and Therapy in Cancer
Start Date: July 1, 2013
Expires: June 30, 2016
Awarded Amount to Date: $369,605
Principal Investigator: Mathukumalli Vidyasagar
Sponsor: University of Texas, Dallas

According to the abstract, these funds will support the investigator's efforts to develop novel algorithms for identifying cancer biomarkers and for predicting the efficacy of multi-drug combinations.


A Computational Framework for Atherosclerotic Plaque Growth Simulations
Start Date: July 1, 2013
Expires: June 30, 2016
Awarded Amount to Date: $27,951
Principal Investigators: Benjamin Seibold, Sunnie Joshi
Sponsor: Temple University

According to the abstract, these funds will support the development of a computational framework for modeling the growth of atherosclerotic plaques in large arteries.


Stochastic Modeling and Inference of Gene Networks
Start Date: Aug 15, 2013
Expires: July 31, 2016
Awarded Amount to Date: $216,565
Principal Investigator: Abhyudai Singh
Sponsor: University of Delaware

These funds will support the development of "computationally tractable methodologies based on moment closure schemes for studying stochastic dynamics of gene regulatory networks," the abstract states.


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