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Funding Update: NSF Bioinformatics Grants Awarded June 27 — Aug. 11, 2014

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An Integrative Approach to Identifying Highly Heritable Subtypes of Complex Phenotypes
Start Date: July 1, 2014
Expires: June 30, 2017
Awarded Amount to Date: $561,717
Principal Investigators: Jinbo Bi, Erin Connor, John Cole, Henry Kranzler
Sponsor: University of Connecticut

According to the abstract, the funds will be used to develop algorithms that can "differentiate homogenous subtypes of a complex phenotype that are most informative in genetic analysis, and identify genetic variants that are associated with the subtypes but cannot be detected by the non-differentiated phenotype."


A New Automated Data Integration, Annotations, and Interaction Network Inference System for Analyzing Drosophila Gene Expression
Start Date: July 1, 2014
Expires: June 30, 2017
Awarded Amount to Date: $610,392
Principal Investigators: Heng Huang, Chris Ding
Sponsor: University of Texas, Arlington

The funds will be used in a project aimed at addressing computational challenges associated with analyzing Drosophila gene expression patterns. Specifically, "it focuses on designing principled bioinformatics and computational biology algorithms and tools that will integrate multi-modal spatial patterns of gene expression for Drosophila embryos' developmental stage recognition and anatomical ontology term annotation, and will infer gene interaction networks to generate a more comprehensive picture of gene function and interaction," the abstract states.


Beyond Ribosomal RNA Gene: Community Tools for Analysis of Whole-Genomes and Metagenomes
Start Date: July 1, 2014
Expires: June 30, 2017
This grant has been awarded to two investigative teams
Konstantinos Konstantinidis; Georgia Tech Research Corporation; $239,126
James Cole, James Tiedje; Michigan State University; $180,108

According to the abstract, the funds will be used to develop computational tools that help scientists explore the "composition, functions and values of the microbial communities" and also to train faculty "in new metagenomics techniques, which are positioned at the interface of microbiology, genomics, bioinformatics, and computational biology."


The Automata Programming Paradigm for Genomic Analysis
Start Date: Aug. 1, 2014
Expires: July 31, 2017
This grant has been awarded to two investigative teams
Michela Becchi, Gavin Conant; University of Missouri-Columbia; $348,219
Jason Bakos; University of South Carolina at Columbia; $173,004

According to the abstract, the funds will be used to develop "novel programmatic descriptions of several genomic analyses" and to map them to two kinds of computing architecture namely; field programmable gate arrays and Micron's automata processor


A Novel Framework for Mining Multi-relation and Labeled Graphs
Start Date: Aug. 1, 2014
Expires: July 31, 2017
Awarded Amount to Date: $345,551
Principal Investigator: Saeed Salem
Sponsor: North Dakota State University, Fargo

According to the abstract, the investigators will use the funds to develop algorithms and analytic methods for "mining cross-graph interesting patterns from multi-relation graphs, and coherent patterns from attributed graphs; and designing computational methods for integrating biological data [such as] gene expression [and] protein-protein interaction networks."


Building Better Genome Assemblies and Gene Models with RNA-seq Data
Start Date: Aug. 15, 2014
Expires: July 31, 2016
Awarded Amount to Date: $458,778
Principal Investigator: Liliana Florea
Sponsor: Johns Hopkins University

The funds will be used to develop improved bioinformatics algorithms and tools for genome assembly and annotation, the abstract states. According to the investigators, "the first set of tools will use contiguity properties of RNAseq reads to recruit unmapped contigs into a draft genome assembly to improve completeness and to discover assembly errors" while "the second set of tools will combine RNAseq and traditional (Sanger) cDNA sequences to produce a comprehensive set of gene and transcript annotations along the genome."


Reconstructing Viral Population without Using a Reference Genome
Start Date: Sept. 1, 2014
Expires: Aug. 31, 2017
Awarded Amount to Date: $333,319
Principal Investigators: Raj Acharya, Mary Poss, Paul Medvedev
Sponsor: Pennsylvania State University, University Park

The funds will be used to develop "probabilistic de Bruijn graphs and network flow on such graphs for the reconstruction of viral population when a reference is not available," the abstract states. "Given NGS data, the algorithms should determine the number, sequences, and relative frequencies of the haplotypes."


Creating Complete and Accurate Alternative Splicing Repertoires from RNA-seq Data
Start Date: Aug. 1, 2014
Expires: July 31, 2017
Awarded Amount to Date: $630,122
Principal Investigator: Liliana Flores
Sponsor: Johns Hopkins University

According to the abstract, the funds will be used to develop a bioinformatics tool that can "identify alternative splicing variations from sequencing reads in more detail and more accurately than previously possible." The funds will also be used to "build a comprehensive catalog of alternative splicing events in several plant species, taking advantage of the growing amounts of data being generated."


VIROME, Bioinformatics Cyberinfrastructure for the Next Wave of Scientific Advancements in Microbiome Research
Start Date: July 1, 2014
Expires: June 30, 2017
This grant has been awarded to two investigative teams
Liliana Flores; University of Maryland, Baltimore; $94,267
K.Wommack, Shawn Polson; University of Delaware; $205,157

According to the abstract, the funds will be used to "enhance a newly developed computational tool, the Viral Informatics Resource for Metagenome Exploration (VIROME)." Specifically, the investigators will use the funds to "leverage sources of long-length DNA sequence data to improve the quality of the information output from the VIROME bioinformatics pipeline; utilize the VIROME gene classification scheme to develop a sustainable database of unknown viral genes; and advance the sustainability of the VIROME resource through virtualization of its underlying computational workflow."


Identifying Phylogentically Informatics Data from Next-generation Sequencing
Start Date: Aug. 1, 2014
Expires: July 31, 2017
Awarded Amount to Date: $686,240
Principal Investigators: Reed Cartwright, Sudhir Kumar
Sponsor: Arizona State University

According to the abstract, the funds will be used to develop methods and software for processing and extracting information from large genomic datasets that help improve current knowledge about evolutionary relationships among species.


A Plug-and-Play Software Platform for Robotics-inspired Algorithms for Modeling Biomolecular Structures and Motions
Start Date: Feb. 1, 2015
Expires: Jan. 31, 2018
This grant has been awarded to three investigative teams
Erion Plaku; Catholic University of America; $215,476
Adrian Roitberg; University of Florida; $67,235
Amarda Shehu; George Mason University; $217,288

This grant will be used to develop open source software that can be used to study biomolecules involved in the activities of diseased cells. According to the investigators, the software will "integrate sophisticated energetic models and molecular representations with powerful search and optimization algorithms for complex modular systems inspired from robot motion planning."


Experimental and Theoretical Analysis of Tree Distance Distributions
Start Date: July 1, 2014
Expires: June 30, 2017
Awarded Amount to Date: $240,000
Principal Investigator: Sean Cleary
Sponsor: CUNY City College

According to the abstract, the project aims to better understand the "distribution of multiple measures of distances on trees." The investigators, it states, will study both "ordered trees, used in computational settings such as data and disk storage techniques; and unordered trees, arising in biological and other scientific studies." They will also work on "computationally feasible" approaches for computing tree distances that can be used for phylogenetic applications.


Algorithms and Models for Distributed Computation of Bayesian Phylogenetics
Start Date: Aug.1, 2014
Expires: July 31, 2017
Awarded Amount to Date: $379,790
Principal Investigators: Christopher Jermaine, Luay Nakhleh
Sponsor: William Marsh Rice University

According to the abstract, investigators involved in the project will develop algorithms for phylogenetic inference that can be used in compute environments such as Amazon EC2.


Algorithms and Tools for Modeling Macromolecular Assemblies
Start Date: July 1, 2014
Expires: June 30, 2017
This grant has been awarded to two investigative teams
Matthew Baker, Steven Ludtke; Baylor College of Medicine; $288,315
Tao Ju; Washington University; $234,668

This grant will be used to develop methods and software for mining structure of large molecular assemblies from imaging data, the abstract states. Specifically, the investigators will develop algorithms for "detecting secondary structure elements … at various non-atomic resolutions, tracing protein backbones in the density volume, and flexibly fitting probe structures into the volume."


A Bayesian Evolutionary Tree Analysis Database
Start Date: July 1, 2014
Expires: June 30, 2017
This grant has been awarded to two investigative teams
Brian Moore; University of California, Davis; $304,169
Robert Thomson; University of Hawaii; $245,559

According to the abstract, the investigators will develop a prototype Bayesian Evolutionary Tree Analysis database called BETAbase that will be an "interactive repository for the output of Bayesian phylogenetic studies."


Algorithms and Tools for Phylogenetic Tree Reconciliation
Start Date: Aug. 1, 2014
Expires: July 31, 2017
Awarded Amount to Date: $220,883
Principal Investigator: Ran Libeskind-Hadas
Sponsor: Harvey Mudd College

According to the abstract, investigator aims to develop "new algorithms, visualization methods, and software tools for studying the evolutionary histories of pairs of entities such as genes and species, hosts and parasites, and species and their geographical habitats and also help to train the next generation of researchers."


Comparative Network Biology to Study the Evolution of Regulatory Networks
Start Date: Aug. 1, 2014
Expires: July 31, 2019
Awarded Amount to Date: $506,579
Principal Investigator: Sushmita Roy
Sponsor: University of Wisconsin, Madison

This grant will support the development of a framework for studying the evolutionary dynamics of regulatory networks. Specifically, the funds will be used to develop "algorithms for regulatory network reconstruction that combine probabilistic models of evolution with network reconstruction," the abstract states. Also to be developed are methods for identifying and correlating "regulatory network patterns of divergence to phenotypic states." The tools developed in this study will be used to study the evolution of stress response, carbon metabolism and plant-microbe relationships using expression datasets from yeast and land plant phylogenies.


Semiparametric ODE Models for Complex Gene Regulatory Networks
Start Date: Aug. 1, 2014
Expires: July 31, 2017
This grant has been awarded to three investigative teams
Hua Liang; George Washington University; $123,983
Guang Yao, Hao Zhang; University of Arizona; $163,989
Guang Cheng; Purdue University; $46,022

According to the abstract, the investigators aim to develop statistical and computational tools that reveal the underlying structure, dynamics, and functionality of gene regulatory networks.


An Integrated Approach to Characterizing Conformational Changes of Large Proteins
Start Date: July 15, 2014
Expires: June 30, 2017
Awarded Amount to Date: $450,000
Principal Investigator: Lydia Kavraki
Sponsor: William Marsh Rice University

This grant will support efforts to "investigate the extent to which computational methods can help discover and visualize conformational changes of large proteins that are in agreement with experiment."


Computational Framework for Characterizing Protein Conformational Landscapes
Start Date: July 1, 2014
Expires: June 30, 2017
Awarded Amount to Date: $320,000
Principal Investigator: Nurit Haspel
Sponsor: University of Massachusetts, Boston

This grant will support efforts to develop algorithms that can "exploit the geometric and biophysical properties of proteins to efficiently characterize their conformational space and detect interesting regions that may be functionally important but are hard to determine experimentally."


Design Tools and the Experimental Validation for Synthetic Biology Systems
Start Date: Aug. 15, 2014
Expires: July 31, 2017
Awarded Amount to Date: $299,774
Principal Investigators: Soha Hassoun, Nikhil Nair
Sponsor: Tufts University

This grant will support efforts to develop computational tools that "increase the role of automation in designing synthetic biological systems."


Persistence and Permanence in Biological Interaction Networks
Start Date: July 15, 2014
Expires: June 30, 2017
Awarded Amount to Date: $272,000
Principal Investigator: Gheorghe Craciun
Sponsor: University of Wisconsin, Madison

According to the abstract, the investigator will develop software "that implements mathematical methods for understanding persistence, and will allow biologists and biomedical scientists to analyze persistence properties of diverse biological networks of interest."


A Reliable and Scalable Approach to Causal Inference for Large-scale Multivariate Data
Start Date: August 15, 2014
Expires: July 31, 2017
Awarded Amount to Date: $38,105
Principal Investigator: Garvesh Raskutti
Sponsor: University of Wisconsin, Madison

The funds will be used to develop algorithms and methods for "inferring causal or functional relationships between genetic, proteomics, and transcriptomic features both for the ENCODE human genome project and data for mice with susceptibility to obesity and diabetes," the abstract states.


Synthetic Biology Open Language (SBOL)
Start Date: July 1, 2014
Expires: June 30, 2018
This grant has been awarded to two investigative teams
Chris Myers; University of Utah; $444,527
Herbert Sauro, John Gennari; University of Washington; $772,192

The funds will support efforts to extend and strengthen the SBOL, a standard for describing biological designs constructed from DNA. The investigators will also develop "validation suites and services, so that systems can verify correct use of the standard; and perform outreach and education to further grow and build our community of users and developers in both academia and industry."

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