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Funding Update: NSF Bioinformatics Grants Awarded Aug. 23 — Sept 19, 2012

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Developing a 3D browser to explore genomes
Start Date: Oct. 1, 2012
Expires: Sept. 30, 2016
This grant is awarded to two investigative teams:
W. Jim Zheng, Deepak Bastia; Medical University of South Carolina; $355,259
Jijun Tang; University of South Carolina Research Foundation; $444,302

These funds will be used to develop a system that enables biologists to build and refine their own 3D genome models for analyzing data. According to the grant abstract, the developers have created a proof-of-concept 3D viewer, Genome3D, which enables the integration and visualization of genomic and epigenomic data in three dimensions. The next steps are to “transform” the prototype into a cloud-based 3D genome browser that can be used on various platforms; add tools that ”analyze 3D features of genomes and support model building and validation;” provide a set of APIs and scripting tools for customized data analysis; and to collaborate with other researchers to explore and visualize new 3D genome models.


Towards robust and scalable discovering of significant associations in massive genetic data
Start Date: Oct. 1, 2012
Expires: Sept. 30, 2016
This grant is awarded to two investigative teams:
Wei Wang, Wei Sun; University of North Carolina, Chapel Hill; $442,303
Xiang Zhang, Jing Li; Case Western Reserve University; $499,591

The funds will support the development of a computational framework for large scale genotype-phenotype association studies. According to the abstract, the infrastructure will include methods for “addressing sample relatedness, capturing confounding factors, and controlling multiple testing errors.” These methods will be tested using simulated and real data collected from yeast, mouse, and human.


An interoperable information infrastructure for biodiversity research
Start Date: Oct. 1, 2012
Expires: Sept. 30, 2014
Awarded Amount to Date: $300,000
Principal Investigator: John Wooley
Sponsor: University of California, San Diego

The funds will support interoperability efforts between the biodiversity community, who use the Darwin Core; and the Genomic Standards Consortium, which has developed the Minimal Information about any Sequence standard for genomics, metagenomics, and marker genes. These groups will develop a reference database that integrates both standards and will create “specific implementations for different database platforms to foster adoption,” the abstract states.


Algorithms and computations for RNA structure prediction
Start Date: Oct. 1, 2012
Expires: Sept. 30, 2015
Awarded Amount to Date: $499,444
Principal Investigators: Daniel Gusfield, Patrice Koehl
Sponsor: University of California, Davis

The project investigators will use the funds to develop and improve algorithms and programs for RNA structure prediction.


Variational multiscale approaches to biomolecular structure, dynamics, and transport
Start Date: Sept. 15, 2012
Expires: Aug. 31, 2015
This grant is awarded to two investigative teams:
Chun Liu; Pennsylvania State University, University Park; $259,469
Guowei Wei; Michigan State University; $319,477

The funds will support efforts to address challenges associated with studying the structure, function, and dynamics of self-organizing biomolecular systems. According to the abstract, the investigators will apply “variational multiscale models” as well as a coarse-grained approach “based on density cluster dynamics, which extracts stable manifolds in molecular dynamics simulations.”


Statistical problems in phylogenetics
Start Date: Sept. 15, 2012
Expires: Aug. 31, 2015
Awarded Amount to Date: $200,000
Principal Investigator: Elizabeth Housworth
Sponsor: Indiana University

The funds will support the development of a “mathematical foundation” for phylogenetic reconstruction methods. Specifically, the investigator plans to study the statistical properties of models used to infer phylogenies from genetic data.


Models and computational strategies in statistical bioinformatics
Start Date: Sept. 15, 2012
Expires: Aug. 31, 2014
Awarded Amount to Date: $46,283
Principal Investigators: James Booth, Martin Wells
Sponsor: Cornell University

The funds will support the development of methods for analyzing high-throughput biological data that are based on statistical tools such as “the use of random effects for regularization, shrinkage estimation, Bayesian statistics, and mixtures for posterior classification and prediction.”


New computational methods through stochastic modeling and analysis
Start Date: Sept. 1, 2012
Expires: Aug. 31, 2017
Awarded Amount to Date: $49,139
Principal Investigator: Sebastien Roch
Sponsor: University of Wisconsin, Madison

The funds will support the application of modeling and analysis techniques to study computational problems in phylogenomics. Specifically, the investigators intend to “improve large-scale likelihood-based gene tree estimation, develop computational methods to assemble species phylogenies from gene histories, and detect network-like signal in molecular data.”


Combinatorial optimization methods for problems in molecular biology and genetics
Start Date: Sept. 1, 2012
Expires: Aug. 31, 2014
Awarded Amount to Date: $263,280
Principal Investigator: Richard Karp
Sponsor: International Computer Science Institute

The funds will support efforts to study problems associated with heuristic algorithms using case studies from molecular biology and genetics


Statistical and computational methods for the analysis of metagenomic count data
Start Date: Sept. 1, 2012
Expires: Aug. 31, 2015
This grant is awarded to two investigative teams:
Zhenqiu Liu; University of Maryland, Baltimore; $96,307
Shili Lin; Ohio State University; $68,727

The funds will support the development of parametric and nonparametric methods for identifying bacterial taxa, predicting clinical outcomes, and bacterial community structure estimation. The investigators will also develop statistical learning methods for evaluating bacterial community dynamics and making causal inferences from longitudinal metagenomic data as well as computational approaches for detecting gene-microbe interactions from metagenomic and genomic data analysis.


Stochastic models of HIV escape from CTL attack
Start Date: Sept. 1, 2012
Expires: Aug. 31, 2015
Awarded Amount to Date: $124,998
Principal Investigator: Sivan Leviyang
Sponsor: Georgetown University

The funds will support the development of mathematical and computational tools through which the effects of cytotoxic T lymphocytes’ attack on HIV genetic diversity can be explored. The investigators also intend to develop statistical methods for inferring HIV “escape dynamics under multi-epitope CTL attack by exploiting both population dynamics and genetic sequence data.”


Mathematical models for pause-induced delays in bioprocesses
Start Date: Sept. 1, 2012
Expires: Aug. 31, 2015
Awarded Amount to Date: $269,648
Principal Investigators: Lisa Davis, Tomas Gedeon
Sponsor: Montana State University

The funds will support efforts to use “a nonlinear hyperbolic partial differential equation as a mathematical model for the transcription process of ribosomal RNA.” The investigators will also develop analytical and numerical methods for verifying, validating, and for sensitivity analysis of the model. “These new tools will be used to determine the limits that transcriptional pauses impose on the mean and variance of the transcription rate of ribosomal RNA,” the abstract states.


Acquisition of computational resource for research in computational and systems biology
Start Date: Sept. 1, 2012
Expires: Aug. 31, 2015
Awarded Amount to Date: $450,000
Principal Investigators: Carlos Camacho, Lillian Chong
Sponsor: University of Pittsburgh

The funds will be used to purchase a 57-node, 3,392-core computing cluster that will be used to develop molecular methods to access biological timescales of interest; generate omics data using high-throughput sequencing technologies; and “to leverage high-resolution multi-modal biomedical images/videos in basic research.”


High performance algorithms and implementations for genome alignment
Start Date: Sept. 1, 2012
Expires: Aug. 31, 2014
Awarded Amount to Date: $200,000
Principal Investigators: Ashfaq Khokhar, Fahad Saeed
Sponsor: University of Illinois, Chicago

The funds will be used to develop genome alignment algorithms that use sampling and domain decomposition strategies. According to the abstract, the algorithms will be implemented on hybrid computing platforms comprised of multicore clusters and graphics processing units.


PathBubbles for dynamic visualization and integration of biological information
Start Date: Aug. 1, 2012
Expires: June 31, 2015
Awarded Amount to Date: $394,007
Principal Investigator: Jian Chen
Sponsor: University of Maryland, Baltimore

The funds will be used to develop PathBubbles, a biological pathway visualization tool that uses the existing Vis- and Code Bubbles as a framework. The investigator plans to provide annotation information for the pathways from data found in specific ontologies, text-mining tools, expression data, and functional information about post-translationally modified proteins from literature.


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