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Funding Update: NSF Bioinformatics Grants Awarded Aug 7 — Sept 9, 2013

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Statistical and Computational Methods for the Analysis of Metagenomic Count Data
Start Date: Feb. 18, 2013
Expires: Aug. 31, 2015
Awarded Amount to Date: $88,824
Principal Investigator: Zhenqiu Liu
Sponsor: Cedars-Sinai Medical Center

The funds will support the development of parametric and nonparametric methods for bacterial taxa identification, clinical outcome prediction, and bacterial community structure estimation. The investigator will also develop statistical learning methods "for evaluating bacterial community dynamics and causal inference with longitudinal metagenomic data" as well as computational methods for "detecting gene-microbe interactions with integrated metagenomic and genomic data analysis."


Machine Learning Approaches for Genome-wide Biological Network Inference
Start Date: Nov. 15, 2012
Expires: April 30, 2014
Awarded Amount to Date: $85,226
Principal Investigator: Xue-Wen Chen
Sponsor: Wayne State University

The funds will support efforts to develop machine learning-based computational methods for studying interaction networks between genes and proteins.


Genome-wide Inference of mRNA Isoforms and Abundance Estimation from Biased RNA-seq Reads
Start Date: Sept. 1, 2013
Expires: Aug. 31, 2016
Awarded Amount to Date: $569,932
Principal Investigator: Tao Jiang
Sponsor: University of California, Riverside

These funds will support the development of methods for "inferring isoforms and estimating their abundance levels from RNA-Seq data where the reads may be sampled non-uniformly." Specifically, the investigators will use a "statistical framework based on quasi-multinomial distributions" and an "expectation-maximization algorithm developed for estimating isoform abundance levels that can handle all above biases in RNA-Seq data."


Next-gen Clustering: Fast and Accurate Ways to Cluster Proteins
Start Date: Sept. 1, 2013
Expires: Aug. 31, 2016
Awarded Amount to Date: $666,969
Principal Investigators: Shira Broschat, Douglas Call, Anantharaman Kalyanaraman
Sponsor: Washington State University

These funds will support the development of a cloud version of pClust, a software program for clustering protein sequences. According to the abstract, the investigators will use the tool to cluster proteins from whole-genome sequences from the Proteobacteria phylum.


Target-template Structural and Functional Relationships in Modeling of Protein-protein Interactions
Start Date: Sept. 1, 2013
Expires: Aug. 31, 2016
Awarded Amount to Date: $240,129
Principal Investigators: Ilya Vasker, Petras Kundrotas
Sponsor: University of Kansas

According to the abstract, the investigators will explore "target-template structural and functional relationships and develop corresponding approaches to modeling of protein-protein interactions."


Acquisition of Computing Equipment for Supporting Data-intensive Bioinformatics Research at the University of Kansas
Start Date: Sept. 1, 2013
Expires: Aug. 31, 2016
Awarded Amount to Date: $500,000
Principal Investigators: Jun Huan, Ilya Vakser, A. Townsend Peterson, Justin Blumenstiel, Krzysztof Kuczera
Sponsor: University of Kansas

The funds will be used to purchase computing infrastructure to support high-throughput sequencing data analysis, molecular dynamics simulation, cell signaling and molecular recognition, and other research activities.


Computational Methods for Macromolecular Binding Analysis
Start Date: Aug. 1, 2013
Expires: July 31, 2016
Awarded Amount to Date: $301,702
Principal Investigator: Changhui Yan
Sponsor: North Dakota State University

According to the abstract, these funds will support the development of graph-based methods for automated discovery of structural and physical-chemical elements that contribute to the affinity and specificity of macromolecular binding.


The iPlant Collaborative: Cyberinfrastructure for the Life Sciences
Start Date: Sept. 1, 2013
Expires: Aug. 31, 2018
Awarded Amount to Date: $11,900,000
Principal Investigators: Stephen Goff, Daniel Stanzione
Sponsor: University of Arizona

According to the abstract, these funds will be used to enhance the infrastructure capabilities of the iPlant collaborative project.


Algorithms and Software Tools for Epigenetics Research
Start Date: Sept. 15, 2013
Expires: Aug. 31, 2016
Awarded Amount to Date: $700,790
Principal Investigators: Stefano Lonardi, Karine Le Roch
Sponsor: University of California, Riverside

These funds will support the development of a computational framework that will help researchers analyze the epigenome of the human malaria parasite. More broadly, the tools will support epigenetics studies in other kinds of eukaryotic organisms.


Development of Generalized-ensemble Algorithms and their Application in Protein Studies
Start Date: Aug. 15, 2013
Expires: July 31, 2016
Awarded Amount to Date: $177,856
Principal Investigator: Ulrich Hansmann
Sponsor: University of Oklahoma

According to the abstract, these funds will support efforts to "develop theoretical and computational approaches aimed at overcoming limitations of generalized-ensemble and replica-exchange techniques in protein folding studies."


Rapid Screening of Interacting Ligands and Proteins
Start Date: Aug. 15, 2013
Expires: July 31, 2016
Awarded Amount to Date: $166,654
Principal Investigator: Daisuke Kihara
Sponsor: Purdue University

According to the abstract, the investigators intend to develop computational methods and databases that "allow fast, real-time screening of various types of three-dimensional structural data of proteins and their interacting molecules."


Interference Selection and the Statistics of Evolution in Microbes
Start Date: Aug. 1, 2013
Expires: July 31, 2016
Awarded Amount to Date: $160,000
Principal Investigator: Michael Desai
Sponsor: Harvard University

These funds will be used to develop mathematical models to predict how "interference selection among … beneficial and deleterious mutations alters evolutionary dynamics and genetic diversity in microbial populations." The investigator will test the predictions using "experimental evolution of budding yeast as a model system."


Ensemble Docking Interrogates Structural Determinants of Ligand-protein Interactions
Start Date: Sept. 1, 2013
Expires: Aug. 31, 2016
Awarded Amount to Date: $400,000
Principal Investigators: Jens Meiler, Gary Sulikowski, Charles Weaver
Sponsor: Vanderbilt University

These funds will be used to develop an "ensemble docking method for the Rosetta Ligand molecular modeling program." The abstract also states that the investigators will use a family of G-protein-coupled receptors and ligand candidates to test drive the method.


Algorithms for Decoding Complex Patterns of Genomic Variation
Start Date: Sept. 1, 2013
Expires: Aug. 31, 2016
Awarded Amount to Date: $311,417
Principal Investigator: Vineet Bafna
Sponsor: University of California, San Diego

According to the abstract, these funds will be used to develop computational techniques for analyzing genetic patterns to identify genes that adapt to "selective constraint[s] such as tolerance to lack of oxygen … or lactose tolerance. The investigators also aim to "reconstruct regions with complex variation patterns such as the killer cell immunoglobulin-like receptor."


Tools to Facilitate Deeper Data Analysis, Exploration, Management, and Sharing of Ensembles of Molecular Dynamics Trajectory Data
Start Date: Sept. 1, 2013
Expires: Aug. 31, 2015
Awarded Amount to Date: $200,000
Principal Investigator: Thomas Cheatham
Sponsor: University of Utah

According to the abstract, these funds will support the development of infrastructure for running biomolecular simulations. Specifically, the investigator intends to create tools that let users "deeply inspect the data generated from these simulations, visualize the results, and ultimately guide the simulation workflow."


Bayesian Ensemble Metabolomic Network Construction
Start Date: Sept. 1, 2013
Expires: Aug. 31, 2016
Awarded Amount to Date: $30,411
Principal Investigator: Seong Ho Kim
Sponsor: Wayne State University

According to the abstract, these funds will be used to develop algorithms that can "infer metabolic networks from the measurements of metabolites." Specifically, the investigators will develop a peak detection algorithm "for simultaneous baseline removal, smoothing, and peak picking steps, as well as the statistical assessment of peak confidence level." They'll then develop a "peak alignment algorithm based on global comparison using point matching algorithm as well as considering measurement error and outlier detection. Once an accurate alignment peak table is created, [the team will create] metabolic networks using a Bayesian ensemble method … to find …pairwise interactions and associations among sets of metabolite peaks as well as to account for uncertainty of network complexity."


Statistical Methods for Integrated Analysis of High-throughput Biomedical Data
Start Date: Sept. 15, 2013
Expires: Aug. 31, 2017
This grant is awarded to three investigative teams:
Pradeep Ravikumar; University of Texas, Austin; $90,723
Genevera Allen; William Marsh Rice University; $117,635
Zhandong Liu; Baylor College of Medicine; $109,609

The investigator intends to develop a statistical framework for integrated analysis of transcriptional, epigenomic, and functional genomics datasets.


Computational Enhancement of Analytical Metagenomics Systems
Start Date: Sept. 1, 2013
Expires: Aug. 31, 2015
Awarded Amount to Date: $560,934
Principal Investigators: Robert Edwards, Elizabeth Dinsdale, Forest Rohwer, Anca Segall
Sponsor: San Diego State University Foundation

These funds will be used to purchase computational infrastructure for metagenomic analysis as well as for training.


Hybrid Computational Models and Robust Numerical Methods for Electrostatic Interactions in Biomolecules
Start Date: Sept. 1, 2013
Expires: Aug. 31, 2016
Awarded Amount to Date: $280,000
Principal Investigators: Bo Li, Li Tien Cheng
Sponsor: University of California, San Diego

These funds will support efforts to develop hybrid computational models and numerical methods for electrostatic interactions in biomolecular systems.


Computational Model-based Statistical Methods in Biomedicine
Start Date: Sept. 1, 2013
Expires: Aug. 31, 2016
Awarded Amount to Date: $280,000
Principal Investigators: Bo Li, Li Tien Cheng
Sponsor: University of California, San Diego

These funds will support efforts to develop hybrid computational models and numerical methods for electrostatic interactions in biomolecular systems.

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