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Funding Update: NSF Bioinformatics Grants Awarded March 20 — April 18, 2012

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Methodology for Pattern Creation, Imprint Validation, and Discovery from the Annotated Biological Web
Start Date: Sept. 1, 2012
Expires: Aug. 31, 2015
This grant is awarded to three investigative teams:
Padmini Srinivasan, University of Iowa, $133,120
Louiqa Raschid; Caren Chang; Zhongchi Liu, University of Maryland, College Park, $271,839
Xiao-Ning Zhang, Saint Bonaventure University, $32,835

Supports the development of methods for mining Arabidopsis gene annotations in the Gene Ontology and Plant Ontology databases. According to the grant abstract, the investigators will use the Patterns in Arabidopsis Annotations, or PattArAn, tool to provide a graphical representations of patterns of Arabidopsis genes and associated GO and PO terms. They will also develop graph data-mining techniques and algorithms to identify dense subgraphs and to perform graph summarization as well as algorithms to mine the literature for relevant sentences for extracted patterns.


Achieving Long Timescale Sampling in Biomolecular Simulations
Start Date: May 1, 2012
Expires: April 30, 2015
Awarded Amount to Date: $633,041
Principal Investigator: Wei Yang
Sponsor: Florida State University

Supports the development of molecular dynamics simulation methods to describe complex biomolecular phenomena that "usually occur in much longer timescales than what conventional techniques can achieve." These methods will include algorithms "to enhance the sampling power of biomolecular simulations." The investigators expect to apply their methods to the "prediction of protein electrostatic effects and understanding their coupling with protein conformational transitions" and to develop an "understanding [of] how slow enzyme fluctuations prepare unique catalytic environments to activate chemical reactions," the abstract states.


Building a Community Resource for Neuroscientists
Start Date: May 1, 2012
Expires: April 30, 2015
This grant is awarded to two investigative teams:
Nicholas Carnevale, Yale University, $99,317
Amitava Majumdar; Maryann Martone, University of California, San Diego, $706,608

Supports the development of a Neuroscience Gateway that will facilitate access and use of high-performance computing resources by neuroscientists. According to the abstract, the resource will offer computer time to neuroscience users and will include "a simple web portal-based environment for uploading models, specifying job parameters, querying running job status and receiving job completion notices, and retrieving and storing output data."


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The Scan

Study Finds Sorghum Genetic Loci Influencing Composition, Function of Human Gut Microbes

Focusing on microbes found in the human gut microbiome, researchers in Nature Communications identified 10 sorghum loci that appear to influence the microbial taxa or microbial metabolite features.

Treatment Costs May Not Coincide With R&D Investment, Study Suggests

Researchers in JAMA Network Open did not find an association between ultimate treatment costs and investments in a drug when they analyzed available data on 60 approved drugs.

Sleep-Related Variants Show Low Penetrance in Large Population Analysis

A limited number of variants had documented sleep effects in an investigation in PLOS Genetics of 10 genes with reported sleep ties in nearly 192,000 participants in four population studies.

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.