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Funding Update: NSF Bioinformatics Grants Awarded April 19 — June 11, 2012

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Association of Protein Helices in Membranes: From Physics to Biology
Start Date: July 1, 2012
Expires: June 30, 2015
Awarded Amount to Date: $224,411
Principal Investigators: Andrei Lomize, Irina Pogozheva
Sponsor: University of Michigan, Ann Arbor

Supports the development of a computational method, associated web server, and a database for structural studies of transmembrane alpha-helical complexes. According to the abstract, the investigators intend to create web resources, including a tool called TMDOCK, that will be used for modeling alpha-helix association in membranes.


Computational Studies of Membrane Proteins Based on NMR Observables
Start Date: July 1, 2012
Expires: June 30, 2015
Awarded Amount to Date: $562,801
Principal Investigator: Wonpil Im
Sponsor: University of Kansas

According to the abstract, this grant will fund the development of computational methods that can be used to acquire "novel insights" into membrane proteins' dynamics and interactions with lipids, which are "important determinants of their functions."


Gramene — Exploring Function through Comparative Genomics and Network Analysis
Start Date: June 1, 2012
Expires: May 31, 2017
Awarded Amount to Date: $1,762,326
Principal Investigators: Doreen Ware, Pankaj Jaiswal
Sponsor: Cold Spring Harbor Laboratory

The funds will support the expansion of the Gramene database — a resource for information about gene structure and function for several plant species. According to the abstract, the investigators intend to "expand the number of plant genomes incorporated into the portal, add new capabilities for studying gene expression, pathways, and networks, and fundamentally improve the database architecture and user interfaces to facilitate sophisticated systems-level analyses." Additionally, the Gramene database will adopt two new tools: the Reactome platform, which can be used to represent curated pathways and for performing pathways-based analyses; and the ATLAS platform, which can be used to display and analyze expression profiles, the abstract states.


Development and Application of Graphical User Interfaces for System Building and Analysis of Membrane Simulations
Start Date: June 1, 2012
Expires: May 31, 2015
This grant is awarded to two investigative teams:
Jeffery Klauda, University of Maryland, College Park, $40,070
Wonpil Im, University of Kansas, $109,149

Supports the development of graphical user interfaces that allow users to run and analyze various membrane simulations. According to the abstract, the investigators intend to, among other activities, develop a standalone GUI toolset for analyzing membrane simulation trajectories from simulation programs such as Amber and NAMD; further develop the Membrane Builder software to include more lipid molecules and provide simulation outputs for GROMACS and Amber software packages; and study the influences of chain saturation, length, and cholesterol concentration.


An Extensible Software Platform for Integrating Multiple Sources of Data and Uncertainty Using Hierarchical Statistical Models
Start Date: June 1, 2012
Expires: May 31, 2015
Awarded Amount to Date: $912,896
Principal Investigators: Perry de Valpine, Duncan Temple Lang, Christopher Paciorek
Sponsor: University of California, Berkeley

Supports the development of an open source software environment for flexible composition of hierarchical models and algorithms. According to the abstract, it will include "low-level components in which algorithms will be executed for speed; high-level components in which algorithms can be composed and managed from the R statistical software environment; and middle-level components to interface the first two."


Modeling made easy: Extending systems biology modeling approaches to genetics and ecology
Start Date: June 1, 2012
Expires: May 31, 2017
Awarded Amount to Date: $208,578
Principal Investigator: Laurence Loewe
Sponsor: University of Wisconsin, Madison

Supports the implementation of a model description language for forward simulation problems in biology that purportedly "makes it easy to read and write such models for humans and for computers." The investigators plan to develop a link to two sources of large-scale computing power to help with analyzing biological models and a new standard for storing and sharing simulation results. Additionally, the investigators plan to "address combinatorial explosions in genetics and ecology models with algorithms and representations that work efficiently with both systems biology and genetics simulations, and that also allow for distributions of event times other than the standard assumption."


Analysis, Construction, and Visualization of 3D Genome Structures
Start Date: June 1, 2012
Expires: May 31, 2017
Awarded Amount to Date: $241,160
Principal Investigator: Jianlin Cheng
Sponsor: University of Missouri, Columbia

The funds will support efforts to investigate 3D structure of genomes. Specifically, the investigator intends to develop "contact-based computational methods to analyze, construct, and visualize 3D structures of genomes" by using "chromosomal contact (interaction) data generated by genome conformation capturing techniques and next-generation sequencing," the abstract states.


Dissecting the Mechanisms of Genetic Control of Biological Systems via High-Dimensional Sparse Graphical Models
Start Date: June 1, 2012
Expires: May 31, 2017
Awarded Amount to Date: $337,411
Principal Investigator: Seyoung Kim
Sponsor: Carnegie-Mellon University

Will support the development of statistical machine learning methods that are based on "high-dimensional sparse graphical models" which will be used to extract information on the genetic control of gene regulation systems in genomic datasets.


A Computational Framework to Study Epigenetic Regulation
Start Date: June 1, 2012
Expires: May 31, 2017
Awarded Amount to Date: $259,609
Principal Investigator: Haiyan Hu
Sponsor: University of Central Florida

The abstract states that the funds will support the development of computational algorithms and tools to model epigenetic modifications from high-throughput sequencing data; mine epigenetic modification patterns; and model gene regulation.


Multi-Resolution Framework for the Characterization of Protein Mechanisms
Start Date: June 1, 2012
Expires: May 31, 2015
Awarded Amount to Date: $420,000
Principal Investigator: Cecilia Clementi
Sponsor: William Marsh Rice University

The abstract states that the funds will support the development of multiscale protein models and "new strategies" for exploring complex free energy landscapes.


AVATOL — Next Generation Phenomics for the Tree of Life
Start Date: June 1, 2012
Expires: May 31, 2015
This grant is awarded to eleven investigative teams:
Robert Thacker, University of Alabama at Birmingham, $79,110
Hong Cui, University of Arizona, $335,421
John Burleigh, University of Florida, $362,025
Lisa Moore, University of Southern Maine, $296,865
Carrine Blank, University of Montana, $144,385
Maureen O'Leary, State University of New York at Stony Brook, $772,630
Marymegan Daly, Ohio State University, $85,859
Thomas Dietterich, Oregon State University, $863,285
Edward Theriot, University of Texas at Austin, $103,238
Nancy Simmons, American Museum of Natural History, $64,843
Dennis Stevenson, New York Botanical Garden, $90,739

These funds will support efforts to use methods from computer vision, machine learning, crowd-sourcing, and natural language processing to study of phenotypes for the Tree of Life project.


Improved Computational Tools for Plant Gene Assembly and Synteny Detection
Start Date: June 1, 2012
Expires: May 31, 2014
Awarded Amount to Date: $211,212
Principal Investigators: David Nelson, Osamu Gotoh
Sponsor: University of Tennessee, Memphis

The abstract states that the funds will be used to improve "automated" plant gene assembly and annotation. The investigators will implement gene prediction algorithms and develop tools for identifying ohnologous genes — which are created by whole genome duplication events — in plant genomes


Parallel Algorithms and Software for High-Throughput Sequence Assembly
Start Date: May 1, 2012
Expires: April 30, 2015
Awarded Amount to Date: $562,500
Principal Investigators: Srinivas Aluru, Patrick Schnable, Karin Dorman
Sponsor: Iowa State University

The funds will be used to develop algorithms and an integrated software framework for genome and transcriptome assembly.


Arbor: Comparative Analysis Workflows for the Tree of Life
Start Date: May 1, 2012
Expires: April 30, 2015
This grant is awarded to four investigative teams:
Robert Thacker, University of Alabama at Birmingham, $499,999
Chelsea Specht, University of California at Berkeley, $609,623
Luke Harmon, University of Idaho, $2,299,244
Jorge Soberon, University of Kansas, $600,000

According to the abstract, these funds will be used to create a visual workflow software program, dubbed Arbor, that will enable users to create and share analyses workflows for data from the Tree of Life project.


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