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NSF Bioinformatics Grants Awarded Jan. 18, 2007 — Feb. 29, 2008

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The iPlant Collaborative: A Cyberinfrastructure-Centered Community for a New Plant Biology. Start date: Feb. 1, 2008. Expires: Jan. 31, 2013. Awarded amount to date: $6,629,200. Principal investigator: Richard Jorgensen. Sponsor: University of Arizona.
 
Funds the iPlant Collaborative, or iPC, a “cyberinfrastructure collaborative for the plant sciences,” according to the grant abstract. The iPC cyberinfrastructure will provide access to an IT infrastructure for storage and computational power via local and national resources, “and it will provide services that promote interactions, communications and collaborations and that advance the understanding and use of computational thinking in plant biology,” the abstract states.
 

 
Biomesh: A Digital Resource Collection at the Biology-Engineering Interface. Start date: March 1, 2008. Expires: Feb. 28, 2009. Awarded amount to date: $294,700.
Principal investigator: Elizabeth Dumont. Sponsor: University of Massachusetts, Amherst.
 
Supports development of a shared digital resource collection of finite element models of biological systems. Finite element analysis “has the ability to transform the way that biologists approach problems in areas ranging from functional morphology to paleobiology, developmental biology, and cellular mechanics,” according to the grant abstract. In addition to finite element models, the resource will include an integrated set of web-enabled ontologies for sharing finite element modeling metadata, mechanical property values of biological materials, software tools for visualizing FEA models and results, FEA utilities supporting the development of biological finite element models, and a threaded discussion.
 

 
PREVALT: Prediction and Validation of Alternative Splicing in Plants. Start date: March 1, 2008. Expires: Feb. 28, 2009. Awarded amount to date: $252,263. Principal investigator: Asa Ben-Hur. Sponsor: Colorado State University.
 
Supports a project to develop machine-learning methods to detect alternative splicing in plants and to experimentally validate selected predictions. The researchers plan to develop computational tools to predict novel alternative splicing events and the cis-elements involved in regulated alternative splicing. The initial focus will be in Arabidopsis, and the methods will be extended to rice and other plants.
 

 
A Computational Design Approach for Predicting and Reengineering Plasticity and Selectivity in Protein-Protein Interfaces. Start date: March 1, 2008. Expires: Feb. 28, 2009. Awarded amount to date: $140,000. Principal investigator: Tanja Kortemme. Sponsor: University of California, San Francisco.
 
Supports the development of computational modeling and design approaches focused on protein-protein interactions, “to facilitate engineering of selective molecules to characterize, perform, and control biological functions,” according to the grant abstract. The grantees first plan to develop a model that will help researchers optimize the fitness of a protein sequence for multiple selective criteria, “such as binding to preferred partners while simultaneously avoiding unwanted interactions.” The investigators also plan to improve methods to more accurately model changes in protein conformation in response to binding events and designed mutations.
 

 
Predicting RNA Secondary Structures with Pseudoknots: 2-Interval Graph and 3D Triangular Lattice. Start date: March 1, 2008. Expires: Feb. 28, 2011. Awarded amount to date: $208,090. Principal investigator: Minghui Jiang. Sponsor: Utah State University.
 
Funds development of a hierarchical method for predicting RNA secondary structures with pseudoknots. The proposed method “mirrors the natural hierarchy of RNA folding by considering both secondary structures and tertiary interactions, and strives for the right balance in rigor and tractability by combining approximation and heuristics at both helix and base-pair resolutions,” according to the grant abstract. The proposed method is based on two concepts: 2-interval graph, which models the computational paradigm of all existing helix-resolution algorithms; and 3D triangular lattice, which is “superior to other lattices terms of regularity, density, and parity,” according to the researchers.
 

 
Simulation Studies of Protein Dynamics in Membranes. Start date: March 1, 2008. Expires: Feb. 28, 2011. Awarded amount to date: $407,673. Principal investigator: Douglas Tobias. Sponsor: University of California-Irvine.
 
Funds development of simulation methods for protein dynamics in membranes. According to the grant abstract, the researchers intend to carry out four projects: molecular dynamics simulations and single-particle dynamics studies of bacteriorhodopsin in purple membranes and phospholipid bilayers; a study of collective dynamics in membranes through normal mode analyses of bacteriorhodopsin; comparison of the results from the first two projects on bacteriorhodopsin to maltose binding protein; and the development of a novel normal mode analysis using elastic network models for membrane proteins.
 

 
Modeling and Simulation of Biological Networks. Start date: May 1, 2008
Expires: April 30, 2009. Awarded amount to date: $62,700. Principal investigator: Reinhard Laubenbacher. Sponsor: Virginia Polytechnic Institute and State University.
 
Supports a program to provide a 10-week residential summer research experience for undergraduate students “with the goal of increasing their desire and preparation to enter a PhD program in mathematics or computational biology,” according to the grant abstract. In the program, students will be paired with mentors working on research projects focusing on mathematical models of biological networks.

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