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NSF Bioinformatics Grants July 28 — Sept. 16, 2006

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Community Annotation Database for Magnaporthe grisea and its Interactions with Rice. Start date: Dec. 1, 2006. Expires: Nov. 30, 2008. Awarded amount to date: $522,458. Principal investigator: Carol Soderlund. Sponsor: University of Arizona.
 
This grant will open the MGOS database (www.mgosdb.org) to the community for annotation of genes, submission of microarray data, and incorporation of other relevant data related to rice and Magnaporthegrisea. The interface and database will be upgraded to provide tools for submission and enhanced integration of data.
 

 
Integrated Biological Sequence Data Management. Start date: Oct. 1, 2006. Expires: April 30, 2008. Awarded amount to date: $30,5715. Principal investigator: Jignesh Patel. Sponsor: University of Michigan, Ann Arbor.
 
Funds development of a system called SEQ that will support “complex declarative and efficient querying on biological sequences,” according to the grant abstract. The grantees will extend a relational database engine with methods for querying on sequences. “Extending a relational database engine, rather than build a stand-alone sequence query processing tool, is a much more challenging task, but is essential as it allows the end-user to combine the power of analytical facilities already provided by SQL engines with the added ability to query sequences,” according to the grantees.
 

 
MSPA-MCS: Small-sample Network Inference in Computational Vision and Biology. Start date: Sept. 15, 2006. Expires: Aug. 31, 2009. Awarded amount to date: $479,999. Principal investigator: Donald Geman. Sponsor: Johns Hopkins University.
 
Supports development of theoretical models and statistical procedures designed to address the “small-sample dilemma” in the computational sciences. The investigators will concentrate on problems in molecular biology and image analysis. According to the grantees, the small-sample dilemma refers to “the disparity between the high dimensionality of the raw data, for example the large number of variables necessary to convey the states of genes and proteins or to encode the content of digital images, and the relatively small number of actual samples (repetitions, replications, etc.) available for obtaining useful information.”
 

 
Bayesian Analysis of Shapes and Curves with Applications in Structural Bioinformatics. Start date: Sept. 1, 2006. Expires: Aug. 31, 2007. Awarded amount to date: $39,870. Principal investigator: Scott Schmidler. Sponsor: Duke University.
 
Funds development of new probabilistic and Bayesian statistical models for the analysis of three-dimensional structures of biological macromolecules. The project will also focus on developing statistical methods for characterizing the biomechanical behavior of molecules under applied forces, such as those that arise in the study of cellular proteins.
 

 
Context Sensitive Hidden Markov Models and Application in Computational Biology. Start date: Sept. 1, 2006. Expires: Aug. 31, 2007. Awarded amount to date: $89,527. Principal investigator: P. Vaidyanathan. Sponsor: California Institute of Technology.
 
Funds development of fast algorithms for finding the optimal state sequence of an observed symbol sequence and for training context-sensitive hidden Markov models for computationally identifying non-coding RNAs. Algorithms that can be used for solving the alignment, scoring, and training problems of csHMMs for more complex correlations will be developed and tested on “a large variety” of documented sequences, according to the grant abstract.
 

 
PLEXdb: Plant Expression Database. Start date: Sept. 1, 2006. Expires: Aug. 31, 2007. Awarded amount to date: $354,418. Principal investigator: Julie Dickerson. Sponsor: Iowa State University.
 
Funds development of PLEXdb (Plant Expression Database), a MIAME-compliant public resource for large-scale plant gene expression data. “Currently, there is no resource in the plant community that integrates the rapidly expanding number of gene expression profile data sets with traditional structural genomics and phenotypic data,” the investigators note in the grant abstract.
 

 
CompBio: Integration of Bioinformatics Modeling and Coarse Grain Dynamics: A New Computational Approach to Solve Complex Biological Problems. Start date: Sept. 1, 2006. Expires: Aug. 31, 2009. Awarded amount to date: $275,000. Principal investigator: Preston Moore. Sponsor: University of the Sciences in Philadelphia.
 
Supports development of a computational approach for studying a small part of the signal transduction pathway used in chemotaxis. The approach combines bioinformatics-assisted molecular modeling techniques with a coarse-grain molecular dynamics method.
 

 
CompBio: A New Paradigm of Protein Threading: simultaneous backbone threading and side-chain packing prediction. Start date: Sept. 1, 2006. Expires: Aug. 31, 2009. Awarded amount to date: $275,000. Principal investigator: Ying Xu. Sponsor: University of Georgia Research Foundation.
 
Proposal to develop a new paradigm for threading-based protein structure prediction using side-chain information. “While residue-based approaches have made threading computationally feasible to predict protein structures in the past decade, we clearly see an urgent need now for more accurate prediction techniques that can provide structural data at higher resolution, to meet the rapidly growing need of structural and functional genomics studies,” the investigators note in the grant abstract. In the proposed computational framework, backbone threading and side-chain packing will be predicted simultaneously through use of a new energy function that combines residue-level information for backbone threading and atom-level information for side-chain packing. The investigators will also develop a new algorithmic framework for solving the generalized threading problem.
 

 
Organelle DB / Organelle View: A Community Resource of Protein Localization and Function. Start date: Sept. 1, 2006. Expires: Aug. 31, 2009. Awarded amount to date: $525,356. Principal investigator: Anuj Kumar. Sponsor: University of Michigan, Ann Arbor.
 
Funds further development of Organelle DB (http://organelledb.lsi.umich.edu/), a web-based relational database containing organelle-localized proteins and major protein complexes. Organelle DB includes data on 25,000 proteins from 154 eukaryotes. Each protein is presented with its subcellular localization, protein sequence, and, as available, a detailed description of its function.
 

 
Microscale Stochastic Modeling of Biological Mechanics. Start date: Sept. 1, 2006.
Expires: Aug. 31, 2009. Awarded amount to date: $91,342. Principal investigator: Paul Atzberger. Sponsor: University of California-Santa Barbara.
 
Supports development of a general mathematical framework and computational method to extend the Immersed Boundary Method to account for thermal fluctuations. These methods will be applied to study the dynamic membrane rearrangements involved in the functions of two cell organelles, the golgi apparatus and mitochondria.
 

 
Mining the Figures and Text of the Biological Literature. Start date: Sept. 1, 2006. Expires: Aug. 31, 2009. Awarded amount to date: $150,580. Principal investigator: Robert Futrelle. Sponsor: Northeastern University.
 
Funds development of a system that analyzes figures in biological literature. According to the grantees, approximately 50 percent of the content of a typical biology research paper is comprised of figures and discussions of figure content. The proposed system analyzes the figures and the text to “build indexes of their content and figure-text interrelations,” according to the grant abstract, and includes visually based interactive systems for users to drill down to specific information in individual papers.
 

 
New Shape Analysis Methods for Structural Bioinformatics. Start date: Aug. 15, 2006. Expires: July 31, 2007. Awarded amount to date: $199,318. Principal investigator: Thomas Funkhouser. Sponsor: Princeton University.
 
Proposal to develop algorithms for analyzing protein structures, detecting similarities between them, visualizing how they interact with other molecules, and automatically providing functional classifications for them.
 

 
Constraint Based Algorithms for Protein Folding. Start date: Aug. 15, 2006. Expires: July 31, 2008. Awarded amount to date: $200,000. Principal investigator: Veit Elser. Sponsor: Cornell University.
 
Supports theoretical and computational research in the area of protein folding and the solution of inverse problems. The investigators will apply a successful solution search strategy in the area of phase retrieval to the problem of protein folding. A key component of the project is the development of a work environment called “semiprotein world.” The investigators define semiproteins as “model proteins with highly simplified properties, but which pose many of the same challenges posed by real proteins,” according to the grant abstract. The project will provide a collection of software tools, including a web-based semiprotein data bank, to enable researchers to design and fold semiproteins, and then deposit their findings in a database.
 

 
Rodeo: A Platform for Discovery and Analysis of Protein Network Motifs. Start date: Aug. 15, 2006. Expires: July 31, 2007. Awarded amount to date: $237,753. Principal investigator: Dennis Wall. Sponsor: Harvard University.
 
Supports development of a publicly available informatics tool called Rodeo that will integrate data relevant to deciphering protein-protein interaction networks and will provide a number of methods for analyzing such data, including graph-theoretic mathematics. Rodeo will integrate several databases including a comprehensive set of orthologs from over 50 genomes, a new set of protein-protein interaction data from humans together with more than 70,000 protein-protein interactions from other organisms, gene expression data from new experiments and experiments hosted by NCBI, and a database of almost 100,000 ESTs from the acorn worm.
 

 
Mathematical Modeling of Biomolecular Surfaces. Start date: Aug. 1, 2006. Expires: July 31, 2009. Awarded amount to date: $303,310. Principal investigator: Guowei Wei. Sponsor: Michigan State University.
 
Supports development of a partial differential equation-based approach to molecular surface modeling. The investigators have designed a set of curvature-controlled PDEs for molecular surface generation and introduce two new concepts, molecular multiresolution surfaces and minimal molecular surfaces, which naturally arise in the proposed PDE modeling.

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The Scan

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The New York Times reports the US Food and Drug Administration is expected to authorize a booster dose of the Pfizer-BioNTech SARS-CoV-2 vaccine this week for individuals over 65 or at high risk.

Snipping HIV Out

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PLOS Papers on Cancer Risk Scores, Typhoid Fever in Colombia, Streptococcus Protection

In PLOS this week: application of cancer polygenic risk scores across ancestries, genetic diversity of typhoid fever-causing Salmonella, and more.