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NSF Bioinformatics Grants Awarded June 3 – June 30, 2007

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A Phylogenomic Toolbox for Assembling the Tree of Life. Start date: Feb. 22, 2007. Expires: Oct. 31, 2008. Awarded amount to date: $682,623. Principal investigator: Michael Sanderson. Sponsor: University of Arizona.
 
Supports a project to develop new methods and software tools to construct the phylogenetic tree for all biological species. The project will focus on extracting information from molecular sequence databases to build collections of smaller trees that can be assembled into larger, more comprehensive trees. “Whereas extensive research has focused on the problem of building a tree from a single data set; relatively little is known about extracting these data sets en masse from sequence databases and then assembling a synthesis,” according to the grant abstract.
 

 
Function/Structure Annotation of Lipid Binding Domains in Arabidopsis thaliana Proteins: Computational Modeling of Subcellular Targeting. Start date: March 1, 2007. Expires: July 31, 2007. Awarded amount to date: $123,225. Principal investigator: Diana Murray. Sponsor: Columbia University.
 
This project aims to understand, at the molecular level, how lipid-binding domains are recruited to different cellular membranes and how proteins and lipid signals are organized laterally at membrane surfaces to regulate cellular processes. The investigators will develop an automated high-throughput comparative modeling pipeline to detect new instances of lipid-binding domains in the Arabidopsis genome and predict the structures of their amino acid sequences using known structures as templates.
 

 
CRD Acquisition of a High-Performance Shared-Memory Computer for Biological and Medical Research in South Carolina. Start date: June 1, 2007. Expires: May 31, 2010. Awarded amount to date: $461,065. Principal investigator: Jijun Tang. Sponsor: University South Carolina Research Foundation.
 
Supports the purchase of a high-performance shared-memory computer for research in the areas of bioinformatics, computational biology, medical research, and nanotechnology.
 

 
Computational Study of DNA Repair Enzyme Photolyase. Start date: June 15, 2007. Expires: May 31, 2008. Awarded amount to date: $135,000. Principal investigator: Alexei Stuchebrukhov. Sponsor: University of California, Davis.
 
Supports a project to apply previously developed computational techniques to new X-ray structural data in order to study different aspects of photorepair of thymine dimers by the DNA-repair enzyme photolyase. Specific aims include studying the mechanism of electron transfer between the enzyme FADH redox co-factor and the thymine dimer of DNA; the repair reaction itself; the mechanism by which photolyase finds the dimer on DNA; and the mechanism by which the dimer flips out of the DNA helix in the process of complex formation and dimer recognition.
 

 
Computational Modeling of Sequence-Dependent DNA Curvature Using Hydrodynamics. Start date: June 15, 2007. Expires: May 31, 2010. Awarded amount to date: $166,898. Principal investigator: Oscar Gonzalez. Sponsor: University of Texas at Austin.
 
Funds development of a computational method for estimating local, sequence-dependent curvature parameters for DNA from hydrodynamic data. “The objective of this project is to exploit the stiffness of DNA at short length scales and develop a method for estimating local, sequence-dependent curvature parameters from hydrodynamic data on short fragments,” according to the grant abstract. The project plans to study the theoretical sedimentation speed of a stiff polymer in a Stokes-type fluid with thermal fluctuations in different asymptotic limits, design fast boundary element methods for computing the theoretical sedimentation speed based on a kernel-adapted Nystrom method, and design fast methods for minimizing a least-squares sedimentation functional over a space of sequence-dependent curvature parameters.
 

 
Statistical and Computational Tools for Identifying Microarray-based Expression and Single Feature Polymorphism Markers in Crops. Start date: June 15, 2007.
Expires: May 31, 2010. Awarded amount to date: $319,997. Principal investigator: Xinping Cui. Sponsor: University of California, Riverside Office of Research.
 
Funds development of statistical algorithms to identify single-feature polymorphism markers and gene expression markers in crops. The investigator has developed an algorithm based on robust projection pursuit to identify SFPs between two genotypes. The project aims to extend the RPP method in order to identify SFPs among multiple genotypes. Another aim is to build a mixture model-based method for identifying gene expression markers. The investigators also plan to validate the detected SFPs and GEMs using expressed sequence tags and direct sequencing and to combine SFPs and GEMs for genotyping.
 

 
Improving the Performance of Motif Finding Tools through Novel Reliable Significance Estimation and a Study of DNA Replication Origins. Start date: July 1, 2007. Expires: June 30, 2008. Awarded amount to date: $123,156. Principal investigator: Uri Keich. Sponsor: Cornell University.
 
Supports a project to develop a “reliable significance analysis” for profile-based de novo motif finders. This can be used to analyze the results of motif finders that integrate phylogeny or localization data in order to improve their performance.
 

 
Bioinformatics of Protein Post-Translational Modifications. Start date: July 1, 2007. Expires: June 30, 2008. Awarded amount to date: $122,001. Principal investigator: Predrag Radivojac. Sponsor: Indiana University.
 
Supports the development of new methods to study protein post-translational modifications. The investigators intend to develop models for automated annotation of PTM sites; analyze structural and functional properties of PTM sites; and integrate protein bioinformatics and proteomics to construct a functional map of all major PTMs.
 

 
Design and Implementation of Effective Solutions for Archiving and Processing Systems Biology Data: Research Integrated with an Ongoing High School Education Program. Start date: July 1, 2007. Expires: June 30, 2009. Awarded amount to date: $906,818. Principal investigator: Nitin Baliga. Sponsor: Institute for Systems Biology.
 
Funds development of an informatics system to integrate systems biology data in order to expedite network inference and knowledge discovery. Specific aims include: the definition of a flexible data standard for capturing experiment and sample information in digital form; the development of tools to assist data curation, retrieval, and statistical analysis; and the creation of database extensions for high-school training programs.
 

 
A Software and Data Resource for Multidomain Homology and Protein Classification. Start date: July 1, 2007. Expires: June 30, 2010. Awarded amount to date: $677,319. Principal investigator: Marie Dannie Durand. Sponsor: Carnegie-Mellon University.
 
Funds the development of software for homology detection and classification of multi-domain sequence families. The project will develop a resource of hand-curated validation data sets; methods for detecting multi-domain homologs and orthologs; methods for automated classification of multi-domain families; and a publicly available database with a web-based interface and visualization tools for exploratory analysis of the data. “A key component of the proposed platform is a novel and accurate method for inferring multi-domain family relationships by exploiting the local structure of the sequence similarity network,” according to the grant abstract.
 

 
Model-Based and Model-Free Dimension Reduction with Applications to Bioinformatics. Start date: July 1, 2007. Expires: June 30, 2010. This grant was awarded to two investigative teams: 
  • Pennsylvania State University. Principal investigator: Bing Li. Awarded amount to date: $260,000.
  • University of Minnesota-Twin Cities. Principal investigator: Ralph Cook. Awarded amount to date: $184,564.
Supports the development of sufficient dimension reduction methods, which reduce the dimension of the predictor vector X in reference to the response Y in regression or classification problems in bioinformatics. The project will introduce inverse reductive models that describe the stochastic structure of X given Y, and not Y given X as in traditional regression, the investigators note in the grant abstract.
 

 
Nonparametric Methods for Emerging Technologies in Bioinformatics. Start date: Sept. 1, 2007. Expires: Aug. 31, 2008. Principal investigator: Jianhua Hu. Awarded amount to date: $55,187. Sponsor: University of Texas, M.D. Anderson Cancer Center.
 
Supports a project to study two statistical problems in protein and gene expression microarray experiments: quantification of protein lysate arrays; and modeling probe level gene expression data. The investigators have developed a statistical framework that allows for unknown regressor values in a nonparametric regression model, with applications to the quantification of protein lysate array data. They are also developing a quantile regression approach for mixed-effect models “that are appropriate for detecting treatment and/or interaction effects without parametric distributional assumptions on the model,” according to the grant abstract.

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