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BioInform s Funding Update: NSF Awards in Bioinformatics through April 12, 2003


A Systems Approach to Study Redox Regulation of Functions of Photosynthetic Organisms. Start date: March 15, 2003. Expires: February 29, 2004. Expected total amount: $50,000. Principal Investigator: Himadri Pakrasi. Sponsor: Washington University.

Project will study four cyanobacterial species with completed sequenced genomes. Methods from molecular biology, biochemistry, bioinformatics, and systems engineering will be used to build network models and study the interactions between molecular components of cyanobacterial cells.


Genomics Databases: Striking a Balance for Information Sharing. Start Date: March 15, 2003. Expires: February 29, 2004. Expected total amount: $120,000. Principal investigator: Frances Sharples. Sponsor: National Academy of Sciences.

Supports a one-day workshop and subsequent report that will identify issues surrounding the release of genomic data for bioterrorism threat agents. The project will be completed before August 31, 2003.


Statistical and Computational Tools for the Analysis of High-Dimensional Genetic Data. Start Date: June 1, 2003. Expires: May 31, 2008. Expected total amount: $400,000. Principal investigator: Chiara Sabatti. Sponsor: University of California Los Angeles.

Project to create new statistical models and computational tools for the analysis of data in high-dimensional spaces, with particular applications in genomics.


Sparse Spatial Reasoning for High-Throughput Protein Structure. Start Date: April 1, 2003. Expires: March 31, 2008. Expected total amount: $488,063. Principal investigator: Christopher Bailey-Kellogg. Sponsor: Purdue University.

Research to develop new tools for analyzing the structure of protein molecules using spatial data sets containing significant noise and sparse information content. Project will create algorithms to address data interpretation and experimental design problems associated with sparse spatial data.


Advanced Approaches for Integration and Analysis of Genomic Data. Start date: May 1, 2003. Expires: April 30, 2008. Expected total amount: $1,628,007. Principal investigator: Aidong Zhang. Sponsor: State University at Buffalo.

Project team will investigate approaches to analyze gene expression data and integrate it into biological research. Strategies include a metadata hierarchy for integration of heterogeneous data, cluster-based indexing for high-dimensional data, inter-dimensional analysis for classification, and dynamic interactive visualization for pattern analysis.


Development of Vector Space-based Methods for Protein Structure Prediction. Start date: July 1, 2003. Expires: June 30, 2006. Expected total amount: $364,598. Principal investigators: Weili Wu/ Haesun Park. Sponsors: University of Texas Dallas/University of Minnesota Twin Cities.

Collaborative project to design knowledge-based prediction systems based on optimal vector space representations of proteins that have previously been represented by character strings. Kernel-based nonlinear classifiers and nonlinear dimension reduction as well as visualization methods will be developed.


Identification, Modeling, and Prediction of Arabidopsis thaliana mRNA 3’ Processing Sites. Start Date: January 1, 2003. Expires: August 31, 2005. Expected total amount: $254,727. Principal investigator: Joel Graber. Sponsor: Jackson Laboratory.

Project aims to establish a curated database and web-server interface for experimentally determined 3’-processing sites for Arabidopsis.


Novel Tools for the Vertical Analysis of Genomic Data. Start Date: May 1, 2003. Expires: April 30, 2008. Expected total amount: $1,222,334. Principal investigator: Sorin Draghici. Sponsor: Wayne State University.

Proposal to provide a suite of turnkey bioinformatics tools that can process extremely large amounts of data and provide vertical inferences to assemble system-level information from component-level data.


Computational and Mathematical Study in Protein Interactions and Functions. Start Date: July 1, 2003. Expires: June 30, 2007. Expected total amount: $1,036,000. Principal Investigator: Fengzhu Sun. Sponsor: University of Southern California.

Research focuses on the development of statistical and computational methods for the analysis of protein interaction data coming from yeast two-hybrid assays and mass spectrometry, as well as protein function data coming from databases of large-scale function annotations. In particular, tools will be created to identify domain-domain interactions and protein-domain interactions.

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The Scan

Interfering With Invasive Mussels

The Chicago Tribune reports that researchers are studying whether RNA interference- or CRISPR-based approaches can combat invasive freshwater mussels.

Participation Analysis

A new study finds that women tend to participate less at scientific meetings but that some changes can lead to increased involvement, the Guardian reports.

Right Whales' Decline

A research study plans to use genetic analysis to gain insight into population decline among North American right whales, according to CBC.

Science Papers Tie Rare Mutations to Short Stature, Immunodeficiency; Present Single-Cell Transcriptomics Map

In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.