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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

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.

Study Reviews Family, Provider Responses to Rapid Whole-Genome Sequencing Follow-up

Investigators identified in the European Journal of Human Genetics variable follow-up practices after rapid whole-genome sequencing.

BMI-Related Variants Show Age-Related Stability in UK Biobank Participants

Researchers followed body mass index variant stability with genomic structural equation modeling and genome-wide association studies of 40- to 72-year olds in PLOS Genetics.

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.