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BioInform s Funding Update: NSF Bioinformatics Awards to Dec. 15, 2004


HEPbaseTM: Specialized Software for Storage, Retrieval and Linkage of Hepatitis Data. Start date: January 2005. Expires: June 2005. Awarded amount to date: $100,000. Principal investigator: Johanna Craig. Sponsor: GATACA.

Phase I SBIR supports development of software for managing and analyzing hepatitis data. This project will provide a solution for hepatitis C virologists initially, and will expand to accommodate data from other hepatitis virus strains during Phase II funding and beyond. The software will contain applications for integrating multiple sources of disparate data into an automated high-dimensional warehouse, applications for performing repetitious tasks common to HCV genetic research projects, a tool for automatic alignment of HCV protein sequences, and the ability to link HCV protein sequences with host microarray expression data.

Statistical Approaches to the Analysis of Genome-wide Measurements: Significance of Periodic Gene Expression and Correlations of Gene Content in Completely Sequenced Genomes. Start date: December 2004. Expires: November 2005. Awarded amount to date: $90,548. Principal investigator: Jie Chen. Sponsor: University of Missouri-Kansas City.

Funds development of new statistical modeling techniques for analyzing genetic data sets. Researchers will develop statistical methods to identify statistically significant periodically expressed genes in cell cycle expression data sets; establish an optimal clustering strategy that produces biologically meaningful clusters for gene expression data sets; and investigate the canonical correlation between gene content vectors to reveal optimal relations between genes or protein vectors.

Acquisition of a 64-Processor 64-Bit Parallel Computer Cluster. Start date: January 2005. Expires: December 2007. Awarded amount to date: $141,553. Principal investigator: Preston Moore. Sponsor: University of the Sciences in Philadelphia.

Provides funding to acquire a 64-processor 64-bit parallel computer cluster that will be used for a number of applications, including the investigation of the role of structure and conformation changes in protein-DNA complexes; the binding of molecules and small peptides to unilamellar vesicles and lipid bilayers; and the development of a computer-based drug design system.

The Evolution of Protein Structure, Function, and Folding. Start date: January 2005. Expires: December 2007. Awarded amount to date: $446,630. Principal investigator: Zaida Luthey-Schulten. Sponsor: University of Illinois at Urbana-Champaign.

Funds a project to develop evolutionary profiles that preserve the phylogenetic tree topology of homologous proteins using a multidimensional QR algorithm developed in a preliminary study. Non-redundant sets of sequences and structures that best span the evolutionary space of the proteins will be constructed from combined sequence and structural alignment information. The QR algorithms and evolutionary profiles developed in the project will be made available as part of a sequence and structure bioinformatics plug-in for the VMD visualization program.

New Methods and Applications for the Dynamic Characterization of Proteins by the Combination of NMR Spectroscopy and Computer Simulations. Start date: January 2005. Expires: June 2005. Awarded amount to date: $148,242. Principal investigator: Rafael Bruschweiler. Sponsor: Florida State University.

Supports a project to study protein dynamics by nuclear magnetic resonance and computational approaches. Realistic analytical motional models will be developed to characterize motions of local protein fragments as well as collective motions involving amino-acid groups and whole secondary structural elements.

NeTS-NR ROSS.Net: A Platform for Integrated Large-Scale Network Design of Experiments and Simulation. Start date: January 2005. Expires: December 2005. Awarded amount to date: $165,738. Principal investigator: Shivkumar Kalyanaraman. Sponsor: Rensselaer Polytechnic Institute.

Funds a project to develop tools that will improve the way the networking community designs, tunes, and studies network protocols, especially for target deployment in large-scale, heterogeneous, and time-varying conditions. In particular, the project will develop an experimentation platform, called ROSS.Net, with meta-simulation and simulation capabilities. According to the grantees, the work has immediate impact in applications where large-scale design is crucial. Specifically, features like fast-approximation and sparse modeling will have potential impact in areas such as industrial quality control, agriculture, and bioinformatics.


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The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.