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BioInform s Funding Update: NSF Bioinformatics Awards to July 17, 2004


Hidden Markov Models for Non-sequential Alignments. Start date: July 2004. Expires: June 2006. Amount: $174,951. Principal investigator: Christopher Bystroff. Sponsor: Rensselaer Polytechnic Institute.

Project to develop predictive models for protein structures using the SCALI (Structural Core ALIgnment) software package, which aligns proteins that share a certain part of their folding arrangement, and then clusters these alignments to find the recurrent themes.

Methodology for Statistical Computing in Massive Datasets: Parallel Approaches to Cluster and MCMC Estimation. Start date: July 2003. Expires: June 2007. Amount: $172,467. Principal investigator: Ranjan Maitra. Sponsor: Iowa State University.

Funds development of a methodology for statistical analysis and estimation in massively sized databases. A particular application area for this approach is in bioinformatics, “where the goal is to cluster microarray data and also to analyze two-dimensional proteomic gel images,” according to the reserachers.

Rich Probabilistic Models for Genomic Data. Start date: July 2004. Expires: June 2009. Amount: $370,026. Investigator: Daphne Koller. Sponsor: Stanford University.

Funds development of a framework for integrating sequence, expression, pathway, and interaction data into a probabilistic relational modeling environment to help understand complex interactions at the subcellular level. The project will develop a dedicated modeling language as part of the framework.

Reconstruction and Annotation of Transcribed Sequences in Plants. Start date: July 2004. Expires: June 2007. Amount: $578,246. Principal investigator: John Quackenbush. Sponsor: The Institute for Genomic Research.

Funds continued development of the TIGR Plant Gene Indices ( to add new features, such as the identification of SNPs, prediction of a collection of 70-mer sequences for microarrays, and the creation of a plant version of the Resourcer tool.

Plant RNA Binding Proteins: Tools for Functional Genomics and Application to Chloroplast Biogenesis. Start date: July 2004. Expires: June 2009. Amount: $833,397. Principal investigator: Alice Barkan. Sponsor: University of Oregon, Eugene.

Project will develop a relational database of predicted plant RNA binding proteins that will integrate data from rice, maize, and Arabidopsis. The database will feature cross-referenced orthologs and paralogs, annotated with gene models, intracellular targeting predictions, experimental data, and literature citations.

Virtual Center for Analysis of Rice Genome Transcription. Start date: September 2004. Expires: August 2007. Amount: $791,128. Principal investigator: Xing-Wang Deng. Sponsor: Yale University.

Project will attempt to discover all possible transcription units of the recently sequenced Japonica rice genome using a high-density genome tiling oligonucleotide microarray. The data will be integrated into the current and ongoing genome annotation to test predicted gene models and to define structures of novel transcription units. Data will be deposited in the GEO database and also made available through a project web site, which will be online by August 2005.

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

Funds the acquisition of a 64-processor 64-bit parallel computer cluster for the department of chemistry and biochemistry at the University of the Sciences in Philadelphia. The system will support the investigation of the role of structure and conformation changes in protein-DNA complexes, the development of ab initio-based methods that will allow NMR chemical shifts to be used as sources of structural constraints, and the development of a computer-based drug design system.

Evobeaker: Simulation Software for Teaching Evolutionary Biology. Start date: July 2004. Expires: June 2005. Amount: $160,000. Principal investigator: Eli Meir. Sponsor: SimBiotic Software.

Supports development of EvoBeaker, a prototype computer simulation program for teaching evolutionary biology at the undergraduate level.

ChromDB: Integrating Information about Plant Chromatin Proteins and Complexes. Start date: September 2004. Expires: August 2008. Amount: $393,799. Principal investigator: Carolyn Napoli. Sponsor: University of Arizona.

Supports the expansion of ChromDB ( from a project-oriented database to a community database supporting the entire plant biology community. ChromDB will integrate and display all available community data regarding gene function, such as mutant phenotypes, biochemical activities and properties, transcript and protein expression patterns, physical and genetic interactions between genes and proteins, and localization of chromatin proteins within the nucleus.

Acquisition of Large-scale Parallel Computational Resources for Biological and Materials Modeling. Start date: September 2004. Expires: August 2007. Amount: $374,609. Principal investigator: Mark Tuckerman. Sponsor: New York University.

Funds the acquisition of a large-scale parallel computational resource for biological and materials modeling at the department of chemistry at New York University. The equipment will be used in a number of areas, including the application of novel conformational sampling tools to protein structure prediction; modeling of DNA polymerase mechanisms; studies of metalloenzyme mechanisms; analysis of protein-ligand binding; accurate treatment of hydrogen-bond dynamics in supramolecular complexes; and computationally aided design of novel RNAs.

Acquisition of a Beowulf Cluster for Use in Research and Research Training. Start date: August 2004. Expires: July 2007. Amount: $308,909. Principal investigator: Manish Mehta. Sponsor: Oberlin College.

Funds purchase of a Beowulf cluster for the department of chemistry at Oberlin College. Application areas include electronic structure calculations of preferential salvation around peptides and the development of algorithms for multiple whole-genome alignments.

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