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BioInform s Funding Update: Some Recent NIH Awards in Bioinformatics: Jul 21, 2003


Haplotype-Based Methods/Software for Analyzing SNP Data. Amount: $133,750. Start date: June 2003. Expires: Dec. 2003. Principal Investigator: Lue Zhao. Institution: Enodar Biologic. NIH Institute: NHGRI.

Phase I SBIR that supports development of the SNIP-Lus software module, a haplotype-based method for analyzing multiple SNP markers from candidate genes.

Discovery of Novel RNA Genes in Genomic DNA Sequences. Amount: $377,162. Start date: June 2003. Expires: April 2006. Principal investigator: Stephan Holbrook. Institution: University of California/Lawrence Berkeley National Lab. NIH Institute: NHGRI.

Proposal to develop a computational approach to identify novel RNA genes and functional RNA elements in complete genomes using machine learning techniques to recognize functional RNA coding sequences by comparison with sequences that do not encode RNAs.

Computation and mechanical modeling of chromosome dynamics. Amount: $376,108. Start date: June 2003. Expires: May 2007. Principal investigator: Peter Sorger. Institution: Massachusetts Institute of Technology. NIH Institute: NIGMS.

Study to determine how S. cerevisiae kinetochores bind to microtubules and how the forces required for chromosome movement are generated. Algorithms incorporating biological prior knowledge will be developed to track chromosome movement in living cells.

Improving Bayesian Phylogeny. Amount: $403,684. Start date: June 2003. Expires: May 2007. Principal investigator: Bret Larget. Institution: University of Wisconsin, Madison. NIH Institute: NIGMS.

Supports a project to improve the Bayesian approach to phylogeny estimation and to build practical tools capable of analyzing very large genetic data sets. Specific aims of the proposal are to improve models for genome-scale rearrangement; to improve methods for ancestral sequence estimation; to develop visualization-based interfaces for exploring distributions of phylogeny; and to develop computational algorithms to apply Bayesian methods to very large phylogenies.

Computational modeling. Start date: June 2003. Expires: May 2008. Principal investigator: Russ Altman. Institution: Stanford University. NIH Institute: NIGMS.

Project has three specific aims: to compute static three-dimensional protein models from experimental data; to augment static models with ensemble and dynamic information as necessary; and to use the resulting models to generate new experiments that either test or clarify the structural models that are built.

Structure-based prediction of folding mechanism. Amount: $231,391. Start date: June 2003. Expires: May 2008. Principal investigator: Yaoqi Zhou. Institution: State University of New York at Buffalo. NIH Institute: NIGMS.

Project to uncover the fundamental mechanisms of protein folding and misfolding, and to predict protein structures from sequences using computational methods. Goals include an all-atom model based on simplified potentials that will permit practical folding simulations using regular PCs.

Software to Handle Missing Values in Large Data. Amount: $99,847. Start date: July 2003. Expires: Dec. 2003. Principal investigator: James Schimert. Institute: Insightful. NIH Institute: NCRR.

Phase I SBIR aims to produce commercial software for handling missing data in large data sets, such as microarray data, genomic data, and high-throughput screening data. A variable-by-variable approach using a recursive partitioning data-mining technique will be used to impute missing values.

In Silico Assessment of Drug Metabolism and Toxicity. Start date: July 2003. Expires: Jan. 2004. Principal investigator: Andrej Bugrim. Institution: GeneGo. NIH Institute: NIGMS.

Project to develop in silico platform called MetaDrug for predicting metabolism and possible toxic effects of novel drug candidates. The platform will integrate QSAR and expert system approaches with a database of human pathways and software for the reconstruction and visualization of metabolic and cell signaling networks.

Tools for mapping transcriptional networks. Start date: July 2003. Expires: June 2005. Principal investigator: Uri Alon. Institution: Weizmann Institute of Science. NIH Institute: NHGRI.

Supports development of a combined computational and experimental approach for mapping transcriptional networks in E. coli. An experimental method based on reporter plasmids for measuring the activity of many promoters in parallel will be developed that will generate kinetic expression data. Analysis algorithms will use this kinetic data to produce maps of the regulatory structure.

Computational Analysis of Gene Expression Pattern Images. Start date: July 2003. Expires: June 2006. Principal investigator: Sudhir Kumar. Institution: Arizona State University. NIH Institute: NHGRI.

Proposal to build a bioinformatics framework called FlyExpress to visualize spatial and temporal
patterns of gene expression in Drosophila embryos. The framework will enable researchers to search for genes with similar expression patterns in temporal-, spatial-, and organ-specific contexts. It will also provide a search tool for gene expression patterns called Fx-BEST that will be analogous to Blast for molecular sequence analysis.

Updating Chromosome Aberration Simulator (CAS) Software. Start date: July 2003. Expires: June 2007. Principal investigator: Rainer Sachs. Institution: University of California, Berkeley. NIH Institute: NIGMS.

Project to update CAS (chromosome aberration simulator), software that simulates chromosome aberrations via Monte Carlo and Markov chain calculations of break mis-rejoining.

Maintenance of blocks-based tools for functional genomics. Amount: $245,734. Start date: July 2003. Expires: June 2007. Principal investigator: Steven Henikoff. Institution: Fred Hutchinson Cancer Research Center. NIH Institute: NIGMS.

Update of protein alignment software tools based on conserved regions of proteins (blocks), including the Blocks database, BLOSUM amino acid substitution matrices, position-based searching strategies, position-specific score matrix and weighting methods, and a PCR primer design strategy for isolating distantly related homologs. Also supports a new reverse genetics strategy that provides an allelic series of point mutations in genes of interest that are analyzed using the blocks-based tools.

Statistical, Computational, and Genetic Analysis of HIV. Amount: $243,180. Start date: July 2003. Expires: June 2007. Principal investigator: Karin Dorman. Institution: Iowa State University of Science and Technology.
NIH Institute: NIGMS.

An informatics-based project to identify recombination promoting sequence features by simultaneously examining HIV-1 recombinants in a Bayesian framework. The project will also create a database of statistically confirmed HIV-1 recombinants and their crossover points.

Computation-Guided Protein Recombination and Evolution. Start date: July 2003. Expires: June 2007. Principal investigator: Frances Arnold. Institution: California Institute of Technology. NIH Institute: NIGMS.

Supports development of an algorithm called SCHEMA to predict what elements, or schemata, of a protein can be swapped among homologous proteins without disrupting the folded structure.

Combined Methods for Protein-Structure Prediction. Amount: $203,318. Start date: July 2003. Expires: June 2008. Principal investigator: Kevin Karplus. Institute: University of California, Santa Cruz. NIH Institute: NIGMS.

Project to develop a program for automatic protein structure prediction that will be available via the web and as a distributable software package. The project combines three different approaches to protein-structure prediction: 1D prediction of local structural properties using neural nets; fold-recognition using hidden Markov models; and conformation generation and scoring using fragment packing and an emprical energy function.


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