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BioInform s Funding Update: Some Recent NIH Awards in Bioinformatics: Sep 29, 2003


Prototype disease marker genome annotation system. Amount: $99,783. Start date: Aug. 2003. Expires: Nov. 2003. Principal investigator: Martin Reese. Institution: Omicia. NIH Institute: NHGRI.

SBIR grant to support development of a system that integrates existing clinical databases with genomic data. Phase I will develop methods to directly map Mendelian mutations within the current human genome sequence. Grantees will build a prototype computer system that identifies the exact nucleotide positions of OMIM mutations within annotated genes of the latest human genome sequence assembly.

Flexible NLP system for MEDLINE information extraction. Amount: $100,000. Start date: Aug. 2003. Expires: Jan. 2004. Principal investigator: Nikolai Daraselia. Institution: Ariadne Genomics. NIH Institute: NIGMS.

SBIR Phase I project to develop a fully automatic system for extraction of the protein function information from Medline abstracts and convert it into a conceptual graph.

HIV phenotype/genotype database resources. Amount: $277,411. Start date: Aug. 2003. Expires: July 2005. Principal Investigator: Colombe Chappey. Institution: Virologic. NIH Institute: NIAID.

Supports development of a relational database to store and analyze data from the phenotypic and genotypic resistance tests of over 15,000 HIV-l-infected patient samples.

Robust Portable Software for Location Proteomics. Amount: $259,000. Start date: Aug. 2003. Expires: July 2006. Principal investigator: Robert Murphy. Institution: Carnegie-Mellon University. NIH Institute: NIGMS.

Project to develop automated systems that can recognize all major subcellular protein patterns in 2D and 3D images along with fast methods for retrieving images from distributed databases based on similarity of protein location patterns.

Reliable Assembler for Whole Genome Shotgun Data. Amount: $145,251. Start date: Aug. 2003. Expires: July 2006. Principal investigator: James Yorke. Institution: University of Maryland, College Park. NIH Institute: NHGRI.

Funds development of a whole-genome shotgun assembler for large repetitive genomes with improved capabilities for finding the sequence in repeat regions.

Comparative Genomic Analysis of Microarray Data. Amount: $210,474. Project Start: Aug. 2003. Expires: July 2006. Principal investigator: Kyle Furge. Institution: Van Andel Research Institute. NIH Institute: NCI.

Project will implement a set of comparative genomic microarray analysis (CGMA) algorithms — which are based on the observation that gene expression values show expression biases in regions of chromosomal gain and loss — to improve cytogenic predictions.

In Silico Analysis of Ocular Genes and Proteins. Amount: $166,328. Start date: Aug. 2003. Expires: July 2007. Principal investigator: John Michon. Institution: Duke University. NIH Institute: NEI.

Project for in silico analysis of genes and their protein products expressed in ocular tissues using statistical and machine learning techniques.

Analytical Tools for Comparative Microbial Genomics. Amount: $156,771. Start date: Aug. 2003. Expires: July 2007. Principal investigator: David Relman. Institution: Stanford University. NIH Institute: NIAID.

Proposal to develop a set of computational tools for the automatic analysis of comparative genome hybridization data. The project will classify conserved and divergent sequences based on microarray hybridization intensity ratios using a mixture model and infer phylogenetic relationships between strains. Grantees will also develop a Java-based visualization tool that integrates graphical representations of microarray data and genome annotation.

Rational Design Tools for Antisense Nucleic Acids. Amount: $283,132. Start date: Aug. 2003. Expires: July 2007. Principal Investigator: Ye Ding. Institution: New York State Department of Health. NIH Institute: NIGMS.

Supports development of novel algorithms and methods for improved prediction of RNA higher-order structures and for the rational and efficient design of antisense nucleic acids.

Clustering Software for Biomedical Applications. Amount: $99,913. Start date: Sept. 2003. Expires: Feb. 2004. Principal investigator: Krzystof Koperski. Institution: Insightful Corp. NIH Institute: NCRR.

SBIR grant supports development of clustering software for large biological databases and for categorical data. Phase I will focus on user requirements, one method for clustering large datasets, two methods for clustering categorical data, and prototype visualization tools.

HIVBase 1.0, The Genetic Data Solution. Amount: $100,000. Start date: Sept. 2003. Expires: Aug. 2004. Principal investigator: Susanna Lamers. Institution: Gene Johnson Inc. NIAID.

Project to develop software called HIVbase to integrate HIV data from multiple sources into an automated high-dimensional warehouse.

A signal transduction pathway database/modeling system. Amount: $156,834. Start date: Sept. 2003. Expires: Aug. 2004. Principal investigator: Eric Mjolsness. Institution: University of California, Irvine. NIH Institute: NIGMS.

Project to develop a computational framework for cell signaling networks, and create high-quality models for several pathways of biological interest. A database called Sigmoid will be developed to capture and organize pathway data and generate computational models.

Bioinformatics Software for Analyzing Microbial Genomes. Amount: $194,875. Start date: Sept. 2003. Expires: Aug. 2007. Principal investigator: Steven Salzberg. Institution: Institute for Genomic Research. NIH Institute: NLM.

Project supports development and maintenance of four bioinformatics systems for microbial genomics research: Glimmer, a gene finder for bacteria, viruses, archaea, and simple eukaryotes; Panda, a system for creating non-redundant protein sequence databases; TransTerm, which finds transcription terminators in microbial genomes; and a fourth system that predicts operons in microbial genomes using conserved synteny across species.

Mining the Structural Genomics Pipeline. Amount: $39,700. Start date: Feb. 2004. Expires: NA. Principal investigator: Chern-Sing Goh. Institution: Yale University. NIH Institute: NIGMS.

Project will analyze data generated by the structural genomics consortia to determine those protein sequence features that affect a protein’s ability to be structurally determined. This set of features will be integrated into a decision-tree algorithm that can be used to predict a user-defined protein characteristic, such as solubility.


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