Multi-dimensional Bio-informatics for Genomic Data. Start date: July 2004. Expires: July 2005. Amount: NA. Principal investigator: Munther Dahleh. Institution: Infolenz. NIH institute: NHGRI.
Project to extend Infolenz’s proprietary technology for building multi-dimensional multi-resolution association models with high predictive power to the analysis of DNA microarray data.
DAS2: A Distributed Genome Annotation Sequence. Start date: July 2004. Expires: May 2006. Amount: $366,248. Principal investigator: Gregg Helt. Institution: Affymetrix. NIH institute: NHGRI
Proposal to extend and enhance the Distributed Annotation System (DAS), a specification for sharing distributed annotations of biological sequences. A new version of DAS, DAS2, will include a formal specification, and freely available open-source implementations of a DAS2 compatibility checker, server, and client.
The project is a collaboration between Affymetrix, Cold Spring Harbor Laboratory, and the Sanger Institute, with consulting provided by Dalke Scientific, according to the companies.
Algorithm and genome-wide database of functional siRNAs. Start date: August 2004. Expires: August 2005. Amount: $100,000. Principal investigator: Alex Chenchik. Institution: System Biosciences. NIH institute: NHGRI
Project to develop software for the prediction of effective siRNAs and a database with a functionally verified set of siRNAs for all currently discovered human, mouse, and rat genes.
Resolving Biological Entity References (Text/Databases). Start date: August 2004. Expires: July 2006. Amount: $199,156. Principal investigator: Frederick Baldwin. Institution: Alias-I. NIH institute: NCRR.
Proposal to extend the existing LingPipe suite of linguistic-processing tools to the challenges of bioinformatics, resulting in LingPipe-Bio.
GenMAPP: A tool for pathway analysis of genomic data. Start date: August 2004. Expires: July 2007. Amount: $350,000. Principal investigator: Bruce Conklin. Institution: J. David Gladstone Institute. NIH institute: NHGRI.
Supports development of GenMAPP 3.0, a free, open-source application that adds drawing and editing enhancements and integrates MAPPFinder functions to the existing GenMapp software program.
Automated Clone Evaluation for Functional Proteomics. Start date: August 2004. Expires: July 2007. Amount: $350,000. Principal investigator: Joshua Labaer. Institution: Harvard University Medical School. NIH institute: NHGRI
Funds development of software that will automate and facilitate the process of biologically evaluating protein expression cDNA clones. This software will compare the assembled sequence of a cDNA clone to a user-specified reference sequence to identify and categorize all discrepancies.
Inferring regulatory circuitry from microarray data. Start date: August 2004. Expires: May 2008. Amount: $340,000. Principal investigator: Harmen Bussemaker. Institution: Columbia University. NIH institute: NHGRI
Project to extend the statistical capabilities of REDUCE, a motif-based regression analysis tool for discovering cis-regulatory elements in non-coding DNA and inferring the activity of the regulatory factors binding to these elements.
Integrated Tool for Biological Parametric Mapping. Start date: August 2004. Expires: May 2008. Amount: $515,816. Principal investigator: Joseph Maldjian. Institution: Wake Forest University Health Sciences. NIH institute: NIBIB.
Phase I SBIR project to create an investigative tool for the real-time integration of data from emerging imaging modalities (fMRI, PET, SPECT, MRS, and diffusion imaging). This tool will allow analysis of an array of biological processes involving multiple cross-platform modalities recording activation, stimulation, biochemistry, and tissue contrast.
Macromolecular Docking. Start date: August 2004. Expires: July 2008. Amount: $356,630. Principal investigator: Ruben Abagyan. Institution: Scripps Research Institute. NIH institute: NIGMS
Proposal to create a new docking methodology that incorporates density-matching algorithms and a new five-dimensional fast Fourier transform method for simultaneous determination of rotation and translation to protein docking.
A Web-Based Automatic Molecular Docking System. Start date: August 2004. Expires: July 2008. Amount: $268,280. Principal investigator: Brian Shoichet. Institution: University of California San Francisco. NIH institute: NIGMS
Proposal to develop public tools and databases for molecular docking. Specific aims include building a public docking service as a research tool, developing public databases suitable for docking, developing an interface to allow non-experts to screen these databases against target structures, developing scripts to completely automate the docking procedure, and developing a computational platform to distribute the calculations.
Extending Bayesian Phylogenetic Analysis. Start date: August 2004. Expires: July 2008. Amount: $223,659. Principal investigator: John Huelsenbeck. Institution: University of California, San Diego. NIH institute: NIGMS
Project to extend Bayesian analysis of genetic data in order to identify site and branch combinations under positive selection, to estimate large phylogenetic trees, and to estimate divergence times.
Development and validation of models for gene regulation. Start date: August 2004. Expires: July 2008. Amount: $302,581. Principal investigator: Jeff Hasty. Institution: University of California San Diego. NIH institute: NIGMS.
Funds the computational modeling and experimental construction of synthetic gene regulatory networks.
Analysis of Large-Scale Biochemical Systems. Start date: August 2004. Expires: July 2008. Amount: $296,343. Principal investigator: Daniel Beard. Institution: Medical College of Wisconsin. NIH institute: NIGMS.
Supports the implementation of new thermodynamic-based constraints on biochemical fluxes and concentration that augments the flux-balance analysis approach currently used in quantitative modeling of biochemical systems. According to the grantees, this methodology allows them to make predictions not available from flux-based analysis alone, including predictions of reactant concentrations, reaction potentials, and enzyme activities.
Gene Regulation E. coli Database Integrated Modeling. Start date: August 2004. Expires: July 2008. Amount: $487,500. Principal investigator: Julio Collado-Vides. Institution: Autonomous University of Morelos, Mexico. NIH institute: NIGMS.
Supports an annotation project on transcriptional regulation and operon organization of Escherichia coil K-12 that will combine literature knowledge with computational predictions in order to put together transcription, transport, signal transduction and metabolism.
Bioinformatics Strategies: Biodefense Vaccine Research. Start date: August 2004. Expires: May 2009. Amount: $486,051. Principal investigator: Jason Moore. Institution: Dartmouth College. NIH institute: NIAID.
Proposal to develop a comprehensive analytical strategy for identifying biomarkers of adverse events following smallpox vaccination. The proposed strategy will combine novel and traditional statistical and computational methods for detecting GxG and GxE interactions with knowledge about hierarchical biological systems.
Quantitative and Computational Biology Graduate Program. Start date: August 2004. Expires: July 2009. Amount: $134,639. Principal investigator: David Botstein. Institution: Princeton University. NIH institute: NHGRI.
Supports a new multi-disciplinary training program in genomics at Princeton University, aimed at educating genome scientists with the quantitative and computational tools “likely to be required for the biology of the future.” The genome training program will support students in Princeton’s new Graduate Program in Quantitative and Computational Biology (QCB).
Bioscience Research Integration Software Platform. Start date: September 2004. Expires: March 2005. Amount: $409,447. Principal investigator: Steven Bova. Institution: Biofortis. NIH institute: NCI
Supports development of a prototype software application, Labmatrix, a platform for the collection, manipulation, and interrelation of molecular, genomic, and clinical data.
Comprehensive Analysis of Microarray Gene Expression. Start date: September 2004. Expires: August 2005. Amount: $149,499. Principal investigator: Yue Wang. Institution: Virginia Polytechnic Institute and State University. NIH institute: NCI.
Supports the development of bioinformatics tools to interpret information derived by gene microarrays about underlying cancer biology, and to facilitate molecular classification/prediction of cancer and response to therapy.
Developing tools for Bio-Molecular Image Informatics. Start date: September 2004. Expires: August 2006. Amount: $146,344. Principal investigator: Bangalore Manjunath. Institution: Mayachitra. NIH institute: NIGMS.
Funds development of image information processing and database tools for biomolecular image data from immunofluorescence microscopy, electron microscopy, GFP visualization, and atomic force microscopy.
Computational discovery of cis-regulatory sequences. Start date: September 2004. Expires: August 2008. Amount: $481,361. Principal investigator: John Stamatoyannopoulos. Institution: Regulome. NIH institute: NIGMS.
Project to combine computational and functional methodologies to develop a set of algorithms with high positive predictive value for identifying and classifying candidate cis-regulatory sequences sites in the vicinity of any gene of interest.
Computational Methods for Fine Mapping. Start date: September 2004. Expires: August 2008. Amount: $487,500. Principal investigator: Paul Marjoram. Institution: University of Southern California. NIH institute: NIGMS.
Funds development of computationally intensive methods to fine-map genes involved in complex traits. Particular emphasis is on methods that exploit the underlying genealogy of a sample of interest and Bayes methods, which abstract out the effects of the genealogy using hierarchical clustering techniques.
Computational Genomics of Signal Transduction. Start date: September 2004. Expires: August 2009. Amount: $224,952. Principal investigator: Igor Zhulin. Institution: Georgia Institute of Technology. NIH institute: NIGMS.
Supports development of a high-throughput computational approach to improve function prediction for signal transduction proteins in microbial genomes combined with experimental validation of selected targets.
Center for Quantitative Biology. Start date: September 2004. Expires: August 2009. Amount: $3,132,249. Principal investigator: David Botstein. Institution: Princeton University. NIH institute: NIGMS.
Proposal to create a multidisciplinary Center for Quantitative Biology at Princeton University.
Physics-based Simulation of Biological Structures. Start date: September 2004. Expires: July 2009. Amount: $350,000. Principal investigator: Russ Altman. Institution: Stanford University. NIH institute: NIGMS.
Proposal to establish the National Center for Simulation of Biological Structures (SimBioS), which will develop, disseminate, and support a simulation toolkit (SimTK) that enables users to create and visualize accurate models and simulations of biological structures at all scales — from atoms to organisms.