Statistical and Computational Approaches for Integrated Genomics and Proteomics Analysis and their Applications to Modeling G1/S Transition During Yeast Cell Cycle. Start date: Jan. 1, 2003. Expires Dec. 31, 2005. Expected total amount: $1,200,000. Principal investigator: Hongyu Zhao. Sponsor: Yale University.
Project will employ an interdisciplinary team of researchers to develop an integrated approach to reconstructing biological pathways. Goals include the development of new statistical and computational methods to identify transcription factor targets.
Facilitating Database Curation via Natural Language Processing. Start date: Feb. 1, 2003. Expires: Jan. 31, 2004. Expected total amount: $100,000. Principal investigator: Carol Friedman. Sponsor: Columbia University.
This project will investigate the effectiveness of a natural language processing method developed at Columbia called GENIES (Genomics Information Extraction System) for aiding curation and ontological development efforts of model organism databases.
New Physics-Based Approaches to Predictive Protein Modeling, with Applications to Cellular Regulation. Start date: Feb. 1, 2003. Expires: Jan. 31, 2004. Expected total amount: $50,000. Principal investigator: Matthew Jacobson. Sponsor: University of California, San Francisco.
Research will focus on computational methods for protein structure prediction based on all-atom physics-based models. New sampling methods will be developed to efficiently explore the energetic landscape of proteins.
Bioinformatics Analysis of Regulatory Sites in Genomic DNA Sequences. Start date: Feb. 1, 2003. Expires: Jan. 31, 2006. Expected total amount: $310,191. Principal investigator: Maria Ermolaeva. Sponsor: The Institute for Genomic Research.
Project will develop new methods for predicting regulatory sites based on statistical properties of sequence data and on conservation of sequence across species.
Bioinformatics of Voltage-Gated Ion Channels. Start date: March 1, 2003. Expires: Jan. 31, 2006. Expected total amount: $386,162. Principal investigator: Eric Jakobsson. Sponsor: University of Illinois, Urbana-Champaign.
Project will correlate sequence data with knowledge about the structure and function of some members of the potassium channel family, and use that to predict functional details for potassium channel genes lacking direct structural and functional data.
New Methods for Simulating Biomolecules of Several Microns in Length. Start date: March 1, 2003. Expires: Feb. 29, 2008. Expected total amount: $672,154. Principal investigator: Jianpeng Ma. Sponsor: Baylor College of Medicine.
Project goal is to develop several new computational methods for simulating molecular motions at any desired length scale without losing the details of atomic calculations. The work will be based on a “substructure synthesis method” that regards a given structure as an assemblage of substructures acting together in some way.
Cellular Control through the Development of Engineered Gene Circuits. Start date: March 1, 2003. Expires: Feb. 29, 2008. Expected total amount: $400,000. Principal investigator: Jeff Hasty. Sponsor: University of California, San Diego.
Project will model a “synthetic gene oscillator” based on the biochemistry of the feedback loops associated with protein-DNA interactions. The proposed engineered gene circuits will enable testable predictions about the behavior of complex biological networks.
Efficient Simulation of Protein-Membrane Interactions by Implicit Solvent Algorithms. Start date: May 1, 2003. Expires: April 30, 2006. Expected total amount: $520,479. Principal investigator: Dexuan Xie. Sponsor: University of Wisconsin, Milwaukee.
Project aims to develop a new computational model for studying protein conformation changes during membrane interactions using new algorithms for constrained molecular dynamics simulations.
New Technologies for Biosequence Comparison. Start date: July 1, 2003. Expires: June 30, 2008. Expected total amount: $757,133. Principal investigator: Jeremy Buhler. Sponsor: Washington University.
Project will develop new algorithms for sequence comparison using enhanced pattern-matching algorithms specialized for particular feature types, such as coding sequence, or to groups of organisms.
Gene Prediction — The Final Step. Start date: Nov. 1, 2003. Expires: Oct. 31, 2008. Expected total amount: $600,152. Principal investigator: Artemis-Georgia Hatzigeorgiou. Sponsor: University of Pennsylvania.
Project will develop a self-trained gene prediction program that will first build a training set from existing resources for transcribed regions. The set will then be combined with a structure model into a gene finder.