Selected Research Projects
Molecular Environmental Sciences and Genomic Evolution (Dr. Patrick Gillevet): Development of a prototype database to integrate phenotypic, metabolic, and genotypic data; new capillary technology technology for high throughput genomic sequencing and environmental monitoring. Applications include the toxic dinoflagellate Pfiesteria piscicida, and monitoring soil ecosystems during bioremediation processes.
Learning and Optimization Algorithms for Computational Biology (Dr. John Grefenstette): Genetic algorithms for protein and RNA structure prediction; induction algorithms for biological network models; machine learning methods for molecular diagnostics.
Genomic Analysis for Agricultural Improvements (Dr. John Grefenstette): Analyze microarray data to identify genes that improve resistance response in soybean to invasion by soybean cyst nematode, the major pest of soybean. This project also include haplotyping methods with applications to the analysis of the bovine genome.
RNA Structure Prediction (Dr. John Grefenstette): Develop improved algorithms for RNA secondary structure prediction using massively parallel genetic algorithms for energy minimization; provide more complete coverage of optimal and sub-optimal structures, and provide data for the analysis of the folding pathway, leading to a fuller understanding of the RNA folding process.
Cellular Modeling (Dr. Saleet Jafri): Improve understanding of heart disease through modeling of cardiac cells; models of cardiac excitation contraction coupling, cardiac energy metabolism; cellular signaling and biochemical reaction networks.
Image Processing Methods (Dr. Jason Kinser): Image registration, display, lane tracking, and base-calling from DNA sequencing machines. Development of new autowave approaches to phylogenetic tree construction. Optical computing application to DNA sequence analysis. New methods for pulse image processing with applications to biometrics: the measurement of humans using a myriad of data types (fingerprints, faces, DNA, shoe prints, speech, etc.)
Protein Aggregation and Unfolding (Dr. Dmitri Klimov) Computational models of protein aggregation with a focus on the assembly of Abeta amyloids, which cause Alzheimer's disease; computational models of forced (mechanical) unfolding of proteins. Methods include the all-atom molecular dynamics (MD) simulations of proteins or peptides in explicit solvent. These topics are critical to understanding the molecular aspects of Alzheimer's disease and mechanical functions of proteins in living organisms.
Sequencing Human Adenoviruses (Dr. Donald Seto): Efficient methods of sequencing and data alignment using consensus sequences. This rapid approach is a model for sequencing and analyzing related genomes and loci (comparative genomics). Software tools for whole genome analysis, currently being applied to the poxvirus genomes.
Protein Structural Analysis Through Computational Geometry (Dr. Iosif Vaisman): Development of new methods for protein structure compariosn and alignment based on topological substructure descriptors. Potential applications include ligand effect on protein topology in the inhibitor complexes with HIV and SIV proteases or topological changes in DNA polymerases in protein-DNA complexes.
Microarray Databases and Analysis Methods (Dr. Jennifer Weller): Organize large microarray datasets for sharing, analysis and data mining; analysis methods that provide insight into biological processes based on microarray data; Develop a reference implementation of the MAGE model (GeneX). Populate the GeneX database to test and refine performance; Develop APIs to the database for ease in testing new analysis methods.
Metabolic System Analysis (Dr. James Willett): Rapid assays for effectors using the nematode Caenorhabditis elegans. Recording responses of biochemical pathways to physiologic state modifiers with applications to elucidating the mechanisms of action of neurotoxicants, and dietary supplements purported to have life extending properties. Analysis of alterations in signaling arrays in nematodes as a function of age.