Projects

Here is a sampling of current projects.

Chromatin Structure and Function - How do the chromatin modification patterns look in different states and what do they mean? What is the relationship between gene expression patterns and chromatin structure? Global mapping of histone modifications using tiling arrays is providing data for understanding the relationship.

Mechanism of Dosage Compensation by the MSL Complex in Drosophila (with Mitzi Kuroda Lab) - How does the male fly up-regulate gene expression from the single X chromosome to achieve similar level of expression as in females (XX) ? More generally, what is the mechanism for the targeting and regulation of active chromatin domains? We are using expression arrays and tiling arrays to understand the binding properties of the Male Specific Lethal (MSL) complex.

Pathway Analysis from Expression Data - Can we predict the pathways that are involved in experiments based on gene expression data? A list of differentially expressed genes alone can be difficult to interpret and coordinated changes of small effects cannot be detected from the list alone. We are developing new algorithms and a database of pathways.

Network Analysis of Expression and Protein Interaction Data - Can we detect modules in the network of genes? Can we predict novel interactions based on the current protein-protein interaction maps? We are using graph-theoretic methods to design new algorithms for detecting features of these networks.

Cross-platform Analysis - Can we combine data from different microarray platforms to gain new insights? A large gene expression study may also involve more than one platform or multiple generations of same platform. We are studying for integrating data from multiple studies and several public databases.

Detecting Chromosomal Abberations - What is the best way to detect chromosomal amplifications and deletions from array CGH (comparative genomic hybridization) data? How can we integrate this information with gene expression to identify the gene essential in the development and progression of cancers? We are developing new detection algorithms and methods for data integration.

Characterizing Expression and Genomic DNA Signatures in Brain Tumors (with Mark Johnson Lab) - What are the gene that characterize different types of these tumors? What are the differences between Glioblastoma Multiforme and low grade gliomas, or between subtypes of low-grades? We are identifying such signatures both in expression data and in array CGH data.