Projects

Broadly speaking, we are interested in these two areas:

(1) Epigenomics

(2) Integrative analysis of multiple genomic data sets

Here are some current projects:

Genome-Wide Mapping of Chromosomal Proteins in Drosophilia (Model organism ENCODE Consortium) - 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? We are part of the national consortium that aim to identify all sequence-based functional elements in the c. elegans and drosophila melanogaster genomes. Our specific project is in mapping of histone modification and chromosomal proteins in multiple tissues and stages. We are also involved in the integrative analysis of the entire modENCODE data.

Epigenomic states in differentiation (with Bob Kingston Lab and David Scadden Lab) - We are mapping nucleosome positions and histone modifications in various stages of development in model systems.

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.

Cancer Genomics (Cancer Genome Atlas Project) - We are part of a comprehensive and coordinated effort to characterize the cancer genome through the application of a wide range of the latest genome analysis technologies. The data types include gene expression, DNA copy number, microRNA expression, DNA methylation, SNP, and genome sequencing for mutations. We are particularly interested in DNA copy number and their relationships to other data types.

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.

Informatics for Integrating Biology and the Bedside (i2b2) - A part of a National Center for Biomedical Computing, this project aims to translate the advances in genomics to patient care. We are interested in the development of informatics framework and statistical methodology that will help bridge the gap between genomic technologies and clinical research.

Systems-Based Consortium for Organ Design and Engineering (SysCODE) - This interdisciplinary consortium brings the experts in organogenesis, gene regulatory networks, progenitor cells and tissue engineering to develop a systematic framework for synthesizing organs in vitro. We are contributing our expertise in computational analysis of genomic data.

Analysis of Data from Next-Generation Sequencing - These next-generation sequencing machines are producing 1-4 gigabases in a single run. We are very excited about this technology and are interested in various analytical issues related to this type of data as well as in their applications.

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.

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.