My research advisors are Terry Speed and Mary Wildermuth.
My main projects are listed below.
Identification of gene expression markers predictive of relapse in prostate cancer patients
Collaborators: Yipeng Wang (Sidney Kimmel Cancer Center), Michael McClelland (Sidney Kimmel Cancer Center), and Terry Speed
Description: We are analyzing the relation between gene expression levels and clinical outcomes in prostate cancer patients.
For this study, gene expression data was collected from fresh frozen prostate biopsy samples.
Each sample contains a mixture of several different cell types.
We have developed models to estimate the mean expression level across samples for each gene in each cell type.
We are working to identify genes that show significant differences in mean expression for different clinical outcomes.
Our work could lead to insights about the mechanisms of prostate cancer
and diagnostic tests to help doctors make treatment decisions.
Gene expression analysis of pathogen infected laser microdissected Arabidopsis leaves
Collaborators: Divya Chandran (UC Berkeley Department of Plant and Microbial Biology) and Mary Wildermuth
Description: We are studying the means by which plants defend themselves from pathogens.
As a model system, we are using Arabidopsis thaliana infected with the powdery mildew Golovinomyces orontii.
Mary Wildermuth's lab has used laser microdissection to collect samples of specific plant cell types from infected leaf tissue.
The lab has performed gene expression measurements on these samples, and we are now analyzing the data.
Since laser microdissection of plant tissue is a relatively new technique,
we must pay particular attention to assessing the quality of the data.
We eventually plan to identify genes that are differentially expressed in response to infection in a cell type specific manner.
Analysis of genomic data involving the Drosophila Myb complex
Collaborators: Michael Botchan (UC Berkeley Department of Molecular and Cell Biology) and Terry Speed
Description: The Myb complex in Drosophila is a DNA binding complex that is involved in regulating development and DNA replication.
Recent experiments on Drosophila cell cultures have produced genomic data associated with the complex.
The data includes ChIP-chip tiling array data for several of the proteins in the complex.
The data also includes genome wide expression data for cells which had certain members of the complex knocked down by RNA interference.
By analyzing the data, we hope to gain a better understanding of how the Myb complex assembles and regulates gene expression.
A semiparametric mixture model for identifying cis-acting regulatory elements
Collaborators: Terry Speed and Mary Wildermuth
Description: A recent article by Wei Wang et al. proposed a method for identifying cis-acting regulatory elements
by combining gene expression data and nucleotide sequence data.
We have developed a modified version of Wang's model that can better accommodate cases
where there are multiple instances of the motif within a gene's promoter.
Our model is also semiparametric, so that fewer assumptions are made about the data.
We have applied our method to data from Arabidopsis and yeast.
Design of oncology phase I clinical studies
Collaborators: Wei Yu (Genentech) and Howard Mackey (Genentech)
Description: Several different designs have been proposed for finding a drug's maximum tolerable dose
in Phase I clinical trials. We performed simulations to compare the safety and efficiency of various designs.