Research Overview
We develop quantitative methods and software for genomics and epigenomics. We focus on microarrays and second generation sequencing. These technologies are used to measure diverse high genomic endpoints including genotype, chromosomal abnormalities including deletions/insertions, protein binding sites, methylation, and alternative splicing.
With these technologies, a number of steps are required to convert raw measures into the results relied upon by biologists and clinicians. These data manipulations influence the quality of the ultimate measurements and studies that rely upon them. We specialize in using modern statistical methodology to improve the accuracy and precision of these measurements, relative to ad-hoc procedures introduced by manufacturers of the technology. Specific problems we are currently working on include:
- RMA,GCRMA: Preprocessing algorithms for Affymetrix arrays.
- CRLMM: Genotyping and copy number tools for Affymetrix and Illumina SNP chips.
- CHARM: Microarray method for high-throughput measurement of DNA methylation.
- Expression Barcode: Single array classification based on calling expressed genes.
- New CpG Islands: New definition based on Hidden Markov Model.
- Synthetic Lethality: Identifying synthetic lethal genetic interactions in yeast.
- Second Generation Sequencing: Developing analysis tools for various applications.
The Publications Section provides links to papers on all these topics. The Software and Data Section provides Bioconductor tools. Open positions are listed in the People Section.