We develop quantitative methods and software for genomics and epigenetics. We focus on microarrays and second generation sequencing. We are interested in leveraging our expertise in handling these data to help translate scientific research into medical practice.
Specific problems we are currently working on include:
- RMA, fRMA, 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.