In the Rafa Lab, we develop quantitative methods and software for genomics and epigenetics. We focus on microarrays and next generation sequencing. We are interested in leveraging our expertise in handling these data to help translate scientific research into medical practice with a focus on cancer.

Specific problems we are currently working on include:

  • Next Generation Sequencing: Developing analysis tools for various applications.
  • Quantitative Epigenetics: Analyzing high throughput DNA methylation data.
  • RMA, fRMA, GCRMA: Preprocessing algorithms for Affymetrix arrays.
  • CRLMM: Genotyping and copy number tools for Affymetrix and Illumina SNP chips.
  • minfi, CHARM: Microarray method for high-throughput measurement of DNA methylation.
  • Expression Barcode: Single array classification based on calling expressed genes.