Technical development

We provide consultation on study design, methodology, and data analysis issues both within and outside Stanford.

The techniques we currently use in our group include RT-PCR (both SYBRGreen-based and Taqman), spotted DNA arrays, and SAGE (longSAGE, followed by tag-specific PCR to recover original cDNA clones).

We have also evaluated a number of commercially available technologies, including microarrays from Agilent, Illumina (with ongoing evaluations of the ABI and Amersham arrays), long-oligo libraries (for printing custom arrays), and MPSS by Lynx.

We develop our own protocols for defining reference genes in RT-PCR experiments; for using gene ontology for unbiased interpretation of microarray results--in fact, nearly all publicly available tools are biased in favor of gene sets with co-regulated genes); and for developing statistical models to control for the multiple biological and technical signals that are always blended in real biological samples, often with unknown ratios.