Analysis of Transcriptomes by Deep Sequencing

Genome-wide studies of transcriptional phenomena in individual tissues is now possible with the recent advent of deep, or next-generation, sequencing technology. We have developed computational methods for analyzing such data, including the alignment tool GSNAP for mapping short reads to a genome and a pipeline GSTRUCT for inferring gene structures from mapping results. An early version of our pipeline gave the highest accuracy results in a recent worldwide contest. We have a particular interest in understanding transcription in cancer, and have studied a particular splicing phenomenon called transcription-induced chimeras (TICs) in human prostate adenocarcinoma and normal tissues, as well as brain and universal reference samples. We have identified and characterized in these samples a large number of novel TIC events, several of which are candidates for having a functional role in prostate cancer

Speaker: Dr. Thomas Wu is currently Senior Scientist in the Department of Bioinformatics at Genentech, where he has been working since December 1999. At Genentech, he has been involved in the development of computational infrastructure for the analysis of microarrays and highthroughput sequencing data.