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Workshop 4: Emerging Genomic Technologies and Data Integration Problems (February 21-24, 2005)

Organizers: Terry Speed and Hongyu Zhao

It is arguable that the genomics revolution is largely technology-driven. Whatever one's view on this question, it is hard to imagine genomics without the polymerase chain reaction (PCR), invented as recently as the mid-1980s, or without high-throughput DNA sequencing, which emerged a little later. More recently, we have had the advent of the microarray (DNA chip) and high-throughput mass spectrometry (MS), which have greatly enriched functional genomics and proteomics, respectively. An inevitable consequence of the wider perspective of genomics and proteomics is the desire to extend assays, once carried out with one gene or one protein, to be as effective with hundreds of thousands of genes at a time, aiming at genome-wide or proteome-wide coverage. Thus, we now have a wide variety of high-throughput assays for measuring gene expression, at both the mRNA and protein levels, emerging ones for measuring DNA-protein and protein-protein interactions, and a constant drive to narrow the focus of the assay (e.g., to a single cell) and reduce the quantity of reagents needed.

Each advance of this kind brings with it many computational, mathematical, and statistical questions, both in the generation and initial processing, and in the analysis and interpretation of the data. While the details of the different technologies necessarily differ, many common themes emerge. These include issues, such as signal processing, signal manipulation, and quantification algorithms, as well as a host of common analysis tasks, such as classification, clustering, and the analysis of time course data. The purpose of this workshop is to introduce participants to some of these emerging technologies, and to have talks, which outline their quantitative needs so that we can highlight common analytical themes.