Peter G. Webb

Designing Specific Oligonucleotide Probes for the Entire S. cerevisiae Transcriptome

Probe specificity plays a central role in designing accurate microarray hybridization assays. Current literature on specific probe design studies algorithmic approaches and their relationship with hybridization thermodynamics. In this work we address probe specificity properties under a stochastic model assumption and compare the results to actual behavior in genomic data.We develop efficient specificity search algorithms. Our methods incorporate existing transcript expression level data and handle a variety of cross-hybridization models. We analyze the performance of our methods. Applying our algorithm to the entire S. cerevisiae transcriptome we provide probe specificity maps for all yeast ORFs that may be used as the basis for selection of sensitive probes.

Functional model based object-oriented development framework for mechatronic systems

This paper presents a functional model based object-oriented framework for mechatronic system development. The approach has been applied to conceptual design of a new generation plate making system for DNA micro-array manufacturing automation. The contributions of this paper include the functional model and object-oriented development framework for mechatronic systems, and concepts of cost and design optimization at the system functional model level.