Approved: ____________________________________ Thesis Supervisor ____________________________________ Title and Department ____________________________________ Date

. OSCAR3 is an open extensible system for the automated annotation of chemistry in scientific articles, which can process thousands of articles per hour. This XML annotation supports applications such as interactive browsing and chemically-aware searching, and has been designed for integration with larger text-analysis systems. We report its application to the high-throughput analysis of the sm...

We describe a trainable computer vision system enabling the automated analysis of complex mouse behaviors. We also collect and manually annotate a very large video database used for training and testing the system. Our system performs on par with human scoring, as measured from the ground-truth manual annotations. Our video-based software should complement existing sensor based automated approa...

& &

Traditionally, protocols in wireless sensor networks focus on low-power operation with low data-rates. In addition, a small set of protocols provides high throughput communication. With sensor networks developing into general propose networks, we argue that protocols need to provide both: low data-rates at high energy-efficiency and, additionally, a high throughput mode. This is essential, for ...

Supplemental nFuse pipeline overview The nFuse method builds upon Comrad (McPherson et al., 2011b), our previous work on rearrangement detection in matched RNA-seq and WGSS. We begin this section by briefly describing Comrad, then describe significant differences between Comrad and nFuse. An overview of the nFuse pipeline is shown in Figure 1.

The advance of Internet and Sensor technology has brought about new challenges evoked by the emergence of continuous data streams. While existing data stream management systems allow for high-throughput stream processing, they lack complex reasoning capacities. We address this shortcoming and elaborate upon an approach to knowledge-intense stream reasoning, based on Answer Set Programming (ASP)...

SUMMARY Current genome browsers are designed for linear browsing of individual genomic regions, but the high-throughput nature of experiments aiming to elucidate the genetic component of human disease makes it very important to develop user-friendly tools for comparing several genomic regions in parallel and prioritizing them based on their functional content. We introduce VISTA Region Viewer (...

We introduce an approach to detecting inconsistencies in large biological networks by using Answer Set Programming (ASP). To this end, we build upon a recently proposed notion of consistency between biochemical/genetic reactions and high-throughput profiles of cell activity. We then present an approach based on ASP to check the consistency of large-scale data sets. Moreover, we extend this meth...

GeoChip is a comprehensive functional gene array that targets key functional genes involved in the geochemical cycling of N, C, and P, sulfate reduction, metal resistance and reduction, and contaminant degradation. Studies have shown the GeoChip to be a sensitive, specific, and high-throughput tool for microbial community analysis that has the power to link geochemical processes with microbial ...