Words in natural language documents exhibit a small world network structure. Thus the physics community provides us with an extensive supply of algorithms for extracting community structure. We present a novel method for semantically clustering a large collection of documents using small world communities. This method combines modified physics algorithms… (More)
The emerging " Computational Grid " infrastructure poses many new opportunities for the developing science of large scale multi-agent simulation. The ability to migrate agent experiments seamlessly from simple, local single-processor development tools to large-scale distributed simulation environments provides valuable new models for experimentation and… (More)
Personal health messages - inter patient communications within online communities; represent a new path towards providing continuous information about patient derived health status. We apply natural language processing techniques to personal health messages from online message boards to demonstrate the ability to track trends in people's positive or… (More)
Seeking health-related information on the Internet is becoming commonplace. Patients use the Internet to learn about their conditions and medications, and to discuss symptoms and concerns with other patients on chat forums. Physicians also browse these chat sites to understand concerns, symptoms, and beliefs of patients that might not be revealed to the… (More)
BACKGROUND Large-scale genomic studies often identify large gene lists, for example, the genes sharing the same expression patterns. The interpretation of these gene lists is generally achieved by extracting concepts overrepresented in the gene lists. This analysis often depends on manual annotation of genes based on controlled vocabularies, in particular,… (More)
With the rapid decrease in cost of genome sequencing, the classification of gene function is becoming a primary problem. Such classification has been performed by human curators who read biological literature to extract evidence. BeeSpace Navigator is a prototype software for exploratory analysis of gene function using biological literature. The software… (More)
Bioinformatics of gene regulation, evolution of gene regulatory networks, comparative genomics, statistical and systems genetics Grading and discussion sessions for the course " Cellular and Developmental Biology " .