Progress Report 2005

Prof Gerstein was previously co-PI on NSF award (grant no: BDI-0135442; original duration: 11/1/2002-10/31/2004; no-cost extension until 10/31/2006; total amount including REU supplement: $492,485) titled: “Exploring Approaches for Microarray Databases that Enable Flexible Design and Integrative Analysis”. Prof. Kei Cheung (Yale Center for Medical Informatics) was the PI on this grant. The bioinformatics research has been conducted in the context of the Yale Microarray Database (YMD) effort (http://info.med.yale.edu/microarray), which is a university-wide database facilitating large-scale management and analysis of gene expression data. Since the inception of this NSF funding, Prof Gerstein worked on the YeastHub project. This involved exploring the use of a variety of semantic web technologies to integrate diverse types of yeast genome data (including gene expression data, transposon insertion data, protein-protein interactions, etc) provided by different web resources in different formats. Mining such integrated data will be beneficial to a variety of biomedical research studies including microarray experiments. We have also involved undergraduate students in this project. As a result, we were awarded an REU (Research Experience for Undergraduates) supplement to continue and broaden this research involvement with undergraduate students. A paper describing the YeastHub work was published as a supplemental issue of Bioinformatics (Cheung et al., 2005). The YeastHub work was also presented at ISMB 2005 (http://www.iscb.org/ismb2005).