The University of Rochester's Computer Science Department and the Center for Funtional Genomics at the University Medical Center have been co-operating over the last couple of years to produce ground-breaking bioinformatics research. I have been lucky to participate in this partnership almost since its inception, under the guidance of Dr. Mitsunori Ogihara, Dr. Andrew Brooks and Dr. David Pearce. Until now, my research has focussed primarily on three areas: data mining of gene expression profiles, functional annotation of the mouse genome, and designing a LIMS (Laboratory Information Management System) with ERP (Enterprise-wide Resource Planning) capabilities.
Our data mining project involved Dr. Ogihara, Dr. Brooks, Yinhe Cheng (a CS graduate student) and myself. Microarrays are a cutting-edge medical research tool that provide genetic 'snapshots' of biological sample, simultaneously recording the expression levels of thousands of genes. Extracting useful information from the resulting mountains of data, is, however, a very challenging task. We tackled the 'classification' problem, which involved creating a system that would 'learn' the association between microarray snapshots and various biological states or classes, which could then be used to identify microarray data samples with unknown class membership. Our tool, which we have acronymed 'ICED ', has proven more reliable in this classification problem than any other published algorithm. It is designed not only to classify microarray samples, but also identify genes that could prove to be potential drug discovery targets. We have trained ICED to distinguish between two types of leukemia as well as between healthy brain tissue samples, and those sufferring from a debilitating neurodegenerative disease. We have applied for a patent on ICED, and our paper on this research was accepted by the journal 'Bioinformatics' in May 2002. Currently, I am working with Dr. Brooks at the Functional Genomics Center on ICED analysis of various other experiments, while Dr. Ogihara and Yinhe Cheng are working on expanding the algorithm's functionality. The mouse genome annotation project, acronymed FAD, was executed by Dr. Pearce, Dr. Brooks and myself. It involved extracting generic annotation for the entire mouse genome from publicly available databases, and processing it exhaustively to produce a simplified annotation code, identifying functional characteristics of every identified gene in the geonome. We are planning to make this database available to the URMC community, and possibly the public domain sometime in the near future.
Lastly, the LIMS/ERP project is a medical informatics project that aims to use computer networks, PDAs and barcode scanners to increase lab efficiency, organize inventory management, as well as create electronic records of every experiment carried out in the Functional Genomics Center, which has a very high experiment turnover. The project is a collaboration between the Functional Genomics Center, which is headed by Dr. Broooks, and where I am currently employed, and a software company in Pune, India. We hope to install the system at the Functional Genomics Center, and eventually license the technology.
Mitsu Ogihara's Web Page
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