Bioinformatics
Core Director David Dyer, Ph.D.
Professor
Microbial Pathogenesis and Microbial Genomics
University of Oklahoma Health Sciences Center
Biomedical Research Center, room 362
975 NE 10th Street
Oklahoma City, OK 73104
405.271.1201 x1
Microgen at the University of Oklahoma Health Sciences Center
CORE PROFILE
The Bioinformatics Core Facility is located within the University of Oklahoma Health Sciences Center Laboratory for Genomics and Bioinformatics (LGB). The focus of the original Oklahoma BRIN bioinformatics core was specific to the analysis and database management of microarray data. The INBRE Bioinformatics Core, by contrast, is more flexible and diverse in its offerings. The core facility provides genomics and informatics support to the OUHSC community, DNA sequence analysis and data cleanup, advice on taxonomic analysis of this DNA sequence data, in addition to supporting proposed microarray experiments. Efforts are collaborated with the INBRE Microarray Core, located at the Oklahoma Medical Research Foundation, and the satellite bioinformatics cores located on the University of Oklahoma Norman campus, Oklahoma State University and The University of Tulsa. Activities are directed towards integrating these groups into a coherent whole. The Bioinformatics Core acts as a central repository of data for submission to the national repository GEO. The Core works directly with the newly hired bioinformatics faculty members in the OUHSC Department of Biostatistics and Epidemiology, to provide training and advice on the design of microarray experiments.
The Core recently implemented the Oklahoma Bioinformatics User's Group (OBUG) (http://obug.ouhsc.edu) that is used as a clearinghouse for bioinformatics exchanges in Oklahoma. In addition, a quarterly newsletter and other information is available at http://microgen.ouhsc.edu.
Oklahoma Re-Annotation (OKRA) Project
The Bioinformatics •Core will engage students from the INBRE undergraduate campuses in the re-annotation of microbial genome sequence databases. The one-semester project directs students to the primary literature to evaluate experimental “proof” of function. Students will update and enhance the annotation of existing microbial genome sequence databases. The re-annotated genome sequence database will be made publicly available on the website of the Bioinformatics Core http://microgen.ouhsc.edu. AAt the end of each project period, a one-day symposium will be held where two or three nationally-recognized investigators who work on this organism will present seminars and meet with students. •Database papers will be published with students as co-authors.
Currently, one of the most vexing problems faced by the discipline of microbial genomics is the paucity of efforts for ongoing curation of the existing microbial genome sequence databases. For instance, the Haemophilus influenzae genome sequence database was first published in 1995, and has not been updated since then. This leads to a gradual degradation of the usefulness of this resource since no new studies are being incorporated into this database and the scientific community thus cannot derive its full benefit. Funding agencies have typically been reluctant to devote resources to curation or “re-annotation” of these genome sequence databases, once established. Re-annotation of these resources has therefore typically been an ad hoc process, generally performed by the original group that sequenced the genome. The process of updating these databases has generally been haphazard and non-uniform. Further, re-annotation of a genome sequence database typically involves considerable effort but little explicit academic reward, which acts as a disincentive. The OKRA project will allow for microbial genome sequence re-annotation as a way to introduce Oklahoma undergraduate students to bioinformatic analyses of genome sequence data, and at the same time update and enhance the annotation of existing microbial genome sequence databases.
