Request for Funding

Medical Student Research Fellowship for Summer 2002

Mentor: Harold "Skip" Garner
Department: McDermott Center/CBI - Biochemistry & Internal Med.
Room number: NA2.508A
Mail Code: 8591
Phone number: 81661
E-mail: garner@swmed.edu

Human subjects IRB approved project number (where applicable): N/A

Two Projects:

Brief Description of Project 1:

We have begun to develop codes to cluster and then integrate information from a variety of databases, especially Medline. We wish to develop several new applications to exploit that data. For example, there are several modules that need to be written for eTBLAST (check it out on our www page at innovation.swmed.edu). Student will be expected to develop code, in C or Oracle, work on UNIX/Linux multi-processor machines (HP, Sun, etc.). They will also be expected to test/inspect/characterize their results, for which knowledge of medicine and/or biology is of value, but not required.

In addition to this project, we have a number of other analysis packages we create, and are always coming up with more ideas of value and need than we have capable people to do. Check out some of the other codes on our www page as well.

You will be working with Alex Pertsemlidis, Asst. Prof., myself and with the people in our group.

Brief Description of Project 2:

We have developed a code called IRIDESCENT, that analyzes all of Medline for hidden relationships among the biomedical objects (drugs, genes, phenotypes, chemicals, etc.) within it. A network of relationships among these objects can be inspected for any one or set of objects within a query. We have used this code to generate hypothesis, find missing elements (genes in a set, a pathway, for example), analyze microarray experiments. We have validated its utility and efficacy by experimentally testing several of its predicted relationships (use an existing drug for a new purpose, develop an entirely new concept for NIDDM, etc.).

We wish to extend this work, and have one or more summer students to test one of its many hypothesis to date, and/or use the code to trigger a hypothesis of interest to the medical student and then have them pursue it within the laboratory. This will not require any hard-core computer knowledge, for IRIDESCENT is fairly complete and has a nice user interface. The student will use their biomedical knowledge to use the code, design an experiment and then complete that experiment in the summer, hopefully resulting in an interesting publication.

Previous Research Activities or Publications with Medical Students:

We have had a number of medical students in the lab each summer. They have successfully completed work, often ending in a publication.

Hyperspectral Imaging: A Novel Approach for Microscopic Analysis, R.A. Schultz, T. Nielsen, J. Zavaleta, R. Ruch, R. Wyatt, H.R. Garner., Cytometry 43: 239-247 (2001)

K. M. O'Brien, J. Wren, V. K. Dave, D. Bai, R. D. Anderson, S. Rayner, G. A. Evans, A. E. Dabiri, and H. R. Garner, "ASTRAL, a Hyperspectral Imaging DNA Sequencer," Review of Scientific Instruments, Vol. 69, No. 5, May, 1998.

Return to UT Southwestern Homepage

Return to Student Research Projects Index