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

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

Three projects are listed below

Project Type (basic research)

Project 1

Project title: Text data mining

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.

Project 2

Brief Description of Project 2:

We have built several devices to exploit TI's DLP micromirror chip. We have built oligo array synthesizers, spectrum generators, light directed tissue engineering systems and most recently 3D Holographic TV prototypes. These projects need additional work on them that spans from programming to engineering/physics to biology, especially biology. For example, we need researchers to take on projects to exploit these technologies, for example we want to characterize the affect of custom light spectra for immune system modulation and melanoma treatment and use custom high precision light patterns to grow cardiac tissues. We can always use a good optics person as well.

You will be working with Michael Huebschman, Ph.D. myself and with the people in our group. Check out our www page for some more information, innovation.swmed.edu

Project 3

Brief Description of Project 3:

We have identified computationally (and published) simple sequence repeat regions that have a high probability of polymorphism. About 9,000 were identified in genes (coding and untranslated regions). Many of these can be candidates genes causative for a given disease. For example 51 are frame shifters, terminating the protein early. We wish to test many of these genes in a collection of specific DNA samples for a given disease. We are investigating cancer, cardiac disease, inflammation, infection and fertility. The student will work to assemble the appropriate collection of DNAs and then sequence them to identify polymorphisms and determine trends and effects.

You will be working with Lena Flood, Ph.D. myself and with the people in our group. Check out our www page for some more information, innovation.swmed.edu

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