Department of Computer Science at UH

University of Houston

Department of Computer Science

In Partial Fulfillment of the Requirements for the Degree of
Master of Science

Karthik Karra

Will defend his thesis

Efficient Algorithms to identify Unique Signatures for silencing mRNA


RNAi is a post-transcriptional gene silencing technique -- a mechanism which inhibits the gene expression at the stage of translation. Cells can inhibit the expression of individual genes (stop proteins from being made) by interfering with an mRNA being transcribed. However, by introducing an artificial RNAi construct with a sequence complementary to a target gene’s mRNA, loss-of-function phenotypes can be generated quickly and easily. Many diseases and conditions might be controlled by suppressing appropriate genes, such as for proteases involved in viral replication or for defective proteins that accumulate in some degenerative diseases (as in Huntington's).

In our work, we have developed efficient algorithms to identify unique signatures that can turn-off a specific transcript. In order to handle transcripts without unique signatures, whether as splicing variants or members of a gene family, we extend our algorithms to identify group-unique signatures that can turn off several closely related transcripts together.

According to the results produced using the above algorithms, out of total 38,851 human mRNA transcripts, we could identify unique-signatures to 20,494 transcripts and covering-signatures to 6,058 groups (corresponding to 14,730 transcripts).

Date: Monday, November 30, 2009
Time: 11:00 AM
Place: 401-SR2
Faculty, students, and the general public are invited.
Advisor: Prof. Yuriy Fofanov