-----------------------------------------------------------

Summer Program Seminars 2006

Thursday, July 6, 2006 @ 10:00AM
Cullimore Hall, Room 611
New Jersey Institute of Technology

Using SVM to Predict Polyadenylation Sites

Yiming Cheng

(on joint work with Robert Miura and Bin Tian)

Department of Mathematical Sciences

New Jersey Institute of Technology

Newark, New Jersey

ABSTRACT

Messenger RNA polyadenylation plays a very important role in cellular processes such as transcription termination, mRNA stability, mRNA translation, and others.  However, it is still not clearly known when and where polyadenylation occurs in the cell, and what controls this special kind of mechanism.  It has been found that a large number of human and mouse genes have multiple polyadenylation sites (poly(A) sites) that lead to variable transcripts with distinct functions.  Alternative polyadenylation in a tissue-specific manner has been discovered by bioinformatics and there is biased alternative polyadenylation in human tissues, suggesting that groups of poly(A) sites can be coordinately regulated.  However, it is completely unclear how coordinate regulation is achieved.  In this study, first we want to use SVM to predict the poly(A) sites based on the gene sequence by bioinformatics, then we plan to systematically characterize coordinate regulation of alternative polyadenylation by mathematical modeling.