Tutorial - Signal and Motif Detection

Presenter: Jagath C. Rajapaske, Nanyang Technological University, Singapore

Description

Signals of genomics sequences refer to specific sites relating to important biological phenomena, for example, transcription start sites (TSS), translation initiation sites (TIS), and splice sides (SS). The computational techniques to detect these signals are becoming popular because of the complexities and difficulties in determining these sites experimentally. This tutorial will introduce computational intelligence techniques, such as neural networks, genetic algorithms, and their hybrids for the detections of TSS, TIS, and SS.

Motifs in genomic sequences refer to short segments of DNA, which are conserved and have some important biological function. Most motifs in DNA sequences have regulatory functions, for examples, transcription factor binding sites (TFBS), promoters, and ribosome binding sites. Motif detection is a difficult problem in computational biology because the motif instances usually present in the sequences with a considerable number of degenerations. We discuss several approaches to motif detection, including profile analysis, neural network methods, the MEME approach, etc. We then proceed to discuss the graphical methods for week motif detection problem where classical techniques fail.

Biosketch of Presenter:

Dr. Jagath C. Rajapakse is an Associate Professor in the School of Computer Engineering (SCE) and the Deputy Director of the BioInformatics Research Centre (BIRC) at the Nanyang Technological University (NTU), Singapore. He is also a Visiting Professor at the Biological Engineering Division, Massachusetts Institute of Technology (MIT), USA. He received B.Sc. (Eng.) degree with First Class Honors in electronic and telecommunication engineering from the University of Moratuwa (Sri Lanka), and M.Sc. and Ph.D. degrees in electrical and computer engineering from the State University of New York at Buffalo (USA). Before joining NTU, he was a Visiting Fellow at the National Institute of Mental Health (Bethesda, USA) and a Visiting Scientist at the Max-Planck-Institute of Cognitive and Brain Sciences (Leipzig, Germany).