Genomic Signal Processing

Monday, May 24, 08:00 - 09:00

Presented by

Dr. P. P. Vaidyanathan, Department of Electrical Engineering, California Institute of Technology, Pasadena, California, U.S.A.

Abstract

In recent years a large amount of genomic data (DNA sequence data) for various organisms has been made available in public databases. This has opened up a unique opportunity which allows scientists to get access to the data and process them to extract useful information out of it. While this is of obvious interest in medicine and biology, this has also generated a great deal of excitement among people with talents in many different areas such as signal processing, computer science, and information theory. In this talk we emphasize some of the signal processing aspects involved in the study of DNA sequences as well as proteins which are sequences of amino acids. We explain how digital filtering, Fourier transform computation, and hidden Markov models have played a role in the identification of protein-coding genes in DNA sequences. We review long-range correlation or 1/f spectra in DNA sequences, and also explain the use of Fourier transform techniques in localizing functionalities in amino acid sequences. The role of signal processing tools such as the hidden Markov models and more general tools such as context-free grammars in biological sequence identification and sequence alignment will be discussed. After a discussion of signal processing problems involved in DNA sequencing and DNA microarrays, we also discuss non-coding genes, and the challenging problem faced today by scientists in identifying them computationally.

Speaker Biography

Prof. P. P. Vaidyanathan received the B.Tech. and M.Tech. degrees in radiophysics and electronics from the University of Calcutta, India, in 1977 and 1979, respectively, and the Ph.D degree in electrical and computer engineering from the University of California at Santa Barbara in 1982. Since 1983 he has been on the faculty of Electrical Engineering at the California Institute of Technology, where he now serves as the Executive officer of Electrical Engineering. His main research interests are in digital signal processing, multirate systems, wavelet transforms, and signal processing for genomics and digital communications. Dr. Vaidyanathan has authored over 300 papers in IEEE journals and conferences, is the author of the book Multirate Systems and Filter Banks, and has written several chapters for various signal processing handbooks. He was a recipient of the Award for Excellence in Teaching at the California Institute of Technology for the years 1983-1984, 1992-93 and 1993-94, and recipient of the IEEE ASSP Senior Paper Award (1987), and the S. K. Mitra Memorial Award from the Institute of Electronics and Telecommunications Engineers for a journal paper (1990). He is a Fellow of the IEEE (1991), and recipient of the F. E. Terman Award of the American Society for Engineering Education (1995). He was a Distinguished Lecturer for the IEEE Signal Processing Society (1996-97). He received the IEEE CAS Society's Golden Jubilee Medal in 1999 and the IEEE Signal Processing Society's Technical Achievement Award in 2002.

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