Systems Seminar
Evolution and Genomic Structure: A Signal Processing Perspective
Prof. Dan Schonfeld
ECE Dept.
University of Illinois at Chicago
Abstract
This talk will explore the use of system theory for the analysis of
genomic and proteomic molecular systems. Protein evolution will be
modeled as a communication system, where the encoded information is
the DNA and the decoder corresponds to the translation process in
biology. The distribution of amino acids will be shown to converge
geometrically to a distribution that is independent of the initial
state. The resulting distribution matches nearly perfectly the
natural abundance of amino acids obtained experimentally. The
structure and role of coding and non-coding regions in the genomic
sequence will be investigated. It is hypothesized that non-coding
segments (introns) serve to reduce the impact of mutations. This
assumption will be used to derive the distribution of the length of
coding segments (exons) that minimizes the probability of error. It
will be shown that the optimal distribution of the length of coding
segments (exons), a diffusive random walk model for the generation of
exons, and experimental data collected from multiple organisms
(eukaryotes) converge to a long-tailed distribution with identical
decay rates. The statistical correlation structure of genomic
sequences will also be explored. Genomic sequences will be shown to
be represented by non-stationary time series whose correlation
structure is more random in the coding segments (exons) and displays
longer correlations in the non-coding regions (introns).
Bio
Dr. Schonfeld received the B.S. degree in Electrical Engineering and
Computer Science from the University of California at Berkeley, and
the M.S. and Ph.D. degrees in Electrical and Computer Engineering
from the Johns Hopkins University, in 1986, 1988, and 1990,
respectively. In 1990, he joined the University of Illinois at
Chicago, where he is currently a Professor in the Department of
Electrical and Computer Engineering. Dr. Schonfeld has authored over
120 technical papers in various journals and conferences. He was co
author of papers that won the Best Student Paper Awards in Visual
Communication and Image Processing 2006 and IEEE International
Conference on Image Processing 2006 and 2007. He is currently serving
as associate editor of the IEEE Transactions on Image Processing on
Image and Video Storage, Retrieval and Analysis and associate editor
of the IEEE Transactions on Circuits and Systems for Video Technology
on Video Analysis. He has served as an associate editor of the IEEE
Transactions on Signal Processing on Multidimensional Signal
Processing and Multimedia Signal Processing as well as an associate
editor of the IEEE Transactions on Image Processing on Nonlinear
Filtering. His current research interests are in multi-dimensional
signal processing; image and video analysis; computer vision; and
genomic signal processing.
Time and Place: Wed., Nov. 19, at 3:30 in 4610 Engr. Hall.
SYSTEMS SEMINAR WEB PAGE:
http://homepages.cae.wisc.edu/~gubner/seminar/schedule.html