REPRESENTATION AND ANALYSIS OF GENOMIC SIGNALS

 Prof. Paul Dan Cristea

Biomedical Engineering Center
"Politehnica" University of Bucharest (Romania)
 

Abstract:

The almost complete sequencing of several genomes, including the human genome, as well as the public access to most of this information, offer the opportunity to data mine and to explore in depth this unique empiric data depository. Most frequently, genomic information is represented by sequences of nucleotide symbols in the strands of DNA and RNA molecules. The main disadvantage of this approach is to limit the methodology of handling genomic information to pattern matching and statistical procedures. Converting the genomic sequences into digital genomic signals offers the possibility to use signal processing methods for handling and analyzing genomic information. Using the genomic signal approach, long range features maintained over distances of 106 - 108 of base pairs, i.e., at the scale of whole chromosomes, have been found. On the other hand, in the context of analyzing large volumes of data and of presenting the results in a easy to read form, the problem of data representability becomes critical. A novel mathematical description of data graphical representability, based on the data scattering ratio for a pixel is defined and is applied for several typical cases of standard signals and for genomic signals. It is shown that the variation of genomic data along nucleotide sequences, specifically the cumulated and unwrapped phase, can be visualized adequately as simple graphic lines for low and large scales, while for medium scales (thousands to tens of thousands of base pairs) the statistical descriptions have to be used.

Biography :

Paul Cristea received his Ph.D. in Technical Physics from the "Politehnica" University of Bucharest in 1970. His research and teaching activities have been in the fields of Genomic Signals, Digital Signal and Image Processing, Connectionist and Evolutionary Systems, Intelligent e-Learning Environments, Computerized Medical Equipment and Special Electrical Batteries. He is the author or co-author of more then 125 published papers, 13 patents, and contributed to more than 20 books in these fields. Currently, he is a Professor and the Coordinator of the Electrical Engineering and Computers Division of the Faculty of Engineering of the "Politehnica" University of Bucharest, General Manager of the Bio-Medical Engineering Center of UPB and the Director of the Romanian Bioinformatics Society.

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