Beyond Genomics: Detecting Codes and Signals in the Cellular Transcriptome
Brendan J. Frey
Electrical and Computer Engineering
University of Toronto
Construction of the discrete genome sequence was the first step in developing a comprehensive understanding of how cellular processes are controlled by bio-molecules and their interactions. That step is now mostly complete and the next step is to determine how DNA subsequences encode instructions for producing RNA transcripts and how continuous abundances of transcripts in cells combine to control activities. This is a much more challenging task than genome assembly, because the encoding of genetic instructions turns out to be far richer than was previously thought, and the detection and analysis of continuous cellular signals is more difficult than discrete symbol detection. Only preliminary progress has been made in assembling and analyzing the "transcriptome" and the first genome-wide data sets enabling the study of transcripts and their interactions have only recently been published. In this talk, I'll describe several open research problems in this area and discuss how they can be approached using representations and algorithms familiar to researchers in the information theory community.
(Wednesday, July 12)
Brendan Frey received his PhD from the University of Toronto in 1997. From 1997 to 1999, he was a Beckman Fellow at the University of Illinois at Urbana Champaign and then he joined the Department of Computer Science at the University of Waterloo as an Assistant Professor. In 2001, Dr. Frey moved to the University of Toronto, where he is now an Associate Professor in Electrical and Computer Engineering, with cross-appointments to Computer Science and the Centre for Cellular and Bio-molecular Research.
He has consulted for Microsoft Research and various startup companies in the Toronto area. Dr. Frey is the author of the book Graphical Models for Machine Learning and Digital Communication and he has published over 100 papers and given over 80 invited talks on machine learning, probabilistic graphical models, molecular biology, computer vision and iterative decoding. Dr. Frey's most highly-cited work is on 'factor graphs and the sum-product algorithm'. In 2005, Dr. Frey's work on computational 'epitomes' with applications in vision received honorable mention for Best Paper at the IEEE Conference on Computer Vision and Pattern Recognition.
Dr. Frey's 2005 Nature Genetics paper reporting the first-ever exon-resolution analysis of the mammalian genome stirred up controversy in the molecular biology and genomics communities, which was reconciled in his favor in the March 2006 issue of Science. Dr. Frey is a Fellow of the Canadian Institute for Advanced Research, a winner of the Premier's Research Excellence Award, a former Fellow of the Beckman Foundation, and a recipient of the NSERC 1967 Science and Engineering Award. In 2005, he received the Outstanding Teaching Award from the Undergraduate Student Society in Electrical and Computer Engineering at the University of Toronto. Dr. Frey's work has been reported in trade journals, including Medical News Today, ACM TechNews, BioMed Central's Most-Viewed Articles and the IEEE Signal Processing Magazine. Dr. Frey was Co-Editor-in-Chief of the February 2001 issue of the IEEE Transactions on Information Theory and was an Associate Editor of the IEEE Transactions on Pattern Analysis and Machine Intelligence from 2002 to 2005. In 2003, he was Co-Chair of the International Conference on Artificial Intelligence and Statistics and the Canadian Workshop on Information Theory.