Title: Stringology and bioinformatics - The art of deciphering genomes Distinguished Lecture Series in Computer Science


Time: Friday, May 3, 2019 9:15 to 10:00 am, reception 10:00 to 12:00 am, Dr. Ukkonen's talk


Location: Integrated Engineering and Visual Arts Complex, EV 1.605 1515 Ste-Catherine St. W., Montreal


Abstract: Since the invention of DNA sequencing in the 1970s, the analysis of molecular biological sequences has been an inspiring source of computational problems. Unlike most data in natural sciences, the biological sequence data such as DNA and amino acid sequences is discrete rather than continuous by nature. Hence biological sequence analysis is, in addition to fields like text processing and information retrieval, another natural application area of combinatorial algorithms for processing text strings, an area sometimes called stringology.

With the advent of high-throughput sequencing the amount of sequence data has exploded, making molecular biology research totally dependent on efficient computation. The talk will discuss some computational problems, algorithmic techniques and future goals of bioinformatics, ranging from the genome reconstruction and sequence matching to the discovery of gene regulatory DNA motifs.

Speaker's bio: Esko Ukkonen (born 1950) is a Professor (since 1985) of Computer Science (emeritus from 2018) of the University of Helsinki. His research interests include algorithms and data structures, combinatorial pattern matching and machine learning as well as applications in biological sequence analysis. Dr. Ukkonen has had visiting positions at the University of California at Berkeley, University of Freiburg, University of Bielefeld, and King's College London. He was Academy Professor of the Academy of Finland in 1999-2004, and Director of a center-of-excellence ('From Data to Knowledge', 'Algorithmic Data Analysis') of the Academy of Finland in 2002-2013. In 2004-2008, he was Research Director of the Helsinki Institute for Information Technology (HIIT), a joint institute of the Aalto University and the University of Helsinki, in 2010-2013 Head of the Department of Computer Science, and in 2014-2017 Vice-dean (research) of the Faculty of Science. Esko Ukkonen is a member of the Finnish Academy of Science and Letters, a foreign member of the Estonian Academy of Sciences, and an honorary doctor of the Aalto University.