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Seminar: What does Information Theory have to say about Biological ...31-01-2020

Speaker: Ercan Engin Kuruoğlu, Institute of Science and Technology of Information-CNR

Title:  What does Information Theory have to say about Biological Evolution?

Date/Time: 5 February, 2020  /  13.40-14.30

Place: FENS L035

Abstract: In this talk, we will study the genetic processes using the principles we learned from telecommunication theory.We envision the molecular evolution process as an information transfer process and provide a quantitative measure for information preservation in terms of the channel capacity according to the channel coding theorem of Shannon. We calculate Information capacities of DNA on the nucleotide (for non-coding DNA) and the amino acid (for coding DNA) level using various substitution models. We extend our results on coding DNA to a discussion about the optimality of the natural codon-amino acid code. We provide the results of an adaptive search algorithm in the code domain and demonstrate the existence of a large number of genetic codes with higher information capacity. Our results support the hypothesis of an ancient extension from a 2-nucleotide codon to the current 3-nucleotide codon code to encode the various amino acids and the frozen accident hypothesis of Francis Crick. The talk presents the potentials of information theory and learning algorithms in computational biology and bioinformatics.

Bio: Ercan Engin Kuruoglu received his BSc and MSc degrees in Electrical and  Electronics Engineering from Bilkent University MPhil and PhD degrees in Information Engineering from the University of Cambridge, Cambridge, United Kingdom, in 1995 and 1998, respectively. In 1998, he joined Xerox Research Center Europe, Cambridge. He was an ERCIM fellow in 2000 with INRIA-Sophia Antipolis, France. In January 2002, he joined the Institute of Science and Technology of Information-CNR (Italian National Council of Research) , Pisa, Italy. He was a visiting professor for periods of 1-3 months with Georgia Tech-China in 2007, 2011 and 2016, Humboldt University in Berlin in 2012, Southern University of Science and Technology of China, Shenzhen in 2017, University of South Australia in 2018-2019 and Zhejiang Gongshang University, Hangzhou in 2019. He is currently a Visiting Professor at Tsinghua-Berkeley Shenzhen Institute, on sabbatical leave from ISTI-CNR where he holds a Chief Scientist (Dirigente di Ricerca) position. He was an associate editor for the IEEE Transactions on Signal Processing and IEEE Transactions on Image Processing. He is currently the editor in chief of Digital Signal Processing: A Review Journal. He acted as a technical co-chair for EUSIPCO 2006 and a tutorials co-chair of ICASSP 2014. He is a member of the IEEE Technical Committees on Signal Processing Theory and Methods, Machine Learning for Signal Processing and Image, Vision and Multidimensional Signal Processing. He was a plenary speaker at DAC  (Data Analysis for Cosmology) 2007, ISSPA (Int. Symposium on Signal Processing and Analysis) 2010, IEEE SIU (Sinyal Isleme ve Uygulamalari) 2017, Entropy 2018, TBSI-WODS  (Workshop on Data Science) 2019 and tutorial speaker at IEEE ICSPCC  (Int. Conf. Signal Processing, Communications and Computing) 2012. He was a Chinese Government 111 Project Foreign Expert 2007-2011. He was an Alexander von Humboldt Experienced Research Fellow in the Max Planck Institute for Molecular Genetics in 2013-2015. His research interests are in the areas of statistical signal and image processing and information and coding theory with applications in computational biology, remote sensing, telecommunications, earth sciences and astrophysics.

Contact: Ersin Göğüş

Faculty of Engineering and Natural Sciences