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Tutorials

The role of the tutorials is to provide a platform for a more intensive scientific exchange amongst researchers interested in a particular topic and as a meeting point for the community. Tutorials complement the depth-oriented technical sessions by providing participants with broad overviews of emerging fields. A tutorial can be scheduled for 1.5 or 3 hours.

Dr. Matthew He, Ph. D.
Director/Full Professor EAI Academician Division of Math, Science, and Technology
Nova Southeastern University
U.S.A.


MATHEMATICS OF BIOINFORMATICS
Theory, Practice and Applications
Tutorial Objectives
Modern science connects many basic secrets of living matter with the genetic codes. Biological organisms belong to a category of very complex natural systems, which correspond to a huge number of biological species with inherited properties. But surprisingly, molecular genetics has discovered that all organisms are identical to each other by their basic molecular-genetic structures. Due to this revolutionary discovery, a great unification of all biological organisms has happened in science. The information genetic line of investigations has become one of the most prospective lines not only in biology, but also in science as a whole. Recent progress in the determination of genomic sequences has yielded many millions of gene sequences. But what do these sequences tell us and what are the generalities and rules that are governed by them? It seems that we understand very little about genetic contexts required to "read" them. Historically, mathematics, probability and statistics have been widely used in biological sciences. Science has a challenge to understand a system organization of molecular genetic ensemble with its unique properties of reliability and productivity. Disclosing of key secrets of this organization means a big step in science about nature in a whole and a big step to create the most productive biotechnologies. Knowledge about this structural organization should become a part of mathematical natural science. Recent advances of mathematical methods and techniques in bioinformatics have been rapidly growing. There is more to life than the genomic blueprint of each organism. Life functions within the natural laws that we know and the ones we do not know. Mathematics can be used to understand life from the molecular to the biosphere level. This tutorial is devoted to the connection and integration between fundamental mathematical methods and biological sequences, DNA and protein structures, biological networks, systems biology, algebraic biology, and cognitive informatics. The materials of the tutorials are selected from a recent book "Mathematics of Bioinformatics: Theory, Practice, and Applications" by Matthew He and Sergey Petoukhov.

Tutorial Topics
The outline of this tutorial includes two main parts consisting of 10 chapters. Part I (Chapters 1-5, 1.5 hours) covers the main topics on genetics codes, biological sequences, DNA and protein structures, and related mathematical theory and methods. Part II (Chapters 6-10, 1.5 hours) will be focusing on biological functions and networks, systems biology, and cognitive informatics.

Part I - Genetic Codes, Biological Sequences, DNA and Protein Structures
    Chapter 1: Bioinformatics and Mathematics
  • 1.1 Introduction
  • 1.2 Genetic Code and Mathematics
  • 1.3 Mathematical Background
  • 1.4 Converting Data to Knowledge
  • 1.5 Big Picture: Informatics
  • 1.6 Challenges and Perspectives
    Chapter 2: Genetic Codes, Matrices, and Symmetrical Techniques
  • 2.1 Introduction
  • 2.2 Matrix Theory and Symmetry Preliminaries
  • 2.3 Genetic Codes and Matrices
  • 2.4 Genetic Matrices, Hydrogen Bonds and the Golden Section
  • 2.5 Symmetrical Patterns, Molecular Genetics and Bioinformatics
  • 2.6 Challenges and Perspectives
    Chapter 3: Biological Sequences, Sequence Alignment, and Statistics
  • 3.1 Introduction
  • 3.2 Mathematical Sequences
  • 3.3 Sequence Alignment
  • 3.4 Sequence Analysis and Further Discussions
  • 3.5 Challenges and Perspectives
    Chapter 4: Structures of DNA and Knot Theory
  • 4.1 Introduction
  • 4.2 Knot Theory Preliminaries
  • 4.3 DNA Knots and Links
  • 4.4 Challenges and Perspectives
    Chapter 5: Protein Structures, Geometry, and Topology
  • 5.1 Introduction
  • 5.2 Computational Geometry and Topology Preliminaries
  • 5.3 Protein Structures and Prediction
  • 5.4 Statistical Approach and Discussions
  • 5.5 Challenges and Perspectives

Part II - Biological Functions, Networks, Systems Biology and Cognitive Informatics
    Chapter 6: Biological Networks and Graph Theory
  • 6.1 Introduction
  • 6.2 Graph Theory Preliminaries and Network Topology
  • 6.3 Models of Biological Networks
  • 6.4 Challenges and Perspectives
    Chapter 7: Biological Systems, Fractals, and Systems Biology
  • 7.1 Introduction
  • 7.2 Fractal Geometry Preliminaries
  • 7.3 Fractal Geometry in Biological Systems
  • 7.4 Systems Biology and Perspectives
  • 7.5 Challenges and Perspectives
    Chapter 8: Matrix Genetics, Hadamard Matrix, and Algebraic Biology
  • 8.1 Introduction
  • 8.2 Genetic Matrices and the Degeneracy of the Genetic Code
  • 8.3 The Genetic Code and Hadamard Matrices
  • 8.4 Genetic Matrices and Matrices of Hypercomplex Numbers
  • 8.5 Some Rules of Evolution of Variants of the Genetic Code
  • 8.6 Challenges and Perspectives
    Chapter 9: Bioinformatics, Living Systems and Cognitive Informatics
  • 9.1 Introduction
  • 9.2 Emerging Pattern, Dissipative Structure, and Evolving Cognition
  • 9.3 Denotational Mathematics and Cognitive Computing
  • 9.4 Challenges and Perspectives
    Chapter 10: The Evolutionary Trends and Central Dogma of Informatics
  • 10.1 Introduction
  • 10.2 Evolutionary Trends of Informatics
  • 10.3 Central Dogma of Informatics
  • 10.4 Challenges and Perspectives


Intended Audience
The main intended audiences are graduate students, researchers, scientists, educators, practitioners, in the fields of bioinformatics, informatics, information engineering, computer informatics, biotechnology, and other related areas.

Biography of Matthew He
Matthew He, Ph.D., is Full Professor and Director of the Division of Math, Science, and Technology of Nova Southeastern University, Florida, USA. He is Full Professor and Grand Ph.D. from the World Information Distributed University since 2004. He has been awarded as an Academician of European Academy of Informatization since 2004. He received the World Academy of Sciences Achievement Awards in recognition of his research contributions in the field of computing in 2003 and 2010. Matthew He received his Ph. D. in Mathematics from University of South Florida in 1991. He was a research associate at the Department of Mathematics and Theoretical Physics, Cambridge University, Cambridge, England in 1986 and at the Department of Mathematics, Eldgenossische Technische Hochschule, Zurich, Switzerland in 1987. He was also a visiting professor at National Key Research Lab of Computational Mathematics of Chinese Science of Academy and University of Rome, Italy in 1998. Dr. Matthew He has authored/edited 8 books/proceedings and published over 120 research papers in the areas of mathematics, bioinformatics, computer vision, information theory, mathematics and engineering techniques in medical and biological sciences. He is an editor of International Journal of Bioinformatics Research and Applications, International Journal of Software Science and Computational Intelligence, International Journal of Cognitive Informatics and Natural Intelligence, International Journal of Biological Systems, and International Journal of Integrative Biology. He is an invited series editor of Biomedical and Life Sciences of Henry Stewart Talk "Using Bioinformatics in Exploration in Genetic Diversity". He is a Chairman of International Society of Symmetry in Bioinformatics and a member of International Advisory Board of "International Symmetry Association (ISA). He is a member of American Mathematical Society (AMS), Association of Computing Machinery (ACM), IEEE Computer Society, World Association of Science Engineering (WASE), and International Advisory Board member of Bioinformatics Group of International Federation for Information Processing (IFIP). He was an international scientific committee co-chair of International Conference of Bioinformatics and its Applications (ICBA 2004), a general co-chair of International Conference of Bioinformatics Research and Applications (ISBRA 2009), general chair of International Conference on Biomedical Engineering and Computer Science 2010 and 2011, and a keynote speaker of many international conferences in the areas of mathematics, bioinformatics, and information science and engineering.

Contacts
e-mail: bioinformatics.secretariat@insticc.org

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