© 2014

Discrete and Topological Models in Molecular Biology

  • Nataša Jonoska
  • Masahico Saito
  • Methods allow researchers to "zoom in" on processes at a molecular level

  • Contributing authors are among the leading scientists in this field

  • Reference for researchers in mathematics, theoretical computer science, mathematical biology and bioinformatics


Part of the Natural Computing Series book series (NCS)

Table of contents

  1. Front Matter
    Pages i-xiii
  2. Discrete and Graph-Theoretic Models for Data Analysis

    1. Front Matter
      Pages 1-1
    2. Angela Angeleska, Sabrina Kleessen, Zoran Nikoloski
      Pages 23-43
    3. Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova, Riccardo Dondi, Teresa M. Przytycka
      Pages 67-83
    4. Vidit Nanda, Radmila Sazdanović
      Pages 109-141
  3. Molecular Arrangements and Structures

    1. Front Matter
      Pages 143-143
    2. Christine Heitsch, Svetlana Poznanović
      Pages 145-166
    3. Meera Sitharam
      Pages 197-216
    4. Paolo Cermelli, Giuliana Indelicato, Reidun Twarock
      Pages 217-240
    5. Joanna Ellis-Monaghan, Greta Pangborn, Laura Beaudin, David Miller, Nick Bruno, Akie Hashimoto
      Pages 241-270
  4. Gene Rearrangements

    1. Front Matter
      Pages 271-271
    2. Aaron David Goldman, Elizabeth M. Stein, John R. Bracht, Laura F. Landweber
      Pages 273-287
    3. Robert Brijder, Hendrik Jan Hoogeboom
      Pages 289-307
    4. Egor Dolzhenko, Karin Valencia
      Pages 309-323
  5. Topological Models and Spatial DNA Embeddings

    1. Front Matter
      Pages 325-325
    2. Isabel K. Darcy, Stephen D. Levene, Robert G. Scharein
      Pages 327-345

About this book


Theoretical tools and insights from discrete mathematics, theoretical computer science, and topology now play essential roles in our understanding of vital biomolecular processes. The related methods are now employed in various fields of mathematical biology as instruments to "zoom in" on processes at a molec­ular level.

 This book contains expository chapters on how contemporary models from discrete mathematics – in do­mains such as algebra, combinatorics, and graph and knot theories – can provide perspective on biomolecular problems ranging from data analysis, molecular and gene arrangements and structures, and knotted DNA embeddings via spatial graph models to the dynamics and kinetics of molecular interactions.

 The contributing authors are among the leading scientists in this field and the book is a reference for re­searchers in mathematics and theoretical computer science who are engaged with modeling molecular and biological phenomena using discrete methods. It may also serve as a guide and supplement for graduate courses in mathematical biology or bioinformatics, introducing nontraditional aspects of mathematical biology.


Cell biology DNA Evolutionary biology Gene assembly Genome analysis Genome processing RNA Recombination Self-assembly Systems biology

Editors and affiliations

  • Nataša Jonoska
    • 1
  • Masahico Saito
    • 2
  1. 1.Dept. Mathematics & StatisticsUniversity of South FloridaTampaUSA
  2. 2.Dept. Mathematics & StatisticsUniversity of South FloridaTampaUSA

About the editors

Prof. Nataša Jonoska is a professor in the Dept. of Mathematics and Statistics of the University of South Florida, Tampa, USA. She received her PhD from the Dept. of Mathematical Sciences, SUNY Binghamton in 1993. Her research is driven by the issue of how biology computes, in particular using formal models such as cellular or other finite types of automata, formal language theory symbolic dynamics, and topological graph theory to describe molecular computation. She is a board member of related prestigious journals such as Theoretical Computer Science, the Int. J. of Foundations of Computer Science, Computability, and Natural Computing. She has edited a number of books, among them the Springer book Nanotechnology: Science and Computation. Dr. Masahico Saito is a researcher in the Dept. of Mathematics and Statistics, University of South Florida, Tampa, USA. He is a member of the Discrete and Topological Methods for DNA Assembly team, and his research interests include knots and quandles.

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