Discrete and Topological Models in Molecular Biology

  • Nataša Jonoska
  • Masahico Saito

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
    3. Kai Ishihara, Koya Shimokawa, Mariel Vazquez
      Pages 387-401
  6. Dynamics and Kinetics of Molecular Interactions

    1. Front Matter
      Pages 403-403
    2. Massa J. Shoura, Stephen D. Levene
      Pages 405-418
    3. Casian Pantea, Ankur Gupta, James B. Rawlings, Gheorghe Craciun
      Pages 419-442
    4. Reinhard Laubenbacher, Franziska Hinkelmann, David Murrugarra, Alan Veliz-Cuba
      Pages 443-474
    5. Michael A. Savageau, Jason G. Lomnitz
      Pages 475-506

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

Bibliographic information