© 2009

Algorithmic Bioprocesses

  • Anne Condon
  • David Harel
  • Joost N. Kok
  • Arto Salomaa
  • Erik Winfree

Part of the Natural Computing Series book series (NCS)

Table of contents

  1. Front Matter
    Pages I-XX
  2. Tribute

    1. Front Matter
      Pages 1-1
  3. Sequence Discovery, Generation, and Analysis

    1. Front Matter
      Pages 13-13
    2. Alberto Apostolico
      Pages 15-29
    3. Alessandra Carbone, Stefan Engelen
      Pages 31-42
    4. Masami Ito, Lila Kari, Zachary Kincaid, Shinnosuke Seki
      Pages 43-61
    5. Yasubumi Sakakibara, Kengo Sato
      Pages 63-79
  4. Gene Assembly in Ciliates

    1. Front Matter
      Pages 81-81
    2. Angela Angeleska, Nataša Jonoska, Masahico Saito, Laura F. Landweber
      Pages 83-98
    3. Robert Brijder, Hendrik Jan Hoogeboom
      Pages 99-115
    4. Mark Daley, Michael Domaratzki
      Pages 117-137
  5. Nanoconstructions and Self-assembly

    1. Front Matter
      Pages 139-139
    2. Nataša Jonoska, Anne Taormina, Reidun Twarock
      Pages 141-158
    3. Sudheer Sahu, Peng Yin, John H. Reif
      Pages 185-204
    4. Nadrian C. Seeman
      Pages 205-214
  6. Membrane Computing

    1. Front Matter
      Pages 227-227
    2. Oscar H. Ibarra, Sara Woodworth
      Pages 229-272

About this book


A fundamental understanding of algorithmic bioprocesses is key to learning how information processing occurs in nature at the cell level. The field is concerned with the interactions between computer science on the one hand and biology, chemistry, and DNA-oriented nanoscience on the other. In particular, this book offers a comprehensive overview of research into algorithmic self-assembly, RNA folding, the algorithmic foundations for biochemical reactions, and the algorithmic nature of developmental processes.

The editors of the book invited 36 chapters, written by the leading researchers in this area, and their contributions include detailed tutorials on the main topics, surveys of the state of the art in research, experimental results, and discussions of specific research goals. The main subjects addressed are sequence discovery, generation, and analysis; nanoconstructions and self-assembly; membrane computing; formal models and analysis; process calculi and automata; biochemical reactions; and other topics from natural computing, including molecular evolution, regulation of gene expression, light-based computing, cellular automata, realistic modelling of biological systems, and evolutionary computing.

This subject is inherently interdisciplinary, and this book will be of value to researchers in computer science and biology who study the impact of the exciting mutual interaction between our understanding of bioprocesses and our understanding of computation.


Algorithmic bioprocesses Algorithmic botany Algorithmic self-assembly Biochemical reactions Bioinformatics Cell biology Developmental processes Grammatical models Information processing Live sequence charts Molecular computing Nanoscience Natu

Editors and affiliations

  • Anne Condon
    • 1
  • David Harel
    • 2
  • Joost N. Kok
    • 3
  • Arto Salomaa
    • 4
  • Erik Winfree
    • 5
  1. 1.Dept. Computer ScienceUniversity of British ColumbiaVancouverCanada
  2. 2.Dept. Applied MathematicsWeizmann Institute of ScienceRehovotIsrael
  3. 3.Leiden Inst. Advanced Computer ScienceLeiden UniversityLeidenNetherlands
  4. 4.Turku Centre for Computer ScienceTurkuFinland
  5. 5.Computer Science, Computation,California Inst. of TechnologyPasadenaU.S.A.

About the editors

The editors and contributors include most of the key researchers working on these topics worldwide.

Bibliographic information

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"In a real sense, this book answers the question, 'What is the cutting edge of research connecting computer science with the biological sciences?' ... [I]ts breadth of content is impressive, and its combination of advanced tutorials with ambitious new proposals is scientifically exciting. ... [The book] will best serve TCS researchers who are looking for new questions to ask, and for new areas in which to apply their skills." (Aaron Sterling, The Book Review Column 43-3, 2012)