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Algebraic Biology

Third International Conference, AB 2008, Castle of Hagenberg, Austria, July 31-August 2, 2008, Proceedings

  • Conference proceedings
  • © 2008

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Editors:
  1. Katsuhisa Horimoto
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  2. Georg Regensburger
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  3. Markus Rosenkranz
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  4. Hiroshi Yoshida
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Part of the book series: Lecture Notes in Computer Science (LNCS, volume 5147)

Part of the book sub series: Theoretical Computer Science and General Issues (LNTCS)

Included in the following conference series:

Conference proceedings info: AB 2008.

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Table of contents (17 papers)

  1. Front Matter

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  2. Algorithms for Inference, Analysis and Control of Boolean Networks

    • Tatsuya Akutsu, Morihiro Hayashida, Takeyuki Tamura
    Pages 1-15

  3. Tutorial on Model Checking: Modelling and Verification in Computer Science

    • Armin Biere
    Pages 16-21

  4. Differential Algebra and System Modeling in Cellular Biology

    • François Boulier, François Lemaire
    Pages 22-39

  5. Hybrid Semantics for Stochastic π-Calculus

    • Luca Bortolussi, Alberto Policriti
    Pages 40-55

  6. Applying a Rigorous Quasi-Steady State Approximation Method for Proving the Absence of Oscillations in Models of Genetic Circuits

    • François Boulier, Marc Lefranc, François Lemaire, Pierre-Emmanuel Morant
    Pages 56-64

  7. On the Computational Power of Biochemistry

    • Luca Cardelli, Gianluigi Zavattaro
    Pages 65-80

  8. The Geometry of the Neighbor-Joining Algorithm for Small Trees

    • Kord Eickmeyer, Ruriko Yoshida
    Pages 81-95

  9. Neural Algebra and Consciousness: A Theory of Structural Functionality in Neural Nets

    • Erwin Engeler
    Pages 96-109

  10. An Algorithm for Qualitative Simulation of Gene Regulatory Networks with Steep Sigmoidal Response Functions

    • Liliana Ironi, Luigi Panzeri, Erik Plahte
    Pages 110-124

  11. Property Preservation along Embedding of Biological Regulatory Networks

    • Mbarka Mabrouki, Marc Aiguier, Jean-Paul Comet, Pascale Le Gall
    Pages 125-138

  12. Process Algebra Models of Population Dynamics

    • Chris McCaig, Rachel Norman, Carron Shankland
    Pages 139-155

  13. Algebraic Analysis of Bifurcation and Limit Cycles for Biological Systems

    • Wei Niu, Dongming Wang
    Pages 156-171

  14. The Smallest Multistationary Mass-Preserving Chemical Reaction Network

    • Anne Shiu
    Pages 172-184

  15. Local Structure and Behavior of Boolean Bioregulatory Networks

    • Heike Siebert
    Pages 185-199

  16. Investigating Generic Methods to Solve Hopf Bifurcation Problems in Algebraic Biology

    • Thomas Sturm, Andreas Weber
    Pages 200-215

  17. An Improved Algorithm for Detecting a Singleton Attractor in a Boolean Network Consisting of AND/OR Nodes

    • Takeyuki Tamura, Tatsuya Akutsu
    Pages 216-229

  18. Constructing a Knowledge Base for Gene Regulatory Dynamics by Formal Concept Analysis Methods

    • Johannes Wollbold, Reinhard Guthke, Bernhard Ganter
    Pages 230-244

  19. Back Matter

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  1. Algebraic Biology

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About this book

This volume contains the proceedings of the Third International Conference on Algebraic Biology (AB 2008). Jointly organized by the National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, and the Research Institute for Symbolic Computation (RISC), Hagenberg, Austria, it was held from July 31 to August 2, 2008 in the Castle of Hagenberg. Algebraic biology is an interdisciplinary forum for research on all aspects of applying symbolic computation in biology. The ?rst conference on algebraic biology (AB 2005) was held November 28–30, 2005 in Tokyo, the second during July 2–4, 2007 in Hagenberg. The AB conference series is intended as a bridge between life sciences and symbolic computation: On the one hand, new insights inbiologyarefoundbypowerfulsymbolicmethods;ontheotherhand,biological problems suggestnew algebraicstructures andalgorithms.While this pro?le has been established in the previous proceedings, the papers in the present volume demonstrate the continuous growth of algebraic biology. We received 27 submissions from 14 countries (Australia, Austria, Canada, China, Colombia, France, Germany, Italy, Japan, Norway, Russia, Switzerland, UK, USA), and 14 papers were accepted for publication. Each submission was assigned to at least three ProgramCommittee members, who carefully reviewed the papers, in many cases with the help of external referees. The reviews were discussedby the ProgramCommittee for oneweekvia the EasyChairconference management system.

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