Chapter 4. Algorithmic Basis for Pathway Visualization

  1. Anton Yuryev PhD
  1. Sergey Simakov1,
  2. Iaroslav Ispolatov PhD2,4,
  3. Sergei Maslov3 and
  4. Alexander Nikitin4

Published Online: 21 APR 2008

DOI: 10.1002/9780470399279.ch4

Pathway Analysis for Drug Discovery: Computational Infrastructure and Applications

Pathway Analysis for Drug Discovery: Computational Infrastructure and Applications

How to Cite

Simakov, S., Ispolatov, I., Maslov, S. and Nikitin, A. (2008) Algorithmic Basis for Pathway Visualization, in Pathway Analysis for Drug Discovery: Computational Infrastructure and Applications (ed A. Yuryev), John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/9780470399279.ch4

Editor Information

  1. Ariadne Genomics Inc., 9430 Key West Avenue, Suite 113, Rockville, MD 20850, USA

Author Information

  1. 1

    Moscow Institute of Physics and Technology, Department of Applied Mathematics, Instituskii Lane, 9, Dolgoprudny, Russia

  2. 2

    Departamento de Fisica, Universidad de Santiago de Chile, Casilla 302, Correo 2, Santiago, Chile

  3. 3

    Department of Physics, Brookhaven National Laboratory, Upton, NY 11973, USA

  4. 4

    Ariadne Genomics Inc., 9430 Key West Avenue, Suite 113, Rockville, MD 20850, USA

Publication History

  1. Published Online: 21 APR 2008
  2. Published Print: 12 SEP 2008

Book Series:

  1. Wiley Series on Technologies for the Pharmaceutical Industry

Book Series Editors:

  1. Sean Ekins

ISBN Information

Print ISBN: 9780470107058

Online ISBN: 9780470399279

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Keywords:

  • pathway visualization - algorithmic basis;
  • cellular localization layout;
  • acyclic core graph construction

Summary

This chapter contains sections titled:

  • Introduction

  • Force-based and Energy Minimization Algorithms

  • Layout by Cellular Localization

  • Symmetrical Algorithm

  • Orthogonal Layout

  • Hierarchical Algorithm

  • Acyclic Core Graph Construction

  • Collapsing Protein Maps

  • References