Computational Modeling of Genetic and Biochemical Networks


The advent of ever more sophisticated molecular manipulation techniques has made it clear that cellular systems are far more complex and dynamic than previously thought. At the same time, experimental techniques are providing an almost overwhelming amount of new data. It is increasingly apparent that linking molecular and cellular structure to function will require the use of new computational tools.

This book provides specific examples, across a wide range of molecular and cellular systems, of how modeling techniques can be used to explore functionally relevant molecular and cellular relationships. The modeling techniques covered are applicable to cell, developmental, structural, and mathematical biology; genetics; and computational neuroscience. The book, intended as a primer for both theoretical and experimental biologists, is organized in two parts: models of gene activity and models of interactions among gene products. Modeling examples are provided at several scales for each subject. Each chapter includes an overview of the biological system in question and extensive references to important work in the area.

Table of Contents

  1. Foreword

    John C. Wooley

  2. Acknowledgments
  3. Introduction: Understanding Living Systems
  4. I. Modeling Genetic Networks
  5. 1. Modeling the Activity of Single Genes

    Michael Andrew Gibson and Eric Mjolsness

  6. 2. A Probabilistic Model of a Prokaryotic Gene and Its Regulation

    Michael Andrew Gibson and Jehoshua Bruck

  7. 3. A Logical Model of -Regulatory Control in a Eukaryotic System

    Chiou-Hwa Yuh, Hamid Bolouri, James M. Bower and Eric H. Davidson

  8. 4. Trainable Gene Regulation Networks with Application to Pattern Formation

    Eric Mjolsness

  9. 5. Genetic Network Inference in Computational Models and Applications to Large-Scale Gene Expression Data

    Roland Somogyi, Stefanie Fuhrman and Xiling Wen

  10. II. Modeling Biochemical Networks
  11. 6. Atomic-Level Simulation and Modeling of Biomacromolecules

    Nagarajan Vaedehi and William A Goddard III

  12. 7. Diffusion

    Guy Bormzann, Fons Brosens and Erik De Schutter

  13. 8. Kinetic Models of Excitable Membranes and Synaptic Interactions

    Alain Destexhe

  14. 9. Stochastic Simulation of Cell Signaling Pathways

    Carl A. J. M. Firth and Dennis Bray

  15. 10. Analysis of Complex Dynamics in Cell Cycle Regulation

    John J. Tyson, Mark T. Borisuk, Kathy Chen and Beta Novak

  16. 11. Simplifying and Reducing Complex Models

    Bard Ermentrout

  17. Contributors
  18. Index
  19. Insert