Computational Modeling of Genetic and Biochemical Networks

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James M. Bower, Hamid Bolouri
MIT Press, 2001 - Computers - 336 pages
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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.

 

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Contents

Modeling the Activity of Single Genes
3
A Probabilistic Model of a Prokaryotic Gene and Its Regulation
49
A Logical Model of cisRegulatory Control in a Eukaryotic System
73
Trainable Gene Regulation Networks with Applications to Drosophila Pattern Formation
101
Genetic Network Inference in Computational Models and Applications to LargeScale Gene Expression Data
119
Modeling Biochemical Networks
159
AtomicLevel Simulation and Modeling of Biomacromolecules
161
Diffusion
189
Kinetic Models of Excitable Membranes and Synaptic Interactions
225
Stochastic Simulation of Cell Signaling Pathways
263
Analysis of Complex Dynamics in Cell Cycle Regulation
287
Simplifying and Reducing Complex Models
307
Contributors
325
Index
327
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About the author (2001)

Hamid Bolouri is Professor of Computational Biology at the Institute for Systems Biology, Seattle, WA.

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