Table of Contents
Preface 1. Graph Theory for Systems Biology: Interval Graphs, Motifs, and Pattern Recognition John R. Jungck and Rama Viswanathan 2. Food Webs and Graphs Margaret Midge Cozzens 3. Adaptation and Fitness Graphs Kristina Crona and Emilie Wiesner 4. Signaling Networks: Asynchronous Boolean Models Réka Albert and Raina Robeva 5. Dynamics of Complex Boolean Networks: Canalization, Stability, and Criticality Qijun He, Matthew Macauley and Robin Davies 6. Steady State Analysis of Boolean Models: A Dimension Reduction Approach Alan Veliz-Cuba and David Murrugarra 7. BioModel Engineering with Petri Nets Mary Ann Blätke, Monika Heiner and Wolfgang Marwan 8. Transmission of Infectious Diseases: Data, Models, and Simulations Winfried Just, Hannah Callender, M. Drew LaMar and Natalia Toporikova 9. Disease Transmission Dynamics on Networks: Network Structure Versus Disease Dynamics Winfried Just, Hannah Callender and M. Drew LaMar 10. Predicting Correlated Responses in Quantitative Traits Under Selection: A Linear Algebra Approach Janet Steven and Bessie Kirkwood 11. Metabolic Analysis: Algebraic and Geometric Methods Terrell L. Hodge, Blair R. Szymczyna and Todd J. Barkman 12. Reconstructing the Phylogeny: Computational Methods Grady Weyenberg and Ruriko Yoshida 13. RNA Secondary Structures: Combinatorial Models and Folding Algorithms Qijun He, Matthew Macauley and Robin Davies 14. RNA Secondary Structures: An Approach Through Pseudoknots and Fatgraphs Christian M. Reidys