Systems Biology

Preface and Commentary vii

List of Contributors ix

Part I Biological Basis of Systems Biology 1

1 Systems Biology 3
Melanie Boerries, Roland Eils, and Hauke Busch

2 Developmental Cell Biology 33
Frank John Dye

3 Principles and Applications of Embryogenomics 51
Vincent VanBuren

4 Interactome 85
Teresa M. Przytycka and Dong-Yeon Cho

5 Protein Abundance Variation 117
Greco Hernandez and Gritta Tettweiler

Part II Systems Biology of Evolution 143

6 Genetic Variation and Molecular Darwinism 145
Werner Arber

7 Systematics and Evolution 169
Jeffrey H. Schwartz

8 Evolution of the Protein Repertoire 207
Aaron David Goldman, Jeremy A. Horst, Ling-Hong Hung, and Ram Samudrala

Part III Modeling of Biological Systems 237

9 Chaos in Biochemistry and Physiology 239
Miguel Antonio Aon, Sonia Cortassa, and David Lloyd

10 Computational Biology 277
Thomas Lengauer, Mario Albrecht, and Francisco S. Domingues

11 Dynamics of Biomolecular Networks 349
Emanuele Cozzo, Joaquin Sanz, and Yamir Moreno

12 E-Cell: Computer Simulation of the Cell 379
Pawan K. Dhar, Kouichi Takahashi, Yoichi Nakayama, and Masaru Tomita

13 Fractals in Biology and Medicine 397
Gabriele Angelo Losa

14 Models of Cell Migration 423
Michael Meyer-Hermann and Tilo Beyer

15 Protein Modeling 469
Marian R. Zlomislic, Valentina Corradi, and D. Peter Tieleman

16 System Models for Inference on Mechanisms of Neuronal Dynamics 505
Klaas E. Stephan and Karl J. Friston

17 Systems Biology of the Liver 539
Ian David Lockhart Bogle, Rajiv Jalan, Elizabeth Shephard, Robert Seymour, Antony Finkelstein, Thomas Sumner, and Anne Warner

Part IV Systems Biology in Medicine and Disease 563

18 Inferring Networks for Diseases 565
Mikael Benson and Michael A. Langston

19 Personalized Medicine (Predictive and Preventive) 593
Alette M. Wessels, Robert R. Bies, and John Urquhart

Part V Systems Biology of Organisms 625

20 Microbiomes 627
Ramana Madupu, Yu-Hui Rogers, Doug Rusch, Jason Miller, Konstantinos Krampis, and Karen E. Nelson

21 Synthetic Biology: Implications and Uses 653
Sanjay Vashee, Mikkel A. Algire, Michael G. Montague, and Michele S. Garfinkel

22 Plant Systems Biology 685
Sonia Osorio and Alisdair R. Fernie

Index 699