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Description
Systems biology is a relatively new biological study field that focuses on the systematic study of complex interactions in biological systems, thus using a new perspective (integration instead of reduction) to study them. Particularly from year 2000 onwards, the term is used widely in the biosciences, and in a variety of contexts. Systems biology is the study of the interconnected aspect of molecular, cellular, tissue, whole animal and ecological processes, and comprises mathematical and mechanistic studies of dynamical, mesoscopic, open, spatiotemporally defined, nonlinear, complex systems that are far from thermodynamic equilibrium.
Table of Contents
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
