Systems Biology (Methods in Molecular Biology)

Contents

Preface. .................................................................... v
Contributors................................................................. xv

1 Conceptual Challenges in the Theoretical Foundations

of Systems Biology. ..................................................... 1

Marta Bertolaso and Emanuele Ratti

2 An Integrative Approach Toward Biology, Organisms, and Cancer............ 15

Carlos Sonnenschein and Ana M. Soto

3 Conceptual Challenges of the Systemic Approach in Understanding

Cell Differentiation ..................................................... 27

Andras Paldi

4 A Primer on Mathematical Modeling in the Study of Organisms

and Their Parts......................................................... 41

Mae ̈l Monte ́vil

5 The Search for System’s Parameters. ...................................... 57

Alessandro Giuliani

6 Inverse Problems in Systems Biology: A Critical Review..................... 69

Rodolfo Guzzi, Teresa Colombo, and Paola Paci

7 Systems Biology Approach and Mathematical Modeling

for Analyzing Phase-Space Switch During Epithelial-Mesenchymal

Transition. ............................................................. 95

Chiara Simeoni, Simona Dinicola, Alessandra Cucina, Corrado Mascia,

and Mariano Bizzarri

8 Parameters Estimation in Phase-Space Landscape Reconstruction

of Cell Fate: A Systems Biology Approach.................................. 125

Sheyla Montero, Reynaldo Martin, Ricardo Mansilla, Germinal Cocho,

and Jose ́ Manuel Nieto-Villar

9 Complexity of Biochemical and Genetic Responses Reduced Using

Simple Theoretical Models. .............................................. 171

Kumar Selvarajoo

10 Systems Biology Modeling of Nonlinear Cancer Dynamics................... 203
Christian Cherubini, Simonetta Filippi, and Alessandro Loppini

11 Endogenous Molecular-Cellular Network Cancer Theory:
A Systems Biology Approach............................................. 215
Gaowei Wang, Ruoshi Yuan, Xiaomei Zhu, and Ping Ao

12 A Network-Based Integrative Workflow to Unravel Mechanisms
Underlying Disease Progression.......................................... 247
Faiz M. Khan, Mehdi Sadeghi, Shailendra K. Gupta, and Olaf Wolkenhauer

xiii