Systems Biology

Description

This volume focuses on methodological aspects of systems biology in order to provide a new theoretical approach with a robust and tailored experimental support. Chapters detail mathematical modeling, methodological issues, modulation of the collective behavior, metabolic, dynamic profiling, and quantitative morphological studies. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Systems Biology aims to ensure successful results in the further study of this vital field. Front Matter ....Pages i-xvii Conceptual Challenges in the Theoretical Foundations of Systems Biology (Marta Bertolaso, Emanuele Ratti)....Pages 1-13 An Integrative Approach Toward Biology, Organisms, and Cancer (Carlos Sonnenschein, Ana M. Soto)....Pages 15-26 Conceptual Challenges of the Systemic Approach in Understanding Cell Differentiation (Andras Paldi)....Pages 27-39 A Primer on Mathematical Modeling in the Study of Organisms and Their Parts (Maël Montévil)....Pages 41-55 The Search for System’s Parameters (Alessandro Giuliani)....Pages 57-68 Inverse Problems in Systems Biology: A Critical Review (Rodolfo Guzzi, Teresa Colombo, Paola Paci)....Pages 69-94 Systems Biology Approach and Mathematical Modeling for Analyzing Phase-Space Switch During Epithelial-Mesenchymal Transition (Chiara Simeoni, Simona Dinicola, Alessandra Cucina, Corrado Mascia, Mariano Bizzarri)....Pages 95-123 Parameters Estimation in Phase-Space Landscape Reconstruction of Cell Fate: A Systems Biology Approach (Sheyla Montero, Reynaldo Martin, Ricardo Mansilla, Germinal Cocho, José Manuel Nieto-Villar)....Pages 125-170 Complexity of Biochemical and Genetic Responses Reduced Using Simple Theoretical Models (Kumar Selvarajoo)....Pages 171-201 Systems Biology Modeling of Nonlinear Cancer Dynamics (Christian Cherubini, Simonetta Filippi, Alessandro Loppini)....Pages 203-213 Endogenous Molecular-Cellular Network Cancer Theory: A Systems Biology Approach (Gaowei Wang, Ruoshi Yuan, Xiaomei Zhu, Ping Ao)....Pages 215-245 A Network-Based Integrative Workflow to Unravel Mechanisms Underlying Disease Progression (Faiz M. Khan, Mehdi Sadeghi, Shailendra K. Gupta, Olaf Wolkenhauer)....Pages 247-276 Spatiotemporal Fluctuation Analysis of Molecular Diffusion Laws in Live-Cell Membranes (Francesco Cardarelli)....Pages 277-290 A Method for Cross-Species Visualization and Analysis of RNA-Sequence Data (Stephen A. Ramsey)....Pages 291-305 Multi-agent Simulations of Population Behavior: A Promising Tool for Systems Biology (Alfredo Colosimo)....Pages 307-326 Metabolomics: Challenges and Opportunities in Systems Biology Studies (Luca Casadei, Mariacristina Valerio, Cesare Manetti)....Pages 327-336 Systems Biology-Driven Hypotheses Tested In Vivo: The Need to Advancing Molecular Imaging Tools (Garima Verma, Alessandro Palombo, Mauro Grigioni, Morena La Monaca, Giuseppe D’Avenio)....Pages 337-359 Back Matter ....Pages 361-364