Systems Biology for Signaling Networks [1 ed.] 1441957960, 9781441957979, 9781441957962, 1441957979

Table of contents :
Front Matter....Pages i-xvi
Front Matter....Pages 1-1
Systems Biology Approaches: Solving New Puzzles in a Symphonic Manner....Pages 3-11
Current Progress in Static and Dynamic Modeling of Biological Networks....Pages 13-73
Getting Started in Biological Pathway Construction....Pages 75-83
From Microarray to Biology....Pages 85-107
Front Matter....Pages 109-109
Computational Procedures for Model Identification....Pages 111-137
Assembly of Logic-Based Diagrams of Biological Pathways....Pages 139-157
Automating Mathematical Modeling of Biochemical Reaction Networks....Pages 159-205
Strategies to Investigate Signal Transduction Pathways with Mathematical Modelling....Pages 207-234
Inferring Transcriptional Regulatory Network....Pages 235-252
Finding Functional Modules....Pages 253-273
Modeling the Dynamics of Biological Networks from Time Course Data....Pages 275-294
Decision Making in Cells....Pages 295-336
Robustness of Neural Network Models....Pages 337-351
Functional Modules in Protein–Protein Interaction Networks....Pages 353-369
Mixture Model on Graphs: A Probabilistic Model for Network-Based Analysis of Proteomic Data....Pages 371-397
Integration of Network Information for Protein Function Prediction....Pages 399-426
Front Matter....Pages 427-427
Cellular-Level Gene Regulatory Networks: Their Derivation and Properties....Pages 429-446
Tyrosine-Phosphoproteome Dynamics....Pages 447-454
Systems Biology of the MAPK1,2 Network....Pages 455-489
Pathway Crosstalk Network....Pages 491-504
Front Matter....Pages 427-427
Crosstalk Between Mitogen-Activated Protein Kinase and Phosphoinositide-3 Kinase Signaling Pathways in Development and Disease....Pages 505-529
Systems-Level Analyses of the Mammalian Innate Immune Response....Pages 531-560
Molecular Basis of Protective Anti-Inflammatory Signalling by Cyclic AMP in the Vascular Endothelium....Pages 561-587
Construction of Cancer-Perturbed Protein–Protein Interaction Network of Apoptosis for Drug Target Discovery....Pages 589-610
Transcriptional Changes in Alzheimer’s Disease....Pages 611-643
Pathogenesis of Obesity-Related Chronic Liver Diseases as the Study Case for the Systems Biology....Pages 645-686
The Evolving Transcriptome of Head and Neck Squamous Cell Carcinoma....Pages 687-702
Peptide Microarrays for a Network Analysis of Changes in Molecular Interactions in Cellular Signalling....Pages 703-718
Front Matter....Pages 719-719
A Primer on Modular Mass-Action Modelling with CellML....Pages 721-750
FERN – Stochastic Simulation and Evaluation of Reaction Networks....Pages 751-775
Programming Biology in BlenX....Pages 777-820
Discrete Modelling: Petri Net and Logical Approaches....Pages 821-855
ProteoLens: A Database-Driven Visual Data Mining Tool for Network Biology....Pages 857-875
MADNet: A Web Server for Contextual Analysis and Visualization of High-Throughput Experiments....Pages 877-888
Erratum to: Functional Modules in Protein–Protein Interaction Networks....Pages E1-E1
Back Matter....Pages 889-908