Systems biology for signaling networks / Sangdun Choi, editor. — New York ; London : Springer, c2010. – (58.15/S995)

Contents

    Contents
    
    Part I Concepts
    1 Systems Biology Approaches: Solving New Puzzles in a Symphonic Manner
    2 Current Progress in Static and Dynamic Modeling of Biological Networks 13
    3 Getting Started in Biological Pathway Construction 75
    4 From Microarray to Biology
    Part II Modeling and Reconstruction
    5 Computational Procedures for Model Identification 111
    6 Assembly of Logic-Based Diagrams of Biological Pathways 139
    7 Automating Mathematical Modeling of Biochemical Reaction Networks 159
    8 Strategies to Investigate Signal Transduction Pathways with Mathematical Modelling 207
    9 Inferring Transcriptional Regulatory Network 235
    10 Finding Functional Modules 253
    11 Modeling the Dynamics of Biological Networks from Time Course Data 275
    12 Decision Making in Cells 295
    13 Robustness of Neural Network Models
    14 Functional Modules in Protein-Protein Interaction Networks
    15 Mixture Model on Graphs: A Probabilistic Model for Network-Based Analysis of Proteomic Data 371
    16 Integration of Network Information for Protein Function Prediction 399
    Part III Applications for Signaling Networks
    17 Cellular-Level Gene Regulatory Networks: Their Derivation and Properties
    18 Tyrosine-Phosphoproteome Dynamics 447
    19 Systems Biology of the MAPK1，2 Network 455
    20 Pathway Crosstalk Network
    21 Crosstalk Between Mitogen-Activated Protein Kinase and Phosphoinositide-3 Kinase Signaling Pathways in Development and Disease 505
    22 Systems-Level Analyses of the Mammalian Innate Immune Response 531
    23 Molecular Basis of Protective Anti-Inflammatory Signalling by Cyclic AMP in the Vascular Endothelium 561
    24 Construction of Cancer-Perturbed Protein-Protein Interaction Network of Apoptosis for Drug Target Discovery 589
    25 Transcriptional Changes in Alzheimer's Disease 611
    26 Pathogenesis of Obesity-Related Chronic Liver Diseases as the Study Case for the Systems Biology 645
    27 The Evolving Transcriptome of Head and Neck Squamous Cell Carcinoma 687
    28 Peptide Microarrays for a Network Analysis of Changes in Molecular Interactions in Cellular Signalling 703
    Part IV Tools for Systems Biology
    29 A Primer on Modular Mass-Action Modelling with CellML 721
    30 FERN - Stochastic Simulation and Evaluation of Reaction Networks 751
    31 Programming Biology in BlenX 777
    32 Discrete Modelling: Petri Net and Logical Approaches 821
    33 ProteoLens: A Database-Driven Visual Data Mining Tool for Network Biology
    34 MADNet: A Web Server for Contextual Analysis and Visualization of High-Throughput Experiments 877
    Subject Index 889