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Advances in systems biology

Andrew B. Goryachev

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Bibliographic Details
Other Authors: Goryanin, Igor I. (Editor) , Goryachev, Andrew B. (Editor)
Format: Book/Monograph
Language:English
Published: New York, NY Springer Science+Business Media, LLC 2012
Edition:1
Series:Advances in experimental medicine and biology 736
In: Advances in experimental medicine and biology (736)

Volumes / Articles: Show Volumes / Articles.
DOI:10.1007/978-1-4419-7210-1
Subjects:
Systembiologie
Online Access:Verlag, Volltext: https://doi.org/10.1007/978-1-4419-7210-1
Resolving-System, lizenzpflichtig, Volltext: http://dx.doi.org/10.1007/978-1-4419-7210-1
Cover: https://swbplus.bsz-bw.de/bsz359118771cov.jpg
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Author Notes:edited by Igor I. Goryanin, Andrew B. Goryachev

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505 8 |a Advances in Systems Biology; Preface; Contents; Contributors; Part I Multiscale Biological Networks: Identification, Modeling and Analysis; Chapter 1 Modular Analysis of Biological Networks; 1 Introduction; 2 Models of Biochemical Networks; 3 Graphs and Community Detection; 4 Stoichiometric Network Analysis and Metabolic Pathways; 5 Modules in Dynamic Networks: Definition by Behavior; 5.1 Local Structure: Network Motifs; 5.2 Global Decomposition: Monotone Systems; 5.3 Retroactivity; 5.4 Interfaces; 6 Applications: Modular Systems Identification and Analysis; 6.1 Control Systems 
505 8 |a 6.2 Modular Response Analysis7 Conclusions and Perspectives; References; Chapter 2 Modeling Signaling Networks Using High-throughput Phospho-proteomics; 1 Introduction; 2 Phospho-proteomics Data Collection; 2.1 Antibody-based Methods; 2.1.1 Intracellular Multicolor Flow Cytometry; 2.1.2 Microwestern Arrays; 2.1.3 Array and Bead-based Methods; 2.2 Mass Spectrometry; 2.2.1 Shotgun MS/MS; 2.2.2 Data Processing Challenges; 2.2.3 Quantitative MS; 2.2.4 MS for PTMs; 2.2.5 Limitations of the Shotgun MS/MS Approach; 2.2.6 Targeted MS/MS 
505 8 |a 3 Computational Analysis of Large Scale Phospho-proteomics Data Sets3.1 ``Descriptive" Approaches; 3.1.1 Global Investigations of the Phospho-proteome; 3.1.2 Analysis of Pathway Utilization Downstream of Receptors; 3.1.3 Analysis of Reciprocal Signaling in Cell-Cell Communication; 3.2 ``Predictive" Approaches; 3.2.1 Input/Output Regression Based Approaches; 3.2.2 Network Inference; 3.2.3 Bayesian Network Inference; 3.2.4 Reaction-based Models; 3.2.5 Rule-based Models; 3.2.6 Logic-based Models; 4 Summary; References 
505 8 |a Chapter 3 An Integrated Bayesian Framework for Identifying Phosphorylation Networks in Stimulated Cells1 Introduction; 2 Algorithm; 2.1 Calculating P(Mi|Kl Si); 2.2 Calculating P(li|KlSi); 2.3 Calculating P(Zlimax,limax|Kl Si); 2.4 The Log Likelihood Function; 2.5 Pseudo Code for the Above Algorithm; 3 Implementation of Our Algorithm to Analyze Phosphoproteomic Data; 3.1 Results; 4 Advantages and Disadvantages of Our Algorithm; 4.1 Advantages; 4.1.1 Inter Kinase Specificity; 4.1.2 Intra Kinase Specificity; 4.1.3 Feedback Interactions; 4.2 Disadvantages; 5 Conclusion; References 
505 8 |a Chapter 4 Signaling Cascades: Consequences of Varying Substrate and Phosphatase Levels1 Introduction; 2 One-Site Linear Signaling Cascades; 2.1 Steady States; 2.2 Concentrations at Steady State; 2.3 Splitting the Cascade; 3 Relationships Between Response Concentrations; 3.1 The Last Layer; 3.2 Intermediate Layers Response; 3.3 Total Amount of Kinase E; 4 Regulation Through Substrate and Phosphatase Variation; 5 Stimulus-Response Curves; 6 Maximal Response; 7 Discussion; References; Chapter 5 Heterogeneous Biological Network Visualization System: Case Study in Context of Medical Image Data 
505 8 |a 1 Introduction 
520 |a Andrew B. Goryachev 
520 |a The International Society for Systems Biology (ISSB) is a society aimed at advancing world-wide systems biology research by providing a forum for scientific discussions and various academic services. The ISSB helps coordinate researchers to form alliances for meeting the unique needs of multidisciplinary and international systems biology research. The annual International Conference on Systems Biology (ICSB) serves as the main meeting for the society and is one of the largest academic and commercial gatherings under the broad heading of 'Systems Biology' 
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