Systems analysis of biological networks [electronic resource] / Arul Jayaraman, Juergen Hahn, editors.
- Boston, Mass. : Artech House, c2009.
- Artech House methods in bioengineering series.
Methods in bioengineering series
1 online resource (328 p.)
- Bacterial genetics.
Cytology -- Technique.
- Electronic books.
- This volume provides a detailed look at the two main aspects of systems biology: the design of sophisticated experimental methods and the development of complex models to analyze the data. Focusing on methods that are being used to solve current problems in biomedical science and engineering, this comprehensive, richly illustrated resource shows you how to design of state-of-the art methods for analyzing biological systems, implement experimental approaches for investigating cellular behavior in health and disease, use algorithms and modeling techniques for quantitatively describing biomedical
- Methods in Bioengineering: Systems Analysis of Biological Networks; Contents; Chapter 1 Quantitative Immunofluorescence for Measuring Spatial Compartmentation of Covalently Modified Signaling Proteins; 1.1 Introduction; 1.2 Experimental Design; 1.3 Materials; 1.3.1 Cell culture; 1.3.2 Buffers/reagents; 1.3.3 Immunofluorescence reagents; 1.4 Methods; 1.4.1 Cell culture and stimulation for phospho-ERK measurements; 1.4.2 Antibody labeling of phosphorylated ERK (ppERK); 1.4.3 Fluorescence microscopy imaging of ppERK and automated imageanalysis
1.5 Data Acquisition, Anticipated Results, and Interpretation1.6 Statistical Guidelines; 1.7 Discussion and Commentary; 1.8 Application Notes; 1.9 Summary Points; Acknowledgments; References; Chapter 2 Development of Green Fluorescent Protein-Based Reporter Cell Lines for Dynamic Profiling of Transcription Factor and Kinase Activation; 2.1 Introduction; 2.2 Materials; 2.2.1 Cell and bacterial culture; 2.2.2 Buffers and reagents; 2.2.3 Cloning; 2.2.4 Microscopy; 2.3 Methods; 2.3.1 3T3-L1 cell culture; 2.3.2 Transcription factor reporter development; 2.3.3 Kinase reporter development
2.4 Application Notes2.4.1 Electroporation of TF reporter plasmids into 3T3-L1 preadipocytes; 2.4.2 Monitoring activation of ERK in HepG2 cells; 2.5 Data Acquisition, Anticipated Results, and Interpretation; 2.6 Discussion and Commentary; 2.7 Summary Points; Acknowledgments; References; Chapter 3 Comparison of Algorithms for Analyzing Fluorescent Microscopy Images and Computation of Transcription Factor Profiles; 3.1 Introduction; 3.2 Preliminaries; 3.2.1 Principles of GFP reporter systems; 3.2.2 Wavelets; 3.2.3 K-means clustering; 3.2.4 Principal component analysis
3.2.5 Mathematical description of digital images and image analysis3.3 Methods; 3.3.1 Image analysis based on wavelets and a bidirectional search; 3.3.2 Image analysis based on K-means clustering and PCA; 3.3.3 Determining fluorescence intensity of an image; 3.3.4 Comparison of the two image analysis procedures; 3.4 Data Acquisition, Anticipated Results, and Interpretation; 3.4.1 Developing a model describing the relationship between the transcription factor concentration and the observed fluorescence intensity
3.4.2 Solution of an inverse problem for determining transcription factor concentrations3.5 Application Notes; 3.6 Summary and Conclusions; Acknowledgments; References; Chapter 4 Data-Driven, Mechanistic Modeling of Biochemical Reaction Networks; 4.1 Introduction; 4.2 Principles of Data-Driven Modeling; 4.2.1 Types of experimental data; 4.2.2 Data processing and normalization; 4.2.3 Suitability of models used in conjunction with quantitative data; 4.2.4 Issues related to parameter specification and estimation; 4.3 Examples of Data-Driven Modeling
4.3.1 Example 1: Systematic analysis of crosstalk in the PDGF receptor signaling network
- Description based upon print version of record.
Includes bibliographical references and index.
- Hahn, Juergen.
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