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| List of contributors | |
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| Introduction | |
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| Network views of the cell | |
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| The network hypothesis | |
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| The central dogma and gene regulatory networks | |
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| Protein-protein interaction networks | |
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| Metabolic networks | |
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| Signaling networks | |
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| Networked networks and cell functionality | |
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| Concluding remarks | |
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| Transcriptional regulatory networks | |
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| Introduction | |
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| Transcriptional regulation in prokaryotes and eukaryotes | |
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| Structure of transcriptional regulatory networks | |
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| Evolution of transcriptional regulatory networks | |
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| Dynamics of transcriptional regulatory networks | |
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| Conclusions | |
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| Transcription factors and gene regulatory networks | |
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| Introduction | |
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| Promoters' complexity/eukaryotic gene promoters | |
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| Transcription factors | |
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| Bioinformatics of regulatory networks | |
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| Experimental methods for protein interaction identification | |
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| Introduction | |
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| Protein complementation techniques | |
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| Affinity purification methods | |
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| Protein complex purification and mass spectrometry | |
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| Protein and peptide chips | |
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| Other methods for interaction detection and functional analysis | |
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| Quality of large-scale interaction data | |
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| Comparison of methods | |
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| Conclusions | |
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| Modeling protein interaction networks | |
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| Introduction | |
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| Scaling laws and network topology | |
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| Predicting protein interactions | |
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| Towards models at an atomic level of resolution | |
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| Concluding remarks | |
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| Dynamics and evolution of metabolic networks | |
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| Introduction | |
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| Cellular metabolism and its regulation | |
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| Metabolism across disciplines | |
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| Dynamics of a metabolic system | |
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| Stoichiometric analysis | |
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| Constraint-based modeling: feasible states and optimality | |
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| Predicting genetic perturbations | |
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| Double perturbations and epistatic interactions | |
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| The ancient history of metabolism: from cell-scale to biosphere-scale | |
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| Conclusions | |
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| Hierarchical modularity in biological networks: the case of metabolic networks | |
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| Introduction | |
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| Modularity and hubs in biological networks | |
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| Scaling of the clustering coefficient: a signature of hierarchy | |
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| Method for finding network modules | |
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| A case study: the E. coli metabolic network | |
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| Hierarchy, fractality and the small world of networks | |
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| Conclusions | |
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| Signalling networks | |
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| Introduction | |
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| Chemical signalling: many pathways following a few general themes | |
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| Cross-talks among signal transduction pathways | |
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| Signalling networks, system organization and modelling | |
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| Conclusions and outlook | |
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| Complex networks: from local to global properties | |
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| Modelling the local structure of networks | |
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| Higher-order topological properties | |
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| Elementary mathematical concepts | |
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| References | |
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| Index | |