List of contributors |
Introduction / M. Buchanan ; G. Caldarelli ; P. De Los Rios ; F. Rao ; M. Vendruscolo |
Network views of the cell / Paolo De Los Rios ; Michele Vendruscolo1: |
The network hypothesis / 1.1: |
The central dogma and gene regulatory networks / 1.2: |
Protein-protein interaction networks / 1.3: |
Metabolic networks / 1.4: |
Signaling networks / 1.5: |
Networked networks and cell functionality / 1.6: |
Concluding remarks / 1.7: |
Transcriptional regulatory networks / Sarath Chandra Janga ; M. Madan Babu2: |
Transcriptional regulation in prokaryotes and eukaryotes / 2.1: |
Structure of transcriptional regulatory networks / 2.3: |
Evolution of transcriptional regulatory networks / 2.4: |
Dynamics of transcriptional regulatory networks / 2.5: |
Conclusions / 2.6: |
Transcription factors and gene regulatory networks / Matteo Brilli ; Elisa Calistri ; Pietro Lió3: |
Promoters' complexity/eukaryotic gene promoters / 3.1: |
Transcription factors / 3.3: |
Bioinformatics of regulatory networks / 3.4: |
Experimental methods for protein interaction identification / Peter Uetz ; Björn Titz ; Seesandra V. Rajagopala ; Gerard Cagney4: |
Protein complementation techniques / 4.1: |
Affinity purification methods / 4.3: |
Protein complex purification and mass spectrometry / 4.4: |
Protein and peptide chips / 4.5: |
Other methods for interaction detection and functional analysis / 4.6: |
Quality of large-scale interaction data / 4.7: |
Comparison of methods / 4.8: |
Modeling protein interaction networks / Francesco Rao4.9: |
Scaling laws and network topology / 5.1: |
Predicting protein interactions / 5.3: |
Towards models at an atomic level of resolution / 5.4: |
Dynamics and evolution of metabolic networks / Daniel Segrè5.5: |
Cellular metabolism and its regulation / 6.1: |
Metabolism across disciplines / 6.3: |
Dynamics of a metabolic system / 6.4: |
Stoichiometric analysis / 6.5: |
Constraint-based modeling: feasible states and optimality / 6.6: |
Predicting genetic perturbations / 6.7: |
Double perturbations and epistatic interactions / 6.8: |
The ancient history of metabolism: from cell-scale to biosphere-scale / 6.9: |
Hierarchical modularity in biological networks: the case of metabolic networks / Erzsébet Ravasz Regan6.10: |
Modularity and hubs in biological networks / 7.1: |
Scaling of the clustering coefficient: a signature of hierarchy / 7.3: |
Method for finding network modules / 7.4: |
A case study: the E. coli metabolic network / 7.5: |
Hierarchy, fractality and the small world of networks / 7.6: |
Signalling networks / Gian Paolo Rossini7.7: |
Chemical signalling: many pathways following a few general themes / 8.1: |
Cross-talks among signal transduction pathways / 8.3: |
Signalling networks, system organization and modelling / 8.4: |
Conclusions and outlook / 8.5: |
Complex networks: from local to global properties / D. GarlaschelliAppendix A: |
Modelling the local structure of networks / Appendix B: |
Higher-order topological properties / S. Ahnert ; T. FinkAppendix C: |
Elementary mathematical concepts / A. GabrielliAppendix D: |
References |
Index |
List of contributors |
Introduction / M. Buchanan ; G. Caldarelli ; P. De Los Rios ; F. Rao ; M. Vendruscolo |
Network views of the cell / Paolo De Los Rios ; Michele Vendruscolo1: |