Toward the dynamic interactome: it's about time

@article{Przytycka2010TowardTD,
  title={Toward the dynamic interactome: it's about time},
  author={Teresa M. Przytycka and Mona Singh and Donna K. Slonim},
  journal={Briefings in bioinformatics},
  year={2010},
  volume={11 1},
  pages={
          15-29
        }
}
Dynamic molecular interactions play a central role in regulating the functioning of cells and organisms. The availability of experimentally determined large-scale cellular networks, along with other high-throughput experimental data sets that provide snapshots of biological systems at different times and conditions, is increasingly helpful in elucidating interaction dynamics. Here we review the beginnings of a new subfield within computational biology, one focused on the global inference and… 
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References

SHOWING 1-10 OF 191 REFERENCES
Revealing static and dynamic modular architecture of the eukaryotic protein interaction network
TLDR
It is found that constitutively expressed and dynamically co‐regulated proteins cluster in distinct functionally specialized network neighborhoods to form static and dynamic functional modules, respectively, and it is shown that whereas dynamic modules are mainly responsible for condition‐dependent regulation of cell behavior, static modules provide robustness to the cell against genetic perturbations or protein expression noise.
Modeling cellular machinery through biological network comparison
TLDR
This review surveys the field of comparative biological network analysis and describes its applications to elucidate cellular machinery and to predict protein function and interaction, and highlights the open problems in the field.
An in Vivo Map of the Yeast Protein Interactome
TLDR
A genome-wide in vivo screen for protein-protein interactions in Saccharomyces cerevisiae by means of a protein-fragment complementation assay (PCA) identified 2770 interactions among 1124 endogenously expressed proteins, revealing a previously unexplored subspace of the yeast protein interactome.
Integrating molecular and network biology to decode endocytosis
TLDR
It is shown here how a careful understanding of a given biological pathway can refine an interactome approach, which permits the elucidation of additional design principles and of spatio-temporal dynamics behind pathways, and aids in experimental design and interpretation.
A Map of the Interactome Network of the Metazoan C. elegans
TLDR
A large fraction of the Caenorhabditis elegans interactome network is mapped, starting with a subset of metazoan-specific proteins, and more than 4000 interactions were identified from high-throughput, yeast two-hybrid screens.
Lethality and centrality in protein networks
TLDR
It is demonstrated that the phenotypic consequence of a single gene deletion in the yeast Saccharomyces cerevisiae is affected to a large extent by the topological position of its protein product in the complex hierarchical web of molecular interactions.
Dynamic Complex Formation During the Yeast Cell Cycle
TLDR
It is shown that additional regulation through targeted degradation and phosphorylation by Cdc28p (Cdk1) specifically affects the periodically expressed proteins.
Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks.
TLDR
It is found that the protein-protein interaction networks in three eukaryotes have remarkably similar structure, such that the number of interactors per protein and the centrality of proteins in the networks have similar distributions.
Reconstructing dynamic regulatory maps
TLDR
A novel computational method that uses an input–output hidden Markov model to model these regulatory networks while taking into account their dynamic nature is developed, leading to new roles for Ino4 and Gcn4 in controlling yeast response to stress.
...
1
2
3
4
5
...