Biological network analysis: insights into structure and functions.

@article{Ma2012BiologicalNA,
  title={Biological network analysis: insights into structure and functions.},
  author={Xiaoke Ma and Lin Gao},
  journal={Briefings in functional genomics},
  year={2012},
  volume={11 6},
  pages={
          434-42
        }
}
  • Xiaoke Ma, Lin Gao
  • Published 1 November 2012
  • Materials Science
  • Briefings in functional genomics
In the past two decades, great efforts have been devoted to extract the dependence and interplay between structure and functions in biological networks because they have strong relevance to biological processes. In this article, we reviewed the recent development in the biological network analysis. In detail, we first reviewed the interactome topological properties of biological networks, the methods for structure and functional patterns. 

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References

SHOWING 1-10 OF 131 REFERENCES
Getting connected: analysis and principles of biological networks.
TLDR
Systematic approaches to study large numbers of proteins, metabolites, and their modification have revealed complex molecular networks which provide novel insights in understanding basic mechanisms controlling normal cellular processes and disease pathologies.
Diseases as network perturbations.
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.
Network biology: understanding the cell's functional organization
TLDR
This work states that rapid advances in network biology indicate that cellular networks are governed by universal laws and offer a new conceptual framework that could potentially revolutionize the view of biology and disease pathologies in the twenty-first century.
Toward the dynamic interactome: it's about time
TLDR
The beginnings of a new subfield within computational biology, one focused on the global inference and analysis of the dynamic interactome, are reviewed, which promises to be a major step forward in the ability to model and reason about cellular function and behavior.
An algorithm for modularity analysis of directed and weighted biological networks based on edge-betweenness centrality
TLDR
A novel modularity analysis algorithm based on edge-betweenness centrality is presented, which facilitates the use of directional information and measurable biochemical data.
A review on models and algorithms for motif discovery in protein-protein interaction networks.
TLDR
This review presents in a systematic way the different computational settings outlining their main features and limitations of motifs in biological networks, particularly in protein-protein interaction networks.
Network motifs: theory and experimental approaches
  • U. Alon
  • Biology
    Nature Reviews Genetics
  • 2007
TLDR
Network motifs are reviewed, suggesting that they serve as basic building blocks of transcription networks, including signalling and neuronal networks, in diverse organisms from bacteria to humans.
Comparative assessment of large-scale data sets of protein–protein interactions
TLDR
Comprehensive protein–protein interaction maps promise to reveal many aspects of the complex regulatory network underlying cellular function and are compared with each other and with a reference set of previously reported protein interactions.
Modular organization of cellular networks
TLDR
This work investigated the organization of interacting proteins and protein complexes into networks of modules and identified module-organizer proteins and module-connector proteins that suggest that they are important for module function and intermodule communication.
...
1
2
3
4
5
...