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Updated: May 31, 2026

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells
Published on: March 3, 2015
Generative probabilistic models for protein-protein interaction networks--the biclique perspective
Regev Schweiger1, Michal Linial, Nathan Linial
1School of Computer Science and Engineering, Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences and The Sudarsky Center for Computational Biology, The Hebrew University, Jerusalem, 91904 Israel. regevs01@cs.huji.ac.il
The duplication-divergence (DD) model better explains Saccharomyces cerevisiae protein-protein interaction (PPI) network evolution than the Barabási-Albert (BA) model. Analysis of maximal biclique distribution favors DD, indicating its ability to capture key network growth patterns.
Area of Science:
- Systems Biology
- Computational Biology
- Network Science
Background:
- Cellular systems biology relies on network representations of molecular data.
- Protein-protein interaction (PPI) networks, with proteins as nodes and interactions as edges, are crucial for understanding cellular processes.
- Developing accurate mathematical models for PPI network evolution is essential but challenging.
Purpose of the Study:
- To evaluate generative network models for their ability to reproduce properties of the Saccharomyces cerevisiae PPI network.
- To distinguish between neighbor-copying models (duplication-divergence, DD) and non-neighbor-copying models (e.g., Barabási-Albert, BA).
- To assess which model best captures the evolutionary patterns of PPI networks.
Main Methods:
- Utilized the distribution of maximal bicliques as a novel criterion to differentiate between network growth models.
- Compared the predictions of the duplication-divergence (DD) model against the Barabási-Albert (BA) preferential attachment model.
- Analyzed the embedding of bicliques within the seed graphs of each model.
Main Results:
- The maximal biclique distribution analysis strongly favors the duplication-divergence (DD) model over the Barabási-Albert (BA) model.
- For the BA model, 92.9% of bicliques (both sides ≥4) were pre-existing in the seed graph, compared to only 5.1% for the DD model.
- This biclique-based perspective demonstrates the DD model's capacity to represent key aspects of PPI network growth.
Conclusions:
- The duplication-divergence (DD) model provides a more accurate representation of Saccharomyces cerevisiae PPI network evolution.
- Maximal biclique distribution serves as an effective metric for evaluating the biological relevance of network growth models.
- A standard DD model can effectively capture essential features of biological PPI networks.
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